Data from: Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact

Le Moan A, Gagnaire P-A, Bonhomme F

Date Published: March 29, 2016

DOI: http://dx.doi.org/10.5061/dryad.h7vb0

 

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Title LeMoan_Atlantic_anchovy_working_dataset_MAC1_1SNPperRAD
Downloaded 12 times
Description The Atlantic subdataset containing 5260 SNPs typed 41 non-admixed individuals that were classified either as pure marine (30 PM) or pure coastal (11 PC) ecotypes using a 95% assignment probability threshold in NewHybrids. The minor allele count (MAC) threshold is 1 and only one SNP per RAD was kept.
Download ATL_mac_1.vcf (4.027 Mb)
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Title LeMoan_Mediterranean_anchovy_working_dataset_MAC1_1SNPperRAD
Downloaded 4 times
Description The Mediterranean subdataset containing 6554 SNPs typed in 48 non-admixed individuals that were classified either as pure marine (17 PM) or pure coastal (31 PC) ecotypes using a 95% assignment probability threshold in NewHybrids. The minor allele count (MAC) threshold is 1 and only one SNP per RAD was kept.
Download MED_mac_1.vcf (5.698 Mb)
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Title LeMoan_4_pops_no_hybrid_anchovy_working_dataset_MAC1_1SNPperRAD
Downloaded 2 times
Description The 4 populations dataset containing 3056 SNPs typed in 89 non-admixed individuals that were classified either as pure marine or pure coastal ecotypes using a 95% assignment probability threshold in NewHybrids. The minor allele count (MAC) threshold is 1 and only one SNP per RAD was kept.
Download 4pop_no_hybrid_mac_1.vcf (4.901 Mb)
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Title LeMoan_4_pops_all_samples_anchovy_working_dataset_MAC2_1SNPperRAD
Downloaded 2 times
Description The global SNP dataset used in NewHybrids analysis and in the PCA analysis containing hybrids (Figure 1A). The VCF file contains 5638 SNPs typed in 128 individuals. The minor allele count (MAC) threshold is 2 and only one SNP per RAD was kept.
Download 4pop_all_samples_mac_2.vcf (12.83 Mb)
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Title LeMoan_Atlantic_anchovy_JAFS
Downloaded 8 times
Description The JAFS dadi input file for the Atlantic ecotype pair.
Download ATL.fs (5.478 Kb)
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Title LeMoan_Mediterranean_anchovy_JAFS
Downloaded 4 times
Description The JAFS dadi input file for the Mediterranean ecotype pair.
Download MED.fs (5.475 Kb)
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When using this data, please cite the original publication:

Le Moan A, Gagnaire P-A, Bonhomme F (2016) Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact. Molecular Ecology 25(13): 3187-3202. http://dx.doi.org/10.1111/mec.13627

Additionally, please cite the Dryad data package:

Le Moan A, Gagnaire P-A, Bonhomme F (2016) Data from: Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.h7vb0
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