Resolving postglacial phylogeography using high-throughput sequencing

by Shank Lab Journal Club

Authors: Kevin J. EmersonClayton R. Merz, Julian M. Catchen, Paul A. Hohenlohe,William A. Cresko, William E. Bradshaw, and Christina M. Holzapfel

Abstract: The distinction between model and nonmodel organisms is becoming increasingly blurred. High-throughput, second-generation sequencing approaches are being applied to organisms based on their interesting ecological, physiological, developmental, or evolutionary properties and not on the depth of genetic information available for them. Here, we illustrate this point using a low-cost, efficient technique to determine the fine-scale phylogenetic relationships among recently diverged populations in a species. This application of restriction site-associated DNA tags (RAD tags) reveals previously unresolved genetic structure and direction of evolution in the pitcher plant mosquito, Wyeomyia smithii, from a southern Appalachian Mountain refugium following recession of the Laurentide Ice Sheet at 22,000–19,000 B.P. The RAD tag method can be used to identify detailed patterns of phylogeography in any organism regardless of existing genomic data, and, more broadly, to identify incipient speciation and genome-wide variation in natural populations in general.

2. Chromosome-scale selective sweeps shapeCaenorhabditis elegans genomic diversity

Authors: Erik C Andersen, Justin P Gerke, Joshua A Shapiro, Jonathan R Crissman, Rajarshi Ghosh, Joshua S Bloom, Marie-Anne Félix & Leonid Kruglyak

Abstract: The nematode Caenorhabditis elegans is central to research in molecular, cell and developmental biology, but nearly all of this research has been conducted on a single strain of C. elegans. Little is known about the population genomic and evolutionary history of this species. We characterized C. elegans genetic variation using high-throughput selective sequencing of a worldwide collection of 200 wild strains and identified 41,188 SNPs. Notably, C. elegans genome variation is dominated by a set of commonly shared haplotypes on four of its six chromosomes, each spanning many megabases. Population genetic modeling showed that this pattern was generated by chromosome-scale selective sweeps that have reduced variation worldwide; at least one of these sweeps probably occurred in the last few hundred years. These sweeps, which we hypothesize to be a result of human activity, have drastically reshaped the global C. elegans population in the recent past.

Presented by S. Herrera on 15 Feb 2012