Results (1239 products found)

Product Year NESCent Contributor Altmetrics
Software and Datasets
Crawford, Jeremy Chase and Drea, Christine M.. 2015, Data from: Baby on board: olfactory cues indicate pregnancy and fetal sex in a non-human primate, Dryad Digital Repository 2015 Jeremy Chase Crawford
Plooij, Frans X., van de Rijt-Plooij, Hetty, Fischer, Martha and Pusey, Anne. 2015, Data from: Longitudinal recordings of the vocalizations of immature Gombe chimpanzees for developmental studies, Dryad Digital Repository 2015 Anne Pusey
Conner, Jeffrey K., Mills, Cynthia J., Koelling, Vanessa A. and Karoly, Keith. 2014, Data from: Artificial selection on anther exsertion in wild radish, Raphanus raphanistrum, Dryad Digital Repository 2014
The Tree of Sex Consortium,, Ashman, Tia-Lynn, Bachtrog, Doris, Blackmon, Heath, Goldberg, Emma E., Hahn, Matthew W., Kirkpatrick, Mark, Kitano, Jun, Mank, Judith E., Mayrose, Itay, Ming, Ray, Otto, Sarah P., Peichel, Catherine L., Pennell, Matthew W., Perrin, Nicolas, Ross, Laura, Valenzuela, Nicole and Vamosi, Jana C.. 2014, Data from: Tree of sex: a database of sexual systems, Dryad Digital Repository 2014 Tia-Lynn Ashman, Doris Bachtrog, Heath Blackmon, Mark Kirkpatrick, Jun Kitano, Itay Mayrose, Ray Ming, Nicolas Perrin, Laura Ross, Nicole Valenzuela
This product consists of an updated, new version of this software for conducting phylogenetic mixed meta-analysis models using likelihood methods. One of our working group members, Dr. Wolfgang Viechtbauer, responded to our group needs (and the needs of the broader scientific community) by adding the capability of fitting arbitrary random effects and one or more phylogenies in his meta-analysis package in R, metafor. This package was already the most powerful in R for meta-analysis with maximum likelihood model fitting, and now has significantly broader applicability to a wide range of model structures. Working group members provided significant feedback about the desired capabilities in this package, and Dr. Viechtbauer has since completed an official release of the new version of the package. New is the rma.mv function, which allows specification of an arbitrary number of random effects, and known correlation matrices. This new version was released on 5/5/2014. 2014 Jason Hoeksema
Zehr, Sarah M., Roach, Richard G., Haring, David, Taylor, Julie, Cameron, Freda H. and Yoder, Anne D.. 2014, Data from: Life history profiles for 27 strepsirrhine primate taxa generated using captive data from the Duke Lemur Center, Dryad Digital Repository 2014
Alberts SC, Altmann J, Brockman DK, Cords M, Fedigan LM, Pusey A, Stoinski TS, Strier KB, Morris WF, Bronikowski AM (2013) Data from: Reproductive aging patterns in primates reveal that humans are distinct. Dryad Digital Repository. doi:10.5061/dryad.m327n 2013 Susan C Alberts, Jeanne Altmann, Diane K. Brockman, Marina Cords, Linda M Fedigan, Anne Pusey, Tara Stoinski, Karen B Strier, Bill Morris, Anne Bronikowski
A tool for converting a VUE diagram document to an OWL ontology. 2013 Jim P Balhoff
Davis AM, Unmack PJ, Pusey BJ, Pearson RG, Morgan DL (2013) Data from: Ontogenetic development of intestinal length and relationships to diet in an Australasian fish family (Terapontidae). Dryad Digital Repository. doi:10.5061/dryad.h30t5 2013 Peter J Unmack
Dragan, M., Priyam, A., & Wurm, Y. 2013. GeneValidator: Identify problems with gene predictions. GeneValidator identifies problems with gene predictions and provides information based on the similarities to genes in public databases. Results of prediction validation can inform sequencing curation and improvement of approaches and tools for gene prediction. GeneValidator was designed for use by biologists who want to validate data obtained in their own laboratories. 2013 Yannick Wurm, Monica-Andreea Dragan, Anurag Priyam
Fanaswala, I., Rambaut, A. Suchard, M., & Guindon, S. 2013. Optimizing tree evaluation in PhyML with the BEAGLE Library. Optimized PhyML with BEAGLE to parallelize (1) partial likelihoods computations and (2) P-matrix updating (i.e. matrix multiplication). 2013 Andrew Rambaut, Marc Suchard, Stephane Guindon, Imran Fanaswala
Frandsen, P. Lanfear, R., & Calcott, B. 2013. Extending PartitionFinder to automatically partition DNA and protein alignments. Implements a new algorithm that uses site rates or site likelihoods to automatically partition sites in DNA and protein alignments into a best fit partitioning scheme. PartitionFinder can be downloaded from: http://www.robertlanfear.com/partitionfinder/ or github. 2013 Paul Frandsen, Brett Calcott, Robert Lanfear
Hertweck KL (2013) Data from: Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales. Dryad Digital Repository. doi:10.5061/dryad.43g64 2013 Kate Hertweck
Lynch, J., Iverson, K., Zaher Md. Faridee, A. 2013. Implementing machine learning algorithms for classification and feature selection in mothur. Extended mothur through implementation of the support vector machine algorithm to support a new classification and feature selection command in mothur. Project-specific code is available at https://github.com/jklynch/mothur; mothur can be downloaded from http://www.mothur.org/ and github. 2013 Joshua Lynch, Kathryn Iverson, Abu Zaher Md Faridee
Nowak, MD, C. Simpson, and D. Zwickl. 2007. Single Node Age Prior Estimator (SNAPE) v. 1.0. SNAPE calculates informative prior probabilities on divergence times based on fossil occurrence data retrieved from the Paleobiology Database. 2013 Derrick Zwickl, Carl Simpson, Mike Nowak
Owlet is a query expansion preprocessor for SPARQL. It parses embedded OWL class expressions (in Manchester Syntax) and uses an OWL reasoner to replace them with FILTER statements containing the URIs of subclasses of the given class expression (or superclasses, equivalent classes, or instances). 2013 Jim P Balhoff
Phelan, C., Harp, G., & Smith, S.A. 2013. Phylet: Open Tree of Life graph visualization and navigation. Phylet is a visualization tool for phylogenetic graphs, powered by the graph database Neo4j and visualized by the JavaScript library D3. Hierarchical (rather than network) graphs are used to represent tree structures. In addition to other types of relationships, conflicts are also displayed. This application can be used by specialists and general lay audiences. 2013 Gabriel Harp, Stephen Smith, Chanda Phelan
Ruan, Z., Talevich, E., & Cock, P. 2013. CodonAlign: Codon alignment and analysis in Biopython. The CodonAlign (Bio.CodonAlign) module extends biopython to support estimations of nonsynonymous substitutions per site (dN) and synonymous substitutions per site (dS), and neutrality testing. CodonAlign currently support three counting based methods (NG86, LWL85, YN00) and maximum likelihood method to estimate dN and dS. Project specific code is available at: https://github.com/zruan/biopython/tree/master/Bio/CodonAlign. 2013 Zheng Ruan, Eric Talevich, Peter Cock
Scowl is a Scala library allowing a declarative approach to composing OWL expressions and axioms using the OWL API. 2013 Jim P Balhoff
Shrestha M, Dyer AG, Boyd-Gerny S, Wong BBM, Burd M (2013) Data from: Shades of red: bird-pollinated flowers target the specific colour discrimination abilities of avian vision. Dryad Digital Repository. doi:10.5061/dryad.pj860 2013 Martin Burd
Soltis DE, Mort ME, Latvis M, Mavrodiev EV, O'Meara BC, Soltis PS, Burleigh JG, de Casas RR (2013) Data from: Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach. Dryad Digital Repository. doi:10.5061/dryad.h4070 Note: This dataset is also associated with Pamela Soltis's visiting scholar project (Title: Reconstructing the Great Tree of Life) 2013 Douglas Soltis, Pamela S Soltis
Unmack PJ, Hammer MP, Adams M, Johnson JB, Dowling TE. 2013. Data from: The role of continental shelf width in determining freshwater phylogeographic patterns in southeastern Australian pygmy perches (Teleostei: Percichthyidae). Dryad Digital Repository. doi:10.5061/dryad.9v852 2013 Peter J Unmack
Vaidya, G. 2013. Species Autocomplete. This tool provides basic Javascript and PHP code to run an autocompletion script. An included Perl script allows the ITIS-DwCA resource to be used to generate the autocompletion database (in SQLite). Further improvements may allow this software program to be integrated into websites which would like to validate the input of scientific names, either for data entry or to power searches. 2013 Gaurav Vaidya
Ye, Yanbo; Holder, Mark; Sukumaran, Jeet; Talevich, Eric. 2013. Phylogenetics in Biopython: Filling in the gaps. TreeConstruction and Consensus modules for Bio.Phylo were constructed to extend biopython support for tree construction and consensus tree algorithms. These modules add UPGMA, NJ, MP, strict consensus, majority rule, adam consensus with some branch support, and bootstrap algorithms to the current package. 2013 Yanbo Ye, Mark Holder, Jeet Sukumaran, Eric Talevich
A major upgrade to this well-used tool. Phylomatic version 3 is a fork of the phylocom phylomatic code and exists only as a web service. I can now: read in trees as NeXML and CDAO, graft in taxa to the megatree, and write out in a number of formats. 2012 Campbell O Webb
A PoC javascript framework that invokes the right Phylotastic REST services at the right time. 2012 Helena Deus
A proof-of-concept SADI-based web service which uses RDF and SPARQL to return subtrees from larger phylogenetic trees. 2012 Jim P Balhoff
Caruso CM, Case A (2012) Data from: Testing models of sex ratio evolution in a gynodioecious plant: female frequency covaries with the cost of male fertility restoration. Dryad Digital Repository. doi:10.5061/dryad.v5n09 2012 Christina M Caruso
Gates, D., Banbury, B., O'Meara, B. 2012. Optimization of TreEvo R code for approximate Bayesian computation (ABC). This project project took the original TreEvo code, found and fixed ineffeciencies within the code, and added parallelization and checkpointing. 2012 Daniel Gates, Brian C O'Meara, Barbara Banbury
Goyal, P. & Baron, C. 2012. jMatrixBrowse: Coordinate-based browsing for matrices. jQuery plugin for browsing large matrices using dragging (like Google Maps). The main features of the tool include a browsable canvas that can be panned and zoomed easily. 2012 Pulkit Goyal, Chris Baron
Hauser, E., & Lapp, H. 2012. MIAPA-ETL: NeXML to MIAPA Mapping & ISAtab Transformation. MIAPA-ETL is a conversion tool to Extract, Transform, and Load (ETL) MIAPA-compliant data from NeXML files into valid ISAtab format. 2012 Hilmar Lapp, Elliott Hauser
Ismailov, I., Degnan, J., Stadler, T. 2012. Ranked gene tree topologies probability computation. Ranked Gene Trees is a polynomial-time algorithm implementation for computing probabilities of ranked gene tree topologies given species trees. 2012 Islam Ismailov, James Degnan, Tanja Stadler
Jim Balhoff, Karen A. Cranston, Mark T. Holder, Hilmar Lapp, Emily J. McTavish, and Enrico Pontelli. June, 2012. PhylotasticTreeStore. PhylotasticTreeStore RESTful adaptor for RDF-based tree store. It is a web2py application, which provides a RESTful interface by translating queries for trees into SPARQL queries to a triple store and then using DendroPy to translate the resulting RDF to NeXML. Built at the Phylotastic hackathon. Christopher Baron, Jeet Sukumaran, and Cam Webb provided helpful feedback. 2012 Mark Holder, Jim P Balhoff, Karen Cranston, Hilmar Lapp, Emily Jane McTavish, Enrico Pontelli, Chris Baron, Jeet Sukumaran, Campbell O Webb
Landing page for the Phylotastic project 2012 Megan Pirrung
Landis, M., & Bedford, T. 2012. Phylowood.js: Browser-based Interactive Animations of Ancestral Dispersal and Diversity Patterns. Phylowood enables users to visualize geographic dispersal patterns of phylogenetic units on maps overtime. 2012 Michael Landis, Trevor Bedford
Lapp H. 2012. Ontology and RDF model for Taxonomic Name Resolution Service (TNRS) results. The ontology describes the entities that make up a TNRS result and the relationship between those and those between an OTU and a TNRS resolution result. The RDF model is accompanied by an instance document and a graph visualization. 2012 Hilmar Lapp
Menard, A., Ponty, Y., & Procter, J. Towards a fully RNA-aware alignment editor with Jalview and VARNA. This project focused on the synchronization of Jalview and VARNA to improve jalview RNA support, with emphasis on tertiary interactions. Tertiary interactions can now be loaded from XML files (RNAML format), directly annotated from 3D experimental models (PDB files), and displayed graphically using an integrated version of the Varna software. 2012 Yann Ponty, Jim Procter, Anne Menard
Midford, P.E., 2012, CMAPOBO, This is a simple command line tool to generate simple OBO format (syntax version 1.2) files from ontology graphs created in the CMAP tool. 2012 Peter E Midford
Midford, P. E. 2012. Mesquite-o-tastic - a Mesquite package for retrieving trees from Phylotastic. This is a prototype package that allows a user to retrieve a tree from phylotastic that matches the taxa present in a Mesquite character matrix. See the demo video by Arlin Stoltzfus at http://www.youtube.com/watch?v=Lak-zjwFuhQ&feature=youtube_gdata_player 2012 Peter E Midford, Arlin Stoltzfus
Midford, P. E. 2012. Taxonomy Ontology Tool (VTOTool). This tool constructs taxonomic ontologies (e.g., Phenoscape's VTO) from multiple taxonomic sources - existing ontologies (e.g., TTO) as well as other taxonomic sources (e.g., NCBI, CoL, PBDB). As of July 2012 it generates the ontologies in an OBO format where taxonomic groups are classes and follows the conventions of the OBO rendering of the full NCBI taxonomic ontology. A earlier version of this tool was used in support of a working group. 2012 Peter E Midford
New release of the Phenex annotation software with new features supporting collaborative editing across file sharing systems such as Dropbox. 2012 Jim P Balhoff
O'Meara, B.C., L. Harmon, J. Eastman, P. Midford, T. Heath, J. Brown, M. Pennell, M. Alfaro. 2012. DateLife.org. Online database and software for returning ages of most recent common ancestors given a string of taxon names. 2012 Brian C O'Meara
Plugin for the Protege ontology editing environment which displays axioms which can not be represented in an OBO format serialization of the ontology. 2012 Jim P Balhoff
Reconcili-o-tastic starts with a gene tree, discovers the species sources, gets a tree for the species on the fly (phylotastically), then runs reconciliation software to identify which branchings represent speciations vs duplications. 2012 Chris Baron
Rutger Vos, 2012. A phylotastic pruning service based on MapReduce. HIP working group of NESCent. This pruner was developed to provide automated pruning services, as part of the Phylotastic project. Given a set { S } of OTU names, and the name of a source tree, the pruner returns a topology for the OTUs that it can match from { S }. This kind of pruning can be done by recursive calls into a database (which probably would need to hit the database many times) or by loading the whole tree into memory (which might take a while to read in the file, and cost a bit of memory). The way it is done here is much cooler, because it never requires the whole tree to be in memory or in a database: the pruning is done in parallel using MapReduce. Some tests on the entire dump of the Tree of Life Web Project showed that this returns a pruned subtree within a few seconds, fast enough for a web service. The pruner has two interfaces, a web forms interface (with explanatory text and examples) and a web-services interface. The code and some documentation is available at a location indicated on the web page. 2012 Arlin Stoltzfus, Rutger Vos
Taxosaurus is a meta TNRS that implements the TNRastic API. It's composed by 2 main modules (the handler_library and the processor) that sit behind an http handler. The handler_library implements the TNRastic API whereas the processor coordinates the execution of the downstream calls to the sources. The processor itself has a modular design that allows the addition of new service via adaptors that are registered through a simple JSON description. 2012 Naim Matasci
The CDAO Comparative Data Analysis Ontology was revised to meet OBO library ontology standards, such as numeric class identifiers. 2012 Jim P Balhoff
The Newick to CDAO ingestor is a Perl module. The module takes as input a tree described in Newick format and produces a CDAO representation of the tree. The module is capable of contacting the Phylotastic TNRS to resolve names and adds the result of the name resolution to the CDAO representation of the tree. 2012 Enrico Pontelli
The Perl controller coordinates stub CGI implementations of the Phylotastic TNRS, tree store, topology, and branch length services which produce correct output for one example input. However, the user may substitute real service implementations into the controller workflow via CGI parameters, allowing the services to be tested for conformance to the Phylotastic specification. Usage instructions for the CGI controller, along with example input/output files for the stub services, are provided at https://github.com/phylotastic/cgi. 2012 Ben Vandervalk
The phylogeny from Goloboff, et al. "Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups" (Cladistics 2009, 25:211-230) is a valuable resource, useful for the Phylotastic project. However, it is available only in TNT format, a nested-parenthesis format like Newick. The tree file has only numeric codes, with names encoded in a separate file. Converting this information into a single Newick tree is a 3-step process: 1. convert the TNT trees (in any of the *.tre files) to newick 2. pick the tree you want and put it in a file by itself 3. replace the numeric codes in the tree with species names from Taxon_Names_Only.tnt I developed and tested Perl scripts for steps 1 and 3. The scripts contain documentation using POD. They are available from a public repository using the URL below. 2012 Arlin Stoltzfus
The TNRastic API is a lightweight RESTful API specification that provides a generalized framework to access Taxonomic Name Resolution Services. It's composed of a set of services that are essential for name resolution. 2012 Naim Matasci
The TNRS group contacted David Mitchell, ITIS Data Specialist at the NMNH, who gave us permission to make the entire ITIS database available as a DarwinCore Archive. This file was generated by dwca-hunter (https://github.com/GlobalNamesArchitecture/dwca-hunter), a Ruby program developed by the Global Names Architecture. I wrote a small script to automatically organize dwca-hunter's results, and have been running it regularly and uploading the results to http://gaurav.github.com/itis-dwca/. 2012 Gaurav Vaidya
To provide end-users with a familiar graphical user interface with which to access PhyloTastic services I have developed several wrapper classes that enable interaction with TNRS, DateLife, BabelPhysh and pruning functionality within the Galaxy web application. A demo Galaxy instance is available at http://galaxy.phylotastic.org, the source code at https://github.com/phylotastic/arch-galaxy and a screen cast that demonstrates the currently available functionality is available at http://youtu.be/kMME658xOu4 2012 Rutger Vos
Using the OpenSim software, a 6 region grid was set up on virtual machine instances at Amazon's EC2 to host the 3D environments for this project. The EC2 API tools were used to automate starting and stopping the server instances in order to reduce costs by not running the instances at night when they are not used. Monitoring software was set up to restart the OpenSim software in case of errors. 2012 Mattison T Ward, Corey Hart
Zaher Md. Faridee, A., Iverson, K., Westcott, S. 2012. Random Forest for Mothur: A machine learning algorithm for ecology data. This implementation of the random forest algorithm enables ecologists to identify bacterial populations that are associated with differences between health and disease using mothur. 2012 Sarah Westcott, Kathryn Iverson, Abu Zaher Md Faridee
Zarins, J., Rambaut, A., Cranston, K., Redelings, B. 2012. MASTodon: Summary and visualization of phylogenetic tree sets. MASTodon looks for a common subtree in a large set of phylogenetic trees. Suitability of a subtree is measured with a MAP (maximum a-posteriori probability) score. MASTodon prunes some taxa from all trees and compares each against the MAP tree. This is the same as counting the trees that contain the subtree that is obtained if you remove the selected taxa from the trees. Command line and graphical interfaces are provided. Several pruning algorithms are available, and it is possible to add more. 2012 Justs Zarins, Andrew Rambaut, Karen Cranston
A plugin for the Protege ontology editing environment which displays images depicting instances of the selected ontology class. 2011 Jim P Balhoff
C.E. Wall, V. Gapeyev, X. Liu, and H. Lapp (2011) Feeding Experiments End-user Database. http://feedexp.org, source code at https://github.com/NESCent/feedingdb 2011 Christine E Wall, Vladimir Gapeyev, Xianhua Liu, Hilmar Lapp
Engelhardt, J., & Procter, J. 2011. Extending Jalview to handle RNA with VARNA (Visualization Applet for RNA). 2011 Jan Engelhardt, Jim Procter
Ginsca, A.L., Balhoff, J. 2011. ontophenotype-eol. A Java library that generates human readable text from ontologies containing phenotype data for integration into the Encyclopedia of Life (EoL). 2011 Alexandru Lucian Ginsca, Jim P Balhoff
Hird, S., Brown, J., Chapman, B. 2011. lociNGS: a simple database for reformatting and displaying multi-locus datasets. 2011 Sarah Hird, Jeremy Brown, Brad Chapman
Hoffman, P., Savidge, K., & Brown, J. 2011. CUDA graphics optimization for DIM SUM simulations with large scale populations and landscapes. 2011 Peter Hoffmann, Kevin Savidge, Jeremy Brown
Packer, D. & Estill, J. 2011. TreeRecXML. Perl/BioPerl implementation of tree reconciliation representations in XML. A contribution to the Tree of Life for the Plant Sciences (iPToL) project (via https://pods.iplantcollaborative.org/wiki/display/iptol/Reconciled+Trees+in+XML). 2011 Daniel Packer, James Estill
Piwowar HA (2011) Data from: Who shares? Who doesn't? Factors associated with openly archiving raw research data. Dryad Digital Repository. doi:10.5061/dryad.mf1sd 2011 Heather Piwowar
Piwowar HA, Vision TJ, Whitlock MC (2011) Data from: Data archiving is a good investment. Dryad Digital Repository. doi:10.5061/dryad.j1fd7 2011 Todd Vision, Michael Whitlock, Heather Piwowar
Popescu, A.-A., Huber, K., & Paradis, E. 2011. APE (Analyses of Phylogenetics and Evolution) incomplete distance extension. Extends APE to handle evolutionary reconstruction from incomplete distance matrices. 2011 Andrei-Alin Popescu, Katharina Huber, Emmanuel Paradis
Revell, L. J. 2011. phytools: Phylogenetic Tools for comparative biology (and other things). R package version 0.0-8. http://CRAN.R-project.org/package=phytools 2011 Liam J Revell
Verma, A., & Iverson, K.D. 2011. PhyloGeoRef. Java library that takes a phylogenetic tree and metadata associated with taxonomic units in the tree as input; and creates a kml file that can be viewed in Google Earth. This project focused on enhancing phyloGeoRef through the addition of a GUI for non-Java users; and weighted means for node positioning. 2011 Apurv Verma, Kathryn Iverson
Web application, database, and reasoning system integrating phenotypic data from over 50 phylogenetic publications across teleost fish with developmental genetic phenotype data from the Zebrafish Information Network (ZFIN). 2011 Jim P Balhoff
Yohe, L., Vos, R., & Piel, W. 2011. Towards automated submission of NeXML data to TreeBASE. This project contributed to automation of NeXML formatted data to TreeBASE, and to related data display functionality. 2011 Laurel Yohe, Rutger Vos, William H Piel
Piwowar HA and Priem J. total-impact. http://total-impact.org, code at https://github.com/total-impact 2010-present Heather Piwowar
Balejko, F., & Kosakovsky Pond, S.L. 2010. Extending Galaxy: Integration of HyPhy workflows and the SLAC and PARRIS methods for inferring positive selection on coding sequences. 2010 Filip Balejko, Brad Chapman, Anton Nekrutenko
Clements, D., Dauga, D., Balhoff, J., Friesen, M., Yoder, M., Washington, N., Cain, S., Redmond, S., Vgapeyev, V., Ybendana, Y. (2010). GMOD & Chado natural diversity modules: ND revision and proof of concept Rails implementation. GMOD Tools for Evolutionary Biology Hackathon, Natural Diversity and Phenotypes in Chado Subgroup, 8-12 November, 2010. Hackathon code: https://github.com/gmodevohack 2010 Delphine Dauga, Jim P Balhoff, Maren Friesen, Nicole Washington, Scott Cain, Seth Redmond
Fields, C., Lapp, H., Stajich, J., & Jordan, G. (2010). GMOD BioPerl Enhancements. GMOD Tools for Evolutionary Biology Hackathon, BioPerl Subgroup, 8-12 November, 2010. Improved tree handling in BioPerl to enable handling very large trees or large numbers of small trees. BioPerl now supports storing such trees in a lightweight database instead of in memory. Core BioPerl 1.x code: http://bioperl.org 2010 Jason E Stajich, Hilmar Lapp, Chris Fields
Hayes, R.; Buels, R.; McKay, S.. (2010). gmod:GBrowse syn2. GMOD Tools for Evolutionary Biology Hackathon, Visualization of Comparative Genomics: JBrowse syn Subgroup, 8-12 November, 2010. GBrowse_syn refactored to fit GBrowse2 architecture; consolidated image rendering abstracted in a new class. Several new classes created under Bio::Graphics::Browser2 for object representation and rendering. 2010 Richard Hayes, Robert Buels, Sheldon McKay
Hill, A., Leto, J., Pick, S. (2010). Polishing PhyloBox: PhyloBoxWidget, Documentation, Application integration. GMOD Tools for Evolutionary Biology Hackathon, PhyloBox Polishing & API Subgroup, 8-12 November, 2010. 2010 Andrew Hill, Jonathan Leto, Sander Pick
Hitz, B., and Lyons, E. (2010). gmod:GMatchbox: creating a common backend for comparative genomics visualization. GMOD Tools for Evolutionary Biology Hackathon, Visualization of Comparative Genomics: GMatchbox Subgroup, 8-12 November, 2010. 2010 Eric Lyons, Benjamin Hitz
Iverson, K.D., and Kidd, D. 2010. PhyloGeoRef: A Java library for producing phylogenetic data kmls to be rendered in Google Earth. 2010 Kathryn Iverson, David Kidd, Karen Cranston, Xianhua Liu
Lui, L., Procter, J., and Vilella, A. 2010. Extending Jalview: Supporting Rfam RNA sequence and alignment imports and secondary structure visualizations. Extends Jalview functionality to enable RNA sequences and alignments to be imported from the Rfam database (http://rfam.sanger.ac.uk/); and supports RNA secondary structure visualizations, including relevant color schemes. 2010 Lauren Lui, Jim Procter, Albert Vilella
Pond, S.K., Balejko, F. (2010). gmod:Galaxy integration module for interactive tools. GMOD Tools for Evolutionary Biology Hackathon, Galaxy and HyPhy Subgroup, 8-12 November, 2010. Improves Galaxy's ability to integrate interactive tools, using HyPhy as the prototype application. Galaxy web home: http://galaxyproject.org/. 2010 Sergei Kosakovsky Pond, Filip Balejko
Priyam, A., Vos, R., & Aerts, J. 2010. BioRuby API for NeXML I/O and RDF triples. Adds support to work with RDF and NeXML in BioRuby; and provides methods to semantically annotate and query BioRuby objects. 2010 Rutger Vos, Jan Aerts, Anurag Priyam
(Released 7/7/2010) BAli-Phy is a Bayesian MCMC program for estimating phylogenies and sequence alignments jointly from unaligned sequence data. BAli-Phy can estimate phylogenies without bias toward a guide tree, when the alignment is uncertain.

New features in the 2.1.0 release include:
  • Allow multiple separate genes as input
  • Each gene may have a different substitution or indel model
  • Decrease the amount of RAM used.
  • Speed up the analysis for many taxa (e.g. > 30).
  • Auto-detect step sizes in slice sampling.
 2010 Benjamin D Redelings
Stack, J.C., O'Meara, B., Harmon, L. 2010. RBrownie: Ancestral State Reconstruction in R. Extends comparative phylogenetic analysis capabilities in R. 2010 Conrad Stack, Luke Harmon, Brian C O'Meara
TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. A second-generation version of TreeBASE was released in 2010 and is hosted by NESCent.
Source code: http://sf.net/projects/treebase		 2010 Todd Vision, Hilmar Lapp, Vladimir Gapeyev, William H Piel, Rutger Vos, Val Tannen
Wasila Dahdul and Peter Midford. 2010. Phenoscape Ontologies. Phenoscape is using multiple ontologies to describe variation in phenotypes across species. We have developed several new ontologies required for evolutionary biology, including the Teleost Anatomy Ontology (TAO) and the Teleost Taxonomy Ontology (TTO). As community resources, these ontologies are available within the OBO Foundry . Wasila Dahdul and Peter Midford are the maintainers of the ontologies developed by Phenoscape. 2010 Peter E Midford, Wasila Dahdul
Yi, H., Skinner, M., Casstevens, T., Tritt, A., & Mueller, O. (2010). gmod:JBrowse: Visualizing comparative geneomics. GMOD Tools for Evolutionary Biology Hackathon, Visualization of Comparative Genomics: JBrowse syn Subgroup, 8-12 November, 2010. Extended JBrowse through removal of the "single genome" assumption from the code and successfully displayed several genomes in parallel. 2010 Hong Yi, Terry Casstevens, Andrew Tritt, Olaf Mueller
Alexei Drummond. 2009. A project to create an open API and fast implementations of a library for evaluating phylogenetic likelihoods (continuous time Markov processes) of biomolecular sequence evolution. The aim is to provide high performance evaluation 'services' to a wide range of phylogenetic software, both Bayesian samplers and Maximum Likelihood optimizers. This will allow these packages to make use of implementations that make use of optimized hardware such as graphics processing units. 2009 Alexei Drummond
Andrew L. Hipp and Marcial Escudero. 2009. MATICCE - a software package in the R language that employs an information-theoretic approach to infer shifts in continuous character distribution on phylogenetic trees. MATICCE also provides simulation functions for visualizing analysis results, functions for accounting for phylogenetic and model uncertainty, and helper functions for the ouch R package. 2009 Andrew L. Hipp
Ayres, D., Darling, A., Suchard, M. 2009. Extending BEAGLE: GPU acceleration for phylogenetic inference using OpenCL. 2009 Daniel Ayres, Aaron Darling, Marc Suchard
Constable, H and Russell, L. 2009. VertNet is a global museum database of vertebrate natural history collections. Four distributed database networks (MaNIS, HerpNET, ORNIS and FishNet) have been the result of a massive, collaborative effort within the museum and bioinformatics communities to make specimen data interoperable, mappable and publicly available. VertNet was formed as an umbrella project to meet the common needs of the participants, maintain the existing networks, add new members and develop integrated online technologies. 2009 James Hanken
Extension of the SADI (Semantic Automated Discovery and Integration) system to integrate biodiversity data. A demo SADI Web Service was created showing how GBIF (http://vocabularies.gbif.org/) data can be served via SADI (Semantic Automated Discovery and Integration). A second service was constructed that extracts taxonomy information from the UniProt protein record. 2009 Mark Wilkinson
Hayden, K., Midford, P., Balhoff, J. 2009. 'Build a Mesquite package to view Phenex-generated Nexml files', a Google summer of code project. This project resulted in a Mesquite plug-in package that used the nexml library for java to parse and display ontology-based annotations from nexml files generated by Phenex. The tool displays annotations within the Mesquite character matrix editor. 2009 Peter E Midford, Jim P Balhoff, Kasia Hayden
Hyam, R., Gopalan, V., Chisham, B., Pontelli, E., Jensen, M., & Yoder, M. (2009). Semantic API for CDAO. NESCent Hackathon on Evolutionary Database Interoperability, Semantic API for CDAO Subgroup. 9-13 March, 2009, Durham, NC. Hackathon code: https://code.google.com/p/dbhack1/ 2009 Roger Hyam, Vivek Gopalan, Brandon Chisham, Enrico Pontelli, Mark A Jensen
Jaunzeikare, D. & Zmasek, C. 2009. phyloXML support in BioRuby. 2009. Reading and writing capabilities for phyloXML in BioRuby. 2009 Diana Jaunzeikare, Christian M. Zmasek
Jiao, D., & Scherle, R. 2009. Enhanced search functionality in Phylr. Enhanced Phylr service for searching content in a collection of XML files, using Lucene; and new services for searching relational databases. 2009 Dazhi Jiao, Ryan Scherle
Jonathan Payne, Jennifer Stempien, Hilmar Lapp, Xianhua Liu, Michal Kowalewski. 2009. Maximum Size Database. 2009. Phanerozoic Body Size Trends through Time and Space Working Group. National Evolutionary Synthesis Center. Code at http://github.com/NESCent/max-bodysize-evol , web application at http://bodysize.nescent.org 2009 Jonathan Payne, Jennifer Stempien, Hilmar Lapp, Xianhua Liu, Michal Kowalewski
Jordan, Greg; McKay, Sheldon; Seltmann, Katja; Stoltzfus, Arlin. (2009). Enhancing PhyloWidget to provide a generic, customizable web-based interface for interacting with and visualizing phylogenetic trees. NESCent Hackathon on Evolutionary Database Interoperability, Visualization Subgroup. 9-13 March, 2009, Durham, NC. Enhancements implement methods to edit visual parameters (e.g., branch width, color, node shape); simple database searching; and tree transformations. Hackathon code: https://code.google.com/p/dbhack1/ 2009 Sheldon McKay, Katja Seltmann, Arlin Stoltzfus, Gregory E Jordan
Matzke, N., & Smith, S. 2009. Bio.Geography. Bio.geography is a Biophython that enables automated searching, downloading, and parsing of geographic location records from the Global Biodiversity Information Facility (GBIF). 2009 Nick Matzke, Stephen Smith
Midford, P., Balhoff, J., Donnelly, S., & Vos, R. (2009). Java API for the NeXML data model. NESCent Hackathon on Evolutionary Database Interoperability, Java API Library to NeXML Subgroup. 9-13 March, 2009, Durham, NC. 2009 Peter E Midford, Jim P Balhoff, Rutger Vos
Midford, P. E. 2009. Phylontal Phylontal is a tool developed to explore phylogenetically aware alignment of multiple taxon-specific ontologies. 2009 Peter E Midford
Miller, C., Jensen, M., & Vos, R. 2009. NeXML support in BioPerl via Bio::Phylo. 2009 Chase Miller, Mark A Jensen, Rutger Vos
Participants of the Evolutionary Database Interoperability Hackathon. 2009. Phylr is an initial proof-of concept implementation of the PhyloWS API, making phylogenetic information available via a standard set of web services. 2009 Ryan Scherle, Lucie Chan, Vladimir Gapeyev, Hilmar Lapp, Jeet Sukumaran
Piel, W., Cranston, K., Kosnik, M., & Seltmann, K. (2009). A new flavor of PhyloWS to return TreeBASE objects in NeXML. NESCent Hackathon on Evolutionary Database Interoperability, Taxonomic Intelligence Subgroup. 9-13 March, 2009, Durham, NC. 2009 Karen Cranston, Matthew A. Kosnik, Katja Seltmann
Shuai, X., Fields, C., Prins, P. 2009. BioLib mapping for the libsequence population genetic libraries. Extends the BioLib project by adding access to Libsequence, a C++ library for population genetic simulation and the evolutionary analysis of molecular data. Mappings to Perl and Python made available using SWIG. 2009 Xin Shuai, Chris Fields, Pjotr Prins
Smith, A.A., & Prins, P. 2009. Mapping the Bio++ Phylogenetics toolkit to R/BioConductor and BioJAVA: A contribution to the BioLib project. 2009 Adam Smith, Pjotr Prins
Smith, S.A. (2009). PHLAWD: phylogenetic dataset construction. PHLAWD (pronounced flawd) allows for the rapid creation of large (mega) phylogenies using NCBI databases. PHLAWD takes advantage of multi threaded computers and can produce matrices of more than 100,000 taxa. Target audiences for PHLAWD include evolutionary biologists hoping to mine GenBank for data associated with their lineages, and also comparative biologists and ecologists who want to develop phylogenetic hypotheses. Binaries for MacOSX and Linux are available at: http://code.google.com/p/phlawd. It is recommended that you work with the source code for the most updated version (https://github.com/blackrim/phlawd). The manual is at the PHLAWD site: http://phlawd.net/. 2009 Stephen Smith
Talevich, E., & Chapman, B. 2009. Tree and TreeIO. Supports phyloXML use in biophython. 2009 Eric Talevich, Brad Chapman
Todd Vision, Ryan Scherle, Hilmar Lapp, Jane Greenberg, Peggy Schaeffer, Kevin Clarke, Peter Midford, Mark Diggory. 2012. Dryad - a repository of data underlying scientific publications, with an initial focus on evolutionary biology and related fields. Developed by Nescent and the University of North Carolina Metadata Research Center, in coordination with a large group of Journals and Societies in evolutionary biology and ecology.
Source code: http://dryad.googlecode.com/		 2009 Todd Vision, Ryan Scherle, Hilmar Lapp, Jane Greenberg, Peggy Schaeffer, Kevin S Clarke, Peter E Midford
Ackerman, M., Midford P. E., Maddison, W. P. 2008. Pdsimul: A Mesquite implementation of PDAP pdsimul, Google Summer of Code project. Project resulted in a Mesquite package (plugin) that simulated evolutionary change in multiple continuous-valued characters up a tree, effectively an extension of the DOS PDAP application of the same name. 2008 Peter E Midford, Matthew Ackerman, Wayne Maddison
Brian O'Meara (2008). TreeTapper. TreeTapper is a database of methods for using phylogenies to understand evolution. Status: well-developed database schema, work is ongoing on php scripts for adding content to the database and for displaying web pages.
Development site: http://treetapper.nescent.org
Source code: http://code.google.com/p/treetapper/		 2008 Brian C O'Meara
Chen, D., J.G. Burleigh, M.S. Bansal, and D. Fernandez-Baca. 2008. PhyloFinder: an intelligent search engine for phylogenetic tree databases. BMC Evol. Biology 8:90. describes a new software tool for accessing data from tree databases. The software home page at http://pilin.cs.iastate.edu/phylofinder/ has become unavailable, and no other location is known. 2008 Gordon Burleigh
Cowan, P., & Bolker, B. 2008. Tree and data plotting in the phylobase project. Implements a plotting function for visualizing phylo4 and phylo4d data objects. A key feature of the functions is the use of the grid graphics interface. This interface allows more flexible plot resizing and pushing of arbitrary plots to tree tips. 2008 Peter Cowan, Ben Bolker
Ganeshkumar Ganapathy, Nihshanka Debroy. DQ: A python package for multilocus disequilibria. 2008 Ganeshkumar Ganapathy
Han, M., Fields, C. 2008. SAX-based phyloXML support in BioPerl. Extends BioPerl by adding a parser to read and write phyloXML; also enabled addition of general annotations in the BioPerl Node module. 2008 Mira Han, Chris Fields
Helmus, M., Kembel, S., Bolker, B. 2008. Enhancing the representation of ecophylogenetic tools in R Picante. Added methods to assess phylogenetic community structure; the effects of environmental variables on phylogenetic community structure; and phylogenetic structure among species interactions in the R package Picante. 2008 Matthew Helmus, Steven Kembel, Ben Bolker
Hilmar Lapp, Xianhua Liu, members of the Primate Life Histories Working Group. Primate Life Histories Database. Code at http://github.com/NESCent/plhdb , online application at http://plhdb.org 2008 Hilmar Lapp, Xianhua Liu, Susan C Alberts
Jim Balhoff. 2008. Phenex - an application for annotating character matrix files with ontology terms. Character states can be annotated using the Entity-Quality syntax for ontologically describing phenotypes. In addition, taxon entries can be annotated with identifiers from a taxonomy ontology. Phenex saves ontology annotations alongside traditional character matrix data using the new NeXML format standard for evolutionary data 2008 Jim P Balhoff
Jim Balhoff. 2008. Phenote - a Java-based stand-alone phenotype annotation and curation tool. 2008 Jim P Balhoff
Kleikamp, M., Spencer, N.J., Caceres, M., Peet, R.K. 2008. Vegschema 1.4. It is an international exchange standard for plot-based vegetation data that is accepted by the broader vegetation science community. 2008 Robert Peet, Nick Spencer
Lewis, Holder, et al. 2008. Nexus Class Library. The Nexus Class Library (NCL) is a C++ library for interpreting data files created according to the NEXUS file format used in phylogenetic systematics and molecular evolution. 2008 Brian C O'Meara
Maddison, W. P., and M. J. Ramirez. 2006. Simple Image LinKing (SILK): A Mesquite package for associating images with character matrices. 2008 Martin Ramirez
McMillan, P., & O'Meara, B. 2008. DBGraphNav: Graphviz navigation of databases. DBGraphNav facilitates visual graphing of relational information stored in databases. It provides a PHP framework for a website developer to display a graphical map of relational information using AT&T's Graphviz program. 2008 Paul McMillan, Brian C O'Meara
O'Meara, B.C. 2008. Brownie 2.1. Brownie is a program for analyzing rates of continuous character evolution and looking for substantial rate differences in different parts of a tree using likelihood ratio tests and Akaike Information Criterion (AIC) statistics. It now also implements many other methods for examining trait evolution and methods for doing species delimitation. See below for info on downloading the program. http://www.brianomeara.info/brownie 2008 Brian C O'Meara
O'Meara, B.C. 2008. MrFisher. This program a slight modification of MrBayes to do simulated annealing maximum likelihood tree searches (Bayes is credited with inventing Bayesian statistics, Fisher with inventing likelihood). 2008 Brian C O'Meara
O'Meara, B.C. 2008. TreEvo. TreEvo (TREE + EVOlution) is an assortment of methods for understanding evolution using trees. It aims to be compatible and complementary with the wide assortment of existing packages in this area in R. 2008 Brian C O'Meara
Payne JL, Boyer AG, Brown JH, Finnegan S, Kowaleski M, Krause Jr RA, Lyons SK, McClain CR, McShea DW, Novack-Gottshall PM, Smith FA, Stempien JA, Wang SC (2008) Data from: Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity. Dryad Digital Repository. doi:10.5061/dryad.223 2008 Jonathan Payne, Alison G. Boyer, Seth Finnegan, Michal Kowalewski, Richard Krause, Sara Lyons, Craig R McClain, Daniel McShea, Philip Novack-Gottshall, Felisa A Smith, Jennifer Stempien, Steve C Wang
Prosdocimi, F., B. Chisham, E. Pontelli, J.D. Thompson, and A. Stoltzfus. 2008. Comparative Data Analysis Ontology (CDAO), an OWL-DL ontology for evolutionary comparative analysis. 2008 Arlin Stoltzfus, Francisco Prosdocimi, Julie Thompson, Enrico Pontelli, Brandon Chisham
Public interface for the Phenoscape Project. Phenoscape was initiated to create a scalable infrastructure that enables linking descriptive phenotype observations across different fields of biology by the semantic similarity of their free-text descriptions. 2008 Hilmar Lapp, Jim P Balhoff
Qiu, WG. 2007. A collection of data sets for phylogenetic analysis. 2008 Weigang Qiu
Qiu, WG. 2008. A new BioPerl module for reading nexml file. Bio::TreeIO:nexml 2008 Weigang Qiu
Ramirez, M. J., J. A. Coddington, P. Midford. 2007. Spider comparative biology: Ontology of terms. 2008 Martin Ramirez
Stoltzfus, A. 2008. MIAPA annotation tool (proof-of-concept software). To demonstrate the potential for users to construct their own ontology-based MIAPA annotations, as in the knowledge capture experiment below, we have created a proof-of-concept application by adapting Phenote. The result is an interactive graphical tool for user-generated, ontology-bound MIAPA annotations. 2008 Arlin Stoltzfus
Wallinga, M., & Balhoff, J. 2008. Matrix display of phenotype annotations using ontologies in Phenote. Extends Phenote by adding matrix representations of annotation data. The matrix is populated by consolidating phenotype annotations into characters by finding values which descend from the same attribute within the PATO phenotype ontology; and character values are grouped by taxon and character. 2008 Michael Wallinga, Jim P Balhoff
Wehe, A., M.S. Bansal, J.G. Burleigh, and O. Eulenstein. 2008. Dupertree: a program for large-scale gene tree parsimony phylogenetic analyses. Dupertree describes a new program for inferring phylogenies by gene tree parsimony. It is also publicly available. Other software used to build supertrees and identify ancient large-scale duplication events in the above manuscripts will eventually be released to the public. 2008 Gordon Burleigh, Oliver Eulenstein
Alfaro, M., Midford, P., Orme, D., Rabosky, D. (2007). Extending the Laser package to handle diversification rate shifts using combined phylogenetic and taxonomic data. NESCent Hackathon on Comparative Methods in R, Diversification Subgroup, 10-14 December, 2007. 2007 Michael Alfaro, Peter E Midford, David Orme, Dan Rabosky
Bell, C., Loarie, S., Swofford, D., Waddell, P. (2007). Extending Ape with a new tree parameterization (Swofford). NESCent Hackathon on Comparative Methods in R, Divergence Time Estimation Subgroup, 10-14 December, 2007. 2007 Charles Bell, Scott Loarie, David L Swofford, Peter Waddell
Ben Bolker, Marguerite Butler, Peter Cowan, Steven Kembel, Thibaut Jombart, Aaron Mackey, Brian O'Meara, Damien de Vienne, David Orme, Derrick Zwickl, Francois Michonneau, Hilmar Lapp, Klaus Schliep. 2008. Phylobase. Defining the basic S4 classes and methods for representing and manipulating phylogenetic trees and data in R. 2007 Ben Bolker, Marguerite Butler, Peter Cowan, Thibaut Jombart, Steve Kembel, Brian C O'Meara
Bohyun Lee, Richard Holland, 2007. Biojavax phylo package and classes providing NEXUS and phylip file parsing and parsimony as well as UPGMA tree reconstruction for Biojava. 2007 Bohyun Lee, Richard Holland
David Kidd and Xianhua Liu. 2007. GeoPhylobuilder is an ESRI ArcGIS extension that creates a spatial network, a geophylogeny, from a tree file and associated geographical data. 2007 David Kidd, Xianhua Liu
Derrick Zwickl and James Balhoff. 2007. GARLI (Genetic Algorithm for Rapid Likelihood Inference) performs phylogenetic searches on aligned sequence datasets using the maximum-likelihood criterion. Version 0.96 is a major revision from the previous version 0.951. It includes many new features, including the ability to perform tree inference using amino acid and codon-based models, in addition to the standard nucleotide-based models available in previous versions. On a practical level, the program is able to perform maximum-likelihood tree searches on large datasets in a number of hours. 2007 Derrick Zwickl, Jim P Balhoff
Gregory Jordan and William Piel. 2007. PhyloWidget is a user-friendly and web-embeddable GUI based on Java/Processing for creating, navigating, and manipulating phylogenetic trees. 2007 Gregory E Jordan, William H Piel
Harmon, L., Hipp, A., & Hunt. (2007). Extending Geiger with fitCountinuous and fitDiscrete. NESCent Hackathon on Comparative Methods in R, Trait Evolution Subgroup, 10-14 December, 2007. Geiger was modified to give more reliable results by a more thorough search of the likelihood surface (fitContinuous) and to deal with a more general set of discrete character models (fitDiscrete). Geiger's tree transformations improved to work for nonultrametric trees. 2007 Luke Harmon, Andrew L. Hipp, Gene Hunt
H. Lapp and W. Maddison, 2010. RMesquite. The RMesquite package allows one to call Mesquite module methods for comparative analyses and for file input/output. 2007 Hilmar Lapp, Wayne Maddison
Hoeksema J. D. 2007. SAS code for conducting mixed-model meta-regression analysis in SAS. 2007 Jason Hoeksema
Hoeksema J. D. and S. Forde. 2007. Summary data on local adaptation, species traits, and experimental design across 29 cross-inoculation studies of species interactions. 2007 Jason Hoeksema
James Estill and Hilmar Lapp. 2007. Phy* is a command-line topological query suite for BioSQL. http://informatics.nescent.org/wiki/PhyloSoC:Command_Line_Topological_Query_Application_for_BioSQL 2007 Hilmar Lapp, James Estill
Jason E Stajich. 2007. BioPerl Population Genetics Modules. 2007 Jason E Stajich
Klaas Hartmann, Tobias Thierer, Rutger Vos. 2007. BioPrio. BioPrio implements various algorithms that utilize phylogenetic information to prioritize species for biodiversity conservation and provides a GUI that allows these to be utilized by conservation managers. 2007 Tobias Thierer, Rutger Vos, Klaas Hartmann
Lars Barquist and Ian Holmes. 2007. xREI is an AJAX-based web interface and visualization server for xrate and its grammar files. 2007 Lars E Barquist, Ian Holmes
Lee B.Y. and R. Holland. 2007. Phlyogenetics extensions in BioJava 2007 Richard Holland, Bohyun Lee
Leung, J., & Lewis, S. xrateparser. A Perl module that runs as a web application to harnesses xrate for tree generation as .png or .svg images. Trees are generated from raw .tre files (Newick format) of .stk files, and are .png or .svg images of trees to be displayed on a webpage. 2007 James Leung, Suzanna Lewis
Okada, M.O., & Stein, L. 2007. Phylogenetic & haplotype displays for GBrowse. Extended visualization for the GBrowse Genome Browser by dividing the single large image to multiple tracks; and created a data track to display DNA alignment data for multiple target species. 2007 Hisanaga Okada, Lincoln Stein
Osborne, B.I., and S. Cain. 2007. The new GMOD Wiki with complete GMOD documentation. 2007 Brian Osborne
Ree, R. H. and S. A. Smith. 2007. Lagrange: likelihood analysis of geographic range evolution. Lagrange is a Python package implementing likelihood models for geographic range evolution on phylogenetic trees, with methods for inferring rates of dispersal and local extinction and ancestral ranges. 2007 Richard Ree, Stephen Smith
Rutger Vos, Jason Caravas and participants of the EvoInformatics working group. 2007. NeXML is an exchange standard for representing phylogenetic data inspired by the commonly used NEXUS format, but more robust and easier to process. 2007 Rutger Vos, Jason Caravas
Susan Kalisz, Mark Johnston and members of the Mixed Mating Working Group. 2007. The prototype database integrates comprises four separate databases. 1) The mating system database contains information on estimates of selfing/outcrossing rate and/or the inbreeding coefficient measured at the population level for 475 species. 2) The inbreeding depression database contains information on estimates inbreeding depression measured across the life history (3-stage or 4-stage IBD) measured at the population level. 3) The experimental pollination database contains information at the population level on experimental tests of selfing, outcrossing, pollen limitation, reproductive assurance, timing of selfing, etc. 4) The species traits database contains data on the average morphological, phenological, life history and habitat characteristics for all 475 species in the mating system database. Significantly, all four databases contain citations to the original publications from which the data were extracted. 2007 Susan Kalisz, Mark Johnston, Hilmar Lapp, Xianhua Liu
Yi-Hsin Tsai and David Kidd. 2007. PhyloGeoViz is a web based application that generates geographic maps (using the Google Maps API) of DNA haplotype data that are often used in the course of phylogeographic analysis. 2007 Yi-Hsin Tsai, David Kidd
Hilmar Lapp and William Piel. 2006. The PhyloDB module extends the core BioSQL schema to allow storing phylogenetic trees or reticulate networks and metadata in a simple yet extensible way. An associated Perl script loads the ITIS taxonomy into the module. 2006 Hilmar Lapp, William H Piel
Publications
Finnegan, S., S.C. Anderson, P.G. Harnik, C. Simpson, D.P. Tittensor, J.E. Byrnes, Z.V. Finkel, D.R. Lindberg, L.H. Liow, R. Lockwood, H.K. Lotze, C.M. McClain, J.L. McGuire, A. O'Dea, and J.M. Pandolfi. In press. Paleontological baselines for evaluating extinction risk in the modern oceans. Science. In press Paul G Harnik
Orzechowski, E.A., R. Lockwood, J. Byrnes, S.C. Anderson‡, S. Finnegan, Z.V. Finkel, P.G. Harnik, D.R. Lindberg, L.H. Liow, H.K. Lotze, C.R. McClain, J.L. McGuire, A. O’Dea, J.M. Pandolfi, C. Simpson, and D.P. Tittensor. In press. Marine extinction risk shaped by trait-environment interactions over 500 million years. Global Change Biology. In press Paul G Harnik
Robinson, B.W. and Pfennig, D.W. Inducible competitors and adaptive diversification. Current Zoology, in press (3/2013). Special issue: Evolution of phenotypic plasticity. In press Beren Robinson
Dillman, C. B., B. L. Sidlauskas and R. P. Vari. in press. A morphological supermatrix-based phylogeny for the Neotropical fish superfamily Anostomoidea (Ostariophysi: Characiformes): phylogeny, missing data and homology. Cladistics. in press Brian L. Sidlauskas
Smith, N.A. in press. Paleontologia Electronica-Fossil Calibration Series. in press N. Adam Smith
Benton, M.J., P.C.J. Donoghue, R.J. Asher, M. Friedman, T.J. Near and J. Vinther. 2015. Constraints on the timescale of animal evolutionary history. Palaeontologia Electronica 18.1.5FC. 2015 Daniel Ksepka
C J Murren, J R Auld, H Callahan, C K Ghalambor, C A Handelsman, M A Heskel, J G Kingsolver, H J Maclean, J Masel, H Maughan, D W Pfennig, R A Relyea, S Seiter, E Snell-Rood, U K Steiner and C D Schlichting. 2015, Constraints on the evolution of phenotypic plasticity: limits and costs of phenotype and plasticity, Heredity, 2015 Carl Schlichting
D. Kainer and R. Lanfear. 2015, The Effects of Partitioning on Phylogenetic Inference, Molecular Biology and Evolution 2015 Robert Lanfear
D.T. Ksepka, J.F. Parham, J.F. Allman, M.J. Benton, M.T. Carrano, K.A. Cranston, P.C.J. Donoghue, J.J. Head, E.J. Hermsen, R.B. Irmis, W.G. Joyce, M. Kohli, K.S. Lamm, D. Leehr, J.S.L. Patané, P.D. Polly, M.J. Phillips, N.A. Smith, N.D. Smith, M. van Tuinen, J.L. Ware and R.C.M. Warnock. IN REVISION. The Fossil Calibration Database, A New Resource for Divergence Dating. Systematic Biology. 2015 Daniel Ksepka
Hidaka BH, Asghar A, Aktipis CA, Nesse RM, Wolpaw TM, Skursky NK, Bennett KJ, Beyrouty MW, Schwartz MD. The status of evolutionary medicine education in North American medical schools. BMC Medical Education. 2015;15:38-47 2015 Nicole Skursky
J. C. Crawford and C. M. Drea. 2015, Baby on board: olfactory cues indicate pregnancy and fetal sex in a non-human primate, Biology Letters, volume 11, issue 2, pp. 20140831-20140831 2015 Jeremy Chase Crawford
Ksepka, D.T. and J.A. Clarke. 2015. Phylogenetically vetted and stratigraphically constrained fossil calibrations within Aves. Palaeontologia Electronica 18.1.3FC. 2015 Daniel Ksepka
Ksepka, D.T. and M.J. Phillips. IN REVIEW. Avian diversification patterns across the K-Pg boundary: influence of calibrations, datasets and model misspecification. Annals of the Missouri Botanical Garden (invited contribution to systematics symposium volume). 2015 Daniel Ksepka
Laura Ross and Benjamin B. Normark. 2015, Evolutionary problems in centrosome and centriole biology, Journal of Evolutionary Biology, pp. n/a-n/a 2015 Laura Ross, Benjamin Normark
Liggins, L., Booth, D. G., Figueira, W. F., Treml, E. A., Tonk, L., Ridgway, T., Harris, D. A., Riginos, C. 2015. Latitude-wide genetic patterns reveal historical effects and contrasting patterns of turnover and nestedness at the range peripheries of a tropical marine fish. Ecography: 10.1111/ecog.01398 2015 Libby Liggins
L. Ross, H. Blackmon, P. Lorite, V. E. Gokhman and N. B. Hardy. 2015, Recombination, chromosome number and eusociality in the Hymenoptera, Journal of Evolutionary Biology, volume 28, issue 1, pp. 105-116 2015
M. B. Blanco and S. M. Zehr. 2015, Striking longevity in a hibernating lemur, J Zool, pp. n/a-n/a 2015 Sarah Zehr
Paul B Frandsen, Brett Calcott, Christoph Mayer and Robert Lanfear. 2015, Automatic selection of partitioning schemes for phylogenetic analyses using iterative k-means clustering of site rates, BMC Evol Biol, volume 15, issue 1 2015 Paul Frandsen, Brett Calcott, Robert Lanfear
Phillips, M.J. 2015. Four mammal fossil calibrations: balancing competing palaeontological and molecular considerations. Palaeontologia Electronica 18.1.5FC. 2015 Daniel Ksepka
Polly, P.D., D.T. Ksepka and J.F. Parham. 2015. Announcing the Fossil Calibration Series and Database. Palaeontologia Electronica 18: 1-5. 2015 Daniel Ksepka
Smith, N.A. 2015. Sixteen vetted fossil calibrations for divergence dating of Charadriiformes (Aves, Neognathae). Palaeontologia Electronica 18.1.4FC. 2015 Daniel Ksepka
B. B. Normark and L. Ross. 2014, Genetic conflict, kin and the origins of novel genetic systems, Philosophical Transactions of the Royal Society B: Biological Sciences, volume 369, issue 1642, pp. 20130364-20130364 2014
Best EV, Schwartz MD. Fever. Evolution, Medicine, and Public Health. 2014;2014(1):92. 2014 Nicole Skursky
B. Misof, S. Liu, K. Meusemann, R. S. Peters, A. Donath, C. Mayer, P. B. Frandsen, J. Ware, T. Flouri, R. G. Beutel, O. Niehuis, M. Petersen, F. Izquierdo-Carrasco, T. Wappler, J. Rust, A. J. Aberer, U. Aspock, H. Aspock, D. Bartel, A. Blanke, S. Berger, A. Bohm, T. R. Buckley, B. Calcott, J. Chen, F. Friedrich, M. Fukui, M. Fujita, C. Greve, P. Grobe, S. Gu, Y. Huang, L. S. Jermiin, A. Y. Kawahara, L. Krogmann, M. Kubiak, R. Lanfear, H. Letsch, Y. Li, Z. Li, J. Li, H. Lu, R. Machida, Y. Mashimo, P. Kapli, D. D. McKenna, G. Meng, Y. Nakagaki, J. L. Navarrete-Heredia, M. Ott, Y. Ou, G. Pass, L. Podsiadlowski, H. Pohl, B. M. von Reumont, K. Schutte, K. Sekiya, S. Shimizu, A. Slipinski, A. Stamatakis, W. Song, X. Su, N. U. Szucsich, M. Tan, X. Tan, M. Tang, J. Tang, G. Timelthaler, S. Tomizuka, M. Trautwein, X. Tong, T. Uchifune, M. G. Walzl, B. M. Wiegmann, J. Wilbrandt, B. Wipfler, T. K. F. Wong, Q. Wu, G. Wu, Y. Xie, S. Yang, Q. Yang, D. K. Yeates, K. Yoshizawa, Q. Zhang, R. Zhang, W. Zhang, Y. Zhang, J. Zhao, C. Zhou, L. Zhou, T. Ziesmann, S. Zou, Y. Li, X. Xu, Y. Zhang, H. Yang, J. Wang, J. Wang, K. M. Kjer and X. Zhou. 2014, Phylogenomics resolves the timing and pattern of insect evolution, Science, volume 346, issue 6210, pp. 763-767 2014 Robert Lanfear
Burd, M. , C. T. Stayton, M. Shrestha, and A. G. Dyer. 2014. Distinctive convergence in Australian floral colours seen through the eyes of Australian birds. Proceedings of the Royal Scoiety of London B 281:20132862. 2014 Martin Burd
Burd, M. , C. T. Stayton, M. Shrestha, and A. G. Dyer. 2014. The colourful language of Australian flowers. Communicative and Integrative Biology 7:e28940. 2014 Martin Burd
C. Moray, R. Lanfear and L. Bromham. 2014, Domestication and the Mitochondrial Genome: Comparing Patterns and Rates of Molecular Evolution in Domesticated Mammals and Birds and Their Wild Relatives, Genome Biology and Evolution, volume 6, issue 1, pp. 161-169 2014 Robert Lanfear
Courtney J. Murren, Heidi J. Maclean, Sarah E. Diamond, Ulrich K. Steiner, Mary A. Heskel, Corey A. Handelsman, Cameron K. Ghalambor, Josh R. Auld, Hilary S. Callahan, David W. Pfennig, Rick A. Relyea, Carl D. Schlichting and Joel Kingsolver. 2014, Evolutionary Change in Continuous Reaction Norms, The American Naturalist, volume 183, issue 4, pp. 453-467 2014 Courtney Murren, Heidi Maclean , Sarah Diamond, Ulrich Steiner, Mary Heskel, Corey Handelsman, Cameron Ghalambor, Josh R Auld, Hilary Callahan, David Pfennig, Rick Relyea, Carl Schlichting, Joel Kingsolver
Davis, E.B., McGuire, J.L., Orcutt, J. 2014. Niche reconstructions of glacial refugia show consistent bias. Ecography. 37(11): 1133-8. 2014 Jenny L McGuire
Doris Bachtrog, Judith E. Mank, Catherine L. Peichel, Mark Kirkpatrick, Sarah P. Otto, Tia-Lynn Ashman, Matthew W. Hahn, Jun Kitano, Itay Mayrose, Ray Ming, Nicolas Perrin, Laura Ross, Nicole Valenzuela and Jana C. Vamosi. 2014, Sex Determination: Why So Many Ways of Doing It?, PLoS Biol, volume 12, issue 7, pp. e1001899 2014 Doris Bachtrog, Judith Mank, Catherine Peichel, Mark Kirkpatrick, Sarah Otto, Tia-Lynn Ashman, Matthew Hahn, Jun Kitano, Itay Mayrose, Ray Ming, Nicolas Perrin, Laura Ross, Nicole Valenzuela, Jana Vamosi
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J. P. Balhoff, I. Miko, M. J. Yoder, P. L. Mullins and A. R. Deans. 2013. A Semantic Model for Species Description Applied to the Ensign Wasps (Hymenoptera: Evaniidae) of New Caledonia, Systematic Biology, volume 62, issue 5, pp. 639-659 2013 Jim P Balhoff, Matthew Yoder, Andy Deans
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Rafael L. Rodríguez, Janette W. Boughman, David A. Gray, Eileen A. Hebets, Gerlinde Höbel, Laurel B. Symes and Greg GretherDiversification under sexual selection: the relative roles of mate preference strength and the degree of divergence in mate preferences, Ecology Letters, volume 16, issue 8, pp. 964-974 2013 David Gray, Eileen Hebets, Laurel Symes, Rebecca Safran
Robert Lanfear, Simon Y. W. Ho, T. Jonathan Davies, Angela T. Moles, Lonnie Aarssen, Nathan G. Swenson, Laura Warman, Amy E. Zanne and Andrew P. Allen. 2013, Taller plants have lower rates of molecular evolution, Nat Comms, volume 4, pp. 1879 2013 Robert Lanfear, Nathan Swenson, Amy Zanne
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John R. Stinchcombe and Mark Kirkpatrick. 2012, Genetics and evolution of function-valued traits: understanding environmentally responsive phenotypes, Trends in Ecology & Evolution 27(11): 637-647. 2012 John Stinchcombe, Mark Kirkpatrick
Johnson, N. A., D. C. Lahti, and D. T. Blumstein. 2012. Combating the assumption of evolutionary progress: Lessons from the decay and loss of traits. Evolution: Education and Outreach 5: 128-138. 2012 Norman Johnson, David Lahti, Daniel Blumstein
Johnson, N., Smith, J., Pobiner, B., & Schrein, C. 2012. Why are chimps still chimps? American Biology Teacher 74(2): 74-80. 2012 Norman Johnson, James J Smith, Briana Pobiner, Caitlin Schrein
Julie A. Meachen-Samuels. 2012, Morphological convergence of the prey-killing arsenal of sabertooth predators, Paleobiology, volume 38, issue 1, pp. 1-14 2012 Julie A Meachen
Katja Seltmann, Matthew Yoder, Istvan Miko, Mattias Forshage, Matthew Bertone, Donat Agosti, Andrew Austin, James Balhoff, Marek Borowiec, Seán Brady, Gavin Broad, Denis Brothers, Roger Burks, Matthew Buffington, Heather Campbell, Kelly Dew, Andrew Ernst, Jose Fernandez-Triana, Michael Gates, Gary Gibson, John Jennings, Norman Johnson, Dave Karlsson, Ricardo Kawada, Lars Krogmann, Robert Kula, Patricia Mullins, Michael Ohl, Claus Rasmussen, Fredrick Ronquist, Susanne Schulmeister, Michael Sharkey, Elijah Talamas, Erika Tucker, Lars Vilhelmsen, Philip S. Ward, Robert Wharton and Andrew Deans. 2012, A hymenopterists’ guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions, Journal of Hymenoptera Research, volume 27, issue 0, pp. 67 2012 Katja Seltmann, Matthew Yoder, Norman Johnson, Jim P Balhoff
Lens, A., Cooper, L., Gandolfo, M., Groover, A., Jaiswal, P., Lachenbrunch, B., Spicer, R., Stanton, M., Stevenson, D., Walls, R., Wegrzyn, J. (2012). An extension of the plant ontology project supporting wood anatomy and development research. IAWA Journal, 33(2) 113-117. 2012
L. H. Comas, K. E. Mueller, L. L. Taylor, P. E. Midford, H. S. Callahan, and D. J. Beerling 2012. International Journal of Plant Sciences. Vol. 173:584-595. 2012 Peter E Midford, Louise Comas, David Beerling, Hilary Callahan
Liam J. Revell (2012) phytools: an R package for phylogenetic comparative biology (and other things), Methods in Ecology and Evolution, volume 3, issue 2, pp. 217-223 2012 Liam J Revell
Liberles, DA, Teichmann, S, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning APJ, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder M, Lakner C, Lartillot N, Lovell S, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjolander E, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S. 2012. The Interface of Protein Structure, Protein Biophysics, and Molecular Evolution. Protein Science, in press. 2012 David Liberles
M. A. Bertone, I. Miko, M. J. Yoder, K. C. Seltmann, J. P. Balhoff and A. R. Deans. 2012. Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment, Database, volume 2013, issue 0, pp. bas057-bas057 2012
Mcclain, Craig R. 2012. Increased Energy Promotes Size-Based Niche Availability in Marine Mollusks. Integrative & Comparative Biology 52(S1): E117. 2012
McClain, C.R., Taylor Gullet, T., Ricketts, J.J. & Unmack, P.J. 2012. Increased energy promotes size-based niche availability in marine mollusks. Evolution. doi: 10.1111/j.1558-5646.2012.01580.x 2012 Peter J Unmack
Meachen, J. and J.X. Samuels. In Press. Evolution in coyotes (Canis latrans) in response to the megafaunal extinction. Proceedings of the National Academy of Science. 2012 Julie A Meachen
Meachen-Samuels, J. In Press. Morphological convergence of the prey-killing arsenal of sabertooth predators. Paleobiology. 2012 Julie A Meachen
Medina, I. and C.D. Francis. Environmental variability and acoustic signals: A multilevel approach in songbirds. Biology Letters doi:10.1098/rsbl.2012.0522 ** dual first author 2012 Clinton D Francis
Mideo N.M., Acosta-Serrano A., Aebischer T., Brown M.J.F., Fenton A., Friman V-P., Restif O., Reece S.E., Webster J.P. & Brown S.P. (2012) Life in cells, hosts, and vectors: parasite evolution across scales. Infection, Genetics & Immunity. 2012 Nicole Mideo, Andy Fenton, Sarah Reece
Mideo N. & Reece S.E. (2012) Plasticity in parasite phenotypes: evolutionary and ecological implications for disease. Future Microbiology 7(1): 17-24 2012 Nicole Mideo, Sarah Reece
Mideo N., Savill N.J., Chadwick W., Schneider P., Read A.F., Day T. & Reece S.E. (2011) Causes of variation in malaria infection dynamics: insights from theory and data. American Naturalist 178(6): E174-E188 2012 Nicole Mideo, Nick Savill, Petra Schneider, Andrew Read, Troy Day, Sarah Reece
Mira V. Han. 2012, Characterizing gene movements between chromosomes in Drosophila, Fly, volume 6, issue 2, pp. 121-125 2012 Mira Han
Moczek, A. P. 2012. The nature of nurture and the causes of traits: toward a comprehensive theory of developmental evolution. Integrative & Comparative Biology 52, Supplement 1: E123. 2012
M. V. Han and M. W. Hahn Inferring the History of Interchromosomal Gene Transposition in Drosophila Using n-Dimensional Parsimony, Genetics, volume 190, issue 2, pp. 813-825 2012 Mira Han
Nicole Mideo, William A. Nelson, Sarah E. Reece, Andrew S. Bell, Andrew F. Read and Troy DayBRIDGING SCALES IN THE EVOLUTION OF INFECTIOUS DISEASE LIFE HISTORIES: APPLICATION, Evolution, volume 65, issue 11, pp. 3298-3310 2012 Nicole Mideo, Sarah Reece, Andrew Read, Troy Day
Ortega, C. P. and C. D. Francis. 2012. Effects of gas well compressor noise on ability to detect birds during surveys in northwest New Mexico. Ornithological Monographs 74:78-90. 2012 Clinton D Francis
Patricia Mullins, Ricardo Kawada, James Balhoff and Andrew Deans. 2012, A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation, ZooKeys, volume 223, issue 0, pp. 1-38 2012 Jim P Balhoff, Andy Deans
Payne, J.L., F.A. Smith, M. Kowalewski, R.A. Krause, A.G. Boyer, C.R. McClain, S. Finnegan, P.M. Novack-Gottshall, and L. Sheble (2012) A lack of attribution: closing the citation gap through a reform of citation and indexing practices. Taxon 61(6), pp. 1349-1351(3) 2012 Craig R McClain, Jonathan Payne, Felisa A Smith, Michal Kowalewski, Richard Krause, Alison G. Boyer, Seth Finnegan, Philip Novack-Gottshall, Laura Sheble
PETER J. UNMACK, JUAN P. BARRIGA, MIGUEL A. BATTINI, EVELYN M. HABIT and JERALD B. JOHNSON 2012. Phylogeography of the catfish Hatcheria macraei reveals a negligible role of drainage divides in structuring populations, Molecular Ecology, 21: 942-959. 2012 Peter J Unmack, Evelyn Habit
Peter J. Unmack, Justin C. Bagley, Mark Adams, Michael P. Hammer, Jerald B. Johnson and Dirk Steinke. 2012, Molecular Phylogeny and Phylogeography of the Australian Freshwater Fish Genus Galaxiella, with an Emphasis on Dwarf Galaxias (G. pusilla), PLoS ONE, volume 7, issue 6, pp. e38433 2012 Peter J Unmack
Peter S. Ungar, John Sorrentino and Jerome C. RoseEvolution of human teeth and jaws: Implications for dentistry and orthodontics, Evolutionary Anthropology: Issues, News, and Reviews, volume 21, issue 3, pp. 94-95 2012 Peter Ungar, John Sorrentino, Jerome Rose
Plotnick, R. E. 2012. Behavioral biology of trace fossils. Paleobiology 38(3):459-473. 2012 Roy Plotnick
P. Mabee, J. P. Balhoff, W. M. Dahdul, H. Lapp, P. E. Midford, T. J. Vision and M. Westerfield. 2012. 500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton, Journal of Applied Ichthyology, volume 28, issue 3, pp. 300-305 2012 Paula Mabee, Jim P Balhoff, Wasila Dahdul, Hilmar Lapp, Peter E Midford, Todd Vision, Monte Westerfield
Pollitt L.C., Reece S.E., Mideo N., Nussey D.H. & Colegrave N. (2012) The problem of autocorrelation in parasitology. PLoS Pathogens, 8(4): e1002590. doi:10.1371/journal.ppat.1002590 2012 Sarah Reece, Nicole Mideo
Popescu, A.-A., K. T. Huber, and E. Paradis. 2012. ape 3.0: new tools for distance based phylogenetics and evolutionary analysis in R. Bioinformatics published online. 2012 Emmanuel Paradis, Andrei-Alin Popescu, Katharina Huber
Price, S. A.*, Hopkins, S. C.*, Smith, K. K & Roth, V. L. Tempo of trophic evolution and its impact on mammalian diversification. Proceedings of the National Academy of Sciences 109(18), 7008-7012 2012 Samantha Price
R. A. Vos, J. P. Balhoff, J. A. Caravas, M. T. Holder, H. Lapp, W. P. Maddison, P. E. Midford, A. Priyam, J. Sukumaran, X. Xia and A. Stoltzfus. 2012. NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata, Systematic Biology, volume 61, issue 4, pp. 675-689 2012 Rutger Vos, Jim P Balhoff, Mark Holder, Hilmar Lapp, Wayne Maddison, Peter E Midford, Jeet Sukumaran, Xuhua Xia, Jason Caravas, Anurag Priyam, Arlin Stoltzfus
Roy E. Plotnick and Dena M. Smith. 2012, Exceptionally Preserved Fossil Insect Ears from the Eocene Green River Formation of Colorado, Journal of Paleontology, volume 86, issue 1, pp. 19-24 2012 Roy Plotnick, Dena Smith
Rubio de Casas, R. (2012). Seed after-ripening and dormancy determine adult life history independently of germination timing. New Phytologist, 194(3), 868-879. 2012
Safran R.J., Flaxman, S.M, Kopp, M, Irwin, D.E., Briggs, D., Evans, M.R., Funk, W.C., Gray, D.A. Hebets, E.A., Seddon, N., Scordato, E., Symes, L.B., Tobias, J.A., Toews, D.P.L., Uy, J.A.C. 2012. A robust new metric of phenotypic distance to estimate and compare multiple trait differences among populations. Invited for Special Theme Issue on Sexual Selection and Speciation, Current Zoology 58: 423-436. 2012 Rebecca Safran
Sarah M. Hird. 2012. lociNGS: A Lightweight Alternative for Assessing Suitability of Next-Generation Loci for Evolutionary Analysis, PLoS ONE, volume 7, issue 10, pp. e46847 2012 Sarah Hird
Servedio, M. R. & Kopp, M. 2012. Sexual selection and magic traits in speciation with gene flow. Current Zoology 58(3): 510-516. 2012 Maria R Servedio, Michael Kopp
Shilin Chen, Jiang Xu, Chang Liu, Yingjie Zhu, David R. Nelson, Shiguo Zhou, Chunfang Li, Lizhi Wang, Xu Guo, Yongzhen Sun, Hongmei Luo, Ying Li, Jingyuan Song, Bernard Henrissat, Anthony Levasseur, Jun Qian, Jianqin Li, Xiang Luo, Linchun Shi, Liu He, Li Xiang, Xiaolan Xu, Yunyun Niu, Qiushi Li, Mira V. Han, Haixia Yan, Jin Zhang, Haimei Chen, Aiping Lv, Zhen Wang, Mingzhu Liu, David C. Schwartz and Chao Sun. 2012, Genome sequence of the model medicinal mushroom Ganoderma lucidum, Nature Communications, volume 3, pp. 913 2012 David Nelson, Mira Han
Smith, D.M. (2012). Exceptional preservation of insects in Lacustrine environments. PALAIOS, 27(41035) 346-353. doi: 10.2110/palo.2011.p11-107r 2012
Stansbury, M., Moczek, A. 2012. The evolvability of arthropods. Arthropod Structure and Development: Major Features and Evolutionary Patterns. 2012
Tallmon, D.A., Waples, R.S., Gregovich, D., & Schwartz, M.K. (2012). Detecting population recovery using gametic disequilibrium-based effective population size estimates. Conservation Genetics Resources, 4(4), 987-989. doi: 10.1007/s12686-012-9689-3 2012
Thomas J. Near, Michael Sandel, Kristen L. Kuhn, Peter J. Unmack, Peter C. Wainwright and Wm. Leo Smith. 2012, Nuclear gene-inferred phylogenies resolve the relationships of the enigmatic Pygmy Sunfishes, Elassoma (Teleostei: Percomorpha), Molecular Phylogenetics and Evolution, volume 63, issue 2, pp. 388-395 2012 Thomas Near, Peter J Unmack, Peter Wainwright
T. M. Andrews, R. M. Price, L. S. Mead, T. L. McElhinny, A. Thanukos, K. E. Perez, C. F. Herreid, D. R. Terry and P. P. Lemons. 2012, Biology Undergraduates' Misconceptions about Genetic Drift, Cell Biology Education, volume 11, issue 3, pp. 248-259 2012 Rebecca Price
Turner, D., Amit, S., Chalom, S., Penn, O., Pupko, T., Katchman, E., Matus, N., Tellio, H., Katzir, M. and Avidor, B. (2012), Emergence of an HIV-1 cluster harbouring the major protease L90M mutation among treatment-naïve patients in Tel Aviv, Israel. HIV Medicine, 13: 202–206. doi: 10.1111/j.1468-1293.2011.00960.x 2012
Urano, D., Jones, J.C., Wang, H., Matthews, M., Bradford, W., Bennetzen, J.L., & Jones, A.M. (2012). G protein activation without a GEF in the plant kingdom. PLoS Genetics, doi: 10.1371/journal.pgen.1002756 2012
Vendrasco, M., Eernisse, D., Powell, C., Fernandez, C. 2012. Polyplacophora (Mollusca) from the San Diego Formation: a remarkable assemblage of fossil chitons from the Pliocene of Southern California. Contributions in Science 520: 15-72. 2012 Michael Vendrasco, Douglas Eernisse
V. Staszewski, S. E. Reece, A. J. O'Donnell and E. J. A. Cunningham. Drug treatment of malaria infections can reduce levels of protection transferred to offspring via maternal immunity, Proceedings of the Royal Society B: Biological Sciences, volume 279, issue 1737, pp. 2487-2496 2012
Wasila M. Dahdul, James P. Balhoff, David C. Blackburn, Alexander D. Diehl, Melissa A. Haendel, Brian K. Hall, Hilmar Lapp, John G. Lundberg, Christopher J. Mungall, Martin Ringwald, Erik Segerdell, Ceri E. Van Slyke, Matthew K. Vickaryous, Monte Westerfield, Paula M. Mabee and Marc Robinson-Rechavi. 2012. A Unified Anatomy Ontology of the Vertebrate Skeletal System, PLoS ONE, volume 7, issue 12, pp. e51070 2012 Wasila Dahdul, David Blackburn, Alexander Diehl, Melissa A Haendel, Brian Hall, Hilmar Lapp, John Lundberg, Christopher Mungall, Martin Ringwald, Erik Segerdell, Monte Westerfield, Paula Mabee
Willis, C., Greenberg, J. & White, H. (2012). Analysis and synthesis of metadata goals for scientific data, Journal of the American Society for Information Science and Technology, volume 63, issue 8, pp. 1505-1520 2012 Jane Greenberg, Hollie White
Wund, M.A. (2012). Assessing the impacts of phenotypic plasticity on evolution. Integrative and Comparative Biology, 52(1), 5-15. doi: 10.1093/icb/ics050 2012
Wund, M.A., Valena, S., Wood, S. and Baker, J.A. (2012), Ancestral plasticity and allometry in threespine stickleback reveal phenotypes associated with derived, freshwater ecotypes. Biological Journal of the Linnean Society, 105: 573–583. doi: 10.1111/j.1095-8312.2011.01815.x 2012
Yael H. Edrey, Diana Casper, Dorothee Huchon, James Mele, Jonathan A. Gelfond, Deborah M. Kristan, Eviatar Nevo and Rochelle Buffenstein. 2012. Sustained high levels of neuregulin-1 in the longest-lived rodents; a key determinant of rodent longevity, Aging Cell, volume 11, issue 2, pp. 213-222 2012 Dorothee Huchon
A. Barzel, E. Privman, M. Peeri, A. Naor, E. Shachar, D. Burstein, R. Lazary, U. Gophna, T. Pupko and M. Kupiec 2011 Native homing endonucleases can target conserved genes in humans and in animal models, Nucleic Acids Research, volume 39, issue 15, pp. 6646-6659 2011
Alex Dornburg, Brian Sidlauskas, Francesco Santini, Laurie Sorenson, Thomas J. Near and Michael E. Alfaro (2011) THE INFLUENCE OF AN INNOVATIVE LOCOMOTOR STRATEGY ON THE PHENOTYPIC DIVERSIFICATION OF TRIGGERFISH (FAMILY: BALISTIDAE), Evolution, volume 65, issue 7, pp. 1912-1926 2011 Brian L. Sidlauskas, Thomas Near, Michael Alfaro
Alex Garnett, Heather Piwowar, Kim Holmberg, Jason Priem, Christina K. Pikas and Nicholas Weber Shaken and stirred: ASIS&T 2011 attendee reactions to shaking it up: Embracing new methods for publishing, finding, discussing, and measuring our research output, Proceedings of the American Society for Information Science and Technology, volume 48, issue 1, pp. 1-2 2011 Heather Piwowar
Alex Garnett, Kim Holmberg, Christina K. Pikas, Heather Piwowar, Jason Priem and Nicholas Weber Shaking it up: Embracing new methods for publishing, finding, discussing, and measuring our research output, Proceedings of the American Society for Information Science and Technology, volume 48, issue 1, pp. 1-3 2011 Heather Piwowar
A. M. Bronikowski, J. Altmann, D. K. Brockman, M. Cords, L. M. Fedigan, A. Pusey, T. Stoinski, W. F. Morris, K. B. Strier and S. C. Alberts 2011 Aging in the Natural World: Comparative Data Reveal Similar Mortality Patterns Across Primates, Science, volume 331, issue 6022, pp. 1325-1328 2011 Anne Bronikowski, Jeanne Altmann, Diane K. Brockman, Marina Cords, Linda M Fedigan, Anne Pusey, Tara Stoinski, Bill Morris, Karen B Strier, Susan C Alberts
Amy L. Angert, Lisa G. Crozier, Leslie J. Rissler, Sarah E. Gilman, Josh J. Tewksbury and Amanda J. Chunco 2011 Do species traits predict recent shifts at expanding range edges?, Ecology Letters, volume 14, issue 7, pp. 677-689 2011 Amy Angert, Lisa Crozier, Leslie Rissler, Sarah Gilman, Amanda Chunco
Anderson, C.D., and M.S. Rosenberg. 2011. Variation in association with manmade habitat edges exhibited by the Timber Rattlesnake (Crotalus horridus) in St. Louis County, Missouri. Journal of Herpetology 45(1):50-55. 2011 Michael S Rosenberg
ANDREW J. VEALE and SHANE D. LAVERY. 2011. Phylogeography of the snakeskin chiton Sypharochiton pelliserpentis (Mollusca: Polyplacophora) around New Zealand: are seasonal near-shore upwelling events a dynamic barrier to gene flow?, Biological Journal of the Linnean Society 104(3): 552-563. 2011 Shane Lavery
Andrew R. Deans, Matthew J. Yoder and James P. Balhoff. 2011, Time to change how we describe biodiversity, Trends in Ecology & Evolution, volume 27, issue 2, pp. 78-84 2011 Matthew Yoder, Jim P Balhoff, Andy Deans
Anthony D. Barnosky, Nicholas Matzke, Susumu Tomiya, Guinevere O. U. Wogan, Brian Swartz, Tiago B. Quental, Charles Marshall, Jenny L. McGuire, Emily L. Lindsey, Kaitlin C. Maguire, Ben Mersey and Elizabeth A. Ferrer. 2011, Has the Earth’s sixth mass extinction already arrived?, Nature, volume 471, issue 7336, pp. 51-57 2011 Jenny L McGuire, Anthony Barnosky
A. P. Moczek, S. Sultan, S. Foster, C. Ledon-Rettig, I. Dworkin, H. F. Nijhout, E. Abouheif and D. W. Pfennig 2011 The role of developmental plasticity in evolutionary innovation, Proceedings of the Royal Society B: Biological Sciences, volume 278, issue 1719, pp. 2705-2713 2011
Armin P. Moczek. 2011, Evolutionary biology: The origins of novelty, Nature, volume 473, issue 7345, pp. 34-35 2011 Armin Moczek
Auld, J.R. & A. Charmantier. 2011. Life history of breeding partners alters age-related changes of reproductive traits in a natural population of blue tits. Oikos _:_-_. 2011 Josh R Auld
Bachtrog D, Kirkpatrick M, Mank JE, McDaniel SF, Pires JC, Rice W, Valenzuela N. Are all sex chromosomes created equal? (2011). Trends in Genetics, 27(9), 350-7. doi: 10.1016/j.tig.2011.05.005 2011
Balaguer, L., Arroyo-Garcia, R., Jimenez, P., Jimenez, M. D., Villegas, L., Cordero, I., Rubio de Casas, R., Fernandez-Delgado, R., Ron, M. E., Manrique, E., Vargas, P., Cano, E., Pueyo, J. J., Aronson, J. (2011). Forest restoration in a fog oasis: Evidence indicates need for cultural awareness in constructing the reference. PLoS ONE, 6(8), e23004. 2011
Barrio-Amoros, C. L., Rivero, R., Santos, J. C. 2011. A new striking dendrobatid frog (Dendrobatidae: Aromobatinae, Aromobates) from the Venezuelan Andes. ZooTaxa 3063: 39-52. 2011
Barrio-Amoros, C. L., Santos, J. C. 2011. Redescription and generic assignation of Dendrobates rufulus Gorzula, 1990 (Anura: Dendrobatidae) from the Chimanti Massif, Venezuela. Salamandra 47(3): 155-160. 2011
Basey, J. M., and C. D. Francis. 2011. Design of inquiry-oriented science labs: impacts on students' attitudes. Research in Science & Technological Education 29:241-255. 2011 Clinton D Francis
B. M. Wiegmann, M. D. Trautwein, I. S. Winkler, N. B. Barr, J.-W. Kim, C. Lambkin, M. A. Bertone, B. K. Cassel, K. M. Bayless, A. M. Heimberg, B. M. Wheeler, K. J. Peterson, T. Pape, B. J. Sinclair, J. H. Skevington, V. Blagoderov, J. Caravas, S. N. Kutty, U. Schmidt-Ott, G. E. Kampmeier, F. C. Thompson, D. A. Grimaldi, A. T. Beckenbach, G. W. Courtney, M. Friedrich, R. Meier and D. K. Yeates. 2011. Episodic radiations in the fly tree of life, Proceedings of the National Academy of Sciences 108(14): 5690-5695. 2011 Brian M Wiegmann, Michelle Trautwein, Issac Winkler, Matt Bertone, Keith Bayless
Brandon Chisham, Ben Wright, Trung Le, Tran Son and Enrico Pontelli. 2011, CDAO-Store: Ontology-driven Data Integration for Phylogenetic Analysis, BMC Bioinformatics, volume 12, issue 1, pp. 98 2011 Brandon Chisham, Enrico Pontelli
Brian R Barber, Peter J Unmack, Marcos Pérez-Losada, Jerald B Johnson and Keith A Crandall. 2011, Different processes lead to similar patterns: a test of codivergence and the role of sea level and climate changes in shaping a southern temperate freshwater assemblage, BMC Evolutionary Biology, 11:343. 2011 Peter J Unmack, Keith Crandall
B. Shapiro, S. Y. W. Ho, A. J. Drummond, M. A. Suchard, O. G. Pybus and A. Rambaut (2011) A Bayesian Phylogenetic Method to Estimate Unknown Sequence Ages, Molecular Biology and Evolution, volume 28, issue 2, pp. 879-887 2011 Alexei Drummond, Marc Suchard, Andrew Rambaut, Beth Shapiro
Burleigh, J.G., M.S. Bansal, O. Eulenstein, S. Hartmann, A. Wehe, and T.J. Vision (2011). Genome-scale phylogenetics: inferring the plant tree of life from 18,896 discordant gene trees. Systematic Biology, volume 60, issue 2, pp. 117-125. 2011 Gordon Burleigh
Carlos Daniel Cadena, Kenneth H. Kozak, Juan Pablo Gómez, Juan Luis Parra, Christy M. McCain, Rauri C. K. Bowie, Ana C. Carnaval, Craig Moritz, Carsten Rahbek, Trina E. Roberts, Nathan J. Sanders, Christopher J. Schneider, Jeremy VanDerWal, Kelly R. Zamudio, and Catherine H. Graham 2011 Latitude, elevational climatic zonation and speciation in New World vertebrates Proc. R. Soc. B doi:10.1098/rspb.2011.0720 2011 Craig R McClain
Caroline H. Wilson and Daniel K. Hartline 2011 The novel organization and development of copepod myelin. II. Non-glial origin The Journal of Comparative Neurology 2011 Craig R McClain
Ceiridwen J. Edwards, Marc A. Suchard, Philippe Lemey, John J. Welch, Ian Barnes, Tara L. Fulton, Ross Barnett, Tamsin C. O'Connell, Peter Coxon, Nigel Monaghan, Cristina E. Valdiosera, Eline D. Lorenzen, Eske Willerslev, Gennady F. Baryshnikov, Andrew Rambaut, Mark G. Thomas, Daniel G. Bradley and Beth Shapiro. 2011, Ancient Hybridization and an Irish Origin for the Modern Polar Bear Matriline, Current Biology, volume 21, issue 15, pp. 1251-1258 2011 Philippe Lemey, Andrew Rambaut, Marc Suchard, Beth Shapiro
C. E. Wall, C. J. Vinyard, S. H. Williams, V. Gapeyev, X. Liu, H. Lapp and R. Z. German 2011 Overview of FEED, the Feeding Experiments End-user Database, Integrative and Comparative Biology, volume 51, issue 2, pp. 215-223 2011 Suzanne Williams, Vladimir Gapeyev, Xianhua Liu, Hilmar Lapp, Rebecca Z German, Christine E Wall, Chris Vinyard
C. GRANADO-YELA, C. GARCIA-VERDUGO, K. CARRILLO, R. RUBIO DE CASAS, L. A. KLECZKOWSKI and L. BALAGUER 2011 Temporal matching among diurnal photosynthetic patterns within the crown of the evergreen sclerophyll Olea europaea L., Plant, Cell & Environment, volume 34, issue 5, pp. 800-810 2011 Rafael F Rubio de Casas
Claire G. Williams and Patrick Aderkas. 2011. Marking live conifer pollen for long-distance dispersal experiments, Oecologia, volume 165, issue 1, pp. 249-254 2011 Claire Williams
Cohen, O., Gophna, U., Pupko, T. (2011). The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer. Molecular Biology and Evolution, 28(4), 1481-1489. doi: 10.1093/molbev/msq333 2011
Cohen, O., Pupko, T. (2011) Inference of gain and loss events from phyletic patterns using stochastic mapping and maximum parsimony: A simulation study. Genome Biology & Evolution, 3, 1265-1275. doi: 10.1093/gbe/evr101 2011
CR McClain, JC Nekola, L Kuhnz and JP Barry. 2011, Local-scale faunal turnover on the deep Pacific seafloor, Marine Ecology Progress Series, volume 422, pp. 193-200 2011 Craig R McClain
Daniel I. Speiser, Douglas J. Eernisse and Sönke Johnsen. 2011, A Chiton Uses Aragonite Lenses to Form Images, Current Biology, volume 21, issue 8, pp. 665-670 2011
DANIEL E. RUZZANTE and JORGE RABASSA 2011 Palaeogeography and palaeoclimatology of Patagonia: effects on biodiversity, Biological Journal of the Linnean Society, volume 103, issue 2, pp. 221-228 2011 Daniel Ruzzante, Jorge Rabassa
Daniel K. Hartline 2011 The evolutionary origins of glia, Glia, volume 59, issue 9, pp. 1215-1236 2011 Daniel Hartline
Daniel T. Ksepka, Michael J. Benton, Matthew T. Carrano, Maria A. Gandolfo, Jason J. Head, Elizabeth J. Hermsen, Walter G. Joyce, Kristin S. Lamm, José S. L. Patané, Matthew J. Phillips, P. David Polly, Marcel Van Tuinen, Jessica L. Ware, Rachel C. M. Warnock, and James F. Parham 2011 Synthesizing and databasing fossil calibrations: divergence dating and beyond Biol. Lett. doi:10.1098/rsbl.2011.0356 2011 Craig R McClain
Dendrobates rufulus Gorzula, 1990 is a poorly known dendrobatid, described from two specimens from the Chimantá Massif in the Venezuelan Guayana. We redescribe it based on six additional specimens and allocate this species to the genus Anomaloglossus. We also provide data on natural history, such as ecology, habitat, and vocalization. 2011 Juan C Santos
Dennis D. Embry. 2011, Behavioral Vaccines and Evidence-Based Kernels: Nonpharmaceutical Approaches for the Prevention of Mental, Emotional, and Behavioral Disorders, Psychiatric Clinics of North America, volume 34, issue 1, pp. 1-34 2011 Dennis Embry
Diego Carmona, Marc J. Lajeunesse and Marc T.J. Johnson 2011 Plant traits that predict resistance to herbivores, Functional Ecology, volume 25, issue 2, pp. 358-367 2011 Marc J. Lajeunesse
Diggle, P.K., Di Stilio, V.S., Gschwend, A.R., Golenberg, E.M., Moore, R.C., Russell, J.R.W., Sinclair, J.P. (2011). Multiple developmental processes underlie sex differentiation in angiosperms. Trends in Genetics, 27(9), 368-376. doi: 10.1016/j.tig.2011.05.003 2011
Dirk Erpenbeck, Jürgen Schmitz, Gennady Churakov, Dorothée Huchon, Gert Wörheide and Bernard M. Degnan 2011 First evidence of miniature transposable elements in sponges (Porifera) HYDROBIOLOGIA DOI: 10.1007/s10750-011-0775-4 2011 Craig R McClain
D. P. Tittensor, M. A. Rex, C. T. Stuart, C. R. McClain and C. R. Smith. 2011. Species-energy relationships in deep-sea molluscs, Biology Letters, volume 7, issue 5, pp. 718-722. 2011 Derek Tittensor, Craig R McClain
Eileen A. Hebets, Jay A. Stafstrom, Rafael L. Rodriguez and Dustin J. Wilgers. 2011, Enigmatic ornamentation eases male reliance on courtship performance for mating success, Animal Behaviour, volume 81, issue 5, pp. 963-972 2011 Eileen Hebets, Rafael Rodriguez
Escobar, J.S., J.R. Auld, A.C. Correa, J.M. Alonso, Y.K. Bony, J.M. Koene, J.-P. Pointier, P. Jarne & P. David. Patterns of mating system evolution in hermaphroditic animals: correlations among selfing rate, inbreeding depression, and the timing of reproduction. Evolution. 2011 Josh R Auld
Eyal Privman, Osnat Penn, and Tal Pupko 2011 Improving the performance of positive selection inference by filtering unreliable alignment regions Mol Biol Evol doi:10.1093/molbev/msr177 2011 Craig R McClain
Francis, C., C. Ortega, & Cruz, A.. 2011. Different behavioural responses to anthropogenic noise by two closely related passerine birds. Biology Letters. doi:10.1098/rsbl.2011.0359. 2011 Clinton D Francis
Francis, C.D., C. P. Ortega, and J. Hansen. 2011. Importance of juniper to birds nesting in pinyon-juniper woodlands in northwest New Mexico. Journal of Wildlife Management 75:1574-1580. 2011 Clinton D Francis
Francis, C. D., J. Paritsis, C. P. Ortega, & A. Cruz. 2011. Landscape patterns of avian habitat use and nest success are affected by chronic gas well compressor noise. Landscape Ecology 26:1269-1280. (doi:101007/s10980-011-9609-z) 2011 Clinton D Francis
Francis CD, Ortega CP, Cruz A (2011) Noise Pollution Filters Bird Communities Based on Vocal Frequency. PLoS ONE 6(11): e27052. doi:10.1371/journal.pone.0027052 2011 Clinton D Francis
Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, Muir A, Merchant N, Lowry S, Mock S, Helmke M, Kubach A, Narro M, Hopkins N, Micklos D, Hilgert U, Gonzales M, Jordan C, Skidmore E, Dooley R, Cazes J, McLay R, Lu Z, Pasternak S, Koesterke L, Piel WH, Grene R, Noutsos C, Gendler K, Feng X, Tang C, Lent M, Kim S-J, Kvilekval K, Manjunath BS, Tannen V, Stamatakis A, Sanderson M, Welch SM, Cranston KA, Soltis P, Soltis D, O'Meara B, Ane C, Brutnell T, Kleibenstein DJ, White JW, Leebens-Mack J, Donoghue MJ, Spalding EP, Vision TJ, Myers CR, Lowenthal D, Enquist BJ, Boyle B, Akoglu A, Andrews G, Ram S, Ware D, Stein L and Stanzione D (2011) The iPlant collaborative: cyberinfrastructure for plant biology. Front. Plant Sci. 2:34. doi: 10.3389/fpls.2011.00034 2011 Steve Goff, Matthew W Vaughn, Sheldon McKay, Eric Lyons, Naim Matasci, Martha Narro, William H Piel, Christos Noutsos, Karla Gendler , Val Tannen, Alexandros Stamatakis, Mike Sanderson, Karen Cranston, Pamela S Soltis, Douglas Soltis, Brian C O'Meara, Cecile Ane, Jim Leebens-Mack, Michael Donoghue, Todd Vision, Brian Enquist, Brad Boyle, Lincoln Stein
Hal L. Smith. 2011, Bacterial competition in serial transfer culture☆, Mathematical Biosciences, volume 229, issue 2, pp. 149-159 2011 Hal Smith
Heather A. Piwowar. 2011, Who Shares? Who Doesn't? Factors Associated with Openly Archiving Raw Research Data, PLoS ONE, volume 6, issue 7, pp. e18657 2011 Heather Piwowar
Heather A. Piwowar, Jonathan D. Carlson and Todd J. Vision. Beginning to track 1000 datasets from public repositories into the published literature, Proceedings of the American Society for Information Science and Technology, volume 48, issue 1, pp. 1-4 2011 Heather Piwowar, Todd Vision
Heather A. Piwowar, Todd J. Vision and Michael C. Whitlock. 2011, Data archiving is a good investment, Nature, volume 473, issue 7347, pp. 285-285 2011 Heather Piwowar, Todd Vision, Michael Whitlock
Hebets, E. A. 2011 Current status and future directions of research in complex signaling. Current Zoology 57: I-V. 2011 Rebecca Safran
Houle, D. C. Pelabon, G. P. Wagner, T. F. Hansen. 2011. Measurement and meaning in biology. Quarterly Review of Biology 86:1-32. 2011 David Houle
J. Conrad Stack, Luke J. Harmon and Brian O'Meara. RBrownie: an R package for testing hypotheses about rates of evolutionary change, Methods in Ecology and Evolution, volume 2, issue 6, pp. 660-662 2011 Luke Harmon, Brian C O'Meara, Conrad Stack
J. C. Santos and D. C. Cannatella (2011) Phenotypic integration emerges from aposematism and scale in poison frogs, Proceedings of the National Academy of Sciences, volume 108, issue 15, pp. 6175-6180 2011
Jennifer M. GUMM, Tamra C. MENDELSON 2011 The evolution of multi-component visual signals in darters (genus Etheostoma) Acta Zoologica 57(2): 125 - 139 2011 Tamra Mendelson
J. Gurevitch, G. A. Fox, G. M. Wardle,   Inderjit and D. Taub 2011 Emergent insights from the synthesis of conceptual frameworks for biological invasions, Ecology Letters, volume 14, issue 4, pp. 407-418 2011
J. Haven, L. C. Vargas, E. F. Mongodin, V. Xue, Y. Hernandez, P. Pagan, C. M. Fraser-Liggett, S. E. Schutzer, B. J. Luft, S. R. Casjens and W.-G. Qiu. 2011. Pervasive Recombination and Sympatric Genome Diversification Driven by Frequency-Dependent Selection in Borrelia burgdorferi, the Lyme Disease Bacterium, Genetics 189(3): 951-966. 2011
Jonathan L. Payne, Craig R. McClain, Alison G. Boyer, James H. Brown, Seth Finnegan, Michał Kowalewski, Richard A. Krause, S. Kathleen Lyons, Daniel W. McShea, Philip M. Novack-Gottshall, Felisa A. Smith, Paula Spaeth, Jennifer A. Stempien and Steve C. WangThe evolutionary consequences of oxygenic photosynthesis: a body size perspective, Photosynthesis Research, volume 107, issue 1, pp. 37-57 2011 Jonathan Payne, Craig R McClain, Alison G. Boyer, James Brown, Seth Finnegan, Richard Krause, Daniel McShea, Philip Novack-Gottshall, Felisa A Smith, Paula Spaeth, Jennifer Stempien, Steve C Wang
Joost, S., Colli, L., Bonin, A., Biebach, I., Allendorf, F.W., Hoffmann, I., Hanotte, O., Taberlet, P., & Bruford, M.W. (2011). Promoting collaboration between livestock and wildlife conservation genetics communities. Conservation Genetics Resources, 3(4), 785-788. doi: 10.1007/s12686-011-9457-9 2011
Kolbe, J. J., L. J. Revell, B. Szekely, E. D. Brodie III, and J. B. Losos. In press. Convergent evolution of phenotypic integration and its alignment with morphological diversification in Caribbean Anolis ecomorphs. Evolution. 2011 Liam J Revell
KOWALEWSKI, M., PAYNE, J. L., SMITH, F. A., WANG, S. C., MCSHEA, D. W., XIAO, S., NOVACK-GOTTSHALL, P. M., MCCLAIN, C. R., KRAUSE, R. A., BOYER, A. G., FINNEGAN, S., LYONS, S. K., STEMPIEN, J. A., ALROY J., and SPAETH, P. A. 2011. The Geozoic Supereon, PALAIOS 26(5): 251-255. 2011 Michal Kowalewski, Jonathan Payne, Felisa A Smith, Steve C Wang, Daniel McShea, Philip Novack-Gottshall, Craig R McClain, Richard Krause, Alison G. Boyer, Seth Finnegan, Sara Lyons, Jennifer Stempien, John Alroy, Paula Spaeth
Lajeunesse, M.J. (2011) phyloMeta: a program for phylogenetic comparative analyses with meta-analysis. Bioinformatics 27, 2603−2604. 2011 Marc J. Lajeunesse
Lapp, Hilmar, Robert A Morris, Terry Catapano, Donald Hobern, and Norman Morrison. 2011. Organizing Our Knowledge of Biodiversity. ASIST Bulletin 37 (4): 38-42. 2011 Hilmar Lapp, Robert Morris, Donald Hobern
Laura C. Pollitt, Paula MacGregor, Keith Matthews and Sarah E. Reece. 2011, Malaria and trypanosome transmission: different parasites, same rules?, Trends in Parasitology, volume 27, issue 5, pp. 197-203 2011 Keith Matthews, Sarah Reece
Law, S. H. W., B. D. Redelings and S. W. Kullman. In press. Comparative Genomics of Duplicate γ-Glutamyl Transferase Genes in Teleosts: Medaka (Oryzias latipes), Stickleback (Gasterosteus aculeatus), Green Spotted Pufferfish (Tetraodon nigroviridis), Fugu (Takifugu rubripes), and Zebrafish (Danio rerio). JEZ part B. 2011 Benjamin D Redelings
Lovette IJ, Arbogast BS, Curry RL, Zink RM, Botero CA, Sullivan JP, Talaba AL, Harris RB, Rubenstein DR, Ricklefs RE, and E Bermingham (2011). Phylogenetic Relationships of the Mockingbirds and Thrashers (Aves: Mimidae). Molecular Phylogenetics and Evolution. In press 2011 Carlos A. Botero
MacLean, E., Matthews, L. J., Hare, B., Nunn, C. L. et al. in press. How does cognition evolve: Phylogenetic comparative psychology. Animal cognition. 2011 Charles Nunn
M. ADAMS, S. D. WEDDERBURN, P. J. UNMACK, M. P. HAMMER and J. B. JOHNSON 2011 Use of Congeneric Assessment to Reveal the Linked Genetic Histories of Two Threatened Fishes in the Murray-Darling Basin, Australia, Conservation Biology, volume 25, issue 4, pp. 767-776 2011 Peter J Unmack
Margaret E. K. Evans, David J. Hearn, Kathryn E. Theiss, Karen Cranston, Kent E. Holsinger and Michael J. Donoghue 2011 Extreme environments select for reproductive assurance: evidence from evening primroses (Oenothera), New Phytologist, volume 191, issue 2, pp. 555-563 2011 E. Margaret Evans, David Hearn, Karen Cranston, Kent Holsinger, Michael Donoghue
Maria R. Servedio, G. Sander Van Doorn, Michael Kopp, Alicia M. Frame and Patrik Nosil. 2011, Magic traits in speciation: ‘magic’ but not rare?, Trends in Ecology & Evolution, volume 26, issue 8, pp. 389-397 2011 Maria R Servedio, Alicia Frame, Patrik Nosil, Michael Kopp
McDade, L.A., Maddison, D.R., Guralnick, R., Piwowar, H.A., Jameson, M., Helgen, K.M., Herendeen, P.S., Hill, A., & Vis, M.L. 2011. Biology Needs a Modern Assessment System for Professional Productivity BioScience, 61 (8), 619-625 2011 Heather Piwowar
McGuire, J.L. (2011). Identifying California Microtus species using geometric morphometrics documents Quaternary geographic range contractions. Journal of Mammalogy, 92(6), 1383-1394. doi: 10.1644/10-MAMM-A-280.1 2011 Jenny L McGuire
M.L. Smith, G.M. Yanega and A. Ruina. 2011, Elastic instability model of rapid beak closure in hummingbirds, Journal of Theoretical Biology, volume 282, issue 1, pp. 41-51 2011 Gregor Yanega
Morris WF, Altmann J, Brockman DK, Fedigan LM, Pusey AE, Stoinski TA, Bronikowski AM, Alberts SC, Strier KB. Low demographic variability in wild primate populations: fitness impacts of variation, covariation, and serial correlation in vital rates. American Naturalist 177: E14-E28. 2011 Jeanne Altmann, Marina Cords
Nimrod D. Rubinstein, Adi Doron-Faigenboim, Itay Mayrose, and Tal Pupko 2011 Evolutionary models accounting for layers of selection in protein coding genes and their impact on the inference of positive selection Mol Biol Evol doi:10.1093/molbev/msr162 2011 Craig R McClain
Nimrod D. Rubinstein, David Zeevi, Yaara Oren, Gil Segal, and Tal Pupko 2011 The Operonic Location of Auto-Transcriptional Repressors is Highly Conserved in Bacteria Mol Biol Evol doi:10.1093/molbev/msr163 2011 Craig R McClain
O. Popa, E. Hazkani-Covo, G. Landan, W. Martin and T. Dagan (2011) Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes, Genome Research, volume 21, issue 4, pp. 599-609 2011
Otto, S.P., Pannell, J.R., Peichel, C.L., Ashman, T.L., Charlesworth, D., Chippindale, A.K., Delph, L.F., Guerrero, R.F., Scarpino, S.V., McAllister, B.F. (2011). About PAR: The distinct evolutionary dynamics of the pseudoautosomal region.Trends in Genetics, 27(9), 358-367. doi: 10.1016/j.tig.2011.05.001 2011
Peter J. Unmack, Michael P. Hammer, Mark Adams, and Thomas E. Dowling 2011 A Phylogenetic Analysis of Pygmy Perches (Teleostei: Percichthyidae) with an Assessment of the Major Historical Influences on Aquatic Biogeography in Southern Australia Syst Biol (2011) doi:10.1093/sysbio/syr042 2011 Craig R McClain
Pieplow, N. D., and C. D. Francis. 2011. Song Differences Among Subspecies of Yellow-Eyed Juncos (Junco phaeonotus). The Wilson Journal of Ornithology 123:464-471. 2011 Clinton D Francis
Pupko, Tal 2011 Evolution after gene duplication Trends in Evolutionary Biology 10.4081/eb.2011.e1 2011 Craig R McClain
Rafael R. de Casas, Pablo Vargas, Esther Pérez-Corona, Esteban Manrique, Carlos García-Verdugo and Luis Balaguer 2011 Sun and shade leaves of Olea europaea respond differently to plant size, light availability and genetic variation, Functional Ecology, volume 25, issue 4, pp. 802-812 2011 Rafael F Rubio de Casas
Revell, L. J., D. L. Mahler, P. R. Peres-Neto, and B. D. Redelings. In press. A new method for identifying exceptional phenotypic diversification. Evolution. 2011 Benjamin D Redelings
Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller. 2011, BIO::Phylo-phyloinformatic analysis using perl, BMC Bioinformatics, volume 12, issue 1, pp. 63 2011 Rutger Vos, Klaas Hartmann, Mark A Jensen, Chase Miller, Jason Caravas
Sarah E. Reece, Laura C. Pollitt, Nick Colegrave, Andy Gardner and Marianne Manchester. 2011, The Meaning of Death: Evolution and Ecology of Apoptosis in Protozoan Parasites, PLoS Pathogens, volume 7, issue 12, pp. e1002320 2011 Sarah Reece
Servedio, M.R., G.S. Van Doorn, M. Kopp, A.M. Frame, and P. Nosil. 2011. in press Magic traits, pleiotropy, and effect sizes: reply to Haller et al. Trends in Ecology and Evolution 2011 Rebecca Safran
Seth Finnegan, Craig M McClain, Matthew A Kosnik and Jonathan L Payne. 2011, Escargots through time: an energetic comparison of marine gastropod assemblages before and after the Mesozoic Marine Revolution, Paleobiology, volume 37, issue 2, pp. 252-269 2011 Seth Finnegan, Craig R McClain, Matthew A. Kosnik, Jonathan Payne
S. Jung, N. Menda, S. Redmond, R. M. Buels, M. Friesen, Y. Bendana, L.-A. Sanderson, H. Lapp, T. Lee, B. MacCallum, K. E. Bett, S. Cain, D. Clements, L. A. Mueller and D. Main. 2011. The Chado Natural Diversity Module: a New Generic Database Schema for Large-scale Phenotyping and Genotyping Data.€ Database 2011 (November): bar051. 2011 Hilmar Lapp, Seth Redmond, Robert Buels, Maren Friesen, Yuri Bendana, Scott Cain, David Clements
Smith, S. A., J. Beaulieu, A. Stamatakis, and M. J. Donoghue. 2011. Understanding angiosperm diversification using large and small phylogenies. American J. of Botany.98(3): 404-414. doi:10.3732/ajb.1000481 2011 Stephen Smith, Jeremy Beaulieu, Alexandros Stamatakis, Michael Donoghue
Staci D. Bilbo, Gregory A. Wray, Sarah E. Perkins and William Parker 2011 Reconstitution of the human biome as the most reasonable solution for epidemics of allergic and autoimmune diseases Medical Hypotheses doi:10.1016/j.mehy.2011.06.019 2011 Craig R McClain
Stetz, J.B., Kendall, K.C., Vojta, C.D., and the Genetic Monitoring (GeM) Working Group. (2011). Genetic monitoring for managers: a new online resource. Journal of Fish & Wildlife Management, 2(2), 216-219. doi: 10.3996/082011-JFWM-048 2011
Susan K. Wiser, Nick Spencer, Miquel De Cáceres, Martin Kleikamp, Brad Boyle and Robert K. (2011) PeetVeg-X - an exchange standard for plot-based vegetation data, Journal of Vegetation Science, volume 22, issue 4, pp. 598-609 2011 Susan Wiser, Nick Spencer, Martin Kleikamp, Brad Boyle, Robert Peet
Szymon Kaczanowski, Mohammed Sajid and Sarah E Reece. 2011, Evolution of apoptosis-like programmed cell death in unicellular protozoan parasites, Parasites & Vectors, volume 4, issue 1, pp. 44 2011 Sarah Reece
Tomiya, S., McGuire, J. L. et al. 2011. A report on late Quaternary vertebrate fossil assemblages from the eastern San Francisco Bay region, California. PaleoBios 30(2): 50-71. 2011 Jenny L McGuire
Trina E. Roberts, Hayley C. Lanier, Eric J. Sargis and Link E. Olson. 2011, Molecular phylogeny of treeshrews (Mammalia: Scandentia) and the timescale of diversification in Southeast Asia, Molecular Phylogenetics and Evolution, volume 60, issue 3, pp. 358-372 2011 Trina E Roberts
Van Valkenburgh, B., A. Curtis, J. X. Samuels, D. Bird, B. Fulkerson, J. Meachen-Samuels, and G. Slater. 2011. Aquatic adaptations in the nose of carnivorans: evidence from the turbinates. Journal of Anatomy 218: 298-310. 2011 Julie A Meachen
Verdolin, J.L. In Press. Genetic Ancestry. In:Encyclopedia of Race and Racism, 2nd Edition 2011 Jennifer Verdolin
Verdolin, J.L. In Press. Genetic variation of populations. In: Encyclopedia of Race and Racism, 2nd Edition. 2011 Jennifer Verdolin
Vision, T.J., Judith Blake, Hilmar Lapp, Paula Mabee, and Monte Westerfield. 2011. Similarity between semantic description sets: addressing needs beyond data integration. In Proceedings of the First International Workshop on Linked Science (LISC 2011), ed. Tomi Kauppinen, Line C. Pouchard, and Carsten KessŸler. Vol. 783. Bonn, Germany: CEUR Workshop Proceedings. 2011 Hilmar Lapp, Todd Vision, Judith A Blake, Paula Mabee, Monte Westerfield
Waples, R.S., & England, P.R. (2011). Estimating contemporary effective population size on the basis of linkage disequilibrium in the face of migration. Genetics, 189(2), 633-644. doi: 10.1534/genetics.111.132233 2011
Weintraub, J. P. 2011. Evolution education resources from The National Evolutionary Synthesis Center. Integrative & Comparative Biology 51(S1): E147. 2011
William Michener, Dave Vieglais, Todd Vision, John Kunze, Patricia Cruse, Greg Janee (2011) DataONE: Data Observation Network for Earth: Preserving Data and Enabling Innovation in the Biological and Environmental Sciences, D-Lib Magazine 17(1/2) 2011 Todd Vision, Dave Vieglais, William Michener
Williams, C.G. 2011. A history of persistence- and decline- for Southern Hemisphere conifer, Fitzroya cupressoides. Forest History Today 16 (1-2): 37-41. 2011 Claire Williams
Williams, C. G. 2011. Evolutionary dynamics of forests under climate change. Springer. 2011
Williams, C.G., V. Martinez and C. Magni. 2011. Inferring past climate change response for Fitzroya cupressoides. Japanese Journal of Historical Botany 19 (1-2): 101-107. 2011 Claire Williams
Xianfa Xie, Wei-Gang Qiu, and Peter Lipke 2011 Accelerated and adaptive evolution of yeast sexual adhesins Mol Biol Evol doi:10.1093/molbev/msr145 2011 Craig R McClain
Edwards, E.J., C.P. Osborne, C.A.E. Stramberg, and S.A. Smith (2010). The Origins of C4 Grasslands: Integrating Evolutionary and Ecosystem Science. Science 328(5978): 587-591. 2010 Erika J Edwards
J. M. Logsdon 2010 No Sex, Please, Science, volume 328, issue 5976, pp. 310-310 2010
J. M. Logsdon and M. Neiman 2010 Meeting for Sex in Iowa, Journal of Heredity, volume 101, issue Supplement 1, pp. S1-S2 2010
S. A. Smith, J. M. Beaulieu and M. J. Donoghue 2010 An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants, Proceedings of the National Academy of Sciences, volume 107, issue 13, pp. 5897-5902 2010
A. Hodgkinson and A. Eyre-Walker (2010). Human Triallelic Sites: Evidence for a New Mutational Mechanism?, Genetics 184(1): 233-241. 2010
Amir Szitenberg, Chagai Rot, Micha Ilan and Dorothée Huchon. 2010, Diversity of sponge mitochondrial introns revealed by cox 1 sequences of Tetillidae, BMC Evolutionary Biology, volume 10, issue 1, pp. 288 2010
Anderson, C.D., B.K. Epperson, M.-J. Fortin, R. Holderegger, P. James, M.S. Rosenberg, K.T. Scribner, and S. Spear (2010). Considering spatial and temporal scale in landscape-genetic studies of gene flow. Molecular Ecology 19: 3565-3575. 2010 Michael S Rosenberg
Anthes, N., David, P., Auld, J.R., Hoffer, J.N.A., Jarne, P., Koene, J.M., Kokko, H., Lorenzi, M.C., Pelissie, B., Sprenger, D., Staikou, A., and Scharer, L. (2010), Bateman gradients in hermaphrodites: An extended approach to quantify sexual selection. American Naturalist, 146: 249-263. 2010 Josh R Auld
Auld, J. R. (2010). The effects of predation risk on mating system expression in a freshwater snail. Evolution. 2010 Josh R Auld
Auld, J. R. and R. A. Relyea (2010). Adaptive plasticity in predator-induced defenses in a common freshwater snail: altered selection and mode of predation due to prey phenotype. Evolutionary Ecology. 2010 Josh R Auld
Auld, J. R. and R. A. Relyea (2010). Inbreeding depression in adaptive plasticity under predation risk in a freshwater snail. Biology Letters 6: 222-224. 2010 Josh R Auld
Auld, J. R. and R. A. Relyea (2010). Life-history plasticity and inbreeding depression under mate limitation and predation risk: cumulative lifetime fitness dissected with a life table response experiment. Evolutionary Ecology 24(5): 1171-1185. 2010 Josh R Auld
Balhoff, J.P., W.M. Dahdul, C.R. Kothari, H. Lapp, J.G. Lundberg, et al. (2010). Phenex: Ontological Annotation of Phenotypic Diversity. PLoS ONE 5(5): e10500. 2010 Jim P Balhoff
Beall, C.M., G.L. Cavalleri, et al. (2010). Natural selection on EPAS1 (HIF2-alpha) associated with low hemoglobin concentration in Tibetan highlanders. PNAS 107:11459-11464. 2010 Cynthia M Beall
Botero, CA, 29 Nov 2010, Variable environments, fluctuating selection, and why we are the way we are, University of Maryland, College Park 2010 Carlos A. Botero
Botero, C. A., Pen, I., Komdeur, J. and Weissing, F. J. (2010), The evolution of individual variation in communication strategies. Evolution, 64: 3123–3133. doi: 10.1111/j.1558-5646.2010.01065.x 2010
Brendan P. Kelly, Andrew Whiteley and David Tallmon. 2010, The Arctic melting pot, Nature, volume 468, issue 7326, pp. 891-891 2010 David Tallmon
Buckley, L. B., Davies, T. J., Ackerly, D. D., Kraft, N. J. B., Harrison, S. P., Anacker, B. L., Cornell, H. V., Damschen, E. I., Grytnes, J. A., Hawkins, B. A., McCain, C. M., Stephens, P. R., and Wiens, J. J. 2010. Phylogeny, niche conservatism and the latitudinal diversity gradient in mammals, Proceedings of the Royal Society B: Biological Sciences 277(1691): 2131-2138. 2010
Chi, K.-J., and V.L.Roth. 2010. Scaling and mechanics of carnivoran footpads reveal the principles of footpad design. J. R. Soc. Interface 7:1145-1155 doi:10.1098/rsif.2009.0556 2010
Cohen, O., Ashkenazy, H., Belinky, F., Huchon, D., Pupko, T. (2010). GLOOME: gain loss mapping engine. Bioinformatics, 26(22), 2914-2915. doi: 10.1093/bioinformatics/btq549 2010
C. R. McClain and S. M. Hardy. 2010. The dynamics of biogeographic ranges in the deep sea, Proceedings of the Royal Society B: Biological Sciences 277(1700): 3533-3546. 2010 Craig R McClain
Dahdul, W. M., J. G. Lundberg, P. E. Midford, J. P. Balhoff, H. Lapp, T. J. Vision, M. A. Haendel, M. Westerfield, and P. M. Mabee. 2010. The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age. Systematic Biology. Systematic Biology Advance Access published on March 29, 2010. 2010 Wasila Dahdul
Dahdul, W.M., J.P. Balhoff, J. Engeman, et al. (2010). Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature. PLoS One 5(5): e10708. 2010 Wasila Dahdul
Dawn Field, Susanna Sansone, Edward F. DeLong, Peter Sterk, Iddo Friedberg, Pascale Gaudet, Susanna Lewis, Renzo Kottmann, Lynette Hirschman, George Garrity, Guy Cochrane, John Wooley, Folker Meyer, Sarah Hunter, Owen White, Brian Bramlett, Susan Gregurick, Hilmar Lapp, Sandra Orchard, Philippe Rocca-Serra, Alan Ruttenberg, Nigam Shah, Chris Taylor and Anne Thessen. 2010, Meeting Report: BioSharing at ISMB 2010, Standards in Genomic Sciences, volume 3, issue 3, pp. 254-258 2010 George Garrity, Hilmar Lapp, Alan Ruttenberg, Anne Thessen, Susanna-Assunta Sansone, Suzanna Lewis
Donohue, K., R. Rubio de Casas, Liana Burghardt, Katherine Kovach, Charles Willis. 2010. Germination, post-germination adaptation, and species ecological ranges. Annual Review of Ecology and Systematics, Vol. 41: 293-319 2010 Kathleen Donohue, Rafael F Rubio de Casas, Liana Burghardt, Charlie Willis
Eckert, C.G., S. Kalisz, M.A. Geber, R. Sargent, E. Elle, P.-O. Cheptou, C. Goodwillie, M.O. Johnston, J.K. Kelly, and D.A. Moeller (2010). Plant mating systems in a changing world. Trends in Ecology & Evolution 25(1): 35-43. 2010 Christopher G Eckert, Susan Kalisz, Monica Geber, Elizabeth Elle, Pierre-Olivier Cheptou, Carol Goodwillie, Mark Johnston, David Moeller, Risa Sargent
Edwards, E. and S. Smith (2010). Phylogenetic analyses reveal the shady history of C4 grasses. Proceedings of the National Academy of Sciences 107(6): 2532-2537. 2010 Stephen Smith, Erika J Edwards
Eernisse, D., M. Strathmann, and R. Strathmann (2010). Henricia pumila sp. nov.: A brooding seastar (Asteroidea) from the coastal northeastern Pacific. Zootaxa 2329: 22-36. 2010 Douglas Eernisse
E Gaya, BD Redelings, P Navarro-Rosines, Xavier Llimona, Miquel De Cáceres, and Francois M. Lutzoni. 2010. Align, or not to align? Resolving species complexes within the Caloplaca saxicola group as a case study. Mycologia. DOI: 10.3852/10-120 2010 Benjamin D Redelings
Elias, D.O., C.A. Botero, M.C.B. Andrade, A.C. Mason, and M.M. Kasumovic (2010). High resource valuation fuels desperado fighting tactics in female jumping spiders. Behavioral Ecology 21(4): 868-875. 2010 Carlos A. Botero
Epperson, B.K., B.H. McRae, K. Scribner, S.A. Cushman, M.S. Rosenberg, M-J. Fortin, P.M.A. James, M. Murphy, S. Manel, P. Legendre, and M.R.T. Dale (2010). Utility of computer simulations in landscape genetics. Molecular Ecology 19: 3549-3564. 2010 Michael S Rosenberg
E. W. Bloomquist and M. A. Suchard 2010 Unifying Vertical and Nonvertical Evolution: A Stochastic ARG-based Framework, Systematic Biology, volume 59, issue 1, pp. 27-41 2010
Gilman et al. 2010 A framework for community interactions under climate change. Trends in Ecology and Evolution 25:325-331 2010
Goldberg EE, Kohn JR, Lande R, Robertson KA, Smith SA, and Igic B. (2010). Species Selection Maintains Self-Incompatibility, Science, 330(6003): 493-495. doi:10.1126/science.1194513 2010 Boris Igic, Emma Goldberg, Stephen Smith
Greenberg, J. Losee, R., Aguera, J., Scherle, R., White, H., and Willis, C. (2010). HIVE: Helping interdisciplinary vocabulary engineering. Bulletin of the American Society for Information Science and Technology 37(4). 2010 Ryan Scherle, Jane Greenberg, Hollie White
Harmon, L.J., J.B. Losos, J.T. Davies, et al. (2010). Early bursts of body size and shape evolution are rare in comparative data. Evolution 64(8): 2385�2396. 2010 Brian L. Sidlauskas
Hazkani-Covo, E., R.M. Zeller, W. Martin and H.S. Malik (2010). Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes. PLoS Genetics 6(2): e1000834. 2010 Einat Hazkani-Covo
Hereford, J. (2010). Does Selfing Or Outcrossing Promote Local Adaptation? American Journal Of Botany 97(2): 298-302. 2010 Joe Hereford
Hollie C. White. 2010, Considering Personal Organization: Metadata Practices of Scientists, Journal of Library Metadata, volume 10, issue 2-3, pp. 156-172 2010 Hollie White
Hunt, J.H., F. Wolschin, M.T. Henshaw, T.C. Newman, A.L. Toth, and G.V. Amdam (2010). Differential Gene Expression and Protein Abundance Evince Ontogenetic Bias toward Castes in a Primitively Eusocial Wasp. PLoS ONE 5(5): e10674. 2010 James H Hunt
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Jane Greenberg. 2010, Metadata for Scientific Data: Historical Considerations, Current Practice, and Prospects, Journal of Library Metadata, volume 10, issue 2-3, pp. 75-78 2010 Todd Vision, Jane Greenberg
Johnson, M.A., L.J. Revell, and J.B. Losos (2010). Behavioral convergence and adaptive radiation: Effects of habitat use on territorial behavior in Anolis lizards. Evolution 64: 1151-1159. 2010 Liam J Revell
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Laikre, L., F.W. Allendorf, L.C. Aroner, et al. (2010). Neglect of genetic diversity in implementation of the convention on biological diversity. Conservation Biology 24(1): 86-88. 2010 Linda Laikre, Fred Allendorf, Jennifer Jackson, Katherine Kendall, Kevin McKelvey, Maile Neel, Isabelle Olivieri, Nils Ryman, Michael Schwartz, Jeffrey Stetz, David Tallmon, Christina Vojta, Robin Waples, Michael Hansen
Lennart Olsson, Georgy S. Levit and Uwe HoßfeldEvolutionary developmental biology: its concepts and history with a focus on Russian and German contributions, Naturwissenschaften, volume 97, issue 11, pp. 951-969 2010 Lennart Olsson
Linda Laikre, Michael K. Schwartz, Robin S. Waples and Nils Ryman. 2010, Compromising genetic diversity in the wild: unmonitored large-scale release of plants and animals, Trends in Ecology & Evolution, volume 25, issue 9, pp. 520-529 2010 Linda Laikre, Michael Schwartz, Robin Waples, Nils Ryman
Lindenfors, P., L.J. Revell, and C.L. Nunn (2010). Sexual dimorphism in primate aerobic capacity: A phylogenetic test. Journal of Evolutionary Biology 23: 1183-1194. 2010 Liam J Revell
Lovely, K.R., D.L. Mahler, and L.J. Revell (2010). The Rate And Pattern Of Tail Autotomy In Five Species Of Puerto Rican Anoles. Evolutionary Ecology Research 12(1): 67-88. 2010 Liam J Revell
Lovely, K. R., D. L. Mahler, and L. J. Revell. 2010. The rate and pattern of tail autotomy in five species of Puerto Rican anoles. Evolutionary Ecology Research 12: 67-88. 2010 Liam J Revell
Mahler, D. L., L.J. Revell, R.E. Glor, and J.B. Losos (2010). Ecological opportunity and the rate of morphological evolution in the diversification of Greater Antillean anoles. Evolution 64(9): 2731-2745. 2010 Liam J Revell
Manel, S., S. Joost, B.K. Epperson, R. Holderegger, A. Storfer, M.S. Rosenberg, K. Scribner, A. Bonin, and M-J. Fortin (2010). Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field. Molecular Ecology 19: 376. 2010 Michael S Rosenberg
Marc J. Lajeunesse. 2010, Achieving synthesis with meta-analysis by combining and comparing all available studies, Ecology, volume 91, issue 9, pp. 2561-2564 2010 Marc J. Lajeunesse
McClain, C.R. and J.P. Barry (2010). Habitat heterogeneity, disturbance, and productivity work in concert to regulate biodiversity in deep submarine canyons. Ecology 91(4): 964-976. 2010 Craig R McClain
Meachen-Samuels, J. (2010). Comparative scaling of humeral crosssections of felids and canids using radiographic images. Journal of Mammalian Evolution 17: 193-209. 2010 Julie A Meachen
Meachen-Samuels, J.A. and Van Valkenburgh, B. 2010. Radiographs Reveal Exceptional Forelimb Strength in the Sabertooth Cat, Smilodon fatalis. PLoS ONE 5: e11412. 2010 Julie A Meachen
Meachen-Samuels, J.A. and W.J. Binder (2010). Sexual dimorphism and ontogenetic growth in the American lion and sabertoothed cat from Rancho La Brea. Journal of Zoology 280(3): 271-279. 2010 Julie A Meachen
N. Goto, P. Prins, M. Nakao, R. Bonnal, J. Aerts and T. Katayama. 2010. BioRuby: bioinformatics software for the Ruby programming language, Bioinformatics, volume 26, issue 20, pp. 2617-2619 2010 Naohisa Goto, Pjotr Prins, Jan Aerts, Toshiaki Katayama
Paez-Vacas, M. I., Coloma, L. A., Santos, J. C. 2010. Systematics of the Hyloxalus bocagei complex (Anura: Dendrobatidae), description of two new cryptic species, and recognition of H. maculosus. Zootaxa 2711: 1-75 (Monograph) 2010 Juan C Santos
P. D. Keightley and A. Eyre-Walker (2010). What can we learn about the distribution of fitness effects of new mutations from DNA sequence data?, Philosophical Transactions of the Royal Society B: Biological Sciences 365(1544): 1187-1193. 2010
Perez-Aguera, J., Arroyo, J., Greenberg, J., Perez-Iglesias, J., and Fresno, V. Using BM25F for Semantic Search. Semantic Search Workshop at the 19th Int. World Wide Web Conference WWW2010 April 26, 2010, Raleigh, NC, USA. 2010 Jane Greenberg
P. F. Campos, E. Willerslev, A. Sher, L. Orlando, E. Axelsson, A. Tikhonov, K. Aaris-Sorensen, A. D. Greenwood, R.-D. Kahlke, P. Kosintsev, T. Krakhmalnaya, T. Kuznetsova, P. Lemey, R. MacPhee, C. A. Norris, K. Shepherd, M. A. Suchard, G. D. Zazula, B. Shapiro and M. T. P. GilbertAncient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics, Proceedings of the National Academy of Sciences, volume 107, issue 12, pp. 5675-5680 2010
Pfennig, D.W. and M. McGee (2010). Resource Polyphenism Increases Species Richness: A Test Of The Hypothesis. Philosophical Transactions Of The Royal Society B-Biological Sciences 365(1540): 577-591. 2010 David Pfennig
Pfennig, D.W., M.A. Wund, E.C. Snell-Rood, T. Cruickshank, C.D. Schlichting, and A.P. Moczek (2010). Phenotypic plasticity's impacts on diversification and speciation. Trends in Ecology and Evolution 25(8): 459-467 . 2010 David Pfennig
Plotnick, R.E., S.Q. Dornbos, and J. Chen (2010). Information landscapes and sensory ecology of the Cambrian Radiation. Paleobiology 36: 303-317. 2010 Roy Plotnick
Pryer, K., E. Schuettpelz, et al. (2010). DNA barcoding exposes a case of mistaken identity in the fern horticultural trade. Molecular Ecology Resources 10(6): 979-985. 2010 Eric Schuettpelz
Revell, L. J. 2010. Phylogenetic signal and linear regression on species data. Methods in Ecology and Evolution 1: 319-329. 2010 Liam J Revell
Revell, L J., D.L. Mahler, J.R. Sweeney, M. Sobotka, V.E. Fancher, and J.B. Losos (2010). Nonlinear selection and the evolution of variances and covariances for continuous characters in an anole. Journal of Evolutionary Biology 23: 407-421. 2010 Liam J Revell
Richards, C.L., O. Bossdorf, and M. Pigliucci (2010). What Role Does Heritable Epigenetic Variation Play in Phenotypic Evolution? BioScience 60(3): 232-237. 2010 Christina L Richards, Oliver Bossdorf, Massimo Pigliucci
Roberts, T.E., T.R.B. Davenport, K.B.P. Hildebrandt, T. Jones, W.T. Stanley, E.J. Sargis, and L.E. Olson (2010). The biogeography of introgression in the critically endangered African monkey Rungwecebus kipunji. Biology Letters 6(2): 233-237. 2010 Trina E Roberts
Rosenberg, M.S. (2010). A Generalized Formula for Converting Chi-Square Tests to Effect Sizes for Meta-Analysis. PLoS ONE 5(4): e10059. 2010 Michael S Rosenberg
Scott, A.C. F. Kenig, R.E. Plotnick, I.J. Glasspool, W.G. Chaloner, and C.F. Eble (2010). Evidence of multiple late Bashkirian to early Moscovian (Pennsylvanian) fire events preserved in contemporaneous cave fills. Palaeogeography, 291(1-2): 72-84. 2010 Roy Plotnick
Sidlauskas, B., G. Ganapathy, E. Hazkani-Covo, K.P. Jenkins, H. Lapp, L.W. McCall, S. Price, R. Scherle, P.A. Spaeth, and D.M. Kidd (2010). Linking big: the continuing promise of evolutionary synthesis. Evolution 64(4): 871-880. 2010 Brian L. Sidlauskas, Ganeshkumar Ganapathy, Einat Hazkani-Covo, Kristin Jenkins, Hilmar Lapp, Lauren W. McCall, Samantha Price, Ryan Scherle, Paula Spaeth, David Kidd
Slater, G.J., S.A. Price, et al. (2010) Diversity versus disparity and the radiation of modern cetaceans.__ Proceedings of the Royal Society B. 277(1697): 3097-3104. 2010 Samantha Price
Smith, S.A. and M.J. Donoghue (2010). Combining Historical Biogeography With Niche Modeling In The Caprifolium Clade Of Lonicera (Caprifoliaceae, Dipsacales). Systematic Biology 59(3): 322-341. 2010 Stephen Smith
Smith, S. A., R. H. Ree, and M. J. Donoghue. Accuracy of maximum-likelihood inferences of geographic range reconstructions and parameter estimates: a simulation study. [in press, Systematic Biology] 2010 Paul Manos
S.N. Bennett, A.J. Drummond, D.D. Kapan, M.A. Suchard, J.L. Munoz-Jordan, O.G. Pybus, E.C. Holmes and D.J. Gubler 2010 Epidemic Dynamics Revealed in Dengue Evolution, Molecular Biology and Evolution, volume 27, issue 4, pp. 811-818 2010
Steven W. Kembel, Peter D. Cowan, Matthew R. Helmus, William K. Cornwell, Helene Morlon, David D. Ackerly, Simon P. Blomberg, and Campbell O. Webb (2010). Picante: R Tools For Integrating Phylogenies And Ecology. Bioinformatics 26(11): 1463-1464. 2010 Steven Kembel, Peter Cowan, Matthew Helmus, William Cornwell, Helene Morlon, David Ackerly, Campbell O Webb
Strier, K.B., J. Altmann, D.K. Brockman, et al. (2010). The Primate Life History Database: a unique shared ecological data resource. Methods in Ecology and Evolution 1(2): 199-211. 2010 Karen B Strier, Jeanne Altmann, Diane K. Brockman, Anne Bronikowski, Marina Cords, Linda M Fedigan, Hilmar Lapp, Xianhua Liu, Anne Pusey, Tara Stoinski, Susan C Alberts
Tallmon, D.A., Gregovich, D., Waples, R.S., Baker, C.S., Jackson, J., Taylor, B.L., Archer, E., Martien, K.K., Allendorf, F.W., & Schwartz, M.K. (2010), When are genetic methods useful for estimating contemporary abundance and detecting population trends?. Molecular Ecology Resources, 10: 684–692. doi: 10.1111/j.1755-0998.2010.02831.x 2010
Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong-Woo Chun, Jan Aerts, Bruno Aranda, Load Hendrix Barboza, Raoul JP Bonnal, Richard Bruskiewich, Jan C Bryne, Jose M Fernendez, Akira Funahashi, Paul MK Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard Holland, Yoshinobu Kano, Edward A Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehvaslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew Pocock, Pjotr Prins, Rene Ranzinger, Florian Reisinger, Lukasz Salwinski, Mark Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A Vos, Mark D Wilkinson, William York, Christian M Zmasek, Kiyoshi Asai and Toshihisa Takagi. 2010, The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows, Journal of Biomedical Semantics, volume 1, issue 1, pp. 8 2010 Toshiaki Katayama, Jan Aerts, Naohisa Goto, Richard Holland, Hilmar Lapp, Pjotr Prins, Mark Schreiber, Hideaki Sugawara, Rutger Vos, Mark Wilkinson, Christian Zmasek
Tsai, Yi-Hsin Erica. 2010. PhyloGeoViz: a web-based program that visualizes genetic data on maps. Molecular Ecology Resources doi:10.1111/j.1755-0998.2010.02964.x. 2010 Yi-Hsin Tsai
Vision, T.J. (2010). Open Data And The Social Contract Of Scientific Publishing. Bioscience 60(5): 330-331. 2010 Todd Vision
Wall, C. E., Gapeyev, V., German, R. Z., Liu, X., Vinyard, C. J., Williams, S. H. 2010. The Feeding Experiments End-user Database (FEED). Integrative & Comparative Biology 50: E309. 2010
Waples, R.S. (2010), Spatial-temporal stratifications in natural populations and how they affect understanding and estimation of effective population size. Molecular Ecology Resources, 10: 785–796. doi: 10.1111/j.1755-0998.2010.02876.x 2010
Waples, R.S. and C. Do (2010). Linkage Disequilibrium Estimates Of Contemporary N-E Using Highly Variable Genetic Markers: A Largely Untapped Resource For Applied Conservation And Evolution. Evolutionary Applications 3(3): 244-262. 2010 Fred Allendorf
Weintraub, J. P., Jenkins, K. P., Smith, R. A., Wiegmann, B. M. 2010. Evolution education resources from the National Evolutionary Synthesis Center. Integrative & Comparative Biology 50(S1): E187. 2010
Williams, C.G. (2010). Long-distance pine pollen still germinates after meso-scale dispersal. American Journal of Botany 97(5): 1-11. 2010 Claire Williams
Williams, C.G. 2010. Of forests and time in the culture of possession. International Forestry Review 12(4): 407-417. 2010 Claire Williams
Williams, S. H., Gapayev, V., Liu, X. H., German, R. Z., Vinyard, C. J., Wall, C. E. 2010. The feeding experiments end-user database (FEED). American Journal of Physical Anthropology p245. 2010
Yanega, G. M., Meyers, R. A. 2010. Pouch morphology and function in brown pelicans, Pelecanus occidentalis. Integrative & Comparative Biology 50: E316. 2010
Yanega, G.M., & Meyers, R.A. 2010. Pouch morphology and function in brown pelicans, Pelecanus occidentalis. Integrative & Comparative Biology 50: E316. 2010 Gregor Yanega
Zanne, A.E., M. Westoby, D.S. Falster, D.D. Ackerly, S.R. Loarie, S.E.J. Arnold, and D.A. Coomes. 2010. Angiosperm wood structure: Global patterns in vessel anatomy and their relation to wood density and potential conductivity. American Journal of Botany 97: 207-215. 2010 Amy Zanne
E. A. Hadly, P. A. Spaeth and C. Li 2009 Colloquium Papers: Niche conservatism above the species level, Proceedings of the National Academy of Sciences, volume 106, issue Supplement_2, pp. 19707-19714 2009
Alfaro, M.E., F. Santini, C.D. Brock, H. Alamillo, A. Dornburg, G. Carnevale, D. Rabosky, and L.J. Harmon (2009). Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. PNAS 106(32):13410-13414. 2009 Michael Alfaro
B. C. O'Meara (2009) New Heuristic Methods for Joint Species Delimitation and Species Tree Inference, Systematic Biology, volume 59, issue 1, pp. 59-73 2009
Botero, C.A., N.J. Boogert, S.L. Vehrencamp, and I.J. Lovette (2009). Climatic Patterns Predict the Elaboration of Song Displays in Mockingbirds. Current Biology 19: 1-5. 2009 Carlos A. Botero
Byars, S.G., D. Ewbank, D.R. Govindaraju, and S.C. Stearns (2010). Natural selection in a contemporary human population. PNAS 107: 1787-1792. 2009 Stephen Stearns
Cellinese, N., S.A. Smith, E.J. Edwards, et al. (2009). Historical Biogeography Of The Endemic Campanulaceae Of Crete. Journal Of Biogeography 36(7): 1253-1269. 2009 Stephen Smith
Chave, J., D. Coomes, S. Jansen, S. L. Lewis, N. G. Swenson, and A. E. Zanne (2009). Towards a worldwide wood economics spectrum. Ecology Letters 12(4): 351-366. 2009 Amy Zanne
Cione, A.L., W.M. Dahdul, J.G. Lundberg, and A. Machado-Allison (2009). Megapiranha paranensis, a New Genus and Species of Serrasalmidae (Characiformes, Teleostei) from the Upper Miocene of Argentina. Journal of Vertebrate Paleontology 29(2): 350-358. 2009 John Lundberg, Wasila Dahdul
Collar, D.C., B.C. O'Meara, P.C. Wainwright, and T.J. Near (2009). Piscivory Limits Diversification of Feeding Morphology in Centrarchid Fishes. Evolution 63(6): 1557-1573. 2009 Brian C O'Meara
Cornwell, W.K., J.H.C. Cornelissen, S.D. Allison, P. Eggleton, C. Preston, F. Scarff, J.T. Weedon, C. Wirth, and A.E. Zanne (2009). Plant traits and wood fates across the globe: rotted, burned, or consumed? Global Change Biology 15(10): 2431 - 2449. 2009 Amy Zanne
Cronk, Q. (2009) The Molecular Organography of Plants. Oxford University Press. 2009 Quentin Cronk
de Kort, S.R., E.R.B. Eldermire, S. Valderrama, C.A. Botero, and S.L. Vehrencamp (2009). Trill consistency is an age-related assessment signal in banded wrens. Proceedings of the Royal Society B 276(1665): 2315-2321. 2009 Carlos A. Botero
Dornburg, A., B.L. Sidlauskas, L. Sorenson, et al. (2009). Morphological And Mechanical Patterns Of Evolution In Triggerfish Fins. Integrative And Comparative Biology 49. 2009 Brian L. Sidlauskas
Dutheil, J.Y., G. Ganapathy, A. Hobolth, T. Mailund, M.K. Uyenoyama, and M.H. Schierup (2009). Ancestral population genomics: the coalescent hidden Markov model approach. Genetics 183: 259-274. 2009 Ganeshkumar Ganapathy
Faith, D.P., C.A. Lozupone, D. Nipperess, and R. Knight (2009). The cladistic basis for the phylogenetic diversity (PD) measure links evolutionary features to environmental gradients and supports broad applications of microbial ecology�s phylogenetic beta diversity framework. Int. J. Mol. Sci 10(11): 4723-4741. 2009 Daniel Faith
Ganapathy, G. and M.K. Uyenoyama (2009). Site frequency spectra from genomic SNP surveys. Theoretical Population Biology 75(4): 346-354. 2009 Ganeshkumar Ganapathy
Goodwillie, C., R.D. Sargent, C. Eckert, E. Elle, M.A. Geber, M.O. Johnston, S. Kalisz, D. Moeller, R. Ree, M. Vallejo-Marin, A.A. Winn. Correlated evolution of mating system and floral display traits in flowering plants and its implications for the distribution of mating system variation. New Phytologist 2009 Susan Kalisz, Mark Johnston
Govindaraju, D.R., M.G. Larson, X.Y. Yin, et al. (2009). Association Between Snp Heterozygosity And Quantitative Traits In The Framingham Heart Study. Annals Of Human Genetics 73: 465-473. 2009 Diddahally Govindaraju
Greenberg, J., H. White, C. Carrier, and R. Scherle (2009). A Metadata Best Practice for a Scientific Data Repository. Journal of Library Metadata 9(3-4): 194-212. 2009 Ryan Scherle, Jane Greenberg, Hollie White, Sarah Carrier
Hacke, U.G., A.L. Jacobsen, and R.B. Pratt (2009). Xylem Function Of Arid-Land Shrubs From California, Usa: An Ecological And Evolutionary Analysis. Plant Cell And Environment 32(10): 1324-1333. 2009 Amy Zanne
Han, M.V. amd C.M. Zmasek (2009). PhyloXML: XML For Evolutionary Biology And Comparative Genomics. BMC Bioinformatics 10: 356. 2009 Mira Han, Christian M. Zmasek
Hansen, M.M., D.J. Fraser, K. Meier, et al. (2009). Sixty Years Of Anthropogenic Pressure: A Spatio-Temporal Genetic Analysis Of Brown Trout Populations Subject To Stocking And Population Declines. Molecular Ecology 18(12): 2549-2562. 2009 Fred Allendorf
Harris, A.J. and Q.Y. Xiang (2009). Estimating Ancestral Distributions Of Lineages With Uncertain Sister Groups: A Statistical Approach To Dispersal-Vicariance Analysis And A Case Using Aesculus L. (Sapindaceae) Including Fossils. Journal Of Systematics And Evolution 47(5): 349-368. 2009 Nathalie Nagalingum
Harris, A.J., Q.Y. Xiang, and D.T. Thomas (2009). Phylogeny, Origin, And Biogeographic History Of Aesculus L. (Sapindales) - An Update From Combined Analysis Of Dna Sequences, Morphology, And Fossils. Taxon 58(1): 108-126. 2009 Nathalie Nagalingum
Hazkani-Covo, E. (2009). Mitochondrial insertions into primate nuclear genomes suggest the use of numts as a tool for phylogeny. Molecular Biology and Evolution 26(10): 2175-2179. 2009 Einat Hazkani-Covo
Hereford, J. A. (2009). Quantitative Survey of Local Adaptation and Fitness Trade-offs. American Naturalist 173(5): 579-588. 2009 Joe Hereford
Hickerson, M.J., B.C. Carstens, J. Cavender-Bares, et al. (2010). Phylogeography�s past, present, and future: 10 years after Avise, 2000. Molecular Phylogenetics and Evolution 54: 291�301. 2009 Michael Hickerson, Bryan Carstens, Jeannine Cavender-Bares, Keith Crandall, Catherine Graham, Jerry Johnson, Leslie Rissler, Pedro Victoriano, Anne Yoder
Hipp, A. and M. Escudero (2009). MATICCE: mapping transitions in continuous character evolution. Bioinformatics 26(1): 132-133. 2009 Andrew L. Hipp
Hodgkinson, A., E. Ladoukakis, and A. Eyre-Walker (2009). Cryptic Variation In The Human Mutation Rate. Plos Biology 7(2): 226-232. 2009 Adam Eyre-Walker
Hopkins, S.S.B. and E.B. Davis (2009). Quantitative Morphological Proxies For Fossoriality In Small Mammals. Journal Of Mammalogy 90: 1449-1460. 2009 Samantha Hopkins
Jane Greenberg. 2009, Theoretical Considerations of Lifecycle Modeling: An Analysis of the Dryad Repository Demonstrating Automatic Metadata Propagation, Inheritance, and Value System Adoption, Cataloging & Classification Quarterly, volume 47, issue 3-4, pp. 380-402 2009 Todd Vision, Jane Greenberg
Johnston, M.O., E. Porcher, P.E. Cheptou, et al. (2009). Correlations Among Fertility Components Can Maintain Mixed Mating In Plants. American Naturalist 173(1): 1-11. 2009 Mark Johnston
Jon Fjeldså and Martin Irestedt. 2009, DIVERSIFICATION OF THE SOUTH AMERICAN AVIFAUNA:PATTERNS AND IMPLICATIONS FOR CONSERVATION IN THE ANDES, Annals of the Missouri Botanical Garden, volume 96, issue 3, pp. 398-409 2009
J. R. Auld, A. A. Agrawal and R. A. Relyea 2009 Re-evaluating the costs and limits of adaptive phenotypic plasticity, Proceedings of the Royal Society B: Biological Sciences, volume 277, issue 1681, pp. 503-511 2009
Kimmel, C.B., B.L. Sidlauskas, and J. Clack (2009). Linked morphological changes during palate evolution in early tetrapods. Journal of Anatomy 215: 91-109. 2009 Brian L. Sidlauskas
Lahti, D.C., N.A. Johnson, B.C. Ajie, S.P. Otto, A.P. Hendry, D.T. Blumstein, R.G. Coss, K. Donohue, and S.A. Foster (2009). Relaxed selection in the wild.Trends in Ecology & Evolution 24(9): 48. 2009 David Lahti, Norman Johnson, Beverly Ajie, Sarah Otto, Andrew P Hendry, Daniel Blumstein, Richard G Coss, Susan Foster, Kathleen Donohue
Lajeunesse, M.J. (2009). Meta-analysis and the comparative phylogenetic method. American Naturalist 174: 369-381. 2009 Marc J. Lajeunesse
Lemey, P., A. Rambaut, A.J. Drummond, M.A. Suchard, and C. Fraser (2009). Bayesian phylogeography finds its roots. PLoS Computational Biology 5(9): e1000520. 2009 Philippe Lemey, Andrew Rambaut, Alexei Drummond, Marc Suchard
Li, M., J. Li, J. Jiang, C. Fu, and W. Judd (2009). Phylogenetics and Biogeography of Pieris (Lyonieae, Ericaceae): inferred from sequences of nuclear and chloroplast genomes. Systematic Botany 34(3): 553-560. 2009 Paul Manos
Lundsten, L., C.R. McClain, J.P. Barry, G.M. Cailliet, D.A. Clague, and A.P. DeVogelaere (2009). Ichthyofauna on three seamounts off southern and central California, USA. Marine Ecology Progress Series 389: 223-232. 2009 Craig R McClain
L. Z. Garamszegi, S. Calhim, N. Dochtermann, G. Hegyi, P. L. Hurd, C. Jorgensen, N. Kutsukake, M. J. Lajeunesse, K. A. Pollard, H. Schielzeth, M. R.E. Symonds and S. Nakagawa 2009 Changing philosophies and tools for statistical inferences in behavioral ecology, Behavioral Ecology, volume 20, issue 6, pp. 1363-1375 2009
Manchester, S.R., Q.Y.(J.) Xiang, T.M. Kodrul, and M. Akhmetiev (2009). Leaves of Cornus (Cornaceae) from the Paleocene of North America and Asia confirmed by trichome characters. International Journal of Plant sciences 170(1): 132_142. 2009 Jenny Xiang
McCall, L.W. (2009). Cultural adaptations after progressionism. Cross-Cultural Research 43: 62-89. 2009 Lauren W. McCall
McCall, L.W. (2009). Studying cultural evolution at the tips: Human cross-cultural ecology. Evolution Education and Outreach 2: 1936-6426. 2009 Lauren W. McCall
McCall, L.W. (2009). The comparative biology of cultural inheritance. Evolution Education and Outreach 2: 573-574. 2009 Lauren W. McCall
McClain, C.R. and A.G. Boyer (2009). Biodiversity and body size are linked across metazoans. Proceedings of the Royal Society B: Biological Sciences 276(1665): 2209-2215. 2009 Craig R McClain
McClain, C.R., L. Lundsten, J. Barry, and A. DeVogelaere (2010). Assemblage structure, but not diversity or density, change with depth on a northeast Pacific seamount. Marine Ecology 31:14-25. 2009 Craig R McClain
McClain, C.R., L. Lundsten, M. Ream, J. Barry, and A. DeVogelaere (2009). Endemicity, Biogeography, Composition, and Community Structure On a Northeast Pacific Seamount. PLoS ONE 4(1): e4141. 2009 Craig R McClain
Meachen-Samuels, J.A., and B.V. Valkenburgh (2009). Forelimb indicators of prey-size preference in the Felidae. Journal of Morphology 270(6): 729-744. 2009 Julie A Meachen
Miko, I. and A.R. Deans (2009). Masner, A New Genus Of Ceraphronidae (Hymenoptera, Ceraphronoidea) Described Using Controlled Vocabularies. Zookeys. 2009 Paula Mabee
Moles, A.T., D.I. Warton, L. Warman, et al. (2009). Global Patterns In Plant Height. Journal Of Ecology 97(5): 923-932. 2009 Amy Zanne
Moore, B.A. and M.J. Donoghue (2009). Evaluating the impact of historical events on rates of diversification: A Bayesian approach using cross-validation predictive densities. Proc. Nat. Acad. Sci. USA 106(11): 4307-4312. 2009 Paul Manos
Nuismer, S.L., S.P. Otto, and F. Blanquart (2009). Host-parasite interactions and the evolution of non-random mating and parasite speciation. Ecology Letters 11(9): 937-946. 2009 Sarah Otto
Payne, J.L., A.G. Boyer, J.H. Brown, et al. (2009). Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity. Proc. Natl. Acad. Sci 106(1): 24-27. 2009 Jonathan Payne
Pfennig, K.S., and D.W. Pfennig (2009). Character displacement: Ecological and reproductive responses to a common evolutionary problem. Quarterly Review of Biology 84: 253-276. 2009 David Pfennig
Polson, M.P., W.E. Hewson, D.J. Eernisse, et al. (2009). You Say Conchaphila, I Say Lurida: Molecular Evidence For Restricting The Olympia Oyster (Ostrea Lurida Carpenter 1864) To Temperate Western North America. Journal Of Shellfish Research 28(1): 11-21. 2009 Douglas Eernisse
Porcher, E., J.K. Kelly, P.-O. Cheptou, C.G. Eckert, M.O. Johnston, and S. Kalisz (2009). The genetic consequences of fluctuating inbreeding depression and the evolution of plant mating systems. Journal of Evolutionary Biology 22(4): 708-717. 2009 Porcher Emmanuelle
Prosdocimi, F., B. Chisham, E. Pontelli, J.D. Thompson, and A. Stoltzfu (2009). Initial Implementation of a Comparative Data Analysis Ontology. Evolutionary Bioinformatics 5: 47-56. 2009 Arlin Stoltzfus, Francisco Prosdocimi, Julie Thompson, Enrico Pontelli, Brandon Chisham
Puchalski, S.S., C.C. Johnson, E.G. Kauffman, et al. (2009). A New Genus And Two New Species Of Multiplacophorans (Mollusca, Polyplacophora, Neoloricata), Mississippian (Chesterian), Indiana. Journal Of Paleontology 83(3): 422-430. 2009 Douglas Eernisse
Ree, R.H., and I. Sanmartin (2009). Guest Editorial: Prospects and challenges for parametric models in historical biogeographical inference. Journal of Biogeography 36(7): 1211-1220. 2009 ISABEL BASTIDA
Revell, L.J. (2009). Size-correction and principal components for interspecific comparative studies. Evolution 63: 3258-3268. 2009 Liam J Revell
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Sakai, Stacey, Samuels, Joshua, Meachen-Samuels, Julie 2009. POSTCRANIAL MORPHOLOGY AND THE LOCOMOTOR HABITS OF LIVING AND EXTINCT CARNIVORANS. JOURNAL OF VERTEBRATE PALEONTOLOGY 29, Supplement 1, p174A. 2009 Joshua Samuels
Samuels, J.X., J.A. Meachen-Samuels, and P.A. Gensler (2009). The First Mid-blancan Occurrence of Agriotherium (Ursidae) in North America: a Record from Hagerman Fossil Beds National Monument, Idaho. Journal of Paleontology 83(4): 597-603. 2009 Joshua Samuels, Julie A Meachen
Santini, F., L.J. Harmon, G. Carnevale, and M. Alfaro (2009). Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes. BMC Evolutionary Biology 9: 194. 2009 Michael Alfaro
Santos, J.C., L.A. Coloma, K. Summers, et al. (2009). Amazonian Amphibian Diversity Is Primarily Derived From Late Miocene Andean Lineages. Plos Biology 7(3): 448-461. 2009 Juan C Santos
S. A. Smith and J. M. Beaulieu 2009 Life history influences rates of climatic niche evolution in flowering plants, Proceedings of the Royal Society B: Biological Sciences, 276(1677): 4345-4352. doi: 10.1098/rspb.2009.1176 2009 Stephen Smith, Jeremy Beaulieu
Servedio, M.R., S.A. Saether and G.-P. Satre (2009). Reinforcement and learning. Evolutionary Ecology 23: 109-123. 2009 Maria R Servedio
Smith, S.A. (2009). Taking into account phylogenetic and divergence-time uncertainty in a parametric biogeographical analysis of the Northern Hemisphere plant clade Caprifolieae. Journal of Biogeography 36(12): 2324-2337. 2009 Stephen Smith
Smith, S.A. and B.C. O'Meara (2009). Morphogenera, Monophyly, And Macroevolution. Proceedings Of The National Academy Of Sciences Of The United States Of America 106(36): E97-E98. 2009 Stephen Smith
Smith, S.A., J.M. Beaulieu, and M.J. Donoghue (2009). Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evol Biol 9: 37. 2009 Stephen Smith
Spaeth, P.A. (2009). Morphological convergence and coexistence in three sympatric North American species of Microtus (Rodentia:Arvicolinae). Journal of Biogeography 36: 350-361. 2009 Paula Spaeth
Spaeth, P.A., M. van Tuinen, Y.L. Chan, D. Terca, and E.A. Hadly (2009). Phylogeography of Microtus longicaudus in the tectonically and glacially dynamic landscape of the Central Rocky Mountains. Journal of Mammalogy 90: 571-584. 2009 Paula Spaeth
Vences, M., K.C. Wollenberg, D.R. Vieites, et al. (2009). Madagascar As A Model Region Of Species Diversification. Trends In Ecology & Evolution 24(8): 456-465. 2009 Anne Yoder
Vini Pereira, David Enard, Adam Eyre-Walker and I. King Jordan. 2009, The Effect of Transposable Element Insertions on Gene Expression Evolution in Rodents, PLoS ONE 4(2): e4321. 2009 Adam Eyre-Walker
Volz, S.M., and S.S. Renner (2009). Phylogeography of the ancient Eurasian medicinal plant genus Bryonia (Cucurbitaceae) inferred from nuclear and chloroplast sequences. Taxon 58(2): 550-560. 2009 Susanne Renner
Weedon, J., W. Cornwell, H. Cornelissen, A.E. Zanne, C. Wirth, and D. Coomes (2009). Global meta-analysis of wood decomposition rates: the role of wood traits. Ecology Letters 12(1): 45-56. 2009 Amy Zanne
Wiegmann, B.M., M.D. Trautwein, J.-W. Kim, B.K. Cassel, M.A. Bertone, S.L. Winterton, and D.K. Yeates (2009). Single-copy nuclear genes resolve the phylogeny of the holometabolous insects. BMC Biology 7(1): 34. 2009 Brian M Wiegmann, Michelle Trautwein
Xiang, Q.P., Q.-Y.(J.) Xiang, Y.Y. Guo, and X.C. Zhang (2009). Phylogeny of Abies (Pinaceae) inferred from ITS sequence data. Taxon 58(1): 141-152. 2009 Jenny Xiang
Xu, J.W., M. Perez-Losada, C.G. Jara, et al. (2009). Pleistocene Glaciation Leaves Deep Signature On The Freshwater Crab Aegla Alacalufi In Chilean Patagonia. Molecular Ecology 18(5): 904-918. 2009 Daniel Faith
Antonelli, A., J. A. A. Nylander, C. Persson, and I. Sanmartin (2009). Tracing the impact of the Andean uplift on Neotropical plant evolution: evidence from the coffee family. Proceedings of the National Academy of Sciences 106(24): 9749-9754. 2008 Joel Cracraft
Beldade, P., A. Papanicolaou, and W.O. McMillan (2008). Butterfly Genomics Eclosing. Heredity 100: 150_157. 2008 Owen McMillan
Bicca-Marques, J.C., H.M. Prates, F.R.C. de Aguiar, et al. (2008). Survey Of Alouatta Caraya, The Black-And-Gold Howler Monkey, And Alouatta Guariba Clamitans, The Brown Howler Monkey, In A Contact Zone, State Of Rio Grande Do Sul, Brazil: Evidence For Hybridization. Primates 49(4): 246-252. 2008 Clara B. B. Jones
Bininida-Emonds, O.R.P., M. Cardillo, K.E. Jones, R.D.E. MacPhee, R.M.D. Beck, R. Grenyer, S.A. Price, R. Vos, J.L. Gittleman, and A. Purvis (2007). The delayed rise of present-day mammals. Nature 446: 507-512. 2008 Samantha Price
Burleigh, J.G., K.W. Hilu, and D.S. Soltis (2008). Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms. BMC Evol. Biol. 9:61. 2008 Gordon Burleigh
Burleigh, J.G., M.S. Bansa, A. Wehe, and O. Eulenstein (2008). Locating Multiple Gene Duplications Through Reconciled Trees. Research In Computational Molecular Biology, Proceedings. Lecture Notes In Bioinformatics 4955: 273-284. 2008 Gordon Burleigh, Oliver Eulenstein
Carrier, Sarah. 2008. The Dryad Repository Application Profile: Process, Development, and Refinement. SILS Electronic Theses and Dissertations. 2008 Sarah Carrier
Chapman, C.A., K. Kitajima, A.E. Zanne, et al. (2008). A 10-Year Evaluation Of The Functional Basis For Regeneration Habitat Preference Of Trees In An African Evergreen Forest. Forest Ecology And Management 255(11): 3790-3796. 2008 Amy Zanne
Charlesworth, J. and A. Eyre-walker (2008). The McDonald-Kreitman test and slightly deleterious mutations. Mol. Biol. Evol. 25: 1007-1015. 2008 Adam Eyre-Walker
Chen, D., J.G. Burleigh, M.S. Bansal, and D. Fernandez-Baca (2008). PhyloFinder: an intelligent search engine for phylogenetic tree databases. BMC Evol. Biology 8: 90. 2008 Gordon Burleigh
Davis, C.M., and V.L. Roth (2008). The evolution of sexual size dimorphism in cottontail rabbits (Sylvilagus, Leporidae). Biological Journal of the Linnean Society 95(1): 141-156. 2008 V. Louise Roth
Donoghue, M.J. (2008). A phylogenetic perspective on the distribution of plant diversity. Proc. Nat. Acad. Sci. USA 105 (Suppl. 1): 11549-11555. 2008 Michael Donoghue
Fail, J.L., Jr. (2008). A no-holds-barred evolution curriculum for elementary and junior high school students. Evolution Education and Outreach 1(1): 56-64. 2008 Joseph Fail
Fail, J.L., Jr. (2008). Book review: Guns, Germs, and Steel by Jared Diamond. Evolution Education and Outreach 1(2):227-228. 2008 Joseph Fail
Fail, J.L., Jr. 2008, March. Poster: Teaching an Elementary Story of Life. Molecules of Life Conference, NSF/NYU. Atlanta, Ga. 2008 Joseph Fail
Fisher, K. M. (2008). Bayesian reconstruction of ancestral expression of the LEA gene families reveals propagule-derived desiccation tolerance in resurrection plants. American Journal of Botany 95: 506-515. 2008 Kirsten Fisher
G. E. Jordan and W. H. Piel. 2008. PhyloWidget: web-based visualizations for the tree of life, Bioinformatics, volume 24, issue 14, pp. 1641-1642 2008 William H Piel, Gregory E Jordan
Gould, F., Y.X. Huang, M. Legros, et al. (2008). A Killer-Rescue System For Self-Limiting Gene Drive Of Anti-Pathogen Constructs. Proceedings Of The Royal Society B-Biological Sciences 275(1653): 2823-2829. 2008 Steve Sinkins
Hanada, K., C. Zou, M.D. Lehti-Shiu, K. Shinozaki, and S.H. Shiu (2008). Importance of Lineage-Specific Expansion of Plant Tandem Duplicates in the Adaptive Responses to Environmental Stimuli. Plant Physiology 148(2): 993-1003. 2008 Shin-Han Shiu
Harper, G.R. Jr., and D.W. Pfennig (2008). Selection overrides gene flow to break down maladaptive mimicry. Nature 451: 1103-1106. 2008 David Pfennig
Hazkani-Covo, E. and S. Covo (2008). Numt-Mediated Double-Strand Break Repair Mitigates Deletions During Primate Genome Evolution. Plos Genetics 4(10): e1000237. 2008 Einat Hazkani-Covo
Hennequin, S., E. Schuettpelz, K.M. Pryer, et al. (2008). Divergence Times And The Evolution Of Epiphytism In Filmy Ferns (Hymenophyllaceae) Revisited. International Journal Of Plant Sciences 169(9): 1278-1287. 2008 Eric Schuettpelz
Hilu, K., C. Black, D. Diouf, and J.G. Burleigh (2008). Phylogenetic signal in matK vs. trnK: a case study. Molecular Phylogenetics and Evolution 48(3): 1120-1130. 2008 Gordon Burleigh
Hoeksema, J.D., and S. Forde (2008). A meta-analysis of factors affecting local adaptation between species. The American Naturalist 171(3): 275-290. 2008 Jason Hoeksema
Hopkins, S.S.B. (2008). Phylogeny And Evolutionary History Of The Aplodontoidea (Mammalia : Rodentia). Zoological Journal Of The Linnean Society 153(4): 769-838. 2008 Samantha Hopkins
Hopkins, S.S.B. (2008). Reassessing The Mass Of Exceptionally Large Rodents Using Toothrow Length And Area As Proxies For Body Mass. Journal Of Mammalogy 89(1): 232-243. 2008 Samantha Hopkins
Horvath, J.E., D.W. Weisrock, S.L. Embry, et al. (2008). Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs. Genome Research 18: 489-499. 2008 Jim P Balhoff
Jones, C.B., V. Milanov, and R. Hager (2008). Predictors Of Male Residence Patterns In Groups Of Black Howler Monkeys. Journal Of Zoology 275(1): 72-78. 2008 Clara B. B. Jones
Kelly, R. and D. Eernisse (2008). Reconstructing a radiation: the chiton genus Mopalia in the north Pacific. Invertebrate Systematics 22: 17-28. 2008 Douglas Eernisse, Ryan Kelly
Kidd, D.M., and X. Liu (2008). Geophylobuilder 1.0: an ArcGIS extension for creating geophylogenies. Molecular Ecology Resources 8: 88-91. 2008 David Kidd, Xianhua Liu
Kohn, David. (2008.) Darwin's keystone: the principle of divergence In: The Cambridge Companion to the Origin of Species. Robert Richards and Michael Ruse, eds. Cambridge University Press. 2008 David Kohn
Kremen, C., A. Cameron, A. Moilanen, et al. (2008). Aligning Conservation Priorities Across Taxa in Madagascar with High-Resolution Planning Tools. Science 320(5873): 222-226. 2008 David Vieties
Ladoukakis, E.D. and A. Eyre-Walker (2008). The Excess Of Small Inverted Repeats In Prokaryotes. Journal Of Molecular Evolution 67(3): 291-300. 2008 Adam Eyre-Walker
L. Barquist and I. Holmes. 2008, xREI: a phylo-grammar visualization webserver, Nucleic Acids Research, volume 36, issue Web Server, pp. W65-W69 2008 Lars E Barquist
Ledon-Rettig, C., D.W. Pfennig, and N. Nascone-Yoder (2008). Ancestral variation and the potential for genetic accommodation in larval amphibians: Implications for the evolution of novel feeding strategies. Evolution and Development 10(3): 316-325. 2008 David Pfennig
Lin, H.T., J.G. Burleigh, and O. Eulenstein (2008). Triplet supertree heuristics for the tree of life. BMC Bioinformatics. 10(Suppl 1): S8. 2008 Gordon Burleigh
Manchester, S.R., Z. Chen, A. Lu, and K. Uemura (2009). Eastern Asian endemic seed plant genera and their paleogeographic history throughout the Northern Hemisphere. Journal of Systematics and Evolution 47(1): 1_42. 2008 Steven Manchester
Manos, P.S., C.H. Cannon, and S.-H. Oh (2008). Phylogenetic relationships and taxonomic status of the paleoendemic Fagaceae of western North America: recognition of a new genus Notholithocarpus. Madrono 55(3): 183-192. 2008 Paul Manos
McBride, C.S., J.R. Arguello, and B.C. O'Meara (2007). Five Drosophila Genomes Reveal Nonneutral Evolution and the Signature of Host Specialization in the Chemoreceptor Superfamily. Genetics 177: 1395. 2008 Brian C O'Meara
Nylander, J.A.A., U. Olsson, P. Alstr�m, and I. Sanmartin (2008). Accounting for phylogenetic uncertainty in biogeography: A bayesian approach to dispersal-vicariance analysis of the thrushes (Aves: turdus). Systematic Biology 57: 257-268. 2008 Joel Cracraft
O'Meara, B., M. Alfaro, C. Bell, et al. (2008). Comparative methods in R hackathon. Nature Precedings. 2008 Brian C O'Meara
O'Meara, Brian (2008). Using trees: Myrmecocystus phylogeny and character evolution and new methods for investigating trait evolution and species delimitation. Nature Precedings. 2008 Brian C O'Meara
Price, S.A. (2007) A review of Horns, Tusks, and Flippers. Aquatic Mammals 33(2): 254. 2008 Samantha Price
Price, S.A. and J.L. Gittleman (2007). Hunting to extinction: biology and regional economy influence artiodactyl extinction risk and the impact of hunting. Proceedings of the Royal Society of Science B 274: 1845-1851. 2008 Samantha Price
Ramirez, M.J., J.A. Coddington, W.P. Maddison,et al. (2007). Linking of digital images to phylogenetic data matrices using a morphological ontology. Systematic Biology 56(2): 283-294. 2008 Martin Ramirez
Rausher, M.D. (2008). Evolutionary transitions in floral color. Int. J. Plant Sci. 169: 7-21. 2008 Mark Rausher
R. C. G. Holland, T. A. Down, M. Pocock, A. Prlic, D. Huen, K. James, S. Foisy, A. Drager, A. Yates, M. Heuer and M. J. Schreiber. 2008. BioJava: an open-source framework for bioinformatics, Bioinformatics, volume 24, issue 18, pp. 2096-2097 2008 Richard Holland, Mark Schreiber
Ree, R.H. and S.A. Smith (2008). Maximum-likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology 57(1): 4-14. 2008 Richard Ree, Stephen Smith
Renner, S.S., G.W. Grimm, G. Schneeweiss, T.F. Stuessy, and R.E. Ricklefs (2008). Rooting and dating maples (Acer) with an uncorrelated-rates molecular clock: Implications for North American/Asian disjunctions. Syst. Biol. 57(5): 795-808. 2008 Susanne Renner, Paul Manos
Roth, V.L., and J.M. Mercer (2008). Differing rates of macroevolutionary diversification in arboreal squirrels. Current Science 95: 857-861. 2008 V. Louise Roth
Sanmartin, I., P. van der Mark, and F. Ronquist (2008). Inferring dispersal: a Bayesian approach to phylogeny-based island biogeography, with special reference to the Canary Islands. Journal of Biogeography 35: 428-449. 2008 Joel Cracraft
Schug, Malcolm D., J.F. Baines, A. Killon, Atwood, S. Muhanty, A. Das, S.G. Smith, S., Zargham, S.McEvey, W. Stephan. (2008). Evolution of mating isolation between populations of Drosophila ananassae. Molecular Ecology, 17(11), 2706-2721. doi: 10.1111/j.1365-294X.2008.03770.x 2008 Malcolm Schug
Sidlauskas, B.L. (2008). Continuous and Arrested Morphological Diversification in Sister Clades of Characiform Fishes: A Phylomorphospace Approach. Evolution 62: 3135-3156. 2008 Brian L. Sidlauskas
Sidlauskas, B.L. and R. Vari (2008). Phylogenetic relationships within the South American fish family Anostomidae (Teleostei, Ostariophysi, Characiformes). Zoological Journal of the Linnean Society 154: 70-210. 2008 Brian L. Sidlauskas
Wehe, A., M.S. Bansal, J.G. Burleigh, and O. Eulenstein (2008). DupTree: a program for large-scale gene tree parsimony phylogenetic analyses. Bioinformatics 24: 1540-1541. 2008 Gordon Burleigh
White, H.C., S. Carrier, A. Thompson, J. Greenberg, and R. Scherle (2008). The Dryad Data Repository: A Singapore Framework Metadata Architecture in a DSpace Environment. Proceedings of the 2008 International Conference on Dublin Core and Metadata Applications. 2008 Ryan Scherle, Sarah Carrier, Abbey Thompson, Jane Greenberg
Whitlock, M.C. (2008). Evolutionary inference from QST. Molecular Ecology 17(8): 1885-1896. 2008 Michael Whitlock
Whitlock, M. C. Founder effects. Encyclopedia of Islands. University of California Press. 2008 Michael Whitlock
Xiang Q.-Y.(J.) and D.T. Thomas (2008). Tracking character evolution and biogeographic history through time in Cornaceae: Does choice of methods matter? Journal of Systematics and Evolution 46: 349-374. 2008 Jenny Xiang
Xiang Q.-Y.(J), J.L. Thorne, T.K. Seo, W.H. Zhang, D.T. Thomas, and R.E. Ricklefs (2008). Rates of nucleotide substitution in Cornaceae (Cornales) - pattern of variation and underlying causal factors. Molecular Phylogenetics and Evolution 49: 327-342. 2008 Jenny Xiang
Zhang, W.H., Q.-Y.(J.) Xiang, D.T. Thomas, B.M. Wiegmann, M.W. Frohlich and D.E. Soltis (2008). Molecular evolution of PISTILLATA-like genes in the dogwood genus Cornus (Cornaceae). Molecular Phylogenetics and Evolution 47: 175-195. 2008 Jenny Xiang
Beder, J. H., and R. Gomulkiewicz (2007). Optimizing selection for function-valued traits. Journal of Mathematical Biology 55(5-6): 861-882. 2007 Jay Beder
Book: Otto, S. P. and T. Day (2007) A Biologist's Guide to Mathematical Modeling. Princeton University Press This book is intended for undergraduate and graduate students in biology who wish to learn how to develop and analyze their own mathematical models. While at NESCent, I was able to complete the book (finalizing figures, reviewing proofs) and develop the book website (http://www.zoology.ubc.ca/biomath), which includes sample chapters, links of potential interest, and labs for readers to practice the modeling methods described in the book (available for Mathematica). The book is now available for purchase from Princeton University Press. 2007 Sarah Otto
Brenner,E.D., M.S. Katari, D.W. Stevenson, S.A. Rudd, A.W. Douglas, W.N. Moss, R.W. Twigg, S.J. Runko, G.M. Stellari, R.W. McCombie, and G.M. Coruzzi (2005). EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes. BMC Genomics 6: 143. 2007 Dennis Stevenson
Charlesworth, J. and A. Eyre-Walker (2006). The rate of adaptive evolution in enteric bacteria. Mol. Biol. Evol. 23: 1348-1356. 2007 Adam Eyre-Walker
Charlesworth, J. and A. Eyre-walker (2007). The other side of the neutral theory, evidence for slightly advantageous back-mutations. Proc. Natl. Acad. Sci. 104(43):16992-16997. 2007 Adam Eyre-Walker
Chen, D.H., J.G. Burleigh, and D. Fernandez-Baca (2007). Spectral Partitioning Of Phylogenetic Data Sets Based On Compatibility. Systematic Biology 56(4): 623-632. 2007 Gordon Burleigh
Cui, L., J. Leebens-Mack, L. Wang, J. Tang, L. Rymarquis, D. Stern, and C.W. dePamphilis (2006). Adaptive Evolution of Chloroplast Genome Structure Inferred Using a Parametric Bootstrap Approach. BMC Evolutionary Biology 6: 13. 2007 Jijun Tang
de la Torre, J., M.G. Egan, M. Katari, E.D. Brenner, D.W. Stevenson, G.M. Coruzzi, and R. DeSalle (2006). ESTimating plant phylogeny: lessons from partitioning. BMC Evolutionary Biology 6:48-87. 2007 Dennis Stevenson
Dube, J, S. Carrier, and J. Greenberg (2007). Driade: A Data Repository For Evolutionary Biology. Proceedings Of The 7Th Acm/Iee Joint Conference On Digital Libraries - Building & Sustaining The Digital Environment 2007: 481. 2007 Todd Vision
Eyre-Walker, A. (2006). Size does not matter for mitochondrial DNA. Science 312(5773): 537-538. 2007 Adam Eyre-Walker
Eyre-Walker, A. and P.D. Keightley (2007). The distribution of fitness effects of new mutations. Nature Reviews Genetics 8: 610-618 2007 Adam Eyre-Walker
Eyre-Walker, A., M. Woolfit, and T. Phelps (2006). The distribution of fitness effects of new deleterious amino acid mutations in humans. Genetics 173: 891-900. 2007 Adam Eyre-Walker
Fail, J.L., Jr. 2007. A Primer of Biology - A textbook for elementary and junior high school students and teachers. Published as textbook for two teacher workshops - 50 copies by James Madison University. 2007 Joseph Fail
Fail, J.L., Jr. (2007). Biology belongs in ""...elementary school"". American Biology Teacher 69(6): 328. 2007 Joseph Fail
Fisher, K.M., D.P. Wall, K.L. Yip, et al. (2007). Phylogeny Of The Calymperaceae With A Rank-Free Systematic Treatment. Bryologist 110(1): 46-73. 2007 Kirsten Fisher
Gandon, S., and S. P. Otto (2007). The evolution of sex and recombination in response to abiotic or coevolutionary fluctuations in epistasis. Genetics 175: 1835-1853. 2007 Sarah Otto
Gilchrist, G.W., and C. Lee (2007). All stressed out and nowhere to go: does evolvability limit adaptation in invasive species? Genetica 129: 127-132. 2007 George Gilchrist
Griswold, C.K., R. Gomulkiewicz, and N. Heckman (2007). Hypothesis testing in comparative and experimental studies of function-valued traits. Evolution 62(5): 1229-1242. 2007 Richard Gomulkiewicz
Guillaume, F., and M. C. Whitlock (2007). Effects of migration on the genetic covariance matrix. Evolution 61(10): 2398 - 2409. 2007 Michael Whitlock
Hadany, L. and S.P. Otto (2007). The evolution of condition-dependent sex in the face of high costs. Genetics 176: 1713-1727. 2007 Sarah Otto
Hazkani-Covo, E. and D. Graur (2007). A Comparative Analysis Of Numt Evolution In Human And Chimpanzee. Molecular Biology And Evolution 24(1): 13-18. 2007 Einat Hazkani-Covo
Hill, J.A., and S.P. Otto (2007). The role of pleiotropy in the maintenance of sex in yeast. Genetics 175: 1419-1427. 2007 Sarah Otto
Hoeksema, J.D., and J.N. Thompson (2007). Evolved geographic structure in a widespread plant-ectomycorrhizal interaction: Pines and false truffles. Journal of Evolutionary Biology 20: 1148-1163. 2007 Jason Hoeksema
Hopkins, S.S.B. (2007). Causes Of Lineage Decline In The Aplodontidae: Testing For The Influence Of Physical And Biological Change. Palaeogeography Palaeoclimatology Palaeoecology 246: 331-353. 2007 Samantha Hopkins
Jones, C.B. (2007). The evolution of exploitation in humans: surrounded by strangers I thought were my friends. Ethology 113: 499-510. 2007 Clara B. B. Jones
Joron, M., C.D. Jiggins, A. Papanicolaou, and W.O McMillan (2006). Heliconius wing patterns: an evo-devo model for understanding phenotypic diversity. Heredity 97: 157-167. 2007 Owen McMillan
Kelly, J.K. (2007). Mutation-Selection Balance In Mixed Mating Populations. Journal Of Theoretical Biology 246(2): 355-365. 2007 Mark Johnston
Lapp, H., S. Bala, J.P. Balhoff, et al. (2007). The 2006 NESCent phyloinformatics hackathon: A field report. Evolutionary Bioinformatics 3: 287-296. 2007 Todd Vision, Hilmar Lapp, Arlin Stoltzfus, Jim P Balhoff
Lapp, H., S. Bala, J.P. Balhoff, et al. (2007). The 2006 NESCent phyloinformatics hackathon: A field report. Evolutionary Bioinformatics 3: 287�296. 2007 Weigang Qiu, Todd Vision
Little, D.P. and D.W. Stevenson (2007). A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms. Cladistics 22: 1-21. 2007 Dennis Stevenson
Little, D.P., R.C. Moran, E.D. Brenner, and D.W. Stevenson (2007). Nuclear genome size in Selaginella. Genome 50: 351-356. 2007 Dennis Stevenson
Mabee, P.M., G. Arratia, M. Coburn, et al. (2007). Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J. Exp. Zoolog. B Mol. Dev. Evol. 308B(5): 655-668. 2007 Melissa A Haendel
Mabee, P.M., M. Ashburner, Q.C. Cronk, et al. (2007). Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol. Evol. 22(7): 345-350. 2007 Melissa A Haendel
Maddison, W.P., P.E. Midford, and S.P. Otto (2007). Estimating a binary character's effect on speciation and extinction. Systematic Biology 56(5): 701-710. 2007 Sarah Otto
Manchester, S.R., Q.Y.(J.) Xiang, and Q.P. Xiang (2007). Curtisia (Cornales) from the Eocene of Europe and its phytogeographic significance. Botanical Journal of Linnean Soceity 155: 127-137. 2007 Jenny Xiang
Mandegar, M.A., and S.P. Otto (2007). Mitotic recombination counteracts the benefits of genetic segregation. Proceedings of the Royal Society, London B. 274: 1301-1307. 2007 Sarah Otto
McCall, L.W. (2007). Individual invention vs. socioecological innovation: Unifying the behavioral and evolutionary sciences. Brain and Behavior Sciences 30(5): 418-419. 2007 Lauren W. McCall
Moore, B.R. and M.J. Donoghue (2007). Correlates of diversification in the plant clade Dipsacales: Geographic movement and evolutionary innovations. American Naturalist 170(S2): S28-55. 2007 Paul Manos
Otto, S.P. (2007). The evolutionary consequences of polyploidy. Cell 131(3): 452-462. 2007 Sarah Otto
Otto, S.P., S.L. Nuismer, and M.R. Servedio (2008). Frequency-dependent selection and the evolution of assortative mating. Genetics 179: 2091-2112. 2007 Sarah Otto
Papanicolaou, A., S. Gebauer-Jung, M.L. Blaxter, W.O. McMillan, and C.D. Jiggins (2007). ButterflyBase: a platform for Lepidoptera genomics. Nucleic Acids Research. 36(S1): D582-D587. 2007 Owen McMillan
Petersen, G., O. Seberg, J. Davis, & D. Stevenson, 2006. RNA editing and phylogenetic reconstruction in two monocot mitochondrial genes. Taxon 55: 871-886. 2007 Dennis Stevenson
Reed, R.D., W.O. McMillan, and L.M. Nagy (2007). Gene expression underlying adaptive variation in Heliconius wing patterns: non-modular regulation of overlapping cinnabar and vermilion patterns. Proceedings of the Royal Society of London, Series B 275(1630): 37-46. 2007 Owen McMillan
Renner, S.S., L. Beenken, G.W. Grimm, A. Kocyan, and R.E. Ricklefs (2007). The evolution of dioecy, heterodichogamy, and labile sex expression in Acer. Evolution 61(11): 2701-2719. 2007 Susanne Renner
Russell, A.L., J. Ranivo, E.P. Palkovacs, S.M. Goodman, and A.D. Yoder (2007). Working at the interface of phylogenetics and population genetics: a biogeographical analysis of Triaenops spp. (Chiroptera: Hipposideridae). Molecular Ecology 16: 839-851. 2007 Amy Russell
Russell, A.L., S.M. Goodman, and M.P. Cox (2008). Coalescent analyses support multiple main-to-island dispersals in the evolution of Malagasy Triaenops bats (Chiroptera: Hipposideridae). Journal of Biogeography 35(6): 995_-1003. 2007 Amy Russell
Sargent, R.D., C. Goodwillie, S. Kalisz, and R. Ree (2007). Phylogenetic evidence for a flower size and number trade-off. American Journal of Botany 94: 2059-2062. 2007 Risa Sargent
Senkowsky, S. (2007). The ascent of NESCent. Bioscience 57(2): 106-111. 2007
Servedio, M.R. (2007). Male versus female mate choice: sexual selection and the evolution of species recognition via reinforcement. Evolution 61: 2772-2789. 2007 Maria R Servedio
Sidlauskas, B.L. (2007). Testing for unequal rates of morphological diversification in the absence of a detailed phylogeny: a case study from characiform fishes. Evolution 61(2): 299-316. 2007 Brian L. Sidlauskas
Sidlauskas, Brian L., Julio Cesar Garavello and Jennifer Jellen. 2007. A new Schizodon (Characiformes: Anostomidae) from the Rio Orinoco system, with a redescription of S. isognathus from the Rio Paraguay system. Copeia 2007(3):711-725. (This work, save some revisions after review, was completed before arriving at NESCent.) 2007 Brian L. Sidlauskas
Smith, K. (2007). Nescent, The National Evolutionary Synthesis Center. Journal Of Morphology 268(12): 1135-1135. 2007
Stoletzki, N. and A. Eyre-Walker (2007). Synonymous Codon Use in Escherichia coli - Selection for translational accuracy. Mol. Biol. Evol. 24: 374-381. 2007 Adam Eyre-Walker
Terry, M. (2004). One nation, under the designer. Phi Delta Kappan 86: 264-270. 2007 Mark Terry
Terry, M. (2005). Art and evolution. The Science Teacher 72: 22-25. 2007 Mark Terry
Terry, M. 2007. What's design got to do with it?: Independent schools and the teaching of science. Independent School. 66(2):40-47. 2007 Mark Terry
Terry, M. and S. Linneman (2003). Watching the Wedge: How the Discovery Institute seeks to change the teaching of science. Washington State Science Teachers' Journal 43: 12-15. 2007 Mark Terry
Whitlock, M. C., and D. Schluter. 2008. The analysis of biological data. Roberts & Co., ~870pp. 2007 Michael Whitlock
Whitlock, M.C., B.H. Davis, and S. Yeaman (2007). The costs and benefits of resource sharing. Journal of Evolutionary Biology 20: 1772-1782. 2007 Michael Whitlock
Whitton, J., C.J. Sears, E.J. Baack, and S.P. Otto (2007). The dynamic nature of apomixis in the angiosperms. International Journal of Plant Sciences 169(1): 157-_168. 2007 Sarah Otto
Williams, D. and J.C. Clamp (2007). A Molecular Phylogenetic Investigation of Opisthonecta and Related Genera (Ciliophora, Peritrichia, Sessilida). Journal of Eukaryotic Microbiology 54: 317-323. 2007 John Clamp
Xiang, Q.-Y.(J.), D.T. Thomas, W. Zhang, S.R. Manchester, and Z. Murrell (2006). Species level phylogeny of the Dogwood genus Cornus (Cornaceae) based on molecular and morphological evidence- implication in taxonomy and Tertiary intercontinental migration. Taxon 55(1): 9-30. 2007 Jenny Xiang
Zeyl, C.W., and S.P. Otto (2007). A short history of recombination in yeast. Trends in Ecology and Evolution 22: 223-225. 2007 Sarah Otto
Agrawal, A.F. and S.P. Otto (2006). Host-parasite coevolution and selection on sex through the effects of segregation. American Naturalist 168: 617-629. 2006 Sarah Otto
Barrett, R. D. H., L. K. M'Gonigle, and S. P. Otto (2006). The distribution of beneficial mutant effects under strong selection. Genetics 174: 2071-2079. 2006 Sarah Otto
Brenner, E. & D. Stevenson. 2006. Using genomics to study evolutionary origins of seeds. Pp. 1- 21 in C. Williams (ed), Landscapes, Genomics, and Transgenic Conifers. Springer-Verlag, Berlin. 2006 Dennis Stevenson
Citerne, H.L., R.T. Pennington, and Q.C. Cronk (2006). An apparent reversal in floral symmetry in the legume Cadia is a homeotic transformation. Proc Natl Acad Sci U S A. 103(32): 12017-12020. 2006 Quentin Cronk
Cronk, Q.C. (2006). Legume flowers bear fruit. Proc Natl Acad Sci U S A. 103(13): 4801-4802. 2006 Quentin Cronk
Cronk, Q.C., I. Ojeda, and R.T. Pennington (2006). Legume comparative genomics: progress in phylogenetics and phylogenomics. Curr Opin Plant Biol. 9(2):99-103. 2006 Quentin Cronk
Davis, E, D. Prothero, and S. Hopkins (2006). Reexamination Of The North American Proboscidean Datum Using Faunal Similarity Analysis. Journal Of Vertebrate Paleontology 26(3): 54A. 2006 Samantha Hopkins
Duret, L, A. Eyre-Walker, and N. Galtier (2006). A New Perspective On Isochore Evolution. Gene 385: 71-74. 2006 Adam Eyre-Walker
Eyre-Walker, A. (2006). The Genomic Rate Of Adaptive Evolution. Trends In Ecology & Evolution 21(10): 569-575. 2006 Adam Eyre-Walker
Ezenwa, V.O., S.A. Price, S. Altizer, et al. (2006). Host Traits And Parasite Species Richness In Even And Odd-Toed Hoofed Mammals, Artiodactyla And Perissodactyla. Oikos 115(3): 526-536. 2006 Samantha Price
Fail, J.L., Jr. (2006). Letter: Teach Evolution Early. BioScience 56: 877. 2006 Joseph Fail
Gerstein, A. C., H.-J. E. Chun, A. Grant, and S. P. Otto (2006). Genomic convergence toward diploidy in Saccharomyces cerevisiae. PLoS Genetics 2(9): e145. 2006 Sarah Otto
Gilchrist, E.J., G.W. Haughn, C.C. Ying, et al. (2006). Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa. Molecular Ecology 15(5): 1367-1378. 2006 Quentin Cronk
Grimm, G.W., S.S. Renner, A. Stamatakis, and V. Hemleben (2006). A nuclear ribosomal DNA phylogeny of Acer inferred with maximum likelihood, splits graphs, and motif analysis of 606 sequences. Evolutionary Bioinformatics Online 2: 279-294. 2006 Susanne Renner
Hopkins, S. (2006). Comparison Of Quantitative And Qualitative Proxies For Fossoriality (Digging) From The Skeletal Morphology Of Mammals. Journal Of Vertebrate Paleontology 26(3): 78A. 2006 Samantha Hopkins
Jenkins, K.P. and B. Bielec (2006). Running Dna Mini-Gels In 20 Minutes Or Less Using Sodium Boric Acid Buffer. American Biology Teacher 68(9): 544-546. 2006
Johnson N.C., J.D. Hoeksema, J.A. Umbanhowar, et al. (2006). From Lilliput to Brobdingnag: Extending models of mycorrhizal function across scales. BioScience 56(11): 889-900. 2006 Jason Hoeksema
Joron, M., R. Papa, M. Beltrian, J. Maviarez, R. Papa, E. Bermingham, J. Mallet, W.O. McMillan and C.D. Jiggins (2006). A conserved supergene locus controls color pattern convergence and divergence in Heliconius butterflies. PLoS Biology 4(10): e303. 2006 Owen McMillan
Kidd, D.M., and M.G. Ritchie (2006). Phylogeographic information systems: Putting the geography into phylogeography. Journal of Biogeography 33: 1851-1865. 2006 David Kidd
Leebens-Mack, J., T. Vision, E. Brenner, et al. (2006). Taking the first steps towards a standard for reporting in phylogenies: Minimal Information About a Phylogenetic Analysis (MIAPA). OMICS 10: 231-237. 2006 Todd Vision
Petersen, G., O. Seberg, J. Davis, et al. (2006). Mitochondrial data in monocot phylogenetics. Aliso 22: 52-62. 2006 Dennis Stevenson
Pires, J., I. Maureira, T. Givnish, K. Sytsma, O. Seberg, G. Petersen, J. Davis, D. Stevenson, P. Rudall, M. Fay, and M. Chase (2006). Phylogeny, genome size, and chromosome evolution of Asparagales. Aliso 22: 287-304. 2006 Dennis Stevenson
Price, S. (2006). Extrapolating From Extant To Extinct: Reconstruction Of Early Neocete Life-History Strategy And Ecology. Journal Of Vertebrate Paleontology 26(3): 112A. 2006 Samantha Price
Tuskan, G., Q. Cronk, et al. (2006). The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313(5793): 1596-1604. 2006 Quentin Cronk
Cunningham, C. (2005). Aibs Partners With New National Evolutionary Synthesis Center. Bioscience 55(2): 183-184. 2005
Terry, M. 2005. Tending the tree of life in the high school garden, in Evolutionary science and society: educating a new generation (J. Cracraft & R. Bybee, eds.). 78-82. 2005
Terry, M. 2005. Tending the tree of life in the high school garden. Pp. 78-82 in J. Cracraft and R. Bybee, eds. Evolutionary science and society: educating a new generation. BSCS/AIBS, Colorado Springs. 2005 Mark Terry
Terry, M. (2004). One nation, under the Designer. Pp. 402-411 in . J.W. Noll, ed. Taking sides: clashing views on educational issues. 14th ed., expanded. McGraw-Hill, Dubuque, IA. 2004 Mark Terry
McCall, L.W. Group selection or group physiology? Filling in the gaps of multi-level selection theory to explain cultural variation. Lauren W. McCall
McCall, L.W. Locomotor diversification as an indicator of adaptive zone colonization is a good predictor of relative brain size in hominins and other vertebrates. Lauren W. McCall
Moore, B.R., S.A. Smith, R.H. Ree, and M.J. Donoghue (2010). Incorporating fossil data in biogeographic inference: a likelihood approach. Evolution. Paul Manos
Proposals and Grants
A. Town Peterson.  October 2007.  Serving Biodiversity Data for US Institutions.  National Biological Information Infrastructure (NBII). James Hanken
Craig Moritz. July 2008. VertNET: A Distributed Network of Museum Specimen Data for Vertebrate Species. National Biological Information Infrastructure (NBII). James Hanken
Jane Greenberg and Ryan Scherle. 2008. HIVE: Helping Interdisciplinary Vocabulary Engineering. Institute of Museum and Library Services. Ryan Scherle, Jane Greenberg
Arlin Stoltzfus, Enrico Pontelli and Brian O'Meara. 2014. "Collaborative Research: ABI Development: An open infrastructure to disseminate phylogenetic knowledge". National Science Foundation, 3 years funding from July 2015 to 2018. 2015 Arlin Stoltzfus
This is a collaborative grant NSF DEB-1256894-0 with Samantha Hopkins 2013 Samantha Price
Duke University, in collaboration with North Carolina State University and University of North Carolina Chapel Hill, is awarded a grant to enhance the services provided by Dryad (http://datadryad.org), a recently launched repository for data underlying the findings in the scholarly bioscience literature. Dryad is distinguished by the close association of data deposition with the process and business of scholarly publishing, and by using article publication as a model for how researchers can benefit from data sharing infrastructure. In a short time, dozens of journals have adopted Dryad as a mechanism for data archiving, and the repository is now at a point of transition to a sustainable organization that has the capacity to make thousands of new datasets each year openly available for reuse in perpetuity. Technical and organizational innovations supported by this award will enhance the Dryad's scalability and sustainability. The technical goals include: automation of metadata curation and preservation tasks; developing more efficient and scalable processes to integrate the manuscript submission processes of journals with the data submission process of Dryad; enhancing the features and usability of the deposition interface; and improving the machine and human interfaces for filtering, searching and accessing repository contents. Dryad?s business model will be refined through evaluation of the costs and benefits of data archiving and data reuse to stakeholders, and continued evaluation of Dryad's role with respect to the many emergent technologies in the world of publishing and data repositories. Dryad's sustainability will be addressed by implementing a nonprofit governance and revenue model that has been developed over the past three years by diverse stakeholders in the research, publishing, library and funder communities. The Broader Impacts of Dryad stem from its potential to transform the way research data are communicated and preserved. The credibility and effectiveness of the research enterprise is due in large part to the social contract behind scholarly publishing. Researchers are incentivized to disclose their work to their peers in return for professional credit. In so doing, they also expose their findings to be confirmed or refuted, and enable other researchers to build upon their results. Dryad seeks to extend this social contract to research data by providing a model for how a disciplinary repository can incentivize researchers to disclose the data that is of the greatest value for scientific reuse, that associated with publications, and realize the manifold benefits of free access to scientific data in perpetuity. This award will provide resources for Dryad to to reach out to the next generation of researchers through educational initiatives and partnerships with the broader community. As new journal and funder mandates raise demand and expectations for data management, preservation, and dissemination services, Dryad - as a stable, community-governed organization - aims to be in a position to provide the necessary infrastructure, as well as provide a focused forum for participating journals, societies and publishers to take coordinated, and well-informed, steps toward improved policy and practice. 2012 Todd Vision
Piwowar, HA and Priem, J. total-impact grant from the Alfred P. Sloan Foundation. May 2012-April 2013, $125k. 2012 Heather Piwowar
Safran. NSF Grant - CAREER DEB ($850,000, 2012 – 2017) Isolation by Distance or Adaptation: The extent of population genomic differentiation that results from adaptive divergence in sexual signals and migratory behavior. PI: Safran (sole). 2012 Rebecca Safran
Collaborative grants are awarded to the University of South Dakota and the University of North Carolina to develop ontology-driven tools for machine reasoning over large volumes of phenotype data. Human-readable descriptions of "phenotypic" properties such as anatomy and behavior are not well-suited to computational analysis. Yet, in evolutionary biology, genetics and development, computational assistance is necessary to discover patterns within the enormous volumes of descriptive phenotype data that are being reported in the literature and in online databases. Ontologies are structured, controlled vocabularies that can be applied to collections of descriptive data to permit logical reasoning to be used. Using the evolutionary transition from fins to limbs as a test system, this project will develop ontologically-aware software that allows users to discover similar sets of phenotypes for different taxa or mutant genes within large and diverse datasets. A fast semantic similarity engine will be developed to allow searches for evolutionary transitions and mutant genes characterized by similar phenotypic profiles. An ontological framework for reasoning over homology will be developed to allow rigorous reasoning over evolutionary diverse lineages. Natural language processing tools will be developed to improve upon the efficiency of mining phenotype data from the literature and improving data consistency. This suite of tools will be tested on a large number of skeletal phenotypes from diverse fossil and modern vertebrates. Taxonomic and anatomical ontologies for vertebrates will be augmented and hypotheses of anatomical homology formally encoded. The ontologies and software tools, together with phenotypes extracted from the vertebrate systematic literature, will be integrated in the knowledgebase with genetic and phenotype data from three vertebrate model organisms: zebrafish (Danio rerio), African clawed frog (Xenopus laevis), and mouse (Mus musculus). The knowledge base will be exposed to generic reasoners using semantic web standards. The system will be validated by its success in retrieving candidate genes for the well-studied vertebrate fin-limb transition and other major events in skeletal evolution. The evolutionary breadth of the test data requires the development of a rigorous framework for reasoning over hypotheses of homology. Another goal is to develop and evaluate natural language processing tools for efficiently capturing ontological descriptions of phenotype from the descriptions available in the published literature. The suite of tools will be validated by recovering developmental genetic pathways that underlie the evolutionary transition from fin to limb in vertebrates, and refined by iterative testing with domain bioinformaticians on the project and biologists from the broader user community. A broad community of users will participate through the lifecycle of this project in the development of community standards and resources for the interoperability and computability of phenotypic knowledge. This will be achieved through workshops, usability testing sessions, and coordination with key research networks. Stakeholder ownership will be enhanced by rapid and open release of a variety of products that we anticipate to be of immediate and enduring value to the greater biology community, including tools for streamlining data curation and performing large-scale semantic similarity searches, high quality vertebrate taxonomy and anatomy ontologies, and standards for reasoning over homology. We will provide a unique training environment for students, postdocs and summer interns, including Native Americans through outreach at the University of South Dakota and minority and female students though a collaboration with Project Exploration at the University of Chicago. Project progress and outcomes will be disseminated through both traditional and online outlets for scholarly communication (including blog posts and mailing lists); the primary web presence will be at https://www.phenoscape.org/wiki/. 2011 Todd Vision
Cranston, Karen A., Gordon Burleigh, Keith Crandall, Karl Gude, David Hibbett, Mark Holder, Laura Katz, Richard Ree, Stephen Smith, Doug Soltis, Tiffani Williams. 2011. Collaborative Research: Automated and community-driven synthesis of the tree of life (AVATol OpenTree). NSF 2011 Karen Cranston
C. Wall et al. 2011. A novel database and ontology for evolutionary analyses of mammalian feeding physiology. Collaborative grant proposal to the ABI Innovation track. 2011 Christine E Wall, Hilmar Lapp
Rodriguez. (NSF Grant IOS–1120790 ($530,000, 2011–2014). Testing the role of sexual selection by mate choice in promoting divergent local adaptation. (With KD Fowler–Finn).) 2011 Rebecca Safran
Dryad UK is a project which aims to further develop Dryad – an international repository of data underlying scientific publications, with an initial focus on evolution, ecology, and related fields. Dryad enables scientists to validate published findings, explore new analysis methodologies, repurpose data, and perform synthetic studies. 2010 Todd Vision
Duke Postdoctoral Professional Development Award funded to attend SACNAS 2010 conference in Anaheim, CA in the capacity as a mentor, panelist, speaker and poster judge. 2010 Julie A Meachen
K. Donohue, J. Schmitt, PIs; Amity Wilczek Co-PI. 2010-2014. Collaborative research: Integrating genetically informed models of germination and flowering to predict life history responses to changing climate” NSF-DEB 2010 Kathleen Donohue
Gordon Uno. Submitted 2008. University of Oklahoma. Preparing to Prepare the 21st Century Biology Student Using Scientific Societies as Change Agents. NSF (RCN Proposal) This project was funded: one of the two proposals funded in this competition in January. 2009 Gordon Uno
The University of New Mexico (UNM) will develop and deploy DataNetONE (Observation Network for Earth), a sustainable long-term data preservation and access network, with related search and discovery, data integration, and user services and analytic tools. The goal of the DataNetONE (Observation Network for Earth) project is to enable scientists, decision-makers, and citizens to understand the nature and pace of change on Earth and to address associated environmental, social, and technological challenges. The initial focus will be on multi-disciplinary observational data collected by biological and environmental scientists, national and international research networks, and environmental observatories. DataNetONE will be extended to serve a broader range of science domains both directly and through interoperability with other DataNet deployments. The project is under the direction of Dr. William Michener at the UNM. DataNetONE is designed to enable the long-term preservation of diverse and complex multi-scale, multi-discipline, and multi-national science data by providing open, persistent, robust, and secure access to well-described and easily discovered Earth observational data. Expected users include scientists, educators, librarians, resource managers, and the public. The potential impact of long-term preservation and integrated access to diverse and complex multi-scale, multi-discipline, multinational science data is transformative in the speed with which researchers will be able to assemble and analyze data sets and in the types of problems they will be able to address. Scientific investigations that will be greatly facilitated by DataNetONE include understanding the relationships among human population density, atmospheric nitrogen and carbon dioxide, energy consumption and global temperatures; understanding and predicting the emergence and spread of diseases like avian flu; critical areas where local or regional changes may have strong effects on earth system interactions, feedbacks, or teleconnections; the impact of "megapolitan-ization" on ecological systems; and the interrelationships among coupled human and natural systems. 2009 Todd Vision
Price and Zane (2007) NESCent informatics white paper: "Comparative methods in R hackathon" 2008 Samantha Price
Hoeksema J.D., S. Brewer, D. Reed, C. Jackson, M. Holland, C. Ochs, G. Stratton, S. Threlkeld. 2007. University of Mississippi. Graduate Training in Multi-Scale Approaches to Forest Restoration and Management Science. USDA. 2008-2012. $168,000. 2007 Jason Hoeksema
Presentations
2009 Integrating taxonomic, phylogenetic, and fossil data in studies of diversification. Evolution, Moscow, ID. Michael Alfaro
Authors: C. E. Wall, V. Gapeyev, R. Z. German, X. Liu, C. J. Vinyard, and S. H. Williams Date: January, 2010 Title: The Feeding Experiments End-user Database (FEED) Meeting: Society for Integrative and Comparative Biology (SICB) Location: Seattle, Washington Christine E Wall
AUTHORS: Hipp, Andrew L. and Alexander Platt DATE: Monday, July 28th, 2008 TITLE: Estimating the probability of continuous character transitions on phylogenetic trees MEETING: Botany 2008 LOCATION: UBC, Vancouver ABSTRACT: Inferring the evolutionary history of species traits is a basic problem in evolutionary biology and an issue of practical concern for ecologists, developmental biologists, and others testing biological hypotheses using phylogenetic data. Methods of analyzing categorical data in a phylogenetic context have addressed the problem of localizing character transitions to branches. Locating transitions in continuous characters have received less focus, in part because many methods are based on a constant variance (Brownian motion) model, in which the rate of character evolution is modeled as shifting gradually on the tree if at all. Evaluation of Ornstein-Uhlenbeck models that allow shifts in character equilibria or Brownian motion models on subtrees are straightforward methods of modeling transitions in continuous characters. Assessed in an information theoretic framework, these models are useful means of estimating the probability that continuous trait change on a selected phylogenetic branch violates the expectations of a constant variance model. We contrast these methods with a Bayesian association mapping method that directly estimates the probability and magnitude of quantitative trait change on all branches of a phylogeny. In combination, these techniques provide a useful complement to existing methods for investigating the evolution of continuous characters. Andrew L. Hipp
Botero CA. 11 Feb 2009. Talk: The Evolution of Individual Variation in Communication Strategies. U Michigan, Ann Arbor. Carlos A. Botero
Botero C. A. 2009. Climatic patterns Predict the elaboration of song displays in mockingbirds. American Ornithologists' Union Symposium: From phylogeny to physiology: integrative studies of starlings and mockingbirds. University of Pennsylvania, Philadelphia. Carlos A. Botero
Botero, CA. 2009. Climatic variability may explain why good learners are sexy beasts. Duke University. BPCE seminar. Carlos A. Botero
Botero, C. A. 2009. Plenary talk: Genetic algorithms and philogenetic methods for the study of the evolution of communication in animals. II Symposium of the Colombian Network of Evolutionary Biologists. Cali, Colombia. Carlos A. Botero
Botero CA. 20 Feb 2009. Talk: The Evolution of Individual Variation in Communication Strategies. UNC Chapel Hill, NC. Carlos A. Botero
Botero, CA. 20 Nov 2009. Individual-based simulations for the study of animal communication. North Carolina State University (hosted by the labs of Rob Dunn, Kevin Gross, and Nick Haddad) Carlos A. Botero
Botero CA. 21 April 2009. Talk: The Evolution of Individual Variation in Communication Strategies. Duke University, Durham NC. Carlos A. Botero
Botero CA. 6 Feb 2009. Talk: The Evolution of Individual Variation in Communication Strategies. NESCent, Durham NC. Carlos A. Botero
Boyer, A.G. J.H. Brown, S. Finnegan, M. Kowalewski, R.A. Krause, Jr., S.K. Lyons, C.R. McClain, D.W. McShea, P.M. Novack-Gottshall, J.L. Payne, F.A. Smith, P.A. Spaeth, J.A. Stempien, and S.C. Wang. 2009. An upper limit to maximum animal body size through the Phanerozoic. 9th North American Paleontological Convention Abstracts. Cincinnati Museum Center Scientific Contributions Number 3, p. 45. Alison G. Boyer
Boyer, A.G. J.H. Brown, S. Finnegan, M. Kowalewski, R.A. Krause, Jr., S.K. Lyons, C.R. McClain, D.W. McShea, P.M. Novack-Gottshall, J.L. Payne, F.A. Smith, P.A. Spaeth, J.A. Stempien, and S.C. Wang. 2009. An upper limit to maximum body size in animal phyla during the past 500 million years. 94th Ecological Society of America Annual Meeting, Albuquerque, NM. Alison G. Boyer
Consortium for the History and Philosophy of Biology, University of Toronto, 2008. "Teasing apart developmental and evolutionary contributions to adaptation: Cultural group selection and the place of development in multi-level evolution." Lauren W. McCall
Constable H and Russell L. December 2008.  Managing online access to biodiversity data and providing opportunities for collaboration and co-development. National Biological Information Infrastructure (NBII) Developers’ Conference, Denver, Colorado. James Hanken
Constable H, L Russell and Wieczorek J.  April 2009. VertNet: The Next Step in the Biodiversity Informatics Revolution for Natural History Museums.  (Invited speaker) Association of Southeastern Biologists, Birmingham, Alabama. James Hanken
Constable, H. May 2009.  VertNet: Serving Biodiversity Occurrence Data for Spatial Analyst. Geolunch Talk Series Geospatial Innovations Facility, University of California Berkeley, Berkeley, California. James Hanken
Constable H, Spencer C, Wieczorek J and Russell L. June 2009. VertNet: The Next Step in the Biodiversity Informatics Revolution. eBiosphere 09, London, England. [poster] James Hanken
Dave Clements, April 2009, Visualizing and Integrating Next Generation Sequence Data using GMOD, Evolutionary Genetics - the impact of next generation sequencing technologies, Lutherstadt-Wittenberg, Germany David Clements
Dave Clements, August 2009, GMOD Help Desk Update, August 2009 GMOD Meeting, Oxford, UK David Clements
Dave Clements, August 2009, Visualizing NGS Data in GBrowse 2 David Clements
Dave Clements, Ben Faga, Sheldon McKay, and Mark Yandell, June 2009, Database Tools for Evolutionary Genomics: An introduction to GMOD software for managing, annotating and visualizing genomic data, SMBE 2009, Iowa City, IA David Clements
Dave Clements, Brian Osborne, Hilmar Lapp, Xianhua Liu, W. Owen McMillan, Nassib Nassar, and Todd J. Vision, November 2007, Digesting the Genome Glut: Promoting the Use and Extension of GMOD To Emerging Model Organisms, Genome Informatics 2007, Cold Spring Harbor, NY David Clements
Dave Clements, David Riley, Ben Faga, Hervé Tettelin, Sam Angiuoli, and Jonathan Crabtree. April 2008, GMOD Tools for Comparative Genomics, IGERT Symposium on Evolution, Development, and Genomics, Eugene, OR. David Clements
Dave Clements, December 2009, Database Tools for Biologists, Texas A&M Biochemistry and Biophysics Department. David Clements
Dave Clements, Hilmar Lapp, and Todd Vision, April 2008, GMOD: Database Resources for Emerging Model Organisms, 2nd Annual Arthropod Genomics Symposium, Kansas City, MO. David Clements
Dave Clements, Hilmar Lapp, and Todd Vision, April 2008, GMOD: Informatics Resources for Evolutionary Research, IGERT Symposium on Evolution, Development, and Genomics, Eugene, OR. David Clements
Dave Clements, Hilmar Lapp, and Todd Vision, June 2008, GMOD: Genomics Resources for Emerging Model Organisms Poster, American Genetic Association Annual Symposium, Raleigh, NC David Clements
Dave Clements, Hilmar Lapp, Brian Osborne and Todd J. Vision, July 2008, GMOD: Managing genomic data from emerging model organisms, ISMB, Toronto, ON, Canada David Clements
Dave Clements, January 2009, GMOD Help Desk Update, January 2009 GMOD Meeting, San Diego, CA David Clements
Dave Clements, July 2008, GMOD Help Desk Update, July 2008 GMOD Meeting, Toronto, ON, Canada David Clements
Dave Clements, June 2009, Seeing the forest and the trees: visualizing next generation sequence data, Next Generation Genome Analysis in Non-Model Organisms, Storrs, CT David Clements
Dave Clements, Nov 2007, GMOD Help Desk Update, November 2007 GMOD Meeting, Cold Spring Harbor, NY David Clements
Dave Clements, November 2009, GMOD for Comparative Genomics, 1st international workshop on Information Systems for Insect Pests, Rennes, France David Clements
Dave Clements, October 2009, Database Tools for Biologists: A Half-Day GMOD Workshop, Bioinformatics Australia 2009 (BA2009), Melbourne, Australia David Clements
Dave Clements, Scott Cain, Paul Hohenlohe, Nicholas Stiffler, Paul Etter, Eric Johnson, and William Cresko, January 2009, Managing Next Generation Sequence Data With GMOD, Plant and Animal Genome (PAG), San Diego, CA David Clements
Finnegan, S., F.A. Smith, S.K. Lyons, A.G. Boyer, J.H. Brown, M.E. Clapham, Z. Finkel, M.A. Kosnik, M. Kowalewski, R.A. Krause, Jr., R. Lockwood, C.R. McClain, D.W. McShea, P.M. Novack-Gottshall, J.L. Payne, P.A. Spaeth, J.A. Stempien, and S.C. Wang. 2009. Size invariant extinction risk in the marine fossil record. 9th North American Paleontological Convention Abstracts. Cincinnati Museum Center Scientific Contributions Number 3, p. 46. Seth Finnegan
Forde and Gudelj will be running a symposium entitled 'Mathmatical models and microbes as tools for understanding diversity' at the annual meeting of the Ecological Society of America in Aug 2009. Six of the participants in the working group will be presenting research during the symposium, some of which has come out of collaborations established through the NESCent working group. Samantha Forde
Greenberg, J., Carrier, S., White, H., and Scherle, R. (2009). The Dryad Repository Application Profile: Groundwork Towards a Metadata Scheme for Scientific Data. DigCCurr2009, Chapel Hill, NC, April 2, 2009. Ryan Scherle, Jane Greenberg, Sarah Carrier, Hollie White
Invited seminar: Duke University, Behavioral, Community and Population Ecology Seminar, 2008. "The diversification of vertebrate locomotor strategies and the hominin brain." Lauren W. McCall
Novack-Gottshall, P.M., C.R. McClain, P.A. Spaeth, S.C. Wang, A.G. Boyer, J.H. Brown, S. Finnegan, M. Kowalewski, R.A. Krause, Jr., S.K. Lyons, D.W. McShea, J.C. Nekola, S.I. Passy, J.L. Payne, F.A. Smith, and J.A. Stempien. 2009. Variation in local body size distributions of fossil and modern taxonomic groups may reflect habitat and life-history differences. 9th North American Paleontological Convention Abstracts. Cincinnati Museum Center Scientific Contributions Number 3, p. 44. Philip Novack-Gottshall
Scherle, R. (2009). Using DSpace as a Disciplinary Data Repository. International Conference on Open Repositories 2009, Atlanta, GA. Ryan Scherle
Scott Cain and Dave Clements, April 2008, Chado: A Database Schema for Integrating Biological Data, 2nd Annual Arthropod Genomics Symposium, Kansas City, MO. David Clements
Scott Cain, David Clements, and the GMOD Consortium, January 2009, Comparative Genomics Software Packages At GMOD, Plant and Animal Genome (PAG), San Diego, CA David Clements
Sheldon McKay, Scott Cain, and Dave Clements, January 2009, Comparative Genomics with GBrowse_syn: A hands on workshop for visualizing your syntenic data with GBrowse_syn, Plant and Animal Genome (PAG), San Diego, CA David Clements
Symposium at Society for Integrative and Comparative Biology (SICB) annual meeting, 2011. Symposium Conveners: Susan H. Williams, Christopher J. Vinyard, Rebecca Z. German, and Christine E. Wall Date: January, 2011 Symposium Title: Synthesis of Physiologic Data from the Mammalian Feeding Apparatus using FEED, the Feeding Experiments End-user Database. Christine E Wall
Winn, A.A., E. Elle, and S. Kalisz. 2008. Mixed mating, inbreeding depression and the dynamics of plant mating system evolution. Evolution meetings Minneapolis, MN Susan Kalisz
Perez KE and Price RM. 2015. The Echoes of an Adaptationist Legacy: (Not) Teaching Non-adaptive Evolution. 118th Annual Meeting of the Texas Academy of Science, Science Education Section. San Antonio, TX. 2015 Rebecca Price
Authors: Brandon H. Hidaka, Anila Asghar, Randolph M. Nesse, Katelyn J. Bennett, Matthew W. Beyrouty, Nicole K. Skursky, Mark D. Schwartz Date: April 24, 2014 Title: The Role of Evolutionary Concept in Medical Education 10 Years Later Meeting: Society of General Internal Medicine Annual Meeting Location: San Diego, CA 2014 Nicole Skursky
Hiatt A, French D, Perez K, Price RM, Davis G, Terry M. 2014. The EvoDevoCI: A new measure of evolutionary understanding. National Association of Biology Teachers. Atlanta, GA. 2014 Rebecca Price
Price RM and Perez KE. 2014. Can teaching nonadaptive mechanisms of evolution improve understanding of natural selection? Lessons learned from developing concept inventories about evolution. Society for the Advancement of Biology Education Research, Minneapolis, MN. 2014 Rebecca Price
Brandon Routman, April 10 2013, Bounded Rationality Updated, 1st Conference of Herbert Simon Society, New York City 2013 Brandon Routman
Smith, N.A. 2013. Assembly of the pelagic avifauna of North America: including insights gleaned from the fossil record of the Pan-Alcidae. Symposium: Assembly of the North American Avifauna. American Ornithologist's Union, Chicago, IL. 2013 N. Adam Smith
Cranston, K. Freeing scientific data with CC0 and Dryad repository. Opensourceway. April 12, 2013. (video) 2013 Karen Cranston
Hertweck, K. L. 2013. Transposable element proliferation and genome size evolution in Asparagales. Poster at Plant Animal Genome (PAG) XXI Meeting, San Diego, CA 2013 Kate Hertweck
Hertweck, K. L. and M. McKain. Estimation of divergence times in Asparagales in the presence of hybridization. Invited talk in the Paleobotany Symposium at Monocots V: 5th International Conference on Comparative Biology of Monocotyledons. 2013 Kate Hertweck
Hertweck, K. L., M. A., Han, J. L., Phillips, Greer, L. F., Graves, M., Rose, M. R. 2013. Genome-wide transposable element insertion frequencies change with selection for accelerated development. Evolution, Snow Bird, Utah. 2013 Kate Hertweck
Maherali H. 2013. Exploring pattern and process in the evolutionary history of the mycorrhizal symbiosis. Invited symposium presentation. The Missouri Botanical Garden 60th Annual Systematics Symposium, Phylogeny meets Ecology: patterns of diversity, community assembly, and niche evolution, St. Louis, MO. 2013 Hafiz Maherali
Robinson, B.W. Invited Talk. 15 February, 2013. Does resource competition favor adaptive plasticity, and if so, what really is the evidence? Dept. of Biology, UNC Chapel Hill, Biology Lunch Bunch Seminar. 2013 Beren Robinson
Schaeffer, P. Supporting scientific communities by publishing data. Joint OpenAIRE/LIBER workshop: Dealing with Data - what'™s the role for the library? Ghent (Belgium), 28 May 2013 2013 Peggy Schaeffer
Scherle, R. Dryad Curation Process. CurateGear Symposium. Chapel Hill, NC, January 9, 2013. 2013 Ryan Scherle
Scherle, R. & Vision, T. (2013) Dryad: Data as an Integral Part of the Scholarly Record. DataONE Users Group. 2013 Ryan Scherle, Todd Vision
Bailey, M. F., C. M. Caruso, and A. L. Case. 2012. Ecological effects on male fertility restoration in cytonuclear gynodioecy. Oral presentation. First Joint Congress on Evolutionary Biology, Ottawa, ON, Canada. 2012 Christina M Caruso
Smith, N.A. 2012. The fossil record and phylogeny of the Pan-Alcidae. Society and Avian Paleontology and Evolution. Vienna, Austria. 2012 N. Adam Smith
Smith, N.A. & J.A. Clarke. 2012. Variation in the endocranial anatomy of the Charadriiformes (Aves): sensory system evolution associated with the transition to wing-propelled diving. Society of Vertebrate Paleontology, Raleigh, NC. 2012 N. Adam Smith
Caruso, C. M. February 10 2012. The evolutionary ecology of cytonuclear interactions in flowering plants. Department of Biology Lunch Bunch, University of North Carolina. 2012 Christina M Caruso
Caruso, C. M. July 3 2012. The evolutionary ecology of cytonuclear interactions in flowering plants. Mountain Lake Biological Station, University of Virginia. 2012 Christina M Caruso
Case, A. L. and C. M. Caruso. 2012. Testing models of sex ratio evolution in a gynodioecious plant. Oral presentation. First Joint Congress on Evolutionary Biology, Ottawa, ON, Canada. 2012 Christina M Caruso
Cranston, K.A. 2012, "Making the tree of life Phylotastic!", iEvoBio, Ottawa, Canada 2012 Karen Cranston
Cranston, Karen A., July 10, 2012, Open Tree of Life: A community-assembled, continually updated evolutionary history of all life, Evolution 2012, Ottawa, Canada 2012 Karen Cranston
Cruickshank, T and MJ Wade. January 2012. Maternal adjustment of brood sex ratio in the broad-horned flour beetle, Gnathocerus cornutus, Symposium: The Impacts of Developmental Plasticity on Evolutionary Innovation and Diversification, SICB Annual Meeting, Charleston, SC. 2012 Tami Cruickshank
Fitzgerald, R., Dechman, L., Willis, C. (2012). HIVE for LC Web Archives: Web Archives and Automatic Subject Indexing. Presentation given at the International Internet Preservation Consortium 2012 General Assembly, Washington, DC. May 4, 2012. (slides) 2012
Francis, C.D., N.J. Kleist, C.P. Ortega, and A. Cruz. 2012. Anthropogenic noise alters key ecological services provided by birds. 5th North American Ornithological Conference, Vancouver, British Columbia. 2012 Clinton D Francis
Francis, C.D., N.J. Kleist, C.P. Ortega, and A. Cruz. 2012. Anthropogenic noise alters key ecological services provided by birds. 97th Meeting of the Ecological Society of America, Portland, Oregon 2012 Clinton D Francis
Greenberg, J. Digital Libraries for Research Data. Conferencia Inaugural del Segundo Cuatrimestre, Dpto. de Biblioteconom­a y Documentacion, Campus de Colmenarejo, Universidad Carlos III de Madrid, Spain. 2012 Jane Greenberg
Greenberg, J. Dryad's Evolving Proof of Concept and the Metadata Hook. Wolfram Data Summit, Washington DC, September 6, 2012 (slides) 2012 Jane Greenberg
Greenberg, J. The Dryad Repository. Long-term Stewardship of Scientific Data: Your Library Can Participate in DataONE. LITA Session, ALA Annual Conference, Anaheim, CA, June 24, 2012. 2012 Jane Greenberg
Harnik, P.G. June 2012. Biological determinants of extinction risk in the marine bivalve fossil record. American Malacological Society annual meeting, Cherry Hill. 2012 Paul G Harnik
Harnik, P.G., P.C. Fitzgerald, and S.J. Carlson. July 2012. Geographic range and extinction risk among Devonian terebratulide brachiopods. Society for the Study of Evolution annual meeting, Ottawa. 2012 Paul G Harnik
Hertweck, K. L. 2012. From environmental adaptation in plants to human disease: The widespread genomic effects of junk DNA. Society for the Advancement of Chicanos and Native Americans in Science (SACNAS) National Meeting, Seattle, Washington. 2012 Kate Hertweck
Hertweck, K. L. 2012. Genome-wide effects of transposable element evolution. Invited seminar at University of Virginia Ecology and Evolutionary Biology Department. 2012 Kate Hertweck
Hertweck, K. L. and J. C. Pires. 2012. Assembly of repetitive DNA from genome survey sequencing: Lessons from grasses and applications to non-model systems. Evolution, Ottawa, Ontario, Canada. 2012 Kate Hertweck
Hiatt A, Perez KE, Davis G, Terry M, Trujillo C, French D, Price RM. 2012. Evo-devo: target concepts and students’ challenges. National Association of Biology Teachers, Dallas, TX. 2012 Rebecca Price
Hiatt, A., Perez, K.E., Davis, G., Trujillo, C., Terry, M., Price, R. 2012. Evo-Devo in the classroom: target concepts and students' challenges. 1st Joint World Congress on Evolutionary Biology, Ottowa, Canada. 2012 Rebecca Price
H. Lapp, R. Guralnick, and M. Westneat. 2012. Liberating Our Beautiful Trees: A Call to Arms. Lightning talk at 2012 iEvoBio Conference. 2012 Hilmar Lapp, Rob Guralnick, Mark Westneat
James P. Balhoff, Wasila M. Dahdul, Hilmar Lapp, Paula M. Mabee, Peter E. Midford, Todd J. Vision, and Monte J. Westerfield, on behalf of the Phenoscape Project Team. "The Phenoscape Knowledgebase: Integrating phenotypic data across taxonomy, from biodiversity to developmental genetics". Poster at DILS 2012, College Park, MD, June 28, 2012. 2012 Jim P Balhoff
J. Balhoff. 2012. Linking phenotypes using ontologies. Invited department seminar presentation at California Academy of Sciences. 2012 Jim P Balhoff
Luyten, B., Diggory, M., Schaeffer, P. Subject Repositories for Research Data - the Dryad Approach., European Library Automation Group (ELAG) Annual Conference, Mallorca, Spain, May 16, 2012. 2012 Peggy Schaeffer
Maherali H. Invited Talk. 11 January 2012. Phylogenies, functional trait evolution and community assembly: perspectives from the plant-fungal symbiosis. NESCent, Durham, NC. 2012 Hafiz Maherali
Maherali H. Invited Talk. February 17, 2012. Phylogenies, functional trait evolution and community assembly: perspectives from the plant-fungal symbiosis. University Program in Ecology, Department of Biology, Duke University, Durham, NC. 2012 Hafiz Maherali
Maherali H. Invited talk. January 24, 2012. Phylogenies, functional trait evolution and community assembly: perspectives from the plant-fungal symbiosis. Department of Plant Biology, North Carolina State University, Raleigh, NC. 2012 Hafiz Maherali
Maherali H. Invited talk. July 5, 2012. Phylogenies, functional trait evolution and community assembly: perspectives from the plant-fungal symbiosis. Mountain Lake Biological Station & Department of Biology, University of Virginia. 2012 Hafiz Maherali
Maherali H. Invited Talk. March 23, 2012. Phylogenies, functional trait evolution and community assembly: perspectives from the plant-fungal symbiosis. Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC. 2012 Hafiz Maherali
Midford, P. E. July 11, 2012. Arachnolingua: Words about what spiders do. iEvoBio 2012 Lightning Talk. Ottawa ON. 2012 Peter E Midford
M. V. Han and M. W. Hahn, 1/23/2012, Gene transpositions in the Drosophila genome, Biology Department, College of Charleston 2012 Mira Han
O'Meara, B., Brown, J., Eastman, J., Harmon, L., Heath, T., Midford, P., Pennell, M. (July 10, 2012) DateLife. iEvoBio 2012 Challenge entry, Ottawa, ON. 2012 Peter E Midford, Brian C O'Meara, Joseph W Brown, Jonathan Eastman, Luke Harmon, Tracy Heath, Matthew Pennell
O'Meara, B.C., T. Heath, L. Harmon, J. Eastman, P. Midford, J. Brown, M. Pennell, M. Alfaro. 2012. Presentation at iEvoBio on the Phylotastic-generated project, DateLife. The recorded talk is also on YouTube. 2012 Brian C O'Meara
Perez, K.E., Price, R. 2012. Concept inventories to assess student understanding of evolution: genetic drift, population-thinking and evo-devo. 1st Joint World Congress on Evolutionary Biology, Ottowa, Canada 2012 Rebecca Price
Piwowar, HA. Feb 19 2012, Accelerating Scientific Progress Through Public Availability of Research Data. Session organizer and speaker. AAAS 2012, Vancouver Canada. 2012 Heather Piwowar
Piwowar, Heather. March 2012. Big shoulders in scholarly communication: data archiving+#altmetrics. HighWire Spring Publisher Meeting, Palo Alto CA. 2012 Heather Piwowar
Price RM, Andrews TM, Mead LS, McElhinny TL, Thanukos A, Perez KE, Herreid CF, Terry DR, and Lemons PP. 2012. Misconceptions that biology undergraduates have about genetic drift. Society for the Advancement of Biology Education Research, Minneapolis, MN. 2012 Rebecca Price
Priem, Jason and Piwowar, Heather. June 2012. Altmetrics in the Wild: Using Social Media to Explore Scholarly Impact. altmetrics12. Evanston IL. 2012 Heather Piwowar
Priem, Jason and Piwowar, Heather. June 2012. total-impact and altmetrics. Startup Science, San Francisco CA. 2012 Heather Piwowar
Robinson, BW. Invited Talk. 6 February, 2012. Adaptive diversification of post glacial fishes by genetic accommodation. NESCent, Durham, NC 2012 Beren Robinson
Schaeffer, P. Creating a sustainable business model for a digital repository: the Dryad experience. Research Data Access and Preservation Summit, New Orleans, LA, Mar. 22, 2012. 2012 Peggy Schaeffer
Scherle, R., & Diggory, M. (2012) Creating Citable Data Identifiers. International Conference on Open Repositories. 2012 Ryan Scherle
Scherle, R. Dryad and Data Citation. ANDS Data Citation Webinar Series. September 26, 2012. 2012 Ryan Scherle
Vision, T.J. Coupling Research Data to Publications in the Life Sciences. ICSTI Delivering Data in Science workshop Paris, France. 2012 Todd Vision
Vision, T. J. Dryad: Scalable Infrastructure for coupling Research Data to Publications in the Life Sciences, Academic Publishing in Europe 2012 Berlin, Germany. 2012 Todd Vision
Botero, CA and DR Rubenstein (2011) Variable environments, fluctuating selection and the stability of breeding partnerships in birds. Talk presented at Evolution 2011 (Norman, OK) and Behavior 2011 (Bloomington, IN) 2011 Carlos A. Botero
Botero, CA (Sep 2011)Climate change, fluctuating selection and the evolution of adaptive flexibility. East Carolina State University. Departmental Seminar (Biology) 2011 Carlos A. Botero
Smith, N.A. 2011. The paleontologists' perspective on choice of fossil calibrations for divergence analysis. Duke University, Biology Department, Durham, NC. 2011 N. Adam Smith
Caruso, C. M. November 21 2011. The evolutionary ecology of cytonuclear interactions in flowering plants. Department of Biology, College of Charleston. 2011 Christina M Caruso
Caruso, C. M. October 27 2011. The evolutionary ecology of cytonuclear interactions in flowering plants. Department of Biology, East Carolina University. 2011 Christina M Caruso
Clarke, K. Sharing Between Data Repositories. Code4Lib 2011 Conference, Feb. 2011. Bloomington, IN. 2011 Ryan Scherle, Kevin S Clarke
Francis, C. D., C. P. Ortega, and A. Cruz. 2011. Anthropogenic noise filters avian communities nonrandomly. Joint Meeting of the Animal Behavior Society and International Ethological Conference, Bloomington, IN. 2011 Clinton D Francis
Greenberg, J. (2011, June). Instantiation: metadata models, rationales and realities for knowledge organization. NASKO/Toronto, 17 June 2011. 2011 Jane Greenberg
Greenberg J and Vision T, "The Dryad Repository: A New Path for Data Publication in Scholarly Communication", OCLC, April 25, 2011. 2011 Jane Greenberg, Todd Vision
Greenberg J. Beyond Zebra: Taking RDA Beyond MARC; Dublin Core: A Stepping Stone for the Dryad Repository. ALA Annual Conference 2011 Jane Greenberg
Greenberg J, "Metadata Research: Evolution of a Discipline", Drexel University iSchool, May 9, 2011, (abstract) 2011 Jane Greenberg
Greenberg, J. The Dryad Repository. Repositories in Science & Technology: Preserving Access to the Record of Science. CENDI and NFAIS and Hosted by FLICC Library of Congress, November 30, 2011 2011 Jane Greenberg
H. Lapp. 2011. Reasoning over phenotype diversity, character change, and evolutionary descent. Invited department seminar presentation at University of Florida. 2011 Hilmar Lapp
H. Lapp and T.J. Vision. 2011. Open science, open-source, and open data: Collaboration as an emergent property? Panel presentation at the 2011 Cyberinfrastructure for Collaborative Science Workshop at NESCent. 2011 Hilmar Lapp, Todd Vision
James Balhoff, Wasila Dahdul, Hilmar Lapp, Peter Midford, Todd Vision, Monte Westerfield and Paula Mabee (July 26-30, 2011) Poster; "Employing reasoning within the Phenoscape Knowledgebase", International Conference on Biomedical Ontology; University at Buffalo, NY 2011 Hilmar Lapp, Peter E Midford, Jim P Balhoff, Wasila Dahdul, Todd Vision, Monte Westerfield, Paula Mabee
James P. Balhoff (February 24, 2011) "The Phenoscape Knowledgebase: Linking Evolutionary Diversity to Genetic Data Using Phenotype Ontologies", Conference on Semantics in Healthcare and Life Sciences, Cambridge, MA. 2011 Jim P Balhoff
James P. Balhoff, Matthew J. Yoder, Andrew R. Deans. (October 2011) "Linking semantic phenotypes to character matrices and specimens". Poster at TDWG 2011 Biodiversity Information Standards conference, New Orleans, LA. 2011 Jim P Balhoff, Matthew Yoder, Andy Deans
James P. Balhoff, Peter E. Midford, Hilmar Lapp (July 2011) Integrating anatomy and phenotype ontologies with taxonomic hierarchies, International Conference on Biomedical Ontology, Buffalo, NY. 2011 Jim P Balhoff, Peter E Midford, Hilmar Lapp
McGuire, J.L. 2011. How Quaternary climate change patterns morphological variation in Microtus californicus. 71st Annual Meeting, Society of Vertebrate Paleontology, Las Vegas, NV. Presented in invited symposium: Symposium II- Climate Change and Vertebrate Response in the Evolving Arid West of Plio-Pleistocene North America. 2011 Jenny L McGuire
McGuire, J. L. 2011. Mammalian responses to climate change: a paleontological perspective. Department Seminar, Department of Earth and Atmospheric Sciences, University of Nebraska at Lincoln. 2011 Jenny L McGuire
McGuire, J. L. 2011. Mammalian responses to climate change: a paleontological perspective. Lunch Bunch Seminar, Department of Biology, University of North Carolina, Chapel Hill. 2011 Jenny L McGuire
McGuire, J.L. 2011. Past climate set the stage for future responses to climate change: morphological evolution in Microtus californicus. Evolution Annual Meeting, Norman, OK. July 20, 2011. 2011 Jenny L McGuire
McGuire, J.L. and Davis, E.B. 2011. Using the paleontological record of Microtus to test species distribution models and reveal responses to climate change. Geological Society of America Annual Meeting, Minneapolis, MN. October 11, 2011. 2011 Jenny L McGuire
Meachen-Samuels, J. 2011. Carnivore morphology and evolution: past, present and future. Marshall University, Huntington, WV. 2011 Julie A Meachen
Meachen-Samuels, J. and J.X. Samuels. 2011. Bigger, stronger and faster in the Pleistocene: evolutionary change in coyotes (Canis latrans) after the megafaunal extinction. Society for the Study of Evolution Meeting. Norman, OK. 2011 Julie A Meachen
Midford, P. E., Balhoff, J. P., Dahdul, W. M., Lapp, H., Mabee, P. M., Vision, T. J., Westerfield, M. June 22, 2011. Matching Taxonomic and Genetic Phenotypes in the Phenoscape Knowledgebase. iEvoBio Lightning Talk, Norman OK. 2011 Peter E Midford, Jim P Balhoff, Wasila Dahdul, Hilmar Lapp, Paula Mabee, Todd Vision, Monte Westerfield
Panelists to discuss evolution of human brain size, skin color and diet at AAAS meeting. Sunday Feb. 20, 8-9:30 a.m., Washington, DC. 2011 Robin A Smith
Piwowar, Heather. August 2011. Data citation challenges. DataCite Summer Meeting, Berkeley CA. 2011 Heather Piwowar
Piwowar, Heather. Dec 2011. A future were data citation Counts. Int Digital Curation Conference. Bristol, UK 2011 Heather Piwowar
Piwowar, Heather. December 2011. BMJ internal workshop on The Future of Research Dissemination, London. 2011 Heather Piwowar
Piwowar, Heather. June 2011. Tracking Data Reuse: Motivations, Methods, and Obstacles. IASSIST Vancouver. 2011 Heather Piwowar
Piwowar, Heather. March 2011. Citation Challenges. JISC, Managing Research Data, Birmingham UK. 2011 Heather Piwowar
Piwowar, Heather. May 15, 2011. Reputation as incentive. SameAs, London UK. 2011 Heather Piwowar
Piwowar, Heather. November 2011. Open research data: fun, important, + in need of librarians. ACCESS11 Vancouver 2011 Heather Piwowar
Piwowar, Heather. October 2011. Recycle, reuse, research: Using open data in scholarly research, OA week SFU, Vancouver. 2011 Heather Piwowar
Shotton, D., Peroni, S. Semantic annotation of publication entities using the SPAR (Semantic Publishing and Referencing) Ontologies. Beyond the PDF Workshop, Jan. 2011, La Jolla, CA. 2011 Todd Vision
Vision T. Introduction to DryadUK sustainability workshop. April 1 2011, The British Library, London UK. 2011 Todd Vision
BD Redelings. July 2010. Phylogenies Unplugged: Consensus Trees with Wandering Taxa., SIAM Conference on the Life Sciences (LS10).Pittsburgh PA. 2010 Benjamin D Redelings
Beagrie, N. 2010. Dryad and the sustainability of digital repositories. Fourth Bloomsbury Conference on e-publishing, London UK. 2010 Todd Vision
Beagrie, N., Eakin-Richards, L., and Vision, T. Business Models and Cost Estimation: Dryad Repository Case Study, iPRES2010 Vienna, September 2010. 2010 Lori Eakin, Todd Vision
Botero, CA 22 Nov 2010. Environmental and individual variation as agents of selection in the evolution of animal communication. Departamental seminar for the College of Charleston. Charleston NC 2010 Carlos A. Botero
Botero, C. A. March 1, 2010. Phylogenetics and the study of animal communication. Institut fur O–kologie und Evolution, University of Bern. Switzerland. 2010 Carlos A. Botero
Buels, R., and Clements, D., 2010, GMOD for Evolutionary Biology, iEvoBio, Portland, Oregon 2010 David Clements
Cain, S, and Clements D. January 2010, GMOD Project Update, Plant and Animal Genome (PAG) XVIII, San Diego, California 2010 David Clements
Clements, D, September 2010, Help Desk Update, September 2010 GMOD Meeting, Cambridge UK 2010 David Clements
Dave Clements and Scott Cain, January 2010, GMOD Project Update, Plant and Animal Genome XVIII, San Diego, CA, USA. 2010 David Clements
Dave Clements, January 2010, Help Desk Update, January 2010 GMOD Meeting, San Diego, CA, USA 2010 David Clements
Dave Clements, Scott Cain, January 2010, GMOD Project Update, Plant and Animal Genome XVIII (PAG 2010), San Diego, CA, USA 2010 David Clements
Dave Clements, Sheldon McKay, Ken Youens-Clark, Ben Faga, Scott Cain, January 2010, Comparative Genomics Tools In GMOD, Plant and Animal Genome XVIII (PAG 2010), San Diego, CA, USA 2010 David Clements
Greenberg, J, Willis, C., and White, H. Metadata for Scientific Data: An Analysis Targeting Challenges and Opportunity in Our Global Information Ecology, CODATA, Cape Town, South Africa, October, 2010, (slides) 2010 Jane Greenberg
H. Lapp. 2010. Bringing reason to phenotype diversity, character change, and common descent. Web seminar presentation in the NCBO Webinar Series. 2010 Hilmar Lapp
Jenkins, K., February 2010. NESCent Podcast: Speciation in real time. 2010 Carlos A. Botero
Kathleen Donohue (Plenary Speaker), June 2010, "Interactions across seed and adult life stages: ecological and evolutionary consequences," Seed Ecology III Meetings, Salt Lake City, Utah 2010 Kathleen Donohue
McGuire, J.L. 2010. Interpreting recent small-mammal range shifts in Yosemite in light of the Quaternary fossil record. 70th Annual Meeting, Society of Vertebrate Paleontology, Pittsburgh, PA. Romer Student Prize Session. 2010 Jenny L McGuire
Meachen-Samuels, J. 2010. Carnivore morphology and evolution: past, present and future. College of Charleston, Department of Biology departmental seminar, Charleston, SC. 2010 Julie A Meachen
Meachen-Samuels, J. 2010. Changes within carnivore guilds from the Pleistocene and Holocene of North America. 70th Annual Meeting of the Society of Vertebrate Paleontology, Pittsburgh, PA. 2010 Julie A Meachen
MEAS Departmental seminar at NC State University, titled "Morphology and evolution in the Carnivora: past, present and future" given on February 8, 2010 2010 Julie A Meachen
Michener, W., Kunze, J., Cruse, P., and Scherle, R. 2010. The Dryad and DataONE project in the US. DataCite Summer Meeting, Hanover, Germany. 2010 Ryan Scherle, William Michener
Midford, P. E. June 27, 2010. Phylontal: Using phylogenies to align phenotype ontologies. Evolution 2010, Portland, OR, USA. 2010 Peter E Midford
NESCent Professional Development (BBL): April 28 2010 Collaborative seminar presentation with Jory Weintraub,Ph.D. NESCent Associate Director 2010 Claire Williams
NESCent Seminar April 21, 2010 2010 Claire Williams
North Carolina Botanical Garden, Chapel Hill NC Invited Public Lecture 2010 Claire Williams
Piwowar, Heather. October 2010. Researching Open Research Data. Open Access Week, UBC Vancouver 2010 Heather Piwowar
Roberts, Trina E. Sticky tips and misplaced roots: Are models leading us astray in intraspecific phylogenetics? Duke Systematics Discussion Group, April 2010. 2010 Trina E Roberts
Roberts, Trina E. When good models go bad: Sticky tips and misplaced roots in intraspecific phylogenies. NESCent BBL, June 2010. 2010 Trina E Roberts
Scherle, R. and Aguera, J. 2010. HIVE: A New Tool for Working With Vocabularies. Code4Lib conference, Asheville, NC 2010 Ryan Scherle
Sheldon McKay, Robert Buels, and Dave Clements, 2010, GBrowse_syn, iEvoBio, Portland, Oregon 2010 David Clements
Talk: "Alternative paradigms in phylogenetic comparative biology." University of Massachusetts, Boston; University Program in Ecology, Duke University. 2010 Liam J Revell
Talk: "Predation and tail autotomy in Anolis lizards." Society for Integrative and Comparative Biology Meeting, Seattle, Washington. 2010 Liam J Revell
Talk presented at Society for the Study of Evolution Meeting, Portland, OR. 2010 Julie A Meachen
University of Parma, Department of Environmental Sciences 2010 Claire Williams
Vision TJ. The Dryad Digital Repository: Published evolutionary data as part of the greater data ecosystem. iEvoBio, Portland OR, June 2010. 2010 Todd Vision
Vision, T., Scherle, R. The Dryad Digital Data Repository: Coupling the Publication of Scientific Articles and Data. International Digital Curation Conference, December 2010, Chicago, IL. 2010 Ryan Scherle, Todd Vision
Vison, T., Lapp, H. The Dryad Digital Repository: published data as part of the greater data ecosystem. ISMB 2010, Boston MA, July 2010. 2010 Todd Vision, Hilmar Lapp
Whitlock, M. Data Archiving in Evolutionary Biology. Evolution 2010, Portland, OR 2010 Michael Whitlock
Evolution: Intersecting Natural and Social Sciences, Darwin Bicentenary, Siena, Italy, 2009. "Group Selection or Group Physiology? Filling in the Gaps of Multi-level Selection Theory to Explain Cultural Variation" 2009 Lauren W. McCall
Greenberg, J. 2009. Metadata Research Supporting the Dryad Data Repository. Metadata Working Group Forum. Cornell University Library. 2009 Jane Greenberg
Greenberg, J. 2009. Theories of Evolution and Cultural Diffusion: The Dryad Repository Case Study for Understanding Changes in Organizing Information Practices. iSchool Conference, Chapel Hill, NC. http://wiki.datadryad.org/wg/dryad/images/d/d5/ReviSchool-2009.doc 2009
Greenberg, J., Lapp, H., Scherle, R., Vision, T., White, H., Carrier, S., and Schaeffer, P. (2009) The Dryad Repository: Designing a Curation Workflow. 5th International Digital Curation Conference, London, UK. December 2009. 2009 Peggy Schaeffer, Ryan Scherle, Jane Greenberg, Hilmar Lapp, Todd Vision, Hollie White, Sarah Carrier
H.Lapp. 2009. Phyloinformatics VoCamp. Presentation at the 2009 TDWG Conference in Montpellier, France. 2009 Hilmar Lapp
Invited seminar: University of North Carolina at Chapel Hill, Servedio lab, 2009. "Explanations of adaptiveness in cultural evolution and behavioral ecology" 2009 Lauren W. McCall
Midford, P. E. (Jan 2009). Comparative Analysis of Behavior Using Ontologies. Society for Integrative and Comparative Biology, Boston MA. 2009 Peter E Midford
Midford, P., Mabee, P., Vision, T., Lapp, H., Balhoff, J, Dahdul, W., Kothari, C., Lundberg, J., Westerfiedl, M. (July 2009). .Phenoscape: Ontologies for large multi-species phenotype datasets. Poster presented at International Conference on Biomedical Ontologies, Buffalo, NY. 2009 Peter E Midford, Paula Mabee, Todd Vision, Hilmar Lapp, Wasila Dahdul, Cartik Kothari, John Lundberg, Monte Westerfield
Scherle, R. 2009. The Dryad Data Repository. Duke Repository Community, July 2009. 2009 Ryan Scherle
Scherle, R., Bapat, A., Carrier, S., Greenberg, J., Lapp, H., Schaeffer, P., Vision, T., & White, H. (2009) Dryad: a digital repository of data from publications in evolutionary biology and ecology. In Evolution 2009, Moscow, Idaho. 2009 Ryan Scherle, Amol Bapat, Sarah Carrier, Jane Greenberg, Hilmar Lapp, Peggy Schaeffer, Todd Vision, Hollie White
Scherle, R., Lapp, H., Bapat, A., Carrier, S., Greenberg, J., Schaeffer, P., Vision, T., & White, H. (2009) The Dryad Data Repository. In the 2009 The International Conference on Biodiversity Informatics, London. 2009 Ryan Scherle, Hilmar Lapp, Amol Bapat, Sarah Carrier, Jane Greenberg, Peggy Schaeffer, Todd Vision, Hollie White
Talk: "Ecology and evolution of tail autotomy in several lizard species." NESCent Brown Bag Lunch seminar, Durham, North Carolina. 2009 Liam J Revell
Vision, Todd J. 2009. Scientific Publications, Scientific Data, and the Role of Domain-specific Digital Libraries. UNC Scholarly Communications Working Group. 2009 Todd Vision
Duke Society for the Philosophy of Biology Conference: Cooperative Alliances in the History of Life: Aggregation, Individuation, and the Major Evolutionary Transitions, 2008. "Are Human Cultural Institutions Group-Level Adaptations?" 2008 Lauren W. McCall
Greenberg, J. 2008. The DRYAD Repository: Metadata Research and Development. Library of Congress. 2008 Jane Greenberg
Hilmar Lapp, Richard Holland, Aaron Mackey, William Piel, Mark Schreiber. BioSQL Reloaded: 1.0 Release, PhyloDB Module, and Future Features. Bioinformatics Open Source Conference (BOSC) 2008. 2008 Hilmar Lapp, Richard Holland, Aaron Mackey, William H Piel, Mark Schreiber
Lapp H. (2008) Towards a Simple, Standards-Compliant, and Generic Phylogenetic Database. Presentation at the 2008 TDWG Annual Meeting, Perth, Australia. 2008 Hilmar Lapp
Midford, P. E. (June 2008). Names, ranks, clades, and taxonomy ontologies. Ontology workshop at Evolution 2008. Minneapolis, MN. 2008 Peter E Midford
Midford, P. E. (Oct 2008). Taxonomy ontologies: Bridging phylogenetic and taxonomic history. TDWG 2008 Meeting, Fremantle, Australia 2008 Peter E Midford
Ryan Scherle, Sarah Carrier, Jane Greenberg, Hilmar Lapp, Abbey Thompson, Todd Vision, and Hollie White. 2008. Building Support for a Discipline-Based Data Repository. In Proceedings of the 2008 International Conference on Open Repositories. 2008 Ryan Scherle, Sarah Carrier, Jane Greenberg, Hilmar Lapp, Abbey Thompson, Todd Vision, Hollie White
Xianhua Liu and David Kidd. (2008) GeoPhyloBuilder. Mapping and Visualization of Census of Marine Life Workshop, October 2008, The Marine Geospatial Ecology Lab at the Nicholas School of the Environment and Earth Sciences at Duke University, Durham, NC. October 23-25, 2008 2008 Xianhua Liu, David Kidd
Carrier, S., Dube, J., & Greenberg, J. (2007). The DRIADE Project: Phased Application Profile Development in Support of Open Science. In DC-2007: Application Profiles: Theory and Practice. International Conference on Dublin Core and Metadata Applications, Singapore, August 27-31, 2007. 2007 Sarah Carrier, Jed Dube, Jane Greenberg
Carrier, S., Dube, J. Greenberg, J., Lapp, H., Thompson, H., Vision, T., & White, H. (2007) The Dryad Repository: Transforming Scientific Publishing and Data Discovery Via the Convergence of Open Access and eScience. The 2007 Microsoft eScience Workshop at RENCI, Chapel Hill, USA, 21-23 Oct 2007. 2007 Ryan Scherle, Sarah Carrier, Jed Dube, Jane Greenberg, Hilmar Lapp, Abbey Thompson, Todd Vision, Hollie White
Emmanuelle Porcher*, Pierre-Olivier Cheptou, Chris Eckert, Mark O. Johnston, and John. K. Kelly. Promising theoretical solutions to the problem of mixed mating. European Society for Evolutionary Biology XI Congress, Uppsala, Sweden, August 2007. (Invited talk.) Also presented to NESCent September 2007. 2007 Mark Johnston, Susan Kalisz
Greenberg, J. (2007). Classifying Scientific Data Objects with Bibliographic Relationship Taxonomies. ASIS&T 2007 Annual Meeting, Oct 2007. 2007 Jane Greenberg
Greenberg, J. (2007). Consensus Building and Prioritizing Consensus Building and Prioritizing Development for Project DRIADE: A Case Study. DigCCurr 2007, Chapel Hill, NC, April 18, 2007. 2007 Jane Greenberg
Hazkani-Covo E and Covo S. What evolution can teach us about double strand break repair: comparative genome analysis of numt loci enables detection of double strand break repair events at a molecular level. Society of Molecular Biology and Evolution (SMBE), Halifax, Canada. July 2007. 2007 Einat Hazkani-Covo
International Society for the History, Philosophy and Social Studies of Biology, 2007 (Exeter, U.K.) “Isolation vs. Diffustion: A cross-cultural test.” 2007 Lauren W. McCall
Mark O. Johnston*. Understanding the paradox of mixed mating in plants: a NESCent working group. Society for the Study of Evolution meeting. July 2006. 2007 Susan Kalisz, Mark Johnston
Pierre-Oliver Cheptou*. The evolution of the dispersal/outcrossing syndrome in spatially heterogeneous pollination environments: why are there so many dioecious plants on islands? European Society for Evolutionary Biology XI Congress, Uppsala, Sweden, August 2007. 2007 Susan Kalisz, Mark Johnston
News coverage
2009. Huge 'Megapiranha' fossil found in South America. Fox News. http://www.foxnews.com/story/0,2933,529195,00.html Wasila Dahdul
2009. Sabertooth just a pussycat next to feline kin. The Durham Herald-Sun. Robin A Smith
2009. ScienceShots: Fern frenzy. Science Magazine. Eric Schuettpelz
2009. Toothy 3-foot piranha fossil found: Remains bridge evolutionary gap between flesh eaters and plant eaters. MSNBC News. http://www.msnbc.msn.com/id/31553901/ns/technology_and_science-science/ Wasila Dahdul
Alleyne, R. 2009. Birds are better at singing in the rain - and the cold. Daily Telegraph, UK. Carlos A. Botero
Bates, K. 2009. Ferns took to the trees and thrived. Duke University Office of News and Communications. Eric Schuettpelz
Braun, David. 2009. Africa's rarest monkey may have bred with baboons. NatGeo News Watch. National Geographic. Robin A Smith
Bryner, Jeanna. 2009. Monkey business: baboon may have been mate. MSNBC News. Robin A Smith
Bryner, Jeanna. 2009. Rare monkey interbred with baboons, study suggests. LiveScience. Robin A Smith
Callaway, E. 2009. Why geeks get the girls. New Scientist. Carlos A. Botero
Cane, A. 2009. Bird song linked to survival. Financial Times. Carlos A. Botero
Conroy, M. 2009. How geeks get girls. Wired Magazine. Carlos A. Botero
Fields, H. 2009. ScienceNOW Daily News: How the Piranha Got Its Teeth. Science. http://sciencenow.sciencemag.org/cgi/content/full/2009/629/1 Wasila Dahdul
Flam, Faye. 2009. Unearthing the megapiranha. Philadelphia Inquirer. http://www.philly.com/inquirer/magazine/20090706_Unearthing_the_megapiranha.html Wasila Dahdul
Gill, V. 2009. Climate link to mockingbird songs. BBC News. Also ran in the Herald de Paris: http://www.heralddeparis.com/climate-link-to-mockingbird-songs/36495 Carlos A. Botero
Gill, V. 2009. Songbirds sing cross-species duet. BBC News. Carlos A. Botero
Harrell, E. 2009. Darwin Lives! Modern Humans Are Still Evolving. TIME. http://www.time.com/time/health/article/0,8599,1931757,00.html Stephen Stearns
Heger, M. (2009). Climate change may be especially tough on trees. USA Today. http://blogs.usatoday.com/sciencefair/2009/09/climate-change-may-be-especially-tough-on-trees.html Robin A Smith
Hirson, B. 2009. Science Update Radio Interview (AAAS). Climate-enhanced bird songs. Carlos A. Botero
Holden, C. 2009. Brainy birds get more chicks. Science Magazine. Carlos A. Botero
Holden, C. 2009. It's fit to be smart. Science Magazine. Carlos A. Botero
Holmes, B. 2009. Meet future woman: shorter, plumper, more fertile. New Scientist. http://www.newscientist.com/article/dn17997-meet-future-woman-shorter-plumper-more-fertile.html?DCMP=OTC-rss&nsref=online-news Stephen Stearns
Johnson, C. 2009. People are still evolving, heart study numbers say. The Boston Globe. http://www.boston.com/business/healthcare/articles/2009/10/26/evolution_continues_framingham_heart_study_says/ Stephen Stearns
Kessler, M. 2009. Mockingbirds: the tougher the weather, the better they sing. USA Today. Carlos A. Botero
Millius, S. 2009. For some birds, chancy climates mean better singers. Science News 175(13): 8. Carlos A. Botero
Minard, A. 2009. Yard-long Megapiranha Fossil Found. National Geographic News. http://news.nationalgeographic.com/news/2009/06/photogalleries/giant-piranha-pictures-evolution/ Wasila Dahdul
Paddock, C. 2009. Humans Are Still Evolving, Study Shows. Medical News Today. http://www.medicalnewstoday.com/articles/167915.php Stephen Stearns
Palca, J. Natural selection works on humans too. NPR's Science Friday. http://www.npr.org/templates/story/story.php?storyId=114081469&ft=1&f=1007 Stephen Stearns
Pennisi, Elizabeth. 2009. On the origin of cooperation. Science 325:1196-1199. James H Hunt
Smith, R. 2009. Sabertoothed males were pussycats. Duke University Office of News and Communications. Robin A Smith
Smith, R.A. 2009. Mockingbirds in fickle climes sing fancier tunes. Duke University Office of News and Communications. Carlos A. Botero
Suter, S. (2009). Editor's choice: Unable to diversify. Science 325(5936): 12. http://www.scienceonline.org/content/vol325/issue5936/twil.dtl#325/5936/12-a Brian C O'Meara
Switek, Brian. 2009. Q: How do you sex a Smilodon? (A: Very carefully). Laelaps Science Blog. Robin A Smith
Torrice, M. 2009. We're Still Evolving--And We May Be Shrinking. Science Magazine. http://sciencenow.sciencemag.org/cgi/content/full/2009/1022/1 Stephen Stearns
Unknown. 2009. Ancient ferns bum a ride off giant trees. Futurity. Robin A Smith
Unknown. 2009. Animal behaviour: Singing in the Rain. Nature 459: 487. doi:10.1038/459487b; Published online 27 May 2009 Carlos A. Botero
Unknown 2009. Hard times make birds better singers. Australian Broadcasting Corporation. ABC Science. Carlos A. Botero
Unknown. 2009. Humans continuing to evolve. The Colorado Springs Gazette. http://www.gazette.com/articles/continuing-64359-traits-humans.html Stephen Stearns
Unknown. 2009. Sabertooth tigers were relative pussycats. Fox News. Robin A Smith
Unknown. 2009. Study paints sabertooths as relative pussycats. LiveScience. Robin A Smith
Unknown. 2009. Study paints sabertooths as relative pussycats. MSNBC News. Robin A Smith
Unknown. 2009. Women to be shorter, more fertile in future. Deccan Chronicle. http://www.deccanchronicle.com/health/women-be-shorter-more-fertile-future-361 Stephen Stearns
2013. Africa's oldest known penguins are SEVEN MILLION years old: Amazing discovery shows boiling continent had four species but they were wiped out by changing sea levels. UK Daily Mail 2013 Robin A Smith
2013. Bird fossil sheds light on how swift and hummingbird flight came to be. Eurekalert. 2013 Robin A Smith
2013. Fly like a hummingbird, glide like a swift. Science Magazine. 2013 Robin A Smith
2013. Fossil illuminates ancestry of swifts and hummingbirds. Science News. 2013 Robin A Smith
2013. Found: Africa's oldest penguins. Discovery 2013 Robin A Smith
2013. Found: Africa's oldest penguins. Scientific American 2013 Robin A Smith
2013. Hummingbird ancestor reveals evolution of its unique flight. Discover Magazine. 2013 Robin A Smith
2013. Oldest fossils yet of African penguins found. NBC News 2013 Robin A Smith
2013. Penguin fossils discovered in Africa called oldest specimens on continent. Huffington Post 2013 Robin A Smith
2013. Text-mining spat heats up: Scientists & publishers clash over licenses that would let machines read research papers. Nature 2013 Robin A Smith
2013. Uncovering Africa's oldest known penguins. Eurekalert 2013 Robin A Smith
2012. 50-Million-year-old cricket and katydid fossils hint at the origins of insect hearing. Science 360, NSF's Daily News Feed. 2012 Robin A Smith
2012. 50-million-year-old crickets with ears. Futurity. 2012 Robin A Smith
2012. Allergies as a blessing in disguise. New York Times. 2012 Robin A Smith
2012. All that human noise has an effect on nature, too. MSNBC. 2012 Robin A Smith
2012. Ancient crickets hint at the origins of insect hearing. Eurekalert. 2012 Robin A Smith
2012. An evolutionary theory of dentistry. Science Magazine. 2012 Robin A Smith
2012. A song for all seasons: Scientists find birds that live in fluctuating weather are better singers. Daily Mail. 2012 Clinton D Francis
2012. Athletic frogs have faster-changing genomes. Eurekalert. 2012 Robin A Smith
2012. Changes in weather add to birds' marital woes. New York Times. 2012 Robin A Smith
2012. Climate change increases mate-swapping in birds. Scientific American. 2012 Robin A Smith
2012. Compromises between quantity and quality are common in animals, but do the same tradeoffs hold true for plants and their flowers? Eurekalert. 2012 Robin A Smith
2012. Cousin marriage health risks 'greatly exaggerated'. The West Australian. 2012 Robin A Smith
2012. Coyotes shrank, wolves did not, after last ice age and megafaunal extinctions. National Science Foundation. 2012 Robin A Smith
2012. Coyotes were bigger before Ice Age, Canis latrans orcutti fossils show. Huffington Post. 2012 Robin A Smith
2012. Earth's oceans 'facing a man-made major extinction event.' Huffington Post. 2012 Robin A Smith
2012. Earth's Oceans 'Facing A Man-Made Major Extinction Event'. Huffington Post. 2012 Paul G Harnik
2012. End stigma of cousin marriage. West Australia Today. 2012 Robin A Smith
2012. Ethiopians and Tibetans thrive in thin air using similar physiology, but different genes. Eurekalert. 2012 Robin A Smith
2012. Fitness tests reveal frisky frogs have faster-changing genomes. Wired Magazine. 2012 Robin A Smith
2012. For most of human history, being an omnivore was no dilemma. National Public Radio. 2012 Robin A Smith
2012. Fossil record shows species need to spread out to survive. LiveScience. 2012 Robin A Smith
2012. Fossil study helps pinpoint extinction risks for ocean animals. Eurekalert. 2012 Robin A Smith
2012. Hear that? Insects can, and it's the sound of a hunting bat. MSNBC. 2012 Robin A Smith
2012. Honey, I shrunk the coyote. Wired. 2012 Robin A Smith
2012. How industrial noise helps and hurts plants. Scientific American. 2012 Robin A Smith
2012. How island isolation evolves giant rodents. Futurity. 2012 Robin A Smith
2012. Huge hamsters and pint-sized porcupines thrive on islands. Eurekalert. 2012 Robin A Smith
2012. Ice Age coyotes were supersized compared to coyotes today, fossil study reveals. Eurekalert. 2012 Robin A Smith
2012. Industrial roar changes nearby plant reproduction. Science News. 2012 Robin A Smith
2012. In shifty climates, birds sleep around. Discovery News. 2012 Robin A Smith
2012. In uncertain climates, birds will sleep around. MSNBC. 2012 Robin A Smith
2012. John Batchelor Podcasts. WABC Radio New York. 2012 Robin A Smith
2012. Man-made noise can affect plants, as well as animals. Christian Science Monitor. 2012 Robin A Smith
2012. Man-made noise disrupts the growth of plants and trees. BBC News. 2012 Robin A Smith
2012. Model sheds light on the chemistry that sparked the origin of life. Eurekalert. 2012 Robin A Smith
2012. New study traces the evolutionary history of what mammals eat. Eurekalert. 2012 Robin A Smith
2012. Noise pollution affects plants, too. Discovery News. 2012 Robin A Smith
2012. Noise pollution is changing forests. New York Times. 2012 Robin A Smith
2012. Not all altruism is alike. Indiana University News Office. 2012 Robin A Smith
2012. Not all altruism is alike, says new study. Eurekalert. 2012 Robin A Smith
2012. Not just for the birds: Man-made noise has ripple effects on plants, too. Eurekalert. 2012 Robin A Smith
2012. Pipe down! That noise might affect your plants. National Public Radio. 2012 Robin A Smith
2012. Powerful arms saved saber-toothed killers' fearsome fangs, study shows. History Channel. 2012 Robin A Smith
2012. Prehistoric predators with supersized teeth had beefier arm bones. Eurekalert. 2012 Robin A Smith
2012. Prehistoric predators with supersized teeth had beefier arm bones. NSF Press Release. 2012 Robin A Smith
2012. Sabertooth cats hunted with their 'beefy' arms, scientists find. Huffington post. 2012 Robin A Smith
2012. Sabertooth predators packed a punch. Nature. 2012 Robin A Smith
2012. Sabre-toothed cats had weaker teeth than today's house cats - and relied on strong forelimbs to subdue struggling prey. Daily Mail. 2012 Robin A Smith
2012. Scientists trace evolutionary history of what mammals eat. National Science Foundation. 2012 Robin A Smith
2012. Study suggests manmade noise affects plant dispersal and flower pollination. Audubon Magazine. 2012 Robin A Smith
2012. Sturdy arms were secret to the saber-tooth's success. Science Magazine. 2012 Robin A Smith
2012. The burdens of being a biped. Science Magazine. 2012 Robin A Smith
2012. The mysterious case of the vanishing genius. Psychology Today. 2012 Robin A Smith
2012. Turns out, sabertooths had arms like Popeye. MSNBC. 2012 Robin A Smith
2012. Unpredictable weather makes birds unfaithful. The Globe and Mail. 2012 Robin A Smith
2012. What caused big coyotes to shrink to modern-day size. MSNBC. 2012 Robin A Smith
2012. Why not marry your cousin? Millions do. Eurekalert. 2012 Robin A Smith
2012. Why the coyote got small. Science Now. 2012 Robin A Smith
2012. Why we cheat: Bird mating habits used to explain infidelity in new study. Huffington Post. 2012 Robin A Smith
2012. Wrestling ninjas -- why sabre-toothed predators have massive arms. Discover Magazine. 2012 Robin A Smith
Baker, Monya. 19 July 2012. Gene data to hit milestone. Nature 487, 282–283 doi:10.1038/487282a 2012 Heather Piwowar
Crump, B. (Presenter). (2012 July 4). Our tree of life of all and everything. Nights. Radio New Zealand National. (audio) 2012 Karen Cranston
Howard, Jennifer. January 29, 2012. Scholars Seek Better Ways to Track Impact Online. The Chronicle of Higher Education. 2012 Heather Piwowar
Howard, Jennifer. May 6, 2012. Elsevier Experiments With Allowing 'Text Mining' of Its Journals. The Chronicle of Higher Education. 2012 Heather Piwowar
Pushing the Frontier of Access for Text Mining: A Conversation with Heather Piwowar on One Researcher’s Attempt to Break New Ground. May 17, 2012. SPARC. 2012 Heather Piwowar
Zimmer, Carl. (2012, June 4). Tree of Life project aims for every twig and leaf. New York Times (Science section). Retrieved from: http://www.nytimes.com/2012/06/05/science/open-tree-of-life-project-draws-in-every-twig-and-leaf.html?smid=pl-share 2012 Karen Cranston, Robin A Smith
2011. Aging rates, gender gap in mortality similar across all primates. Eurekalert. 2011 Robin A Smith
2011. Ancestry of Polar Bears Traced to Ireland. ScienceDaily. 2011 Robin A Smith
2011. Athletic frogs: Go bold or go home. Futurity. 2011 Robin A Smith
2011. Bigger birds are harder hit by human noise. Eurekalert. 2011 Robin A Smith
2011. Biological clock ticks slower for female birds who choose good mates. Eurekalert. 2011 Robin A Smith
2011. Bird chatter: What's that? I can't hear you! Discovery News. 2011 Robin A Smith
2011. Chimpanzees closer to us than thought. Herald Sun (Melbourne, Victoria). 2011 Robin A Smith
2011. Climate for divorce. Science News. 2011 Robin A Smith
2011. C'mon feel the noise: Related songbirds respond differently to noise pollution, possibly complicating conservation efforts. Science Magazine. 2011 Robin A Smith
2011. Despite long lives, humans age like other primates. NPR's Science Friday. 2011 Robin A Smith
2011. Earth's sixth mass extinction: is it almost here? National Science Foundation. 2011 Robin A Smith
2011. Eating meat drove the evolution of our big, powerful brain. AAAS Meeting Coverage. National Association of Science Writers. 2011 Robin A Smith
2011. Froggy fitness: toxic species prove most athletic. Live Science. 2011 Robin A Smith
2011. How male birds affect female fertility. MSNBC. 2011 Robin A Smith
2011. Human Brain Evolution and Creatine Gene Expression. Scitable. 2011 Robin A Smith
2011. Humans age at same pace as other primates, study finds. US News & World Report. 2011 Robin A Smith
2011. Humans age at same rate as chimps, gorillas. Discovery News. 2011 Robin A Smith
2011. Humans, apes, have similar aging patterns. ABC News. 2011 Robin A Smith
2011. Humans, apes, have similar aging patterns. Seattle Times. 2011 Robin A Smith
2011. Humans, apes, have similar aging patterns. USA Today. 2011 Robin A Smith
2011. Humans, monkeys age the same way. Futurity. 2011 Robin A Smith
2011. Humans, primates age in similar ways. CBS News. 2011 Robin A Smith
2011. Hummingbirds catch flying bugs with the help of fast-closing beaks. Eurekalert. 2011 Robin A Smith
2011. Just how big a deal is milk drinking? Scientific American. 2011 Robin A Smith
2011. Marine snails get a metabolism boost. Eurekalert. 2011 Robin A Smith
2011. New study pinpoints why some microbial genes are more promiscuous than others. Eurekalert. 2011
2011. Noise pollution is driving larger birds away, study says. Southern California Public Radio. 2011 Robin A Smith
2011. Padrao de envelhecimento de primatas pode 'estender' vida humana. Estado de Minas. 2011 Robin A Smith
2011. Padrao de envelhecimento do homem e semelhante ao de outros primatas. Correio Braziliense. 2011 Robin A Smith
2011. Podcast from Science Magazine. 2011 Robin A Smith
2011. Poison dart frogs leap to the top for frog fitness. MSNBC News. 2011 Robin A Smith
2011. Poison frog athletes. California Academy of Sciences. 2011 Robin A Smith
2011. Poisonous lifestyle makes frogs more fit. Wired Science. 2011 Robin A Smith
2011. Songbirds adapt to noisy environments. US News and World Report. 2011 Robin A Smith
2011. Songbirds tweak their tunes in different ways to cope with clamor. Eurekalert. 2011 Robin A Smith
2011. Songbirds tweak their tunes in different ways to cope with clamor. Science 360 news highlights from NSF. 2011 Robin A Smith
2011. Study finds primates age gracefully. National Science Foundation. 2011 Robin A Smith
2011. Study offers warning about next potential mass extinction. USA Today. 2011 Robin A Smith
2011. Thinking big. Science News. 2011 Robin A Smith
2011. To age is primate. Duke News. 2011 Robin A Smith
2011. Treadmill test reveals most poisonous frogs are best frog athletes. Discovery Channel: Animal Planet. 2011 Robin A Smith
2011. Treadmill tests for poison frogs prove toxic species are more physically fit. Eurekalert. 2011 Robin A Smith
2011. What do you mean I'm aging like a baboon?! MSNBC News. 2011 Robin A Smith
2011. When birds go to town: Urban settings offer enterprising critters new opportunities - if they can cope with the challenges. Science News. 2011 Robin A Smith
Corbyn, Zoe. 14 September 2011. Researchers failing to make raw data public. Nature, doi:10.1038/news.2011.536 2011 Heather Piwowar
Pretty Poisons. The Amazon's most color and toxic frogs are also its most physically fit. Audubon: July-August 2011 2011 Juan C Santos
Radio In Vivo. May 4, 2011. Dr. Jenny McGuire discusses conservation paleontology, the sixth mass extinction, and organisms responses to climate change. By Ernie Hood 2011 Jenny L McGuire
Woodsen, M. 2011. Bad vibrations. Living Bird 30: 14-20. 2011 Clinton D Francis
2010. Climate changes, and there goes the neighborhood. ScienceNews. 2010 Robin A Smith
(2010). DNA barcodes could protect plants. The Raleigh News and Observer. 2010
2010. Life history database aids wild primate studies. Eurekalert. 2010 Robin A Smith
2010. Loblolly pine pollen is everywhere. Salisbury Post. 2010 Robin A Smith
2010. Local researchers: Pine pollen pervasive. The Herald-Sun. 2010 Robin A Smith
2010. Lovely weather for ducks and primates. Futurity. 2010 Robin A Smith
2010. Primates are more resilient than other animals to environmental ups and downs. Eurekalert. 2010 Robin A Smith
2010. Primates best at coping with change. St. Louis Globe-Democrat. 2010 Robin A Smith
2010. Primates better adapted to environmental changes. Birmingham Star. 2010 Robin A Smith
(2010). "Protecting plants through DNA testing." The Charlotte Observer. 2010
2010. Scared snails opt for single parenthood rather than wait for a mate. Dallas Morning News. 2010 Robin A Smith
2010. Scared snails opt for single parenthood rather than wait for a mate. USA Today. 2010 Robin A Smith
Ahlstrom, D. 2010. Tibetan gene find may help patients in intensive care. Irish Times. 2010 Robin A Smith
Bryner, M. 2010. How does a wasp become a queen? Life's Little Mysteries. 2010 Robin A Smith
Choi, C. 2010. Saber-toothed cats also had powerful arms. MSNBC. 2010 Robin A Smith
Dickey, G. 2010. Saber-toothed cats strong-armed prey. ScienceNews. 2010 Robin A Smith
Gill, V. Blueprint of the songbird genome. BBC News 2010 Carlos A. Botero
Keim, K. June 17, 2010 Swine Flu Jumps Back to Pigs and Keeps Evolving. Wired Science 2010 Alexei Drummond
Kelly, Whiteley, and Tallmon. 2010. The Arctic melting pot. Nature 468: 891. 2010 Robin A Smith
Kluger, J. 2010. Planet of the Apes...and Monkeys and Humans. TIME Magazine. 2010 Robin A Smith
Krishnaswamy, D. 2010. Saber-tooth tigers add powerful arms to their arsenal. Science Magazine. 2010 Robin A Smith
Loh, S. T. (2010). Saber Equality. The Loh Down on Science, National Public Radio. 2010
Madrigal, A. 2010. Male spiders are all bark, female spiders fight to kill. Wired Science. 2010 Robin A Smith
Millius, S. 2010. Pine pollen gets flight miles. Science News. 2010 Robin A Smith
Moseman, A. 2010. The saber-toothed cat's true secret: its super-strong arms. Discover Magazine. 2010 Robin A Smith
Ovaska, Sarah. 2010. Pollen reaches record levels. News and Observer. 2010 Robin A Smith
Parry, W. 2010. Fearful snail becomes better breeder. LiveScience. 2010 Robin A Smith
Prum, A. (2010). Hummingbirds: Magic in the Air, PBS. 2010 Robin A Smith
Science News. October 15, 2010. Climate changes, and there goes the neighborhood. By Susan Milius. 2010 Jenny L McGuire
Scudellari, Megan. 2010. Stephen Smith: the botanist hacker. The Scientist 24:3 2010 Robin A Smith
Shipley, T. 2010. Tibetans carry unique gene to combat mountain sickness. Discovery News. 2010 Robin A Smith
Smith, R. 2010. Desperate female spiders fight by different rules. Eurekalert. 2010
Smith, R. 2010. Desperate female spiders fight by different rules. U.S. News and World Report. 2010 Robin A Smith
Smith, R. (2010). DNA barcode exposes 'fake' ferns for sale. Futurity. 2010
Smith, R. (2010). DNA barcodes expose fake ferns. Duke News Office. 2010
Smith, R. 2010. Scared snails opt for single parenthood rather than wait for a mate. Eurekalert. 2010 Robin A Smith
Smith, R. 2010. Scientists uncover the genetic secrets that allow Tibetans to thrive in thin air. Eurekalert. 2010 Robin A Smith
Smith, R. 2010. The making of a queen: Road to royalty begins early in paper wasps. Eurekalert. 2010 Robin A Smith
Smith, R. 2010. Why you should never arm wrestle a saber-toothed tiger. Eurekalert. 2010 Robin A Smith
Wade, N. 2010. Scientists cite fastest case of human evolution. New York Times. 2010 Robin A Smith
Weise, E. (2010). Heger, M. (2009). Drier weather 30 million years ago may have led to grass evolution. USA Today. 2010 Robin A Smith
Yong, Ed. 2010. Sabre-tooth cats wrestled prey with powerful front legs. Discover Magazine. 2010 Robin A Smith
Zimmer, C. 2010. Scientists square off on evolutionary value of helping relatives. The New York Times. 2010 Robin A Smith
Feb. 13, 2009, The tree of life grows denser, FEATURED ARTICLE, BMC Evol Biol 2009 Stephen Smith
Williamson, A. 29 July 2009. Feature - Common cheap chips get jobs done faster. iSGTW 2009 Alexei Drummond
Zimmer, C. (2009). Crunching the data for the tree of life. New York Times. New York, NY. http://www.nytimes.com/2009/02/10/science/10tree.html. 2009 Stephen Smith
(2007). ARC-NZ Research Network for Vegetation Function Annual Report. http://www.vegfunction.net/activity/Annual/VFN_AnnReport2007_high.pdf 2008 Nick Spencer
Faculty of 1000 Biology: evaluations for Harper GR & Pfennig DW Nature 2008 Feb 28 451 (7182) :1103-6 http://www.f1000biology.com/article/id/1103333/evaluation 2008 David Pfennig
Joron, M. (2008). Batesian mimicry: can a leopard change its spots and get them back? Current Biology 18(11): R476-R479. 2008 David Pfennig
(2007). An interview with: Dr. Susanne Renner. http://in-cites.com/scientists/SusanneRenner.html. 2007 Susanne Renner
Ng, H. H. (2007). New Schizodon tetra named. Practical Fishkeeping. http://www.practicalfishkeeping.co.uk/pfk/pages/item.php?news=1374 2007 Brian L. Sidlauskas
Toner, B. (2006). NESCent Hosts Hackathon to Jumpstart Development of Phyloinformatics Toolkit. http://www.genomeweb.com/informatics/nescent-hosts-hackathon-jumpstart-development-phyloinformatics-toolkit 2007 Todd Vision
Curriculum/Education Resources
This course presents the principles of evolution, ecology, and behavior for students beginning their study of biology and of the environment. It discusses major ideas and results in a manner accessible to all Yale College undergraduates. Recent advances have energized these fields with results that have implications well beyond their boundaries: ideas, mechanisms, and processes that should form part of the toolkit of all biologists and educated citizens. 2014 Nicole Skursky