Next-generation sequencing and the expanding domain of phylogeography

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.