DOI: 10.5061/dryad.67170
title: Data from: Mito-nuclear discord in six congeneric lineages of Holarctic ducks (genus Anas)

description: Many species have Holarctic distributions that extend across Europe, Asia,
 and North America. Most genetics research on these species has examined
 only mitochondrial (mt) DNA, which has revealed wide variance in
 divergence between Old World (OW) and New World (NW) populations, ranging
 from shallow, unstructured genealogies to deeply divergent lineages. In
 this study, we sequenced 20 nuclear introns to test for concordant
 patterns of OW-NW differentiation between mtDNA and nuclear (nu) DNA for
 six lineages of Holarctic ducks (genus Anas). Genetic differentiation for
 both marker types varied widely among these lineages (idiosyncratic
 population histories), but mtDNA and nuDNA divergence within lineages was
 not significantly correlated. Moreover, compared to the association
 between mtDNA and nuDNA divergence observed among different species, OW-NW
 nuDNA differentiation was generally lower than mtDNA divergence, at least
 for lineages with deeply divergent mtDNA. Furthermore, coalescent
 estimates indicated significantly higher rates of gene flow for nuDNA than
 mtDNA for four of the six lineages. Thus, Holarctic ducks show prominent
 mito-nuclear discord between OW and NW populations, and we reject
 differences in sorting rates as the sole cause of the within-species
 discord. Male-mediated intercontinental gene flow is likely a leading
 contributor to this discord, although selection could also cause elevated
 mtDNA divergence relative to weak nuDNA differentiation. The population
 genetics of these ducks contribute to growing evidence that mtDNA can be
 an unreliable indicator of stage of speciation, and that more holistic
 approaches are needed for species delimitation.
description: 6 Anas species mtDNA
 & 20 introns individual FASTA filesThis zipped folder
 contains 126 FASTA files, each containing aligned sequences (N = ~100
 sequences) from one species (species pair) and one locus (6 species x 21
 loci). The sequences are all introns only, and the gametic phases of
 alleles are resolved with &gt;90% probability. Individual sequences are
 labeled "o" for Old World and "n" for New
 World.6
 Anas species mtDNA & 20 loci individual FASTA
 files.zip6 Anas species 20 loci
 concatenated Nexus FilesThis zipped folder
 contains NEXUS files of 20 concatenated introns for each of 6 species (or
 species pair) of Anas ducks (~100 sequences per species). The sequences
 are all introns only, and the gametic phases of alleles are resolved with
 &gt;90% probability. Individual sequences are labeled "o" for
 Old World and "n" for New World. Locus identification is
 provided at the end of each file.6 Anas species 20 loci
 STRUCTURE input filesThis zipped folder
 contains STRUCTURE input files containing genotypes at 20 introns and 50
 individuals for each of 6 species (or species pair) of Anas ducks (~100
 sequences per species). The second column in each file contains population
 IDs: "1" = Old World, "2" = "New World".
 Prior to designating alleles, singletons were removed from sequences so
 that rare alleles were grouped with closely related
 alleles.6 Anas species mtDNA
 & 20 introns ARLEQUIN filesThis zipped folder
 contains 126 ARLEQUIN files, each containing aligned sequences (N = ~100
 sequences) from one species (species pair) and one locus (6 species x 21
 loci). The sequences are all introns only, and the gametic phases of
 alleles are resolved with &gt;90% probability. Sequences are partitioned
 into two populations "OW" for Old World and "NW" for
 New World.6
 Anas species mtDNA & 20 loci ARLEQUIN
 files.zip6 Anas species mtDNA
 & 20 loci IM input filesThis zipped folder
 contains 12 IM files. SPECIES-mtDNA contains mtDNA control regions
 sequences from up to 100 individuals of the given species. SPECIES-20loci
 contains up to 100 sequences from each of 20 nuclear introns (gametic
 phases of alleles are resolved with &gt;90% probability) for the given
 species. Sequences are partitioned into two populations "OW" for
 Old World and "NW" for New World.