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  • Tuesday, July 13, 2021

SC4ES: National Center for Genome Analysis Support Genomics Research webinar series

Featuring Layla R. Freeborn, Indiana University, this monthly scientific series highlights the research of scientists who use computational resources provided by NCGAS.

Event details

  • Date & time
    Tuesday, July 13, 2021
  • Location
    Online - Zoom

Register here

About this event


The National Center for Genome Analysis Support (Links to an external site.) (NCGAS) helps researchers nationwide with the demanding—and often confusing— computations that genomics research requires. In this monthly series, scientists present their genomics research in pursuit of answers to some of the most confounding biological questions.

"NCGAS serves hundreds of researchers who apply genomics to their research, and we wanted to find out what their individual research projects entail. We hope to learn how they are using genomics in their studies, as an inspiration to other researchers." - Tom Doak, Chief Scientist, National Center for Genome Analysis Support

Talks will take place the second Tuesday of each month, 2-3pm EST.

Title of presentation: 
Red frog, green frog, blue frog: estimating phylogenetic relationships among closely related populations of Oophaga pumilio from Bocas del Toro, Panama.

Layla Freeborn has always been fascinated by how the natural world operates, so she surprised no one when she declared herself a Biology major before officially starting her B.S. at Utica College of Syracuse University. After undergrad, she completed a master's in Biology at Southeastern Louisiana University with the late Dr. David Sever, studying the reproductive morphology of sea snakes. She went on to complete her Ph.D. in Ecology & Evolutionary Biology with Dr. Cori Richards-Zawacki, starting at Tulane University but moving with her lab to the University of Pittsburgh. Her dissertation looked at the cellular, genetic, and evolutionary basis of polymorphic coloration in the strawberry poison frog, Oophaga pumilio, from Central America.

Along her (sometimes literal) winding path through graduate school, she picked up a diverse set of skills, from image analysis and multivariate statistics to phylogenetics and population genomics. She didn't get far before realizing that she finds the tools she employ as fascinating as the biological questions she set out to answer. In particular, bioinformatics tools captured her interest, so her focus transitioned to learning the ins-and-outs of software she used and working toward fluency in R and Unix. She realized a bioinformatics career promised the fun and challenge she sought in her professional life, so when an analyst position opened at NCGAS during her last semester of grad school, "applying was a no-brainer."

Oophaga pumilio has emerged as a popular species for evolutionary biologists interested in the roles of geographic isolation and selection in driving phenotypic divergence. Although this species provides a compelling example of phenotypic variation and incipient speciation, the system is characterized by many of the challenges associated with studying recently separated populations. In this study, Freeborn provides a high-resolution species tree for O. pumilio by incorporating a more focused sampling strategy (greater number of individuals, greater number of collecting sites), the application of NGS, and population genetic analyses. To test whether dorsal coloration is the result of convergent evolution, she uses the topologies and novel spectral reflectance data to perform ancestral character state reconstruction. The topological relationships evident in the phylogenies and the distribution of dorsal color phenotypes suggest that vicariance largely explains genetic differentiation patterns in O. pumilio.

The ancestral character state reconstructions support the convergent evolution of dull colors like green and blue and at least one reversal to bright coloration like yellow, orange or red. Incorporating these species trees with future genetic, morphological, and physiological datasets will provide an integrative approach to study color polymorphism as a driver of speciation.

The series (and archive):

View all the talks in this series as well as links to archive video of each talk (Links to external site.).

The Supercomputing for Everyone Series (S4ES) of workshops and seminars are led by personnel from Research Technologies (Links to external site.), a division of University Information Technology Services (Links to external site.). This series is led by the National Center for Genome Analysis Support (Links to external site.). Both are centers in the Pervasive Technology Institute (Links to external site.) at Indiana University.

The Supercomputing for Everyone Series (Links to external site.) aims to bring more users into the realm of advanced computing, whether it be visualization, computation, analytics, storage, or any related discipline. Let the Research Technologies staff take you to the next level of computing.