Generally, genotypes and phenotypes are expected to be spatially congruent, however, in widespread species complexes with few barriers to dispersal, multiple contact zones, and limited reproductive isolation, discordance between phenotypes and phylogeographic groups is more probable. Wagtails (Aves: Motacilla) are a genus of birds with striking plumage pattern variation across Eurasia. Up to 13 subspecies are recognized within a single species, yet previous studies using mitochondrial DNA have supported phylogeographic groups that are inconsistent with subspecies plumage characteristics. In this study, we investigate the link between phenotypes and genotype by comparing populations thought to be at different stages along the speciation continuum. We take a phylogeographic approach by estimating population structure, testing for isolation by distance, conducting demographic modeling, and estimating the first time-calibrated species tree for the genus. Our study provides strong evidence for species-level patterns of differentiation in wagtails, however population-level differentiation is less pronounced. We find evidence that three of four widespread Eurasian species exhibit an east-west divide that contradicts both subspecies taxonomy and phenotypic variation. Both the geographic location of this divide and time estimates from demographic models are overlapping in two sympatric species, indicating that coincident Pleistocene events shaped their histories.
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