Testing hypotheses of Pleistocene population history using coalescent simulations: phylogeography of the pygmy nuthatch (Sitta pygmaea)

In this paper, we use mitochondrial NADH dehydrogenase subunit 2 sequences to test Pleistocene refugial hypotheses for the pygmy nuthatch (Sitta pygmaea). Pygmy nuthatches are a common resident of long-needle pine forests in western North America and demonstrate a particular affinity with ponderosa pine (Pinus ponderosa). Palaeoecological and genetic data indicate that ponderosa pine was isolated in two Pleistocene refugia corresponding to areas in the southern Sierra Nevada in the west and southern Arizona and New Mexico in the east. We use coalescent simulations to test the hypothesis that pygmy nuthatches tracked the Pleistocene history of their preferred habitat and persisted in two refugia during the periods of glacial maxima. Coalescent simulation of population history does not support the hypothesis of two Pleistocene refugia for the pygmy nuthatch. Instead, our data are consistent with a single refuge model. Nucleotide diversity is greatest in the western populations of southern and coastal California. We suggest that the pygmy nuthatch expanded from a far western glacial refuge into its current distribution since the most recent glacial maximum.