Data from: Genetic admixture supports an ancient hybrid origin of the endangered Hawaiian duck

Speciation is regarded primarily as a bifurcation from an ancestral species into two distinct taxonomic units, but gene flow can create different signals of phylogenetic relationships among different loci. We evaluated several hypotheses that could account for phylogenetic discord between mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) within Hawaiian ducks (Anas wyvilliana), including stochastic lineage sorting, mtDNA capture, and widespread genomic introgression. Our results best support the hypothesis that the contemporary Hawaiian duck is descended from an ancient hybridization event between the mallard (A. platyrhynchos) and Laysan duck (A. laysanensis). Whereas mtDNA clearly shows a sister-relationship between Hawaiian ducks and mallards, nuDNA is consistent with a genetic mosaic with nearly equal contributions from Laysan ducks and mallards. In addition, coalescent analyses suggest that gene flow from either mallard or Laysan duck, depending on the pre-defined tree topology, is necessary to explain contemporary genetic diversity in Hawaiian ducks, and these estimates are more consistent with ancient, rather than contemporary, hybridization. Time since divergence estimates suggest that the genetic admixture event occurred around the Pleistocene-Holocene boundary, which is further supported by circumstantial evidence from the Hawaiian sub-fossil record. Although the extent of reproductive isolation from either putative parental taxon is not currently known, these species are phenotypically, genetically, and ecologically different, and they meet primary criteria used in avian taxonomy for species designation. Thus, the available data are consistent with an admixed origin, and support the hypothesis that the Hawaiian duck may represent a young hybrid species