Data from: Unexpected ancestry of Populus seedlings from a hybrid zone implies a large role for postzygotic selection in the maintenance of species

Lindtke D, Gompert Z, Lexer C, Buerkle CA

Date Published: April 14, 2014

DOI: http://dx.doi.org/10.5061/dryad.kh7sc

 

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Title Sample IDs
Downloaded 20 times
Description Individual IDs for 621 samples; columns give individual number; species (P. alba (AL), hybrid (HY), P. tremula (TR), or family sample (FA)); mom or progeny (MO, PR, NA); family ID; individual ID.
Download IDs.txt (12.57 Kb)
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Title Genotype likelihoods, 32 912 SNPs
Downloaded 10 times
Description Genotype likelihoods in vcf file format for the full data set including all 621 individuals.
Download variants.vcf (336.9 Mb)
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Title Genotype likelihoods, 64 649 SNPs
Downloaded 5 times
Description Genotype likelihoods in vcf file format for the reduced data set without seedlings, 137 individuals.
Download variants_ref.vcf (155.7 Mb)
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Title Input file, 11 979 SNPs
Downloaded 12 times
Description Formatted input file to run ancestry model.
Download input_maf05anc.txt (61.40 Mb)
Download README.txt (651 bytes)
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Title Input file, 5 226 SNPs
Downloaded 13 times
Description Formatted input file to run ancestry model.
Download input_maf05ancred.txt (26.75 Mb)
Download README.txt (651 bytes)
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Title Additional input file, 11 979 SNPs
Downloaded 6 times
Description Initial q values to run ancestry model.
Download ldak2_pcg_maf05.txt (4.937 Kb)
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Title Additional input file, 5 226 SNPs
Downloaded 4 times
Description Initial q values to run ancestry model.
Download ldak2_pcg_maf05red.txt (5.414 Kb)
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Title C source code, main file
Downloaded 24 times
Description C source code for genetic ancestry model.
Download main.C (5.872 Kb)
Download README.txt (591 bytes)
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Title C source code, functions
Downloaded 14 times
Description C source code for genetic ancestry model.
Download func.C (50.59 Kb)
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Title C source code, header
Downloaded 12 times
Description C source code for genetic ancestry model.
Download populusancestry.h (6.439 Kb)
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Title R simulation code, main file
Downloaded 20 times
Download simulations.R (9.227 Kb)
Download README.txt (1.53 Kb)
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Title R simulation code, functions
Downloaded 16 times
Download simulations_func.R (6.928 Kb)
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Title R simulation code, parameters
Downloaded 6 times
Download params.txt (114 bytes)
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Title R simulation code, additional script 1
Downloaded 9 times
Description Additional Perl script to obtain point estimates for genotype likelihoods.
Download gl2genestsims.pl (951 bytes)
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Title R simulation code, additional script 2
Downloaded 5 times
Description R script to obtain starting values for q to run ancestry model.
Download initqsims.R (596 bytes)
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When using this data, please cite the original publication:

Lindtke D, Gompert Z, Lexer C, Buerkle CA (2014) Unexpected ancestry of Populus seedlings from a hybrid zone implies a large role for postzygotic selection in the maintenance of species. Molecular Ecology 23(17): 4316-4330. http://dx.doi.org/10.1111/mec.12759

Additionally, please cite the Dryad data package:

Lindtke D, Gompert Z, Lexer C, Buerkle CA (2014) Data from: Unexpected ancestry of Populus seedlings from a hybrid zone implies a large role for postzygotic selection in the maintenance of species. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.kh7sc
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