The field of phylogeography seeks to shed light on the ecology and evolution of organisms by resolving genetic relationships across a geographic range. This includes comparisons among isolated populations, subspecies partitions, sister species, and more ancient separations. The staple method employed in phylogeographic studies has been mitochondrial DNA sequencing; however, the field has kept abreast of technical developments, with nuclear DNA sequencing and microsatellite fragment analysis now commonly used to resolve genetic patterns, and single nucleotide polymorphisms (SNPs) and next-generation sequencing technologies becoming increasingly popular. This review is focused on the contributions phylogeography has made to understanding reef fish dispersal, evolutionary divergence, and conservation. Examples of these findings include the following: (1) genetic surveys of reef fishes often reveal multiple evolutionary lineages within a species' range; (2) genetic connectivity by larval transport can vary from a few kilometers in anemone fishes, to entire ocean basins in unicorn fishes and other species with long larval stages; (3) biogeographic provinces, defined by species distributions, are often concordant with genetic partitions for widespread species; (4) new species arise in biodiversity hotspots like the Coral Triangle and Caribbean Sea, but these areas can also accumulate species that originate in peripheral oceanic islands; (5) both biodiversity hotspots and peripheral areas of high endemism should be conservation priorities; and (6) parentage analyses with “DNA fingerprints” show that some larvae settle close to their origin, reinforcing the conservation value of marine protected areas (MPAs). We conclude with a discussion of how rapidly developing methods for genomic sequencing are revolutionizing the field, allowing for the first time an in-depth exploration of the ecological and environmental factors that influence genomes, and the genetic building blocks for future biodiversity.

The field of phylogeography incorporates elements of phylogenetics (species trees), biogeography (species distributions), and population genetics [115]. Roots of this field can be found in the first biochemical comparisons of organisms, most commonly with the technique of protein electrophoresis [46]. In a classic application of this technique, seemingly identical bonefishes (Albula spp.) caught in the same location in Hawaiʿi were found to include two species [2307].