Climatic fluctuations shape the phylogeography of a mesic direct‐developing frog from the south‐western Australian biodiversity hotspot

Aim To assess phylogeographic pattern throughout the range of Metacrinia nichollsi in order to develop specific biogeographical hypotheses for the wet forests of south‐western Australia. This was carried out by contrasting a direct‐developing frog species, M. nichollsi, that breeds independently of free surface water with conventional, aquatic breeders and highly specialized direct developers. Location Wet forests of the south‐western Australian biodiversity hotspot – an area of high species richness and endemism for myobatrachid frogs and many other faunal groups. Methods We compiled an extensive phylogeographic data set from field‐collected samples based on mitochondrial ND2 sequences. Phylogenetic analyses combined with estimates of divergence times were used to build a model of major biogeographical events affecting the species. Phylogeographic analyses were used to provide insights into smaller‐scale processes acting within each major lineage. Results Phylogenetic analysis recovered three major lineages, with divergence dates coincident with late Miocene–early Pliocene arid cycles. One lineage was confined to geographically isolated populations in the Stirling Ranges (Stirling Ranges Lineage, SRL). The continuous range of M. nichollsi was split into two: the Main Range Lineage (MRL) and the Southern Coastal Lineage (SCL). The SCL displays a strong drainage‐based population structure, whereas the MRL displays a strong signature of recent expansion, suggesting that these two lineages have had very different biogeographical histories. Main conclusions Late Miocene–Pliocene aridity appears to have isolated populations in the Stirling Ranges and resulted in the formation of two additional lineages on a north–south gradient that are independent of southward‐flowing drainage systems. Our results demonstrate that climatic fluctuations are likely to have generated fine‐scale phylogeographic structure within M. nichollsi and that catchment regions are important refugia during arid cycles.