The southern African marine realm is located at the transition zone between the Atlantic and Indo-Pacific biomes. Its biodiversity is particularly rich and comprises faunal and floral elements from the two major oceanic regions, as well as a large number of endemics. Within this realm, strikingly different biota occur in close geographic proximity to each other, and many of the species with distributions spanning two or more of the region's marine biogeographic provinces are divided into evolutionary units that can often only be distinguished on the basis of genetic data. In this review, we describe the state of marine phylogeography in southern Africa, that is, the study of evolutionary relationships at the species level, or amongst closely related species, in relation to the region's marine environment. We focus particularly on coastal phylogeography, where much progress has recently been made in identifying phylogeographic breaks and explaining how they originated and are maintained. We also highlight numerous shortcomings that should be addressed in the near future. These include: the limited data available for commercially important organisms, particularly offshore species; the paucity of oceanographic data for nearshore areas; a dearth of studies based on multilocus data; and the fact that studying the role of diversifying selection in speciation has been limited to physiological approaches to the exclusion of genetics. It is becoming apparent that the southern African marine realm is one of the world's most interesting environments in which to study the evolutionary processes that shape not only regional, but also global patterns of marine biodiversity.

In March 2012, the authors met at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, USA, to discuss approaches and cooperative ventures in Indo-Pacific phylogeography. The group emerged with a series of findings: (1) Marine population structure is complex, but single locus mtDNA studies continue to provide powerful first assessment of phylogeographic patterns. (2) These patterns gain greater significance/power when resolved in a diversity of taxa. New analytical tools are emerging to address these analyses with multi-taxon approaches. (3) Genome-wide analyses are warranted if selection is indicated by surveys of standard markers. Such indicators can include discordance between genetic loci, or between genetic loci and morphology. Phylogeographic information provides a valuable context for studies of selection and adaptation. (4) Phylogeographic inferences are greatly enhanced by an understanding of the biology and ecology of study organisms. (5) Thorough, range-wide sampling of taxa is the foundation for robust phylogeographic inference. (6) Congruent geographic and taxonomic sampling by the Indo-Pacific community of scientists would facilitate better comparative analyses. The group concluded that at this stage of technology and software development, judicious rather than wholesale application of genomics appears to be the most robust course for marine phylogeographic studies. Therefore, our group intends to affirm the value of traditional (“unplugged”) approaches, such as those based on mtDNA sequencing and microsatellites, along with essential field studies, in an era with increasing emphasis on genomic approaches.