DOI: 10.5061/dryad.vc8ch8r8
title: Data from: Behavioral vs. molecular sources of conflict between nuclear and mitochondrial DNA: the role of male-biased dispersal in a Holarctic sea duck

description: Genetic studies of waterfowl (Anatidae) have observed the full spectrum of
 mitochondrial (mt) DNA population divergence, from panmixia to deep,
 reciprocally monophyletic lineages. Yet these studies generally found weak
 or no nuclear (nu) DNA structure which was often attributed to sex-biased
 gene flow (i.e., male dispersal and female philopatry), a common behavior
 within this family. An alternative explanation for this “conflict” is that
 the smaller effective population size and faster sorting rate of mtDNA
 relative to nuDNA leads to different signals of population structure. To
 test these alternatives, we simulated expected nuDNA differentiation based
 on mtDNA patterns of effective population sizes, gene flow, and divergence
 times in a Holarctic pair of waterfowl subspecies, the goosander (Mergus
 merganser merganser) and common merganser (M. m. americanus). We compared
 simulated results to empirical data from 12 nuDNA introns sampled from the
 species’ global range. Between Europe and North America, nuDNA ФST was
 3.4-fold lower than mtDNA ФST, a result consistent with differences in
 sorting rates. However, despite geographically structured and monophyletic
 mtDNA lineages within continents, nuDNA ФST values were generally &lt;
 0 and significantly lower than predicted. This between- and
 within-continent contrast held when comparing mtDNA and nuDNA among
 published studies of ducks. Thus, male-mediated gene flow is a better
 explanation than slower sorting rates for limited nuDNA differentiation
 within continents, which is also supported by non-molecular data. This
 study illustrates the value of quantitatively testing discrepancies
 between mtDNA and nuDNA to reject the null hypothesis that conflict simply
 reflects different sorting rates.
description: Merg.ANXA11.finalFASTA file containing resolved alleles for gene Annexin A11 (ANXA11), intron 5, sampled from Mergus merganser.MERG.CPD.finalFASTA file containing resolved alleles for carboxypeptidase D (CPD) gene, intron 9, sequenced from Mergus merganser.MERG.CRYAB.finalFASTA file containing resolved alleles for alpha-B crystallin (CRYAB) gene, intron 1, sampled from Mergus merganser.Merg.ENO1.finalFASTA file containing resolved alleles for alpha enolase (ENO1) gene, intron 8, sampled from Mergus merganser.MERG.FAST.finalFASTA file containing resolved alleles for S-acyl fatty acid synthase thioesterase (FAST) gene, intron 2, sequenced from Mergus merganser.Merg.FGB.finalFASTA file containing resolved alleles for beta fibrinogen (FGB) gene, intron 7, sequenced from Mergus merganser.Merg.GH1.finalFASTA file containing resolved alleles for growth hormone 1 (GH1) gene, intron 3, sequenced from Mergus merganser.Merg.LDH1.finalFASTA file containing resolved alleles for lactate dehydrogenase B (LDH-B) gene, intron 3, sequenced from Mergus merganser.Merg.MSTN.finalFASTA file containing resolved alleles for myostatin (MSTN) gene, intron 2, sequenced from Mergus merganser.Merg.ODC1.finalFASTA file containing resolved alleles for ornithine decarboxylase (ODC1) gene, intron 5, sequenced from Mergus merganser.Merg.PCK1.finalFASTA file containing resolved alleles for phosphenolpyruvate carboxykinase (PCK1) gene, intron 9, sequenced for Mergus merganser.Merg.SOAT1.finalFASTA file containing resolved alleles for sterol o-acyltransferase 1 (SOAT1) gene, intron 12, sequenced from Mergus merganser.LAMARC-mtDNA.inputInput file for estimating theta and migration rates under a stepping-stone model for mtDNA sampled from six populations of Mergus merganser.COME-6pops-mtDNA2.menuIM-nuDNA.infileInfile for analysis of an isolation-migration model between goosanders (Old World, OW) and common mergansers (New World, NW) using 12 independent nuclear introns.infile.txtSampling detailsTable providing information on sequence IDs, sampling locations, and subspecies of Mergus merganser sequenced for 12 nuclear loci.