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.
data_readme
A readme file explaining the information loaded to Dryad
NL map file
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
NL_numeric_ids.map
NL genotype file
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.
NL_numeric_ids.ped
NL QTL mapping pedigree
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.
NL_QTL_mapping_pedigree.txt
NL traits
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.
NL_traits.xlsx
UK map file
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
UK_numeric_ids.map
UK genotype file
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.
UK_numeric_ids.ped
UK QTL mapping pedigree
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.
UK_QTL_mapping_pedigree.txt
UK traits
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.
UK_traits.xlsx
framework without LD linkage map
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
framework_without_LD_map.txt
GWAS results
This folder contains the GWAS results for the UK and NL traits, as estimated using the mmscore function in GenABEL
GWAS_results.zip