Population Genomics and Phylogeography

Abstract

Population genetics is the study of genetic variation within populations and how allele frequencies change over space and time. This field largely focuses on the five fundamental evolutionary processes that influence genetic variation: mutation, genetic drift, gene flow, natural selection, and recombination. In this chapter, we review how genomic data from avian species have advanced our understanding of each of these five processes, including an emphasis on their interactions in shaping contemporary genetic diversity on the scale of whole populations. In general, genomic data has increased the potential for fine-scale resolution of population structure and determination of population boundaries and population membership. However, delineating populations is not always straightforward, and populations tend to fall on a continuum from isolation to panmixia. Mutation is the ultimate source of all genetic variation within populations. The ability to sequence whole genomes resulted in better estimates of mutation and substitution rates in particular genomic regions (e.g., coding vs. noncoding DNA) and along different avian lineages. The uncovered variation in these rates will further advance our knowledge of bird evolution. A genomic perspective on other evolutionary forces, such as genetic drift (tightly linked with the concept of effective population size [Ne]), migration, and selection, allows for more detailed reconstructions of demographic and phylogeographic history. In addition, the estimates of genome-wide recombination rates and their relationship with linked selection and GC-biased gene conversion will improve the match between population genetic models and biological reality.