Data from: ddRAD‐seq data reveal significant genome‐wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America

Recently evolved species typically share genetic variation across their
genomes due to incomplete lineage sorting and/or ongoing gene flow. Given
only subtle allele frequency differences at most loci and the expectation
that divergent selection may affect only a tiny fraction of the genome,
distinguishing closely related species based on multi‐locus data requires
substantial genomic coverage. In this study, we used ddRAD‐seq to sample
the genomes of five recently diverged, New World “mallards” (Anas spp.), a
group of dabbling duck species characterized by diagnosable phenotypic
differences but minimal genetic differentiation. With increased genomic
sampling, we aimed to characterize population structure within this group
and identify genomic regions that may have experienced divergent selection
during speciation. We analyzed 3,017 autosomal ddRAD‐seq loci and 177 loci
from the Z‐chromosome. In contrast to previous studies, the ddRAD‐seq data
were sufficient to assign individuals to their respective species or
subspecies and to generate estimates of gene flow in a phylogenetic
framework. We find limited evidence of contemporary gene flow between the
dichromatic mallard and several monochromatic taxa, but find evidence for
historical gene flow between some monochromatic species pairs. We conclude
that the overall genetic similarity of these taxa likely reflects retained
ancestral polymorphism rather than recent and extensive gene flow. Thus,
despite recurring cases of hybridization in this group, our results
challenge the current dogma predicting the genetic extinction of the New
World monochromatic dabbling ducks via introgressive hybridization with
mallards. Moreover, ddRAD‐seq data were sufficient to identify previously
unknown outlier regions across the Z‐chromosome and several autosomal
chromosomes, regions that may have been involved in the diversification of
species in this recent radiation.