DOI: 10.5061/dryad.nv5v1v59
title: Data from: Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history

description: Inferring aspects of the population histories of species using coalescent
 analyses of non-coding nuclear DNA has grown in popularity. These
 inferences, such as divergence, gene flow, and changes in population size,
 assume that genetic data reflect simple population histories and neutral
 evolutionary processes. However, violating model assumptions can result in
 a poor fit between empirical data and the models. We sampled 22 nuclear
 intron sequences from at least 19 different chromosomes (a genomic
 transect) to test for deviations from selective neutrality in the gadwall
 (Anas strepera), a Holarctic duck. Nucleotide diversity among these loci
 varied by nearly two orders of magnitude (from 0.0004 to 0.029), and this
 heterogeneity could not be explained by differences in substitution rates.
 Using two different coalescent methods to infer models of population
 history and then simulating neutral genetic diversity under these models,
 we found that the among-locus heterogeneity in nucleotide diversity was
 significantly higher than expected for these simple models. Defining more
 complex models of population history demonstrated that a pre-divergence
 bottleneck was also unlikely to explain this heterogeneity. However, both
 selection and interspecific hybridization could account for the
 heterogeneity observed among loci. Regardless of the cause of the
 deviation, our results illustrate that violating key assumptions of
 coalescent models can mislead inferences of population history.
description: Microsatellite locus
 A27E1 allelesContains DNA sequences
 for 100 phased and aligned alleles from the microsatellite locus A27E1
 that were sampled from gadwalls (Anas strepera). The first 50 alleles were
 sampled from Eurasia, and the second set of 50 alleles were sampled from
 North America. The sequences were aligned in
 Sequencher.A27E1.fasIntron 1 of CRYAB geneContains DNA sequences for 100 phased and aligned alleles from intron 1 of the CRYAB gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.CRYAB.fasIntron 8 of Sf3A2 geneContains DNA sequences for 100 phased and aligned alleles from intron 8 of Sf3A2 gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.Sf3A2.fasIntron 5 of ANXA11 geneContains DNA sequences for 100 phased and aligned alleles from intron 5 of the ANXA11 gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.ANXA11.fasIntron 5 of CD4 geneContains DNA sequences for 100 phased and aligned alleles from intron 5 of CD4 gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.CD4.fasIntron 19 of CHD1Z geneContains DNA sequences for 100 phased and aligned alleles from intron 19 of CHD1Z gene (sex-linked; Z-chromosome) sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.CHD1Z.fasIntron 9 of CPD geneContains DNA sequences for 100 phased and aligned alleles from intron 9 of CPD gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.CPD.fasIntron 8 of ENO1 geneContains DNA sequences for 100 phased and aligned alleles from intron 8 of ENO1 gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.ENO1.fasIntron 2 of FAST geneContains DNA sequences for 100 phased and aligned alleles from intron 2 of FAST gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.FAST.fasIntron 7 of FGB geneContains DNA sequences for 100 phased and aligned alleles from intron 7 of FGB gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.FGB.fasIntron 3 of GH1 geneContains DNA sequences for 100 phased and aligned alleles from intron 3 of GH1 gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.GH1.fasIntron 3 of GHRL geneContains DNA sequences for 100 phased and aligned alleles from intron 3 of GHRL gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.GHRL.fasIntron 11 of GRIN1 geneContains DNA sequences for 100 phased and aligned alleles from intron 11 of GRIN1 gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.GRIN1.fasIntron 2 of LCAT geneContains DNA sequences for 100 phased and aligned alleles from intron 2 of LCAT gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.LCAT.fasIntron 2 of LDHB geneContains DNA sequences for 100 phased and aligned alleles from intron 2 of LDHB gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.LDHB.fasIntron 2 of MSTN geneContains DNA sequences for 100 phased and aligned alleles from intron 2 of MSTN gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.MSTN.fasIntron 12 of NCL geneContains DNA sequences for 100 phased and aligned alleles from intron 12 of NCL gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.NCL.fasIntron 5 of ODC1 geneContains DNA sequences for 100 phased and aligned alleles from intron 5 of ODC1 gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.ODC1.fasIntron 9 of PCK1 geneContains DNA sequences for 100 phased and aligned alleles from intron 9 of PCK1 gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.PCK1.fasIntron 2 of SAA geneContains DNA sequences for 100 phased and aligned alleles from intron 2 of SAA gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.SAA.fasIntron 12 of SOAT1 geneContains DNA sequences for 100 phased and aligned alleles from intron 12 of SOAT gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.SOAT1.fasIntron 2 of SOX9 geneContains DNA sequences for 100 phased and aligned alleles from intron 2 of SOX9 gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.SOX9.fasIM input file, 22 loci, 2 populations of gadwallContains the input file used in IM analysis with sequences truncated to meet the assumption of no intralocus recombination. Data were filtered using IMgc to optimally remove base pairs and/or chromosomes (a maximum of 5% of chromosomes, N = 5 copises) for each locus.infile-IMgcFiltered.txtCharacteristics and primers of loci sequencedThis table contains full locus names, locus abbreviations, location of each locus within the chicken and zebra finch genomes, length of the intron, and primer sequences used for amplifying each locus.Locus characteristics.docxInput for *BEAST - 8 taxa, 22 lociInput file for analyses of relative substitution rates in *BEAST. This file contains 8 deeply divergent taxa of Anseriformes sequenced at 22 nuclear introns. The command lines direct *BEAST to use a relaxed lognormal clock and the multispecies coalescent for rate calculations.8taxa-22loci-RelaxClock.xmlms.out.v4.2This contains the R-script used to analyze data simulated using the coalescent program MS. This script contains detailed annotations describing the code. Also see the readme file for more details.