Data from: Heteropatric speciation in a duck, Anas crecca

Winker K, McCracken KG, Gibson DD, Peters JL

Date Published: September 13, 2013

DOI: http://dx.doi.org/10.5061/dryad.76d82

 

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Title CHD1Z.nex
Downloaded 6 times
Description NEXUS file containing 175 resolved alleles from intron 19 of the chromo-helicase DNA binding (CHD1Z) gene sampled from 105 Common (Green-winged) Teal (Anas crecca). Populations (OW, Old World; NW, New World; Attu, Aleutian Islands; Shemya, Aleutian Islands; Adak, Aleutian Islands; Ugamak, Aleutian Islands) are defined within the file. Note that CHD1Z is located on the Z-chromosome, and therefore, females only have a single copy.
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Title CRYAB.nex
Downloaded 3 times
Description NEXUS file containing 202 resolved alleles from intron 1 of the alpha-B crystallin (CRYAB) gene sampled from 101 Common (Green-winged) Teal (Anas crecca). Populations (OW, Old World; NW, New World; Attu, Aleutian Islands; Shemya, Aleutian Islands; Adak, Aleutian Islands; Ugamak, Aleutian Islands) are defined within the file.
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Title ENO1.nex
Downloaded 3 times
Description NEXUS file containing 210 resolved alleles from intron 8 of the alpha enolase (ENO1) gene sampled from 105 Common (Green-winged) Teal (Anas crecca). Populations (OW, Old World; NW, New World; Attu, Aleutian Islands; Shemya, Aleutian Islands; Adak, Aleutian Islands; Ugamak, Aleutian Islands) are defined within the file.
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Title FGB.nex
Downloaded 2 times
Description FASTA file containing 210 resolved alleles from intron 7 of the beta fibrinogen (FGB) gene sampled from 105 Common (Green-winged) Teal (Anas crecca). Populations (OW, Old World; NW, New World; Attu, Aleutian Islands; Shemya, Aleutian Islands; Adak, Aleutian Islands; Ugamak, Aleutian Islands) are defined within the file.
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Title GRIN1.nex
Downloaded 3 times
Description FASTA file containing 210 resolved alleles from intron 11 of the N-methyl D-aspartate 1 glutamate receptor (GRIN1) gene sampled from 105 Common (Green-winged) Teal (Anas crecca). Populations (OW, Old World; NW, New World; Attu, Aleutian Islands; Shemya, Aleutian Islands; Adak, Aleutian Islands; Ugamak, Aleutian Islands) are defined within the file.
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Title LDHB.nex
Downloaded 4 times
Description FASTA file containing 210 resolved alleles from intron 3 of the lactate dehydrogenase B (LDHB) gene sampled from 105 Common (Green-winged) Teal (Anas crecca). Populations (OW, Old World; NW, New World; Attu, Aleutian Islands; Shemya, Aleutian Islands; Adak, Aleutian Islands; Ugamak, Aleutian Islands) are defined within the file.
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Title ODC1.nex
Downloaded 1 time
Description FASTA file containing 210 resolved alleles from intron 5 of the ornithine decarboxylase (ODC1) gene sampled from 105 Common (Green-winged) Teal (Anas crecca). Populations (OW, Old World; NW, New World; Attu, Aleutian Islands; Shemya, Aleutian Islands; Adak, Aleutian Islands; Ugamak, Aleutian Islands) are defined within the file.
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Title PCK1.nex
Downloaded 1 time
Description FASTA file containing 210 resolved alleles from intron 8 of the phosphoenolpyruvate carboxykinase (PCK1) gene sampled from 105 Common (Green-winged) Teal (Anas crecca). Populations (OW, Old World; NW, New World; Attu, Aleutian Islands; Shemya, Aleutian Islands; Adak, Aleutian Islands; Ugamak, Aleutian Islands) are defined within the file.
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Title mtDNA control region.nex
Downloaded 11 times
Description FASTA file containing 199 mtDNA control region sequences (987 aligned sites) sampled from Common (Green-winged) Teal (Anas crecca). Populations (OW, Old World; NW, New World; Attu, Aleutian Islands; Shemya, Aleutian Islands; Adak, Aleutian Islands; Ugamak, Aleutian Islands) are defined within the file.
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Title Teal.3pop.8nuDNA.IMa2
Downloaded 7 times
Description Input file for analysis of population history in the program IMa2. The input contains 8 loci sampled from 94 individuals of Anas crecca (25 from North America, population 0; 25 from Eurasia, population 1; 44 from the Aleutian Islands, excluding Shemya, population 2). Note that the data have been filtered for recombination, and therefore, some loci have fewer than the expected number of alleles sampled. The command line for running IM was: -i Teal.3pop.8nuDNA.IMa2.infile -q 25 -m 15 -t 0.75 -b 1000000 -l 12.0 -hfg -hk 50 -hn 50 -ha 0.9 -hb 0.75 -s 7510970185 -p5 -r2 -o outfile.txt
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Title Teal.3pop.mtDNA.IMa2
Downloaded 5 times
Description Input file for analysis of population history from mtDNA control region (987 aligned nucleotides) in the program IM. The input contains 188 individuals of Anas crecca (86 from North America, population 0; 58 from Eurasia, population 1; 44 from the Aleutian Islands, excluding Shemya, population 2). The command line for running IM was: -i Teal.3pop.mtDNA.IMa2.infile -q 150 -m 0.4 -t 20 -b 500000 -l 12.0 -hfg -hk 20 -hn 20 -ha 0.9 -hb 0.85 -s 976267 -p5 -o outfile.txt
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Title CHD1Z.tbs
Downloaded 2 times
Description tbs (to be specified) file defining population-level parameters for simulating neutral genetic diversity in the program MS for CHD1Z in green-winged teal. MS command line: ./ms 210 1000 -t tbs -r tbs tbs -I 3 50 50 110 -n 2 tbs -n 3 tbs -ej tbs 3 2 -en tbs 2 tbs -ej tbs 2 1 -en tbs 1 tbs -m 1 2 tbs -m 1 3 tbs -m 2 1 tbs -m 2 3 tbs -m 3 1 tbs -m 3 2 tbs -em tbs 1 2 tbs -em tbs 2 1 tbs < ALTE-CHD1Z.tbs.ms > ALTE-CHD1Z.ms.out [See the manual for MS for an explanation of the terms; http://home.uchicago.edu/rhudson1/source/mksamples.html]
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Title CRYAB.tbs
Downloaded 1 time
Description tbs (to be specified) file defining population-level parameters for simulating neutral genetic diversity in the program MS for CRYAB in green-winged teal. MS command line: ./ms 210 1000 -t tbs -r tbs tbs -I 3 50 50 110 -n 2 tbs -n 3 tbs -ej tbs 3 2 -en tbs 2 tbs -ej tbs 2 1 -en tbs 1 tbs -m 1 2 tbs -m 1 3 tbs -m 2 1 tbs -m 2 3 tbs -m 3 1 tbs -m 3 2 tbs -em tbs 1 2 tbs -em tbs 2 1 tbs < ALTE-CRYAB.tbs.ms > ALTE-CRYAB.ms.out [See the manual for MS for an explanation of the terms; http://home.uchicago.edu/rhudson1/source/mksamples.html]
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Title FGB.tbs
Downloaded 6 times
Description tbs (to be specified) file defining population-level parameters for simulating neutral genetic diversity in the program MS for FGB in green-winged teal. MS command line: ./ms 210 1000 -t tbs -r tbs tbs -I 3 50 50 110 -n 2 tbs -n 3 tbs -ej tbs 3 2 -en tbs 2 tbs -ej tbs 2 1 -en tbs 1 tbs -m 1 2 tbs -m 1 3 tbs -m 2 1 tbs -m 2 3 tbs -m 3 1 tbs -m 3 2 tbs -em tbs 1 2 tbs -em tbs 2 1 tbs < ALTE-FGB.tbs.ms > ALTE-FGB.ms.out [See the manual for MS for an explanation of the terms; http://home.uchicago.edu/rhudson1/source/mksamples.html]
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Title GRIN1.tbs
Downloaded 3 times
Description tbs (to be specified) file defining population-level parameters for simulating neutral genetic diversity in the program MS for GRIN1 in green-winged teal. MS command line: ./ms 210 1000 -t tbs -r tbs tbs -I 3 50 50 110 -n 2 tbs -n 3 tbs -ej tbs 3 2 -en tbs 2 tbs -ej tbs 2 1 -en tbs 1 tbs -m 1 2 tbs -m 1 3 tbs -m 2 1 tbs -m 2 3 tbs -m 3 1 tbs -m 3 2 tbs -em tbs 1 2 tbs -em tbs 2 1 tbs < ALTE-GRIN1.tbs.ms > ALTE-GRIN1.ms.out [See the manual for MS for an explanation of the terms; http://home.uchicago.edu/rhudson1/source/mksamples.html]
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Title LDHB.tbs
Downloaded 1 time
Description tbs (to be specified) file defining population-level parameters for simulating neutral genetic diversity in the program MS for LDHB in green-winged teal. MS command line: ./ms 210 1000 -t tbs -r tbs tbs -I 3 50 50 110 -n 2 tbs -n 3 tbs -ej tbs 3 2 -en tbs 2 tbs -ej tbs 2 1 -en tbs 1 tbs -m 1 2 tbs -m 1 3 tbs -m 2 1 tbs -m 2 3 tbs -m 3 1 tbs -m 3 2 tbs -em tbs 1 2 tbs -em tbs 2 1 tbs < ALTE-LDHB.tbs.ms > ALTE-LDHB.ms.out [See the manual for MS for an explanation of the terms; http://home.uchicago.edu/rhudson1/source/mksamples.html]
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Title ODC1.tbs
Downloaded 1 time
Description tbs (to be specified) file defining population-level parameters for simulating neutral genetic diversity in the program MS for ODC1 in green-winged teal. MS command line: ./ms 210 1000 -t tbs -r tbs tbs -I 3 50 50 110 -n 2 tbs -n 3 tbs -ej tbs 3 2 -en tbs 2 tbs -ej tbs 2 1 -en tbs 1 tbs -m 1 2 tbs -m 1 3 tbs -m 2 1 tbs -m 2 3 tbs -m 3 1 tbs -m 3 2 tbs -em tbs 1 2 tbs -em tbs 2 1 tbs < ALTE-ODC1.tbs.ms > ALTE-ODC1.ms.out [See the manual for MS for an explanation of the terms; http://home.uchicago.edu/rhudson1/source/mksamples.html]
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Title ENO1.tbs
Downloaded 4 times
Description tbs (to be specified) file defining population-level parameters for simulating neutral genetic diversity in the program MS for ENO1 in green-winged teal. MS command line: ./ms 210 1000 -t tbs -r tbs tbs -I 3 50 50 110 -n 2 tbs -n 3 tbs -ej tbs 3 2 -en tbs 2 tbs -ej tbs 2 1 -en tbs 1 tbs -m 1 2 tbs -m 1 3 tbs -m 2 1 tbs -m 2 3 tbs -m 3 1 tbs -m 3 2 tbs -em tbs 1 2 tbs -em tbs 2 1 tbs < ALTE-ENO1.tbs.ms > ALTE-ENO1.ms.out [See the manual for MS for an explanation of the terms; http://home.uchicago.edu/rhudson1/source/mksamples.html]
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Title PCK1.tbs
Downloaded 3 times
Description tbs (to be specified) file defining population-level parameters for simulating neutral genetic diversity in the program MS for PCK1 in green-winged teal. MS command line: ./ms 210 1000 -t tbs -r tbs tbs -I 3 50 50 110 -n 2 tbs -n 3 tbs -ej tbs 3 2 -en tbs 2 tbs -ej tbs 2 1 -en tbs 1 tbs -m 1 2 tbs -m 1 3 tbs -m 2 1 tbs -m 2 3 tbs -m 3 1 tbs -m 3 2 tbs -em tbs 1 2 tbs -em tbs 2 1 tbs < ALTE-PCK1.tbs.ms > ALTE-PCK1.ms.out [See the manual for MS for an explanation of the terms; http://home.uchicago.edu/rhudson1/source/mksamples.html]
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Title Teal.structure.infile
Downloaded 10 times
Description Input file for the program STRUCTURE containing genotypic data at 8 nuclear loci for 105 individuals of green-winged teal (Anas crecca).
Download Teal.structure.infile (6.173 Kb)
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When using this data, please cite the original publication:

Winker K, McCracken KG, Gibson DD, Peters JL (2013) Heteropatric speciation in a duck, Anas crecca. Molecular Ecology 22(23): 5922–5935. http://dx.doi.org/10.1111/mec.12525

Additionally, please cite the Dryad data package:

Winker K, McCracken KG, Gibson DD, Peters JL (2013) Data from: Heteropatric speciation in a duck, Anas crecca. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.76d82
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