Data from: Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history

 

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Title Microsatellite locus A27E1 alleles
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Description Contains 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.
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Title Intron 1 of CRYAB gene
Downloaded 22 times
Description Contains 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.
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Title Intron 8 of Sf3A2 gene
Downloaded 21 times
Description Contains 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.
Download Sf3A2.fas (32.66 Kb)
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Title Intron 5 of ANXA11 gene
Downloaded 25 times
Description Contains 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.
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Title Intron 5 of CD4 gene
Downloaded 22 times
Description Contains 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.
Download CD4.fas (46.16 Kb)
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Title Intron 19 of CHD1Z gene
Downloaded 26 times
Description Contains 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.
Download CHD1Z.fas (28.96 Kb)
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Title Intron 9 of CPD gene
Downloaded 23 times
Description Contains 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.
Download CPD.fas (34.96 Kb)
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Title Intron 8 of ENO1 gene
Downloaded 24 times
Description Contains 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.
Download ENO1.fas (19.06 Kb)
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Title Intron 2 of FAST gene
Downloaded 20 times
Description Contains 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.
Download FAST.fas (34.06 Kb)
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Title Intron 7 of FGB gene
Downloaded 22 times
Description Contains 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.
Download FGB.fas (45.86 Kb)
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Title Intron 3 of GH1 gene
Downloaded 27 times
Description Contains 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.
Download GH1.fas (38.66 Kb)
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Title Intron 3 of GHRL gene
Downloaded 27 times
Description Contains 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.
Download GHRL.fas (37.07 Kb)
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Title Intron 11 of GRIN1 gene
Downloaded 22 times
Description Contains 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.
Download GRIN1.fas (30.96 Kb)
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Title Intron 2 of LCAT gene
Downloaded 24 times
Description Contains 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.
Download LCAT.fas (36.06 Kb)
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Title Intron 2 of LDHB gene
Downloaded 22 times
Description Contains 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.
Download LDHB.fas (48.58 Kb)
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Title Intron 2 of MSTN gene
Downloaded 23 times
Description Contains 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.
Download MSTN.fas (31.06 Kb)
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Title Intron 12 of NCL gene
Downloaded 24 times
Description Contains 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.
Download NCL.fas (36.26 Kb)
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Title Intron 5 of ODC1 gene
Downloaded 22 times
Description Contains 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.
Download ODC1.fas (31.50 Kb)
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Title Intron 9 of PCK1 gene
Downloaded 19 times
Description Contains 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.
Download PCK1.fas (34.66 Kb)
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Title Intron 2 of SAA gene
Downloaded 26 times
Description Contains 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.
Download SAA.fas (37.26 Kb)
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Title Intron 12 of SOAT1 gene
Downloaded 18 times
Description Contains 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.
Download SOAT1.fas (37.36 Kb)
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Title Intron 2 of SOX9 gene
Downloaded 20 times
Description Contains 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.
Download SOX9.fas (40.76 Kb)
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Title IM input file, 22 loci, 2 populations of gadwall
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Description Contains 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.
Download infile-IMgcFiltered.txt (597.2 Kb)
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Title Characteristics and primers of loci sequenced
Downloaded 53 times
Description This 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.
Download Locus characteristics.docx (20.17 Kb)
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Title Input for *BEAST - 8 taxa, 22 loci
Downloaded 28 times
Description Input 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.
Download 8taxa-22loci-RelaxClock.xml (226.2 Kb)
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Title ms.out.v4.2
Downloaded 112 times
Description This 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.
Download ms.out.v4.2.R (29.47 Kb)
Download README.txt (3.344 Kb)
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When using this data, please cite the original publication:

Peters JL, Robert TE, Winker K, McCracken KG (2012) Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history. PLoS ONE 7(2): e31972. http://dx.doi.org/10.1371/journal.pone.0031972

Additionally, please cite the Dryad data package:

Peters JL, Robert TE, Winker K, McCracken KG (2012) Data from: Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.nv5v1v59
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