Looking forwards or looking backwards in avian phylogeography? A comment on Zink and Barrowclough 2008

In a recent review, Zink & Barrowclough (2008, hereafter ZB08) addressed the question of whether mitochondrial DNA (mtDNA) was sufficient to describe the phylogeographic history of avian species. They offered a number of conclusions, most of which were variants of the central tenet that mtDNA is sufficient to describe the broad picture of avian phylogeographies. Specifically, they concluded that, for questions of phylogeographic pattern, mtDNA does quite well on its own as a descriptor of geographical and taxonomic patterns, and that ‘the case for the primacy of nuclear variation for studies of phylogeography is not so clear to us’. The motivation for their review was a concern about the conclusions of several recent reviews (e.g. Edwards et al. 2005) summarizing several well-known limitations of mtDNA, including evidence for pervasive natural selection, the use of a single maternally inherited molecule to describe population histories and uncertainty over whether the mitochondrial gene trees obtained in hundreds of phylogeographic studies are representative of the histories of the relevant species or populations. One of the main arguments on which their confidence in mtDNA is based is their claim that nuclear genes are ‘lagging indicators’ of population structure compared with mtDNA: the majority of cases in birds (and presumably other taxa) reveal that mtDNA, a ‘leading indicator’ of population structure, exhibits reciprocal monophyly or high differentiation between taxa when nuclear DNA (nuDNA) does not. This enhanced resolving power, they suggest, is reason enough to be content with mitochondrial gene trees in delimiting patterns in species and phylogeographic history. In contrast, they concede that questions of phylogeographic process—demographic histories, gene flow, effective population sizes, population expansions, presumably speciation