Abstract
Phylogeography is experiencing a revolution brought on by next-generation sequencing methods. A historical survey of the phylogeographic literature suggests that phylogeography typically incorporates new questions, expanding on its classical domain, when new technologies offer novel or increased numbers of molecular markers. A variety of methods for subsampling genomic variation, including restriction site associated DNA sequencing (Rad-seq) and other next generation approaches, are proving exceptionally useful in helping to define major phylogeographic lineages within species as well as details of historical demography. Next-generation methods are also blurring the edges of phylogeography and related fields such as association mapping of loci under selection, and the emerging paradigm is one of simultaneously inferring both population history across geography and genomic targets of selection. However, recent examples, including some from our lab on Anolis lizards and songbirds, suggest that genome subsampling methods, while extremely powerful for the classical goals of phylogeography, may fail to allow phylogeography to fully achieve the goals of this new, expanded domain. Specifically, if genome-wide linkage disequilibrium is low, as is the case in many species with large population sizes, most genome subsampling methods will not sample densely enough to detect selected variants, or variants closely linked to them. We suggest that whole-genome resequencing methods will be essential for allowing phylogeographers to robustly identify loci involved in phenotypic divergence and speciation, while at the same time allowing free choice of molecular markers and further resolution of the demographic history of species.
Highlights
Like many fields in evolutionary biology, phylogeography has been consistently transformed by available technologies for assaying genetic variation
A major criticism of sequence based markers or single nucleotide polymorphisms (SNPs) in phylogeography has been the paucity of such markers and their low polymorphism. While these criticisms may have been valid in the polymerase chain reaction (PCR) era, we suggest that they no longer apply meaningfully given the large number of SNPs achievable with next-generation sequencing approaches
We have a growing number of examples of studies in which employment of next-generation sequencing methods has yielded high resolution substructuring within species at a level of detail that far exceeds that formerly yielded by single locus mtDNA or microsatellite studies
Summary
Like many fields in evolutionary biology, phylogeography has been consistently transformed by available technologies for assaying genetic variation. We suggest that the domains of phylogeography have expanded to include surveys of selection and covariation of genes and environment across the landscape as a result of the increasing ability to assay variation at large numbers of loci through next-generation sequencing.
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have