Title: Comparative and population genomics of host-pathogen co-evolution in birds
Abstract: Infectious disease produces some of the strongest selective forces on natural populations across the tree of life. The signatures of pathogen-mediated evolution on host genomes have been described for several model organisms, but few studies of non-model organisms have detected such signatures beyond candidate loci such as MHC genes or toll-like receptors. In my dissertation I use population genomics and comparative genomics to study the dynamics of pathogen-mediated selection at two evolutionary timescales.
In Chapters 1 and 2, I use a combination of geographic and temporal sampling to compare the impacts on genomic variability of recent founder events and an epizootic on the genome of the House Finch (Haeomorhous mexicanus), a common North American songbird with a well-documented recent history of introductions and disease. House Finches, native to the western US and Mexico, were introduced to the Hawaiian Islands in 1870 and the eastern US in 1940. Following substantial population expansions, in 1994, a previously poultry-associated bacterium, Mycoplasma gallisepticum jumped to House Finches and has caused severe declines across both eastern and western populations. In Chapter 1, I genotype ~2,000 loci from across the House Finch genome and demonstrate that demographic shifts brought about by eastern and Hawaiian founder events have much more profound impacts on the genome than natural selection mediated by a bacterial pathogen. In Chapter 2, I use whole-genome resequencing data in House Finches to fully characterize the impacts of both the eastern founder event and epizootic. I show that the population expansion of the native western US population following the last glacial maximum had the largest genome-wide impact on patterns of genetic variation, followed by the eastern founder event. The greater power of this dataset enables me to detect a decrease in genetic diversity immediately following the epizootic. Additionally, the lack of temporal differentiation at individual SNPs with large changes in allele frequency associated with the epizootic suggest that House Finches evolved resistance through polygenic selection.
In Chapter 3, I use comparative genomics to investigate genome-wide signatures of host-pathogen co-evolution across longer temporal scales in birds. Using over 11,000 genes from 39 bird genomes, I show that immune genes characterized as receptors, encoding proteins that interact directly with pathogens, are consistently under selection at a higher proportion of sites and in a larger proportion of lineages than estimates from all genes. Using an unbiased approach with all genes and pathways regardless of function, I also show that immune system functional pathways are enriched for signatures of positive selection. Taken together I demonstrate that host-pathogen interactions play an important role in shaping the bird genome over long evolutionary timescales.