Newsletter Vol. 3 No. 2 May, 2009
In this issue:
Science and Synthesis
- Funding opportunities at NESCent
- Science in the spotlight
- NESCent welcomes new Communications Manager
- Departing NESCentarians look back
- New awards
- Recent publications
Informatics
- Training opportunities: introduction to GMOD software
- Computational Phyloinformatics course now offered in Europe
- Coming soon: ontology workshop at ASIH
- Hackathon to improve interoperability between evolutionary databases
- Data publishing initiative gains momentum
Education and Outreach
- Promoting undergraduate diversity at SSE
- New travel award program for faculty from minority-serving institutions
- Darwin lecture series continues
- Teacher workshop at Evolution 2009 meetings
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Science and Synthesis
Funding opportunities at NESCent: Call for proposals
NESCent is now accepting applications for postdoctoral and sabbatical fellowships, short-term visitors and group meetings.
The next deadline for short-term visitor proposals is July 1. For sabbatical fellowships, working groups, and catalysis meeting proposals, the next deadline is July 10. The deadline for postdoctoral fellowship proposals is December 1 annually. For more information about funding opportunities at NESCent, click here.
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▪NESCent postdoc Carlos Botero received widespread media attention for his recent paper in Current Biology, “Climatic patterns predict the elaboration of song displays in mockingbirds.” His paper was covered by Science News, BBC online, and USA Today, among others. Read more here.
▪Former NESCent postdoc Joe Hereford was recently featured in Faculty of 1000. Based on the recommendations of over 2000 scientists, Faculty of 1000 is an online research service that highlights and reviews the most interesting papers in biology. Faculty of 1000 singled out a paper based on Hereford’s NESCent work titled “A quantitative survey of local adaptation and fitness trade-offs,” which was published in American Naturalist this May.
▪NESCent postdoc Trina Roberts gave an invited talk at the Smithsonian National Museum of Natural History titled "Disentangling treeshrew systematics and biogeography with 'antique' DNA" on May 22, 2009
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NESCent welcomes Robin Smith as Communications Manager
NESCent is pleased to announce that Robin Smith joined our staff as Communications Manager this May. Robin will work with the Directors and the Education and Outreach Group to translate NESCent research to diverse audiences and to promote the scientific and educational activities of the Center. Robin received a PhD in evolutionary biology in 2005 from the Biology Department at Duke University, and was a postdoctoral fellow in the Thompson Writing Program at Duke. Robin has published scholarly articles in Evolution, American Naturalist, and the American Journal of Botany. She has also written for popular audiences under the Duke University Office of News and Communications, and for Scitable, an online learning initiative from the publishers of Nature. If you have ideas for news stories or other NESCent-related research or events that you would like to highlight please contact Robin at rsmith@nescent.org
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Departing NESCentarians look back
As we head into the summer, we say goodbye to a number of NESCent postdocs and sabbatical scholars who will soon be moving on to the next stages of their careers. Several of them shared their thoughts on their time at NESCent with us:
George Gilchrist came to NESCent in August of 2008 as a sabbatical scholar from the College of William and Mary. For Gilchrist, accepting a sabbatical fellowship at NESCent was also a decision to be an active part of the intellectual community. “To me, a sabbatical is a time to refresh yourself and do something new and change your environment, and this has been perfect for that,” Gilchrist says. “But I think it’s also important for a sabbatical scholar to recognize that they’re part of the NESCent community. It means taking time for something that’s not as obviously productive in terms of cranking out papers or grants. I came with the expectation that I would spend time interacting with the postdocs and working groups, and that’s been very rewarding.”
Christian d'Orgeix joined NESCent in September 2008 as a sabbatical scholar from Virginia State University. d'Orgeix decided to apply for a NESCent sabbatical fellowship after participating in a working group titled "Evolution Education at Historically Minority Universities." Inspired by his interactions with the working group, d'Orgeix returned to his home institution and proposed a new course in evolution. “Our students haven’t been exposed to much in the way of evolutionary thought,” d’Orgeix says. “Part of the reason I was interested in coming back to NESCent as a sabbatical scholar was so I could develop that course. I’m able to fill a niche and expose students to an area they’ve never been exposed to before.” d'Orgeix’s time at NESCent has also enabled him to reinvigorate his research program. “Another thing I wanted to do here was to look at data I’ve collected in the past and start writing again,” d’Orgeix says. “I hope NESCent continues to recruit people from minority-serving institutions. It really gives us an opportunity that we don’t have, both in terms of time and in terms of meeting people who are on the cutting edge.”
Brian Sidlauskas joined NESCent as a postdoctoral fellow in September of 2006. For Sidlauskas, the key to being maximally productive was staying open to unexpected collaborations. “To get the best out of NESCent I think it’s important to collaborate and keep your mind open to unexpected possibilities,” says Sidlauskas. “I never would have been involved in some projects without networking with people and taking advantage of what NESCent has to offer. Some of the most important ideas for your science – things that will send you on new trajectories and give you a new perspective on what you’re doing − probably won’t come from your own head. Other people have a huge resource of knowledge. One project can lead to another, even when you’re not necessarily expecting it to.”
Left to right: Brian Sidlauskas, George Gilchrist, Paula Spaeth, Einat Hazkani-Covo, Ganesh Ganapathy, Brian O'Meara
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NESCent is pleased to announce the following new awards:
Postdoctoral Fellows (arriving fall 2009)
Julie Meachen-Samuels, University of California-Los Angeles
Competition, guild structure and evolution in the Carnivora
Benjamin Redelings, North Carolina State University
Improved probabilistic models of insertion/deletion for phylogenetic inference
Liam Revell, Harvard University
Process and pattern in the phylogenetic analysis of comparative data
Juan Santos, University of Texas
Multivariate evolutionary analysis: integrating structural equation modeling and phylogenetics
Eric Schuettpelz, Duke University
A phylogenetic approach to understanding the evolution of the Earth's biomes
Gregor Yanega, University of Connecticut
A comparative phylogenetic approach to the study of insular avian phenotypes
Long-term Sabbatical Scholars (starting Sept. 2009)
James Hunt, North Carolina State University
Michael Rosenberg, Arizona State Univesity, Tempe
Geography, phylogeny, and population: an evolutionary synthesis
Short-term Visitors
Travis Ingram, University of British Columbia
Peter Midford, University of Kansas
Alignment of phenotype ontologies
Catalysis Meeting
David Sloan Wilson, SUNY at Binghamton
Working Groups
Alexei Drummond, University of Auckland
Andrew Rambaut, University of Edinburgh
Marc Suchard, University of California-Los Angeles
Software for Bayesian evolutionary analysis by sampling trees
Margaret Hall, Midwestern University
Christopher Heesy, Midwestern University
Andrew Iwaniuk, University of Lethbridge
Evolutionary shifts in vertebrate visual ecology and visual system morphology
Courtney Murren, College of Charleston
Carl Schlichting, University of Connecticut
Costs of phenotypic plasticity and adaptation to novel environments
Rebecca Safran, University of Colorado at Boulder
Albert Uy, Syracuse University
An integrative evolutionary approach to examine sexual selection as a mechanism of speciation
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Recent publications by NESCent authors
▪Botero, C., Boogert, N., Vehrencamp, S., & Lovette, I. (2009). Climatic patterns predict the elaboration of song displays in mockingbirds. Current Biology, 
doi:10.1016/j.cub.2009.04.061.
▪Dutheil, J., Ganapathy, G., Hobolth, A., Mailund, T., Uyenoyama, M. & Schierup, M. (2009). Ancestral Population Genomics: The Coalescent- Hidden Markov Model Approach. Genetics, in press.
▪Ganapathy, G. and Uyenoyama, M. (2009). Site frequency spectra from genomic SNP surveys. Theoretical Population Biology, doi:10.1016/j.tpb.2009.04.003.
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Informatics
Training Opportunities
Database Tools for Evolutionary Genomics: An introduction to GMOD software for managing, annotating and visualizing genomic data
Where: 2009 Annual Meeting of the Society for Molecular Biology and Evolution (SMBE), Iowa City, Iowa
When: June 6, 2009, 2:30-5:00pm
Learn how you can annotate, visualize, and compare genome data using tools from the Generic Model Organism Database project, or GMOD. GMOD is a collection of open-source software tools for managing a web-accessible genome database. NESCent, through funding from NIH, supports a GMOD Help Desk to provide support for genomic data management within the evolutionary biology community.
Dave Clements, who runs NESCent’s GMOD Help Desk, is organizing a workshop aimed at teaching new users how to get up and running with GMOD. The workshop will introduce the GMOD project and cover some of the most widely used GMOD software components, including the Chado database, the GBrowse genome browser, the CMap comparative map browser, and the Apollo genome curation tool. The workshop will also cover the GBrowse_syn comparative genomics viewer, and the MAKER genome annotation pipeline for eukaryotes. Speakers will address both existing functionality and ongoing developments specifically targeted at better supporting evolutionary data and research. No knowledge of programming is necessary.
For more information, visit:
http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
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Back by popular demand – summer course in computational phyloinformatics now offered in Europe
Where: Instituto Gulbenkian de Ciência, Oeiras, Portugal
When: July 9-19, 2009
Develop your programming skills while discovering Portugal! NESCent has partnered with the Instituto Gulbenkian to offer the 2009 Computational Phyloinformatics Summer Course. The course will be held July 9-19 at the Instituto Gulbenkian near Lisbon, Portugal. This hands-on course aims to teach students how to use the BioPerl and BioPhylo libraries for phylogenetic analyses, and how to store and manipulate phylogenetic data and results in a relational database using SQL. The application deadline is June 8, 2009.
For more information and to apply, visit: http://www.nescent.org/courses/2009/comphy/
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Coming soon: ontology workshop at ASIH
Where: Joint Meeting of Ichtyologists and Herpetologists, Portland, Oregon
When: July 25, 2009
The Phenoscape and AmphibAnat projects are together offering a workshop on "Ontologies for Icthyology and Herpetology" to be held on July 25, 2009 in Portland Oregon, in conjunction with the Joint Meeting of Ichtyologists and Herpetologists. Ontologies − controlled vocabularies with well-defined relations among terms − are a key tool in scientific data integration. By using ontologies, scientists from different disciplines can know when they are referring to the same entity by different names, and computer software can reason across disciplines and over large datasets. Already widely used in genomics, ontologies are of growing importance in systematics, ecology, behavior, development, morphology and physiology. This workshop aims to explore the utility of ontologies for ichthyology and herpetology. Participants will present examples of how ontologies in ichthyology and herpetology are being used for applications in biomedicine, evo-devo, comparative anatomy, and genomics.
For more information, visit: https://www.phenoscape.org/wiki/ASIH09_workshop
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NESCent hosts a hackathon to improve interoperability between evolutionary databases
NESCent sponsored its third hackathon from March 9th-13th, this time on the theme of Evolutionary Database Interoperability. Despite the rich and meticulously curated variety of evolutionary data available online, most of these data are not available in standardized formats with explicit semantics, and can only be queried through interfaces intended for humans. To enable computers to query, access, and understand these valuable data, NESCent brought together developers from a number of popular evolutionary databases, as well the authors of several emerging interoperability standards.
The standards themselves arose from the activities of a NESCent Working Group on Evolutionary Informatics, led by Arlin Stoltzfus and Rutger Vos. They include a machine-readable phylogenetic data exchange format (NeXML), an ontology to formally describe semantics (CDAO), and a web service specification for how applications can query data providers (PhyloWS). The meeting produced several prototypes that demonstrate how these standards can be used, for instance, to convert phylogenetic data into a format that is compatible with semantic web applications, to deliver TreeBASE records to client applications using taxonomic intelligence, and to decorate trees in a tree visualization tool (such as Phylowidget) with data content pulled from remote data providers (such as images from Morphbank). Several developers joined forces to create a general-purpose programming library that others can use to add support for reading and writing the NeXML format to their applications. The event also launched the development of a standards-compliant web services toolkit for phylogenetic data providers.
A report-in-progress is available online. NESCent welcomes ideas for future hackathons at any time. Suggestions can be submitted through the Informatics Whitepaper program.
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Data publishing initiative gains momentum
The first official meeting of the Dryad Consortium Management Board took place at NESCent on May 21-22. Dryad is a digital data library for evolutionary biology, ecology, and related fields with a primary goal of preserving published data for the purpose of validation, re-purposing, scientific synthesis, and education. The Dryad Consortium Management Board consists of representatives from the journals that govern the repository. Representatives from 16 journals were present at the meeting. The board discussed an array of topics, including board governance, repository sustainability, data archiving policies, intellectual property, priorities for development of the repository functionality, and engagement of the user community. An important outcome was that authors at many of the partner journals will soon be provided, at the time when a paper is accepted, with a link to the repository where their data may be published.
For more information about the meeting visit https://www.nescent.org/wg_dryad/Management_Board_Meeting_Spring_2009
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Education and Outreach
NESCent to promote undergraduate diversity at evolution conference
In what has become an ongoing collaboration, NESCent is once again partnering with Dr. Scott Edwards (Harvard) and Dr. Rich Kliman (Cedar Crest College) to sponsor Undergraduate Diversity at Evolution. This program identifies talented undergraduates, particularly from under-represented groups, and provides them with travel awards to attend the annual Evolution (SSE/SSB/ASN) conference. While at the conference, students present their own research during a special poster session for undergraduates, participate in social events and professional development sessions, and receive mentoring from evolutionary biologists. Nearly 20 undergraduates will be attending as part of this year’s program, which will be held at the University of Idaho on June 12-16. For more information contact Jory Weintraub at jory@nescent.org.
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NESCent implements new travel award program for faculty from minority-serving institutions
As part of NESCent's ongoing commitment to promoting diversity in evolutionary biology, we have implemented a new travel award program to send faculty from minority serving institutions (MSIs) to a national evolutionary biology conference. The goal of this program is to increase faculty exposure to current, cutting edge findings and approaches in evolutionary biology research and education, allowing them to update and enhance both classroom and laboratory instruction. This year, the program is sending Dr. Christian D'Orgeix (Virginia State University) and Dr. Hong Qin (Tuskegee University) to the SMBE (Society for Molecular Biology and Evolution) Conference being held in Iowa City, Iowa from June 3-7. While there, Drs. D'Orgeix and Qin will be attending a day-long workshop entitled "Teaching Molecular Evolution: Incorporating the ‘Molecular’ into Evolution Education". Dr. Qin will also be a presenter in the workshop, and both travel award recipients will have opportunities to attend other talks, sessions and workshops. In order to receive the travel awards, Drs. D'Orgeix and Qin were required to outline the ways in which participation in this program would both benefit them professionally and enhance the learning and understanding of evolution by their students. NESCent is committed to sending MSI faculty to a national evolution conference (e.g., SMBE, SSE, SICB) on an annual basis as a way of ultimately increasing diversity in evolutionary science. To apply for future awards please contact Jory Weintraub at jory@nescent.org.
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Darwin lecture series continues
To celebrate the bicentennial of Darwin's birth and the 150th anniversary of the publication of The Origin of Species, NESCent is collaborating with the NC Museum of Natural Sciences and the Keck Center for Behavioral Biology at NCSU to sponsor a series of free public presentations on evolution.
The series kicked off Feb. 12 – Darwin’s 200th birthday – with Carl Zimmer. Mr. Zimmer is a well known science writer who has written widely on evolution. Rob Dunn, assistant professor of zoology at NCSU and author of Every Living Thing, followed in March.
Please consider joining us for the three remaining speakers in the series: Anne Yoder, Director of the Duke Lemur Center and professor of Biology at Duke (pictured right), presents "Madagascar's magnificent biodiversity: What would Darwin say?" Thursday July 9th in the Museum auditorium at 6:30pm. The next speaker will be Dale Russell, geologist/palaeontologist and professor in the Department of Marine Earth and Atmospheric Sciences (MEAS) at North Carolina State University, who will speak on September 29th. Dr. Russell was the first to suggest an extraterrestrial cause for the extinction of the dinosaurs. Finally, Museum paleontologist Paul Brinkman will close out the year’s series on November 24th, the 150th anniversary of the publication of On The Origin Of Species, with a talk on how the discovery of fossil mammals in South America may have inspired Darwin to write his seminal book.
These events are free and open to the public but registration is requested. To register please send an email to museum.reservations@ncmail.net. Speaker presentations will also be posted on the web for educational use and for those who cannot attend. Watch for each of the talks to be posted here.
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Teacher workshop at Evolution 2009 meetings: evolution and biogeography
Where: Evolution 2009 Conference, Moscow, Idaho
Please note off-site location: Connor Museum, Washington State University, Pullman, WA
When: June 12, 2009, 9:00am - 5:00pm
We invite K-12 teachers and biology educators to join us for a teacher workshop on evolution and biogeography, to be held June 12th in Pullman, WA, in conjunction with the Evolution 2009 meetings. Biogeography, or the study of species distribution patterns over space and time, is a keystone approach to evolutionary biology. Modern tools have made this field even more powerful, and biogeography is playing an important role in developing effective conservation strategies.
The workshop will include hands-on demonstrations of resources and materials to effectively teach biogeography and evolutionary biology, presentations by evolutionary biologists about their research, and discussions on improving evolution education. Registration for the workshop is $25 and includes full participation in the Evolution 2009 meeting. Teachers are invited to attend the scientific sessions, symposia, keynote presentations, picnic, and poster sessions to be held at the University of Idaho. Workshop participants may be particularly interested in the evolution education symposium, concurrent sessions on evolution education, and the Public Outreach Lecture by Dr. Eugenie Scott of the National Center for Science Education.
For more information visit: http://www.uiweb.uidaho.edu/evolution09/workshops.html
For information on car-pooling to the workshop from Moscow please e-mail mead@ncseweb.org.
Workshop organizers:
Louise S. Mead: mead@ncseweb.org
Kristin Jenkins: kjenkins@nescent.org
Mike Webster: mwebster@wsu.edu
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NESCent is an NSF-funded collaborative research center operated by Duke University, the University of North Carolina at Chapel Hill, and North Carolina State University. For more information about research and training opportunities at NESCent, visit http://www.nescent.org.
