Estimating gene flow between Black salamander (Aneides flavipunctatus) populations: a multi-locus coalescent approach

Analyzing DNA sequence data from multiple unlinked loci in a coalescent framework is a powerful means for assessing the genetic isolation of populations by estimating population divergence times and gene flow since divergence. This approach was used to study three ecologically and morphological distinguishable populations of the Black Salamander (Aneides flavipunctatus) that are parapatrically distributed in northwestern California. These populations meet at a three way contact zone in northern Mendocino County, where abrupt transitions in color pattern, vertebral number, and microhabitat preference are observed. Analysis of seven presumably independently assorting loci reveals that the northern population diverged simultaneously from both southern populations 2.6 MYA. There has been little gene flow out of the northern population into both southern populations, though there is some gene flow into the northern population. The coastal and inland populations diverged from each other 1.9 MYA, and there apparently has been substantial gene flow between. The effective population sizes were estimated for the coastal and inland populations at 1.1 and 1.4 million individuals respectively, and the ancestral effective population sizes were all estimated at around 900,000 individuals. Based on the divergence times and relative genetic isolation of the southern populations from the northern population, these findings suggest that the main portion of the range contains a northern and southern species.