Newsletter Vol. 2 No. 3 November, 2008


In this issue:

NESCent Searches for a New Director

Science and Synthesis

Call for Proposals

New Awards Announced


Ontology workshop at SICB

NSF Award to Support Data Sharing Initiative

Google Summer of Code(TM)

Education and Outreach

Celebrating Darwin 2009


NESCent at NABT 2008


Visit NESCent's Home Page



NESCent Searches for a New Director

NESCent logo

Applications and nominations are invited for the position of Director of the National Evolutionary Synthesis Center, NESCent.

The Director has overall responsibility for administration of the Center, in collaboration with Associate Directors from the co-sponsoring Universities. The Director reports annually to NSF and to administrators of the associated universities and is advised by an external Advisory Board. The Director provides scientific leadership and fosters an environment that inspires collaboration. The Director should have an outstanding record of research in evolutionary biology with demonstrated organizational and management and interpersonal skills, and a fully articulated commitment to the goals of the Center. The position of Director will be a faculty appointment at the senior level made by Duke University.  More information is available on the NESCent website.

Questions about the position, as well as applications and nominations should be submitted electronically to Review of applications will begin December 1, 2008 and continue until the position is filled.

Back to Table of Contents


Science and Synthesis

Call for Proposals

The deadline for the next round of proposals for post-doctoral fellowships, sabbatical scholars, working groups and catalysis meetings is December 1, 2008.  Applications for short term visitors are accepted four times a year: January 1, April 1, July 1 and September 1.  For more information, visit the Science and Synthesis site.

Back to Table of Contents

New Awards Announced

NESCent recently announced a new set of awards including two working groups and two catalysis meetings.  In addition, two groups of researchers will be coming to NESCent as short term visitors to work on their joint projects.  The project titles and PIs are listed here.  More information can be found in the Science and Synthesis section of the NESCent website. 

bambooWorking groups:

Evolution and development of polyphenisms: Pathways to innovation and diversification

PIs: David Pfennig and Armin Moczek

Analysis and synthesis of physiologic data from the mammalian feeding apparatus

PIs: Christine Wall, Susan Williams, Rebecca German, and Chris Vinyard

Catalysis meetings:

Human evolution and adaptation to high-altitude hypoxia

PIs: Cynthia Beall and Peter Robbins

Toward a new synthesis of the evolutionary history and ecology of C4 grasses

PIs:Erika Edwards, Colin Osborne, and Caroline Stromberg

Short-term Visitors:

Toward a general theory of biological invasions

Jessica Gurevitch, Gordon Fox, Inderjit, Max Taub, and Glenda Wardle

Integrating fossil and molecular data in the study of diversification

Michael Alfaro, Luke Harmon, and Gene Hunt

Back to Table of Contents



Ontology workshop at the Society for Integrative and Comparative Biology (SICB) Meeting

sib_logoNESCent will be cosponsoring a workshop on the application of ontologies to comparative biology at the annual meeting of the Society for Integrative and Comparative Biology (SICB) in Boston, MA, January 6, 2009. The workshop is focused on the application of ontologies to studies in comparative biology, with a particular emphasis on morphological and behavioral phenotypes. The goal is to introduce what ontologies are, how they are built, what makes an ontology useful, how ontologies can help researchers collaborate across disciplines, and to highlight several applications of this approach to comparative biology.  Check the Phenoscape website for more information.

Back to Table of Contents


NSF Award To Support Data Sharing Initiative

NESCent is pleased to announce receipt of a National Science Foundation award in support of the Dryad digital data repository. The four year award from the Biological Databases and Informatics program seeks to promote the archiving of data underlying publications in evolution, ecology and related disciplines.Dryad logo

Dryad is being designed with evolutionary biology and ecology journals as stakeholders, and with individual scientists as the ultimate users and beneficiaries.  Technical goals include: simplifying the process of data deposition during manuscript submission; exchanging metadata with journal-required archives such as Genbank and TreeBASE, and with metadata registries such as MetaCat; and assigning globally unique, stable, resolvable identifiers for each data object, thus enabling data citations; cataloguing of taxonomic, geographic, and other specialized metadata to facilitate data search; implementing web services to allow third-party data search and retrieval; and distributing data backup among several institutions. Dryad is being overseen by a consortium of journals and societies interested in promoting more widespread data archiving.

Dryad will not only help enable the preservation, discovery, sharing and reuse of data for evolutionary biology and ecology, but will serve as a model for the many other “small science” disciplines facing similar challenges in data preservation and sharing.

The awardees include NESCent, the Metadata Research Center at the University of North Carolina, the North Carolina State Digital Library Program, TreeBase, and the LTER directorate at the University of New Mexico.

Back to Table of Contents

GSoC2008 logo


Google Summer of Code(TM) at NESCent

NESCent served as a mentoring organization in the 2008 Google Summer of Code(TM).  In this program, students receive a stipend from Google to spend a summer contributing to any of over 100 distributed open-source programming projects under the mentorship of an experienced programmer.  Google sponsored six students to work with NESCent and a community of mentors drawn from throughout the evolutionary bioinformatics community.  After months of interacting remotely, mentors and students finally met face-to-face at NESCent in mid-August for a highly enjoyable end-of-summer get-together.




Matt Ackerman –An Extension of Mesquite based on PDSIMULackerman photo

Mentor: Peter Midford

ackerman picThis project implemented Theodore Garland, et al's* PDSIMUL in Mesquite, a modular Java based with a phylogenetic focus. In addition to implementing most of the functionality of the dos based PDSIMUL, we also implemented a basic statistical analysis option, the ability to import and export data from PDAP's native .sim files, and the ability to apply bounding procedures at small steps along long branches. Graphs showing the equivalence of the original PDSIMUL and the mesquite implementation are presented on the projects homepage, along with a user guide explaining how to install and use the program, an explanations of basic model behavior, and explanations of the biological relevance of model variables.

*(Jr., Peter E. Midford, Jason A. Jones, Allan W. Dickerman, and Ramon Diaz-Uriarte)


Cowan image

Peter Cowan – Tree and data plotting in the phylobase project

Mentors: Ben Bolker (primary) and Steven Kembel

Cowan photo

The R programming language has become increasingly popular among biologists for writing simulations and statistical tests.  The phylobase package is an add-on that provides data structures and tools for working with phylogenetic trees.  In particular, phylobase is designed to ease working with trees that have associated data such as trait measurements, molecular data, etc. My GSOC project was to write a plotting function for visualizing these trees and associated data. A primary goal was to provide a flexible interface for creating new types to plots with minimal effort. Using this function it is possible to embed subplots of data at tips and nodes as well as embed trees into other plots.


Helmus photoMatt Helmus - Enhancing the representation of ecophylogenetic tools in R

Mentors: Steven Kembel (primary) and Ben Bolker

I greatly expanded the R package picante, a toolbox of comparative methods used to assess phylogenetic community structure. I coded three types of published ecological phylogenetic comparative methods. These methods can be used to assess phylogenetic community structure, the effects of environmental variables on phylogenetic community structure, and phylogenetic structure among species interactions. In other words, the methods can be used to ask questions such as: are closely related species found within the same community; are closely related species found in the same environments; and do closely related species interact with the same species. I also coded data handling routines that quickly randomize large matrices. These routines allow for tests of statistical significance with the methods. The product of my Summer of Code experience was a comprehensive R package of phylogenetic comparative methods that will facilitate the use of phylogenetics in ecological research.



Mira picMira Han - PhyloXML support in BioPerl

Mentors: Chris Fields (primary), Jason Stajich, Rutger Vos, and Christian Zmasek

A shortcoming of current formats for describing phylogenetic trees is the lack of a standardized means to annotate tree nodes and branches with distinct data fields. Without specific definitions on the data types or Mira Hanproper constraints on the structure, previous formats have produced a variety of inconsistent documents that are interoperable in only a subset of phylogenetic programs. phyloXML is a well-defined XML schema that can incorporate new types of annotations in a general and extensible manner, and facilitate data exchange and interoperation between different programs. Our project extended the current BioPerl Node module to add general annotations, and developed a parser for phyloXML, so that users can easily read and write the format.


McMillan photo

McMillan image

Paul McMillan – Graphiviz navigation of databases

Mentor: Brian O’Meara

I developed the DBGraphNav tool to facilitate the 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. The image is generated using AT&T's Graphviz program, and my project provides a relatively easy-to-use interface for defining recursive relational queries on the database, and then drawing a navigation graphic using this data. One usage of this is to allow website visitors to develop a clearer understanding of the relations between the authors and co-authors of scientific papers, as demonstrated in the treetapper implementation from which the example graphic is drawn.


Wallinga image



Wallinga photo


Mike Wallinga - Matrix Display of Phenotype Annotations Using Ontologies in Phenote

Mentors:Jim Balhoff (primary), Mark Gibson, and Nicole Washington

Phenote is an application which facilitates the annotation of biological phenotypes using ontologies.  This summer, I developed a matrix representation for the annotation data entered into Phenote. The matrix is populated by consolidating phenotype annotations into characters by finding values which descend from the same attribute within the PATO phenotype ontology.  It shows character values grouped by taxon and character, and displays the existing annotations in a way that is already familiar to evolutionary biologists. It is hoped that this representation will aid in the evaluation of taxonomic annotation coverage and phylogenetic patterns.


Back to Table of Contents


Education and Outreach

Celebrating Darwin 2009Darwin


In honor of the 150th anniversary of the publication of The Origin of Species and Darwin's 200th birthday, NESCent is co-sponsoring an Evolution Speaker Series with the North Carolina Museum of Natural Science, and NCSU’s Keck Center.  We are pleased to announce that Carl Zimmer will be opening the series for us on Thursday, February 12 – Darwin’s birthday. 

NESCent is also sponsoring a Darwin Day Symposium “Darwin's Legacy: Evolutionary Approaches to World Challenges ” on February 21, 2009.  The focus of this event is demonstrating the societal applications of evolutionary research.  Barbara Schaal will talk about agricultural applications, Katia Koelle will talk about her work with evolutionary theory and pandemic diseases, and Dan Faith will talk about designing conservation strategies based on evolutionary theory.  Steve Benner will talk about the field of synthetic biology, and Fred Gould will give an introduction to evolutionary applications in society.  The symposium is open to the public; teachers and students are particularly encouraged to attend. A free workshop for teachers will be offered February 14.  The focus will be on providing resources to prepare students for the symposium the following Saturday.  Registration for both the symposium and the workshop is free.

Back to Table of Contents


Continuing what has now become an annual event and a major component of our minority outreach efforts, NESCent once again had a strong presence at the annual SACNAS (Society for the Advancement of Chicanos and Native Americans in Science) Conference, which was held on Oct. 8-11 in Salt Lake City, Utah.  With enthusiastic support from the SACNAS programming committee, NESCent (in collaboration with AIBS, NCEAS and SSE) has implemented an annual Evolution and Ecology track of events and activities, in an effort to increase the profile of these disciplines at the SACNAS Conference and, ultimately, to increase diversity in these fields. 

This years events included a mentoring session (“Conversations with Scientists”) during which over 15 evolutionary biologists and ecologists volunteered their time to chat with undergraduate and graduate students to answer questions, share perspectives and provide inspiration.  Additionally, two NESCent postdocs (Drs. Brian Sidlauskas and Paula Spaeth) and an NCEAS postdoc (Dr. Lauren Buckley) participated in a scientific symposium to share their research with students.  And, in what has now become an annual tradition (“Evolution and Ecology Movie Night at SACNAS”), there was a screening of the global warming/climate change documentary “The 11th Hour”.  As evidence of the popularity of these events and the demand for more evolution/ecology activities at SACNAS, all of the events at this year’s conference were held in packed or standing-room-only rooms, and the feedback from SACNAS attendees and organizers was overwhelmingly positive.  We are already planning for SACNAS 2009, which will be held in Dallas next October.

Back to Table of Contents

NABTNESCent at NABT 2008

The National Association of Biology Teachers met in Memphis, TN, October 15 – 18.  NESCent and AIBS co-sponsored the fifth annual Evolution Symposium and accompanying teachers’ workshop.  This year’s topic “Illuminating Biology: an Evolutionary Perspective” included presentations by Joram Piatigorsky on his work with lens crystallins, Robert Blankenship on the evolution of photosynthesis, Trisha Wittkopp on evo-devo, and Georg Streidter on evolution of complex brains.  Presentations will be posted on the website shortly. 

The teachers’ workshop also focused on unexpected applications of evolutionary research.  Understanding Evolution staff introduced teachers to a lesson on the use of DNA barcoding and phylogeny to detect illegal whale meat.  The BioQUEST and NESCent staff collaborated on a lesson about using systematics to inform biocontrol efforts.  Resources for bringing these topics to the classroom may be found on the CD.

In addition, Joel Cracraft and Mark Sidall’s working group “Developing an Integrative Algorithmic Method for Historical Biogeography” decided to use part of their working group resources to give a workshop on biogeography at NABT.  Joel Cracraft, Kathryn Perez and Frank Fontanella came to Memphis to share tools and ideas for introducing biogeography in the classroom. This workshop was co-sponsored by NESCent and the National Center for Science Literacy, Education and Technology, American Museum of Natural History.

Back to Table of Contents

Image Credits: Bamboo by Tenryu Momiji


To unsubscribe from News, get a password reminder, or change your subscription options enter your subscription email address:

If you leave the field blank, you will be prompted for your email address

Back to Table of Contents