DOI: 10.5061/dryad.j05b3
title: Data from: Genetic admixture supports an ancient hybrid origin of the endangered Hawaiian duck

description: 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.
description: PHASED.FASTA.FILESFasta files include the mitochondrial control region and 19 phased nuclear loci for 15 Hawaiian duck, 21 Laysan duck, and 25 mallard individuals (see Supporting information Table S1 & S2 for marker information).IMa2.Input.FILESIMa2 input files consisting of 19 nuclear markers filtered for the largest non-recombinant fragment in the program IMgc for 15 Hawaiian duck, 21 Laysan duck, and 25 mallard individuals. The two files differ in starting phylogenetic relationships with mtDNA-like topology (Hawaiian duck sister to mallard) and nuDNA-like topology (Hawaiian duck sister to Laysan duck).STRUCTURE.Input.FILESInput files for STRUCTURE runs. Three files include analyses between 15 Hawaiian duck, 21 Laysan duck, and 25 mallard samples with data sets where (a) recombination was ignored, (b) loci were filtered for recombination, and (c) 17 diagnostic SNPs ascertained by comparing Laysan ducks and mallards (Table S2). Similar to the latter file, a fourth file (Structure.Multi-species.SNP.Input.FILE.stru) includes 16 diagnostic SNPs assayed across 8 taxonomic units of the mallard complex.SplitsTree.Input.FILEFasta file of 19 nuclear loci concatenated for a total of 6,682 aligned nucleotides for 15 Hawaiian duck, 21 Laysan duck, and 25 mallard samples.Concatenated.Nuclear.file.fas