Phylogeographic information systems: putting the geography into phylogeography

Phylogeography is concerned with the principles and processes governing the geographical distributions of genealogical lineages, especially those at the intraspecific level (Avise, 1998, 2000). Phylogeographic study is undergoing a major expansion as the range of convenient genetic markers available to study geographic variation increases. Ultimately, the aim of phylogeography might be defined as a means to understand microevolution and speciation in its geographic or spatiotemporal context. Detecting coincidence or concordance of geographic variation in genotypes, or their genealogies, and the environment is therefore at the heart of phylogeographic inference. Geographical concordance between genealogies may be across sequence characters within a gene, between significant genealogical partitions across multiple genes within a species, or in the geography of gene-tree partitions across multiple co-distributed species (Fig. 1). The latter has been called comparative phylogeography (Bermingham & Moritz, 1998) and may provide a ‘bridge’ between the historically separate disciplines of phylogeography and historical biogeography (Riddle & Funk, 2004; Riddle & Hafner, 2004; Riddle, 2005). Any of these three types of genetic pattern may be geographically concordant with an environmental feature, for example, a mountain range, river or climatic barrier. A wider definition of phylogeography includes genetically controlled traits, such as morphology or behaviour, for which comparable concordance patterns can be studied (Avise, 1998). Environmental and Evolutionary Biology, School of Biology, University of St. Andrews, St. Andrews, UK