Phylogeography

AbstractPhylogeography is a relatively young discipline, having been introduced into the literature in 1987. Its original focus was the analysis of gene trees (derived from molecular sequence data) in spatial geographic contexts, and for almost a decade, the field was dominated by the use of the mitochondrialdeoxyribonucleic acid(DNA) locus (in animals). Because phylogeography contains an explicit tree‐based focus on population genetic questions, it has successfully linked this discipline to the previously disconnected domain of phylogenetic systematics. From a largely descriptive beginning, phylogeography has become more rigorous by the inclusion of independent nuclear gene loci, more quantitative by incorporation of various statistical methods (nested clade phylogeographic analysis, statistical phylogeography) and more synthetic by incorporation of coalescent theory (using gene trees to estimate species trees) and data and methods from disciplines such as landscape genetics, palaeoecology and palaeoclimatology. Modern phylogeography has many applications to other disciplines of biology.Key concepts:Phylogeography is the study of the spatial and temporal distribution of gene sequences in populations of a single species, or among closely related species.Phylogeographic studies draw heavily on other disciplines, including geology, palynology, GIS layers of environmental records, population biology, coalescent theory and community ecology.Phylogeographic studies are increasingly being used to study multiple unrelated species that share the same geographic distributions, in an attempt to identify shared signals of historical events (such as stream captures, glacial cycles and marine transgressions) that contributed to population divergence and speciation in multiple groups.Phylogeography can contribute to knowledge of speciation and the assembly of community structure and identify geographic areas of high genetic diversity and/or regions where evolutionary processes may be identified and included in conservation planning on regional scales.