NSF smiles upon us. In this era of 4% funding rates, we are particularly appreciative of having been awarded a significant grant from the National Science Foundation for a new study entitled “Quantifying genomic porosity in non-model radiations.” In addition to Irby and Leo Campagna (Leo was a prime mover on this proposal!) from our lab, our collaborators include Adam Siepel from Cold Spring Harbor and Ilan Gronau from the Interdisciplinary Center in Herzliya, Israel. The non-technical summary of this project follows:
Understanding how organisms are related to each other is a central goal of biological research, yet much of the branching structure of the tree of life remains imperfectly known. Comparisons of DNA sequences have been used to build reliable evolutionary trees for many groups of organisms. Yet in cases where species hybridize with one another (or have done so in the past), their descendants become a mosaic of genetic backgrounds, and this genetic mixing makes it more difficult to back-calculate their past relationships. Hybridization is particularly common in groups of species that have undergone rapid radiation–situations when large numbers of species evolve over a relatively short period of time—while at the same time these rapid radiations are models for many other kinds of evolutionary analysis. This project will investigate the type of genomic regions that are exchanged among species during rapid radiations. A central goal of the researchers is to develop a computer program that leverages large-scale genomic data to better understand the phylogenetic relationships among species, improving the ability to incorporate the effects of past hybridization events. This tool will be made available to the research community to help biologists understand evolution at the tips of the tree of life.
The overarching goals of this project are to (A) test questions about the degree and type of genomic regions exchanged among species in rapid radiations, and to (B) explore the implications for phylogenetic inference. These objectives are based on (C) the further development of a new bioinformatics tool (Generalized Phylogenetic Coalescent Sampler – G-PhoCS) that will allow the non-model organism community to test hypotheses about phylogenetic relationships and generate detailed demographic inferences (e.g., quantifying gene flow, effective population sizes and divergence times) across a phylogeny, using a variety of genomic-scale datasets. As empirical test cases the researchers will leverage natural evolutionary experiments in two avian radiations in which pairs of species can be classified as either introgression-prone or introgression-resistant based on external criteria such as ecological overlap and sympatry/allopatry. The research team brings together systematists and computer scientists attempting to realize the full potential of newly emerging high throughput sequence data by developing inference methods that make use of the rich information they provide. This collaboration will more generally broaden the understanding of the patterns and processes underlying genealogical discordance among regions of the genome.