Newsletter Vol. 1 No. 1 May, 2007

 

In this issue:

A Message from the Director

Science and Synthesis

New Short Term Visitors Program

Recent Awards

Call for Proposals

Recent Publications by NESCent Scientists

Informatics

Call for White Papers

Phyloinformatics Hackathon

Recently Funded Informatics Projects

Education and Outreach

Evolution Symposium at the National Association of Biology Teachers Conference

NESCent Databases Aim to Increase Diversity in Evolutionary Biology Fields

Upcoming Evolution Meetings

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Banner Photo Credits (left to right): John Clamp, Zoothamnium niveum; Owen McMillan, Heliconius ; Sally Otto, Sula nebouxii; Amy Zanne, fern.

 

A Message from the Director

Kathleen Smith

I’d like to welcome you to NESCent’s first newsletter.  Our aim is to provide, in this quarterly newsletter, a brief summary of our activities, programs, and funding deadlines.

As we enter our third year, NESCent is establishing itself as a vibrant center for evolutionary biology.  We have currently 14 in house postdocs and 4 sabbatical scholars and an almost constant flow of scientists through the center.  We are on course to host close to 1,000 visitors this year in well over 50 meetings, with an extraordinary variety of topics, approaches and aims.  Our Informatics and our Education and Outreach groups have each developed a wide range of programs.  We hope in the newsletter below we convey a few of these exciting activities, and encourage you to explore the activities of the center further at our website. 

NESCent is here to serve the evolutionary biology community.  We are always interested in feedback, inquiries, and your participation.  Please contact me or any of the other directors at any time with questions or suggestions (kksmith@duke.edu).

 

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Science and Synthesis

 

New Short Term Visitors Program

A new program at NESCent supports short term projects to enable synthetic research on any aspect of evolutionary biology and relevant disciplines. Visitors will work on-site at NESCent for periods of 2 weeks to 3 months. Proposals can include any type of synthetic evolutionary project, but we particularly welcome collaborative projects. Such collaborations might include collaborations with NESCent in-house scientists or informaticians; joint proposals from two or more investigators to spend time together at NESCent; or proposals from leaders of working groups to work on their project with NESCent informatics staff.  

Proposals should project an important evolutionary question, and should reflect NESCent’s mission to facilitate synthesis and analysis of existing data. NESCent will not fund collection of new data or field research, but encourages the mining of public and private databases. Products might include (but are not restricted to):


* Synthetic papers and reviewssmall meeting
* Databases allowing others to build on your foundation
* Software or mathematical tools that solve a major analytical problem

NESCent is committed to making data, databases, software and other products that are developed as part of NESCent activities available to the broader scientific community. Applicants should review the draft Data and Software Policy for NESCent.
Proposals are considered four times a year, with deadlines on January 1, April 1, July 1 and September 1. Proposals will be evaluated in terms of both the scientific value of the project and the qualifications of the applicant. Visitors will receive reimbursement for travel and housing expenses, and an honorarium to cover other incidental expenses (meals, etc). Because of visa restrictions, international scholars should contact us before applying.

Application Information

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Recent Awards

meetingThe results of the December 2006 call for proposals have been announced.  One catalysis meeting and three working groups have been funded, as well as two new post-doctroal fellows and a sabbatical scholar. 

The catalysis meeting, "Myelin,  A New Model for Evolutionary Innovation" will focus on model systems for exploring evolutionary innovations - changes that generate new phylogenetic developments - using myelination of the nervous system and the evolution of image forming eyes as key examples. This meeting will be organized by Daniel Hartline, David Colman, Petra Hoepcke Lenz, Mark Martindale, Elaine Seaver, and Gunter Paul Wagner. 

Charles Nunn and Brian Hare are the PIs for the working group addressing the question "How Does Cognition Evolve?".  This group will bring together comparative psychology with evolutionary research to examine what ecological and life history traits that drive the development of cognitive abilities. 

David Lahti and Susan Foster are the PIs for the "Relaxed Selection and Trait Loss in Evolution" working group.  This group will develop models to explore the evolutionary processes affecting traits under relaxed or exempted from selective pressures.

The "Mechanistic Distribution Models: Energetics, Fitness, and Population Dynamics" working group will develop a more complete understanding of species' distributions by including individual energetics, fitness curves, population dynamics and evolutionary change.  This project is co-funded by the National Center for Ecological Analysis and Synthesis (NCEAS), ant the PIs for this group are Lauren Buckley, Michael Angilletta, Robert Holt and Joshua Tewksbury. 

The post-doctoral fellows are Brian O'Meara and Paula Spaeth. Brian is coming from UC Davis, and will be working on "Methods to examine trait evolution on trees: advancing the field." Paula is coming from Stanford to work on "Competition and meso-evolutionary change in the mammalian fossil record." Malcolm Schug, from UNC Greensboro, will be doing a sabbatical project on "The role of crossing-over and recombination in adaptive evolution".

For more information about these awards and a searchable list of all Supported Projects at NESCent go to the Supported Projects page in Science and Synthesis.

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Call for Proposals

HackathonNESCent’s scientific mission is to advance synthetic research that addresses fundamental questions in evolutionary biology.  Synthetic research in evolutionary biology occurs along a continuum in terms of the scope of the scientific questions, tools and disciplines that may be involved.  At one end of the continuum, synthesis involves integrating available data and models to address important problems within a discipline.    At the other end, methods and perspectives from multiple disciplines are combined to develop new tools for answering-- and creating new-- fundamental scientific questions. 

postdocs

NESCent supports a portfolio of scientific activities that span this spectrum of synthetic research in evolutionary biology and related fields. NESCent sponsors postdoctoral fellows and sabbatical scholars as resident scientists, creating a fertile in-house environment for sustained synthetic research. Short-term visitors are supported to enable synthetic research on any aspect of evolutionary biology and relevant disciplines.  Visitors will work on-site at NESCent for periods of 2 weeks to 3 months. Working groups enable teams of visiting scientists to work intensively over a several-year period.  Catalysis meetings provide a novel mechanism for bringing together diverse research communities and cultures to identify common interests and catalyze new synthetic collaborations.  Proposals for these diverse activities are generated by the scientific community, through our application process and evaluated by an external advisory board.

Proposals for sabbaticals, working groups and catalysis meetings are accepted twice a year, at June 15 and December 1 deadlines.  Proposals for post-doctoral fellowships are accepted at the December 1 deadline. Proposals for short-term visitors are considered four times a year, with deadlines on January 1, April 1, July 1 and September 1. 

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Recent Publications by NESCent Scientists

Publications by NESCent Scientists as well as other information can be found in the News section. 

Doug Eernise
Kelly, R.P. and Eernisse, D.J. 2007, Southern Hospitality: A Latitudinal Gradient in Gene Flow in the Marine Environment. Evolution 61: 700-707
Kelly, R.P., Sarkar, I.N., Eernisse, D.J, and Desalle, R. 2007, DNA Barcoding Using Chitons (genus Mopalia). Molecular Ecology Notes 7:177-183

Joel Kingsolver

Kingsolver, J.G., Massie, K.R., Ragland, G.J. and Smith, M.H. 2007, Rapid population divergence in thermal reaction norms for an invading species: breaking the temperature–size rule. Journal of Evolutionary Biology OnLine Early

Kingsolver, J.K. (2007) Variation in growth and instar number in field and laboratory Manduca sexta. Proceedings of the Royal Society B: Biological Sciences. Vol 274 (No.1612), pp977 - 981.

Sally Otto

A Biologists Guide to Mathematical Modeling in Ecology and Evolution

Samantha Price
Bininda-Emonds, O. R. P., Cardillo, M., Jones, K. E., MacPhee, R. D. E., Beck, R. D.M.,Grenyer, R., Price, S. A., Vos, R. A., Gittleman, J. L. & Purvis, A. 2007 The delayed rise of present-day mammals. Nature 446, 507-512

Maria Servedio

Lorch, P.D. and Servedio, M.R. 2007. The Evolution of conspecific gamete precendence and its effect on reinforcement. J of Evolutionary Biology Vol 20(3):937-949.

Brian Sidlauskas

Sidlauskas, Brian L. 2007. Testing for unequal rates of morphological diversification in the absence of a detailed phylogeny: a case study from characiform fishes. Evolution 61 (online early).

Todd Vision

Bouck A, Vision T. The molecular ecologist's guide to expressed sequence tags. Mol Ecol. 2007 Mar;16(5):907-24.
Gaulton KJ, Mohlke KL, Vision TJ. A computational system to select candidate genes for complex human traits. Bioinformatics. 2007 Jan 19; [Epub ahead of print]


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Informatics

Call for White Papersshout

 

In order to be responsive to user needs and tap into the expertise and creativity of the evolutionary biology community, NESCent is soliciting short whitepapers on potential initiatives to be undertaken by the center in the area of informatics (including, but not limited to, training, software development, and coordination of data standards). The scale of the proposed work may vary widely. Those who submit whitepapers are making no commitment to participate in a project but would be welcome to do so.  More information on white papers is available on the the NESCent website.

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Phyloinformatics Hackathon

A large number of powerful and sophisticated, model-based analysis tools exist for comparison of evolutionary models, inference of phylogenetic trees, and testing of hypotheses in a comparative framework, but very few of these tools phylohackathoninteroperate with each other. Seamlessly incorporating these tools into automated workflows to address advanced questions on large data sets in an evolutionary context is difficult due to incompatible interfaces and data exchange formats. NESCent periodically brings together open source software developers and evolutionary biologists for intensive collaborative coding sessions known as "hackathons", which are used to help overcome barriers to intercompatibility.  NESCent's first Phyloinformatics hackathon in December 2006 jumpstarted the development of common object models and phyloinformatics "glue code" in the widely used Bio* toolkits, led to the first steps in validating and standardizing the use of the NEXUS format for data exchange, as well as to the first definition of a format for exchanging models between analysis programs.

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Recently Funded Informatics Projects

Reusable database components for genomic and natural diversity dataheliconus

The evolutionary biology community faces a data-management challenge due to an overwhelming volume of high-throughput genomic data that is being generated in a wide variety of organisms. To address this, NESCent has partnered with the Generic Model Organism Database (GMOD) project, an open-source software suite that provides a rich and flexible model organism data model, a host of intercompatible web and user interface components, and applications for curating genomic data (such as sequences, genetic maps, and published literature). NESCent aims to further develop the data model for evolutionary datatypes (named organisms, georeferenced collections, genetic and phenotypic variability, and phylogenies), to develop web applications for accessing these types of data, and to provide user support for adoption of the GMOD platform for evolutionary model organisms.  If you have an evolutionary model organism database project underway or in the works, we would love to hear from you. Please send an email to help@gmod.org.

(Heliconius photo: Owen McMillan)

Application of ontologies to phenotypic studies

An ontology is a structured and controlled vocabulary for formalizing knowledge within a particular domain, and is an important technology for computational processing of semantic concepts. NESCent is promoting the development and application of phenotype ontologies to evolutionary morphology, in order to enable computers to reason about phenotypic descriptions of organisms, and to relate descriptions of phenotypes in natural systems with developmental genetic information about mutant phenotypes in model organisms.  This project is a partnership with the Cypriniformes Tree of Life project, the ZFIN database, and the National Center for Biomedical Ontologies.

rose

 

"A rose by any other name..." Wm. Shakespeare

More information about IT projects is available in the Informatics section, under Major Inititatives

 

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Education and Outreach

Evolution Symposium at the National Association of Biology Teachers Conference

The Education and Outreach Group (EOG) at NESCent is charged with communicating evolutionary research to both the scientific community and the general public.  This is a tall order and EOG has several projects that address this goal.  We often partner with other groups to increase the impact of our activities.  One example of this kind of project is the annual Evolution Symposium at the National Association of Biology Teachers (NABT) conference.  The symposium was initiated in 2004, the year NESCent’s grant was awarded, by the American Institute of Biologicial Sciences and the Biological Sciences Curriculum Study.  AIBS is an umbrella organization for professional societies in the biological sciences, and BSCS is a well respected curriculum development group.  Both groups were concerned about the increase in challenges to the teaching of evolution across the country.  The first symposium “Evolutionary Science and Society” was a three day event with multiple speakers and panel sessions.  The products of this meeting include a collection of essays by presenters and a collection of classroom activities, both with the same title as the symposium. 

 

The 2004 symposium was a great success, so AIBS and BSCS decided to continue to offer an evolution symposium on an annual basis scaled down to a single topic for a full day.  NESCent became a co-sponsor of the symposium in 2005, when the topic was “Evolution and the Environment”.  In 2006 the topic was “Macroevolution” and the topic for 2007 is “Evolution and Medicine”.  Each year six leading scientists give short presentations about their research and additional resources are provided for teachers, such as a demonstration of a lesson or a discussion of issues involved with teaching evolution.  In 2006, EOG developed a CD-ROM of resources for educators to use in the classroom and handed it out at the symposium.  This CD includes information about the speakers, appropriate lessons, background information on macroevolution, and video clips from various sources.  In particular, three scientists associated with NESCent gave short video presentations on macroevolution and their work.  For the 2007 symposium, EOG is developing a new CD which will include material from scientists visiting NESCent for a catalysis meeting on “Evolution in Contemporary Human Populations” among other resources.    nabt

 

 

Speakers from the 2007 Macroevolution Symposium (left to right): Jeffery Levinton, David Jablonski, Scott Hodges, Nipam Patel, Philp Gingerich.  Not shown: Nicole King.

 

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NESCent Databases Aim to Increase Diversity in Evolutionary Biology Fields

One of the challenges in diversifying the field of evolutionary biology is a matter of access.  Students and faculty at minority serving institutions (MSIs) have not historically had convenient, one-stop access to a listing of all of the graduate programs in evolutionary biology at PhD-granting institutions across the nation.  At the same time, graduate admissions committees have lacked a single, comprehensive listing of MSIs to facilitate their efforts at targeted recruitment.  As a result, MSI students may not be aware of all their graduate programs options, while the graduate programs have difficulty contacting underrepresented students for recruitment.

In order to address these challenges Dr. John Clamp, a professor of biology at North Carolina Central University, spent part of his time as a NESCent Sabbatical Scholar developing comprehensive databases of both Minority Serving Institutions and Research I universities with graduate programs in evolutionary biology.  Both of these databases can be accessed at NESCent’s Education and Outreach website.  It is our hope that these databases will prove to be valuable resources in addressing the problem of access that has contributed to the lack of diversity in evolutionary biology.  To access these databases, or share them with your colleagues and students, please go to https://www.nescent.org/eog/database.php.

 

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Look for NESCent at these upcoming meetings:

June 18-19, 2007, The Evolution of the Animals: A Linnean Tercentenary Celebration

Royal Society, London

June 16-20, 2007 Evolution 2007

Christchurch, New Zealand

Joint meeting of the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB), and the American Society of Naturalists (ASN)

June 24-28, 2007 SMBE Annual Meeting

Halifax, Nova Scotia, Canada

July 7-11, 2007 Plant Biology and Botany Joint Congress

Chicago, IL

American Fern Society

American Society of Plant Biologists

American Society of Plant Taxonomists

Botanical Society of America

July 11-13, 2007 Mechanisms of Genome Evolution

Bloomington, IN

American Genetic Association Annual Symposium

July 16-21, 2007 8th International Congress of Vertebrate Morphology

Paris, France

July 21-25, 2007 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB)

Vienna, Austria

For more information about upcoming conferences, see Evolution Events in the News section. 

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