Comparative phylogeography: concepts and applications

This special issue of Molecular Ecology celebrates the birth of phylogeography 10 years ago (Avise et al. 1987). Because the discipline has deep roots in historical biogeography and population genetics, phylogeography was heralded as a bridge linking the study of microand macroevolutionary processes. The initial and still dominant infrastructure for this bridge has been mitochondrial DNA (mtDNA) analyses which have permitted genealogical traces to be followed across the genetic boundaries between populations, species and higher taxonomic levels. In his personal reflection, Avise (1998) documents the explosive growth of phylogeography in the decade since its inception and notes many of the hallmark studies that have provided the empirical and conceptual link between systematics and population genetics. Celebrations are often times of renewal, and thus this special issue of Molecular Ecology aims not only to review the past but also to present a blend of theoretical and empirical papers with the hope of invigorating the field. Phylogeography and its predominant reliance on (animal) mtDNA has led to a body of descriptive data that are impressive in terms of their sheer comparative scope. For example, comparisons of mtDNA divergence between sister taxa of North American birds (Bermingham et al. 1992; Klicka & Zink 1997), South American rodents and marsupials (da Silva & Patton 1998) and frogs and reptiles across the Australian Wet Tropics (Schneider et al. 1998) have significantly discounted Late Pleistocene models of speciation and suggested that many species pairs are older than previously appreciated. Several articles in this issue presage the potential of comparative phylogeographic analyses and demonstrate that the shift from RFLP-based assays to direct determination of DNA nucleotide sequence has permitted increasingly fruitful cross-taxa comparisons of evolutionary history. In turn, we project that comparative phylogeographic analysis will permit detailed studies of landscape evolution, including the dispersal of taxa through a region, speciation, adaptive radiation, and extinction; in other words, investigation of the fundamental links between population processes and regional patterns of diversity and biogeography. The (typically) slower evolutionary rate of chloroplast DNA (Schaal et al. 1998) has limited the contribution of plants to phylogeography and our nascent knowledge of landscape evolution. We anticipate that plant phylogeography will increase in importance, thus refining our interpretation of historical landscape assembly and maintenance, as our understanding of the mutational basis of microsatellite evolution improves and permits this class of molecular markers to be used in comparative context. Certainly one clear empirical success of mtDNA-based phylogeography has been the improved description of the geographical distribution, phylogenetic relationships and genetic distances among evolutionary lineages of animals, leading, in turn, to a better understanding of regional biogeography and areas of endemism. Articles presented in this issue summarize and discuss the evolutionary landscapes of North America (Bernatchez & Wilson 1998), lower Central America (Bermingham & Martin 1998), Amazonia (da Silva & Patton 1998), Europe (Taberlet et al. 1998), the Australian Wet Tropics (Schneider et al. 1998) and Hawaii (Roderick & Gillespie 1998; see also Fleischer et al. 1998). These studies demonstrate the importance of combining molecular phylogeographic evidence with independent information on landscape history obtained from geology, palaeopalynology, etc. Of course there is a long way to go. One of the many challenges lying ahead is the comparative phylogeographic description of marine species, owing in part to the vast and disjunct geographical scale of many marine populations (Shulman & Bermingham 1995; Palumbi 1997). Meeting this challenge will undoubtedly provide contrasts and insights as sharp as those emerging from comparisons of temperate and tropical terrestrial evolutionary landscapes. Comparative phylogeographic analyses can contribute to broader studies of ecology and evolution in a number of ways. First, phylogeographic analysis can identify historically and evolutionarily independent regions that can be considered as natural replicates amongst which generalizations about specific processes can be tested statistically. For example, the evolutionary response to selection gradients can be compared across Molecular Ecology (1998) 7, 367–369