DOI: 10.5061/dryad.5t32v
title: Data from: Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations

description: Currently there is much debate on the genetic architecture of quantitative
 traits in wild populations. Is trait variation influenced by many genes of
 small effect or by a few genes of major effect? Where is additive genetic
 variation located in the genome? Do the same loci cause similar phenotypic
 variation in different populations? Great tits (Parus major) have been
 studied extensively in long-term studies across Europe, and consequently
 are considered an ecological 'model organism'. Recently, genomic
 resources have been developed for the great tit, including a custom SNP
 chip and genetic linkage map. In this study, we used a suite of approaches
 to investigate the genetic architecture of eight quantitative traits in
 two long-term study populations of great tit - one in the Netherlands, and
 the other in the United Kingdom. Overall, we found little evidence for the
 presence of genes of large effects in either population. Instead, traits
 appeared to be influenced by many genes of small effect, with conservative
 estimates of the number of contributing loci ranging from 31 to 310.
 Despite concordance between population-specific heritabilities, we found
 no evidence for the presence of loci having similar effects in both
 populations. While population-specific genetic architectures are possible,
 an undetected shared architecture cannot be rejected because of limited
 power to map loci of small and moderate effects. This study is one of few
 examples of genetic architecture analysis in replicated wild populations,
 and highlights some of the challenges and limitations researchers will
 face when attempting similar molecular quantitative genetic studies in
 free-living populations.
description: data_readmeA readme file explaining the information loaded to DryadNL map fileplink-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 LGE22NL_numeric_ids.mapNL genotype fileGenotypes 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.NL_numeric_ids.pedNL QTL mapping pedigreeNot 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.NL_QTL_mapping_pedigree.txtNL traitsSeparate 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.NL_traits.xlsxUK map fileplink-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 LGE22UK_numeric_ids.mapUK genotype fileGenotypes 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.UK_numeric_ids.pedUK QTL mapping pedigreeNot 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.UK_QTL_mapping_pedigree.txtUK traitsSeparate 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.UK_traits.xlsxframework without LD linkage mapThis 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 markersframework_without_LD_map.txtGWAS resultsThis folder contains the GWAS results for the UK and NL traits, as estimated using the mmscore function in GenABELGWAS_results.zip