Data from: Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations

Santure AW, Poissant J, De Cauwer I, van Oers K, Robinson MR, Quinn JL, Groenen MAM, Visser ME, Sheldon BC, Slate J

Date Published: November 4, 2015

DOI: http://dx.doi.org/10.5061/dryad.5t32v

 

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Title data_readme
Downloaded 40 times
Description A readme file explaining the information loaded to Dryad
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Title NL map file
Downloaded 10 times
Description plink-style map file with marker locations for the NL dataset.The map file is in an amended plink format with chromosome in column 1, SNP name in column 2, cM position in column 3 (note this is different from defaul plink map files which have distances in Morgans) and genome order in column 4 (again this is different from the plink format which would usually have bp position in this column). Chromosome codings in the map file (column 1) are as follows: Chromosomes 1-15 and 17-28 are the corresponding chromosomes 1-15 and 17-28 in the great tit genome Chromosome 29 = chromosome 1A Chromosome 30 = chromosome 4A Chromosome 31 = Z chromosome Chromosome 32 = Linkage group LGE22
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Title NL genotype file
Downloaded 9 times
Description Genotypes for the 1,407 NL individuals. These are standard plink files (see http://pngu.mgh.harvard.edu/~purcell/plink/) where the first column gives a family id, the second column an individual id (in this case family id = individual id), the third and fourth columns are paternal and maternal IDs (here, left blank so that ids = 0 for both parents), column five has sex (1=male; 2=female; other=unknown) and finally column 6 phenotype (here all phenotypes = -9 for unknown). Columns 7 onwards contain genotype information for the SNPs listed (in order) in the .map file of the same name.
Download NL_numeric_ids.ped (31.44 Mb)
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Title NL QTL mapping pedigree
Downloaded 13 times
Description Not all genotyped individuals could be linked into a pedigree suitable for QTL mapping, therefore these files contain only related genotyped individuals and their shared (sometimes ungenotyped) relatives. There are two sets of columns, the first column shows the QTL mapping numeric IDs (used only for QTL mapping) while the second column shows the numeric ids that relate to the genotype and trait data.
Download NL_QTL_mapping_pedigree.txt (22.92 Kb)
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Title NL traits
Downloaded 26 times
Description Separate sheets in these excel files contain trait information for the phenotyped and genotyped animals, along with important fixed and random effects fitted in the mixed models. See Supporting Information 1 for more information.
Download NL_traits.xlsx (543.7 Kb)
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Title UK map file
Downloaded 7 times
Description plink-style map file with marker locations for the UK dataset.The map file is in an amended plink format with chromosome in column 1, SNP name in column 2, cM position in column 3 (note this is different from defaul plink map files which have distances in Morgans) and genome order in column 4 (again this is different from the plink format which would usually have bp position in this column). Chromosome codings in the map file (column 1) are as follows: Chromosomes 1-15 and 17-28 are the corresponding chromosomes 1-15 and 17-28 in the great tit genome Chromosome 29 = chromosome 1A Chromosome 30 = chromosome 4A Chromosome 31 = Z chromosome Chromosome 32 = Linkage group LGE22
Download UK_numeric_ids.map (117.4 Kb)
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Title UK genotype file
Downloaded 14 times
Description Genotypes for the 2,497 UK individuals. These are standard plink files (see http://pngu.mgh.harvard.edu/~purcell/plink/) where the first column gives a family id, the second column an individual id (in this case family id = individual id), the third and fourth columns are paternal and maternal IDs (here, left blank so that ids = 0 for both parents), column five has sex (1=male; 2=female; other=unknown) and finally column 6 phenotype (here all phenotypes = -9 for unknown). Columns 7 onwards contain genotype information for the SNPs listed (in order) in the .map file of the same name.
Download UK_numeric_ids.ped (55.90 Mb)
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Title UK QTL mapping pedigree
Downloaded 15 times
Description Not all genotyped individuals could be linked into a pedigree suitable for QTL mapping, therefore these files contain only related genotyped individuals and their shared (sometimes ungenotyped) relatives. There are two sets of columns, the first column shows the QTL mapping numeric IDs (used only for QTL mapping) while the second column shows the numeric ids that relate to the genotype and trait data.
Download UK_QTL_mapping_pedigree.txt (63.54 Kb)
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Title UK traits
Downloaded 24 times
Description Separate sheets in these excel files contain trait information for the phenotyped and genotyped animals, along with important fixed and random effects fitted in the mixed models. See Supporting Information 1 for more information.
Download UK_traits.xlsx (711.7 Kb)
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Title framework without LD linkage map
Downloaded 9 times
Description This contains the cM positions for the framework linkage map. The "without LD" refers to the removal of a few markers from the original framework map that appeared to cause convergence issues during QTL mapping due to high levels of LD with neighbouring markers
Download framework_without_LD_map.txt (24.67 Kb)
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Title GWAS results
Downloaded 20 times
Description This folder contains the GWAS results for the UK and NL traits, as estimated using the mmscore function in GenABEL
Download GWAS_results.zip (4.112 Mb)
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When using this data, please cite the original publication:

Santure AW, Poissant J, De Cauwer I, van Oers K, Robinson MR, Quinn JL, Groenen MAM, Visser ME, Sheldon BC, Slate J (2015) Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology, 24(24): 6148–6162. 10.1111/mec.13452

Additionally, please cite the Dryad data package:

Santure AW, Poissant J, De Cauwer I, van Oers K, Robinson MR, Quinn JL, Groenen MAM, Visser ME, Sheldon BC, Slate J (2015) Data from: Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.5t32v
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