Population Genetics of Tree Swallows, in Collaboration with NCGAS

Abstract

The National Center for Genome Analysis Support (NCGAS) provides training and computational resources in an effort to train biologists to approach historically-difficult, non-model problems with large biological data sets. For example, our collaborators at Baylor University work with Tree Swallow (Tachycineta bicolor), using RNAseq data in population genetics and toxicology. Working with the NCGAS, they assembled a de novo transcriptome assembly for the Tree Swallow, for which there is no genome. Variant calling using the transcriptome identified 66,169 single nucleotide polymorphisms (SNPs) across 144 samples. They were then able to identify phylogeographic structuring across the Great Lakes Region, including accurate grouping populations distributed across smaller geographic scales (e.g. along the Maumee River). SNPs were also used to assess population heterozygosity and genetic diversity. This project required large scale data handling, large memory machines to assembly the transcriptome, and advanced Linux skills to manage the data and analyses. NCGAS provided the computation resources and training on the Linux environment and data management. Further assistance was provided in consultation and problem solving - leading to a high level of independence and competency of the graduate student researcher.