DOI: 10.5061/dryad.76d82
title: Data from: Heteropatric speciation in a duck, Anas crecca

description: Heteropatric differentiation is a mode of speciation with gene flow in
 which divergence occurs between lineages that are in sympatry and
 allopatry at different times during cyclic spatial movements. Empirical
 evidence suggests that heteropatric differentiation may prove to be common
 among seasonally migratory organisms. We examined genetic differentiation
 between the sedentary Aleutian Islands population of green-winged teal
 (Anas crecca nimia) and its close migratory relative, the Eurasian, or Old
 World (OW), Anas c. crecca population, a portion of which passes through
 the range of nimia during its seasonal migrations. We also examined its
 relationship with the parapatric North American, New World (NW), A. c.
 carolinensis population. Sequence data from eight nuclear introns and the
 mtDNA control region showed that the nimia-crecca divergence occurred much
 more recently than the deeper crecca-carolinensis split (~83,000 y vs.
 ~1.1 My). Despite considerable spatial overlap between crecca and nimia
 during seasonal migration, three key predictions of heteropatric
 differentiation are supported: significant genetic divergence (overall
 mean Φst = 0.07), low gene flow (2Nem ~1.8), and an effective population
 size in nimia that is not especially low (Ne ~ 80,000 individuals).
 Similar levels of gene flow have come into nimia from carolinensis, but no
 detectable nuclear gene flow has gone out of nimia into either OW (crecca)
 or NW (carolinensis) populations. We infer that adaptations of these
 populations to local optima in different places (e.g., each matching their
 reproductive effort to different resource blooms) promote genetic
 isolation and divergence despite periods of sympatry between them, as the
 heteropatric model predicts.
description: CHD1Z.nexNEXUS 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.ALTE-CHD1Z.nexCRYAB.nexNEXUS 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.ALTE-CRYAB.nexENO1.nexNEXUS 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.ALTE-ENO1.nexFGB.nexFASTA 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.ALTE-FGB.nexGRIN1.nexFASTA 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.ALTE-GRIN1.nexLDHB.nexFASTA 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.ALTE-LDHB.nexODC1.nexFASTA 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.ALTE-ODC1.nexPCK1.nexFASTA 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.ALTE-PCK1.nexmtDNA control region.nexFASTA 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.ALTE-mtDNA.nexTeal.3pop.8nuDNA.IMa2Input 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.txtTeal.3pop.mtDNA.IMa2Input 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.txtCHD1Z.tbstbs (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 &lt; ALTE-CHD1Z.tbs.ms &gt; ALTE-CHD1Z.ms.out [See the manual for MS for an explanation of the terms; http://home.uchicago.edu/rhudson1/source/mksamples.html]ALTE-CHD1Z.tbs.msCRYAB.tbstbs (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 &lt; ALTE-CRYAB.tbs.ms &gt; ALTE-CRYAB.ms.out [See the manual for MS for an explanation of the terms; http://home.uchicago.edu/rhudson1/source/mksamples.html]ALTE-CRYAB.tbs.msFGB.tbstbs (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 &lt; ALTE-FGB.tbs.ms &gt; ALTE-FGB.ms.out [See the manual for MS for an explanation of the terms; http://home.uchicago.edu/rhudson1/source/mksamples.html]ALTE-FGB.tbs.msGRIN1.tbstbs (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 &lt; ALTE-GRIN1.tbs.ms &gt; ALTE-GRIN1.ms.out [See the manual for MS for an explanation of the terms; http://home.uchicago.edu/rhudson1/source/mksamples.html]ALTE-GRIN1.tbs.msLDHB.tbstbs (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 &lt; ALTE-LDHB.tbs.ms &gt; ALTE-LDHB.ms.out [See the manual for MS for an explanation of the terms; http://home.uchicago.edu/rhudson1/source/mksamples.html]ALTE-LDHB.tbs.msODC1.tbstbs (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 &lt; ALTE-ODC1.tbs.ms &gt; ALTE-ODC1.ms.out [See the manual for MS for an explanation of the terms; http://home.uchicago.edu/rhudson1/source/mksamples.html]ALTE-ODC1.tbs.msENO1.tbstbs (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 &lt; ALTE-ENO1.tbs.ms &gt; ALTE-ENO1.ms.out [See the manual for MS for an explanation of the terms; http://home.uchicago.edu/rhudson1/source/mksamples.html]ALTE-ENO1.tbs.msPCK1.tbstbs (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 &lt; ALTE-PCK1.tbs.ms &gt; ALTE-PCK1.ms.out [See the manual for MS for an explanation of the terms; http://home.uchicago.edu/rhudson1/source/mksamples.html]ALTE-PCK1.tbs.msTeal.structure.infileInput file for the program STRUCTURE containing genotypic data at 8 nuclear loci for 105 individuals of green-winged teal (Anas crecca).