Next-generation phylogenetics takes root

Abstract

It has been a tumultuous 5 years in phylogeography and phylogenetics during which both fields have struggled to harness the power of next-generation sequencing (NGS) (Ekblom & Galindo; McCormack et al.). Fortunately, several methodological approaches appear to be taking root. In this issue of Molecular Ecology, O'Neill et al.) employ one such method - parallel tagged sequencing (PTS) - to elucidate the phylogeography of a tiger salamander (Ambystoma tigrinum) species complex. This study demonstrates a practical application of NGS on a scale appropriate (and not overkill) for most biologists interested in phylogeography (~100 loci for ~100 individuals), and their results highlight several analytical challenges that lie ahead for researchers employing NGS techniques. © 2012 Blackwell Publishing Ltd.