Understanding the genetic architecture of quantitative traits can provide insights into the mechanisms driving phenotypic evolution. Bill morphology is an ecologically important and phenotypically variable trait, which is highly heritable and closely linked to individual fitness. Thus, bill morphology traits are suitable candidates for gene mapping analyses. Previous studies have revealed several genes that may influence bill morphology, but the similarity of gene and allele effects between species and populations is unknown. Here, we develop a custom 200K SNP array and use it to examine the genetic basis of bill morphology in 1857 house sparrow individuals from a large-scale, island metapopulation off the coast of Northern Norway. We found high genomic heritabilities for bill depth and length, which were comparable with previous pedigree estimates. Candidate gene and genome wide association analyses yielded six significant loci, four of which have previously been associated with craniofacial development. Three of these loci are involved in bone morphogenic protein (BMP) signalling, suggesting a role for BMP genes in regulating bill morphology. However, these loci individually explain a small amount of variance. In combination with results from genome partitioning analyses this indicates that bill morphology is a polygenic trait. Any studies of eco-evolutionary processes in bill morphology are therefore dependent on methods that can accommodate polygenic inheritance of the phenotype and molecular-scale evolution of genetic architecture.
All phenotypic measurements for Helgeland house sparrows
File containing all phenotypic measurements for Helgeland individuals used in main analysis (metapopulation location 66°30’N, 12°30’E). Measurements were taken from all adult birds recorded between 1998-2013. id is individual id as determined by ring number. Sex is the genetic sex. Hatch island is the island the bird was first recorded on. Hatch year is the first year recorded if a bird was measured as a nestling, or the year prior to first year recorded if first measured as an adult. Year and month refer to the date the phenotypic measurement was taken. Age is the age of the bird when the measurement was taken. Island is the same as hatch island if hatch island is one of the 8 SNP-typed islands, else the island is that on which the blood sample for SNP typing was taken.
LundreganEtAl_PhenosAll.txt
Single phenotypic measurements for Helgeland house sparrows adjusted to May 2CY
File containing single phenotypic measurements for Helgeland individuals used in main analysis (metapopulation location 66°30’N, 12°30’E). Measurements were taken from all adult birds recorded between 1998-2013. To give a single value for each individual, measurements of adult birds (second calendar year (2CY) and older) were adjusted to May in 2CY using a linear mixed effects model with age, age2 and month as fixed factors, random intercepts for year, cohort and ID number, and a random slope for the effect of age within ID number to account for any between-individual variation. If age and month effects were significant (P < 0.05) in likelihood ratio tests, predicted values from the model were used to adjust measurements to May in 2CY before calculation of mean phenotypic values. ID is individual id determined by ring number. Sex is the genetic sex. Hatchyear is the first year recorded for birds measured as nestlings or fledged juveniles, or the year prior to first year recorded for birds ringed as adults. Hatch island is the island the bird was first recorded on. Island is hatch island if hatch island was one of the 8 SNP typed islands, else it is the island on which the blood sample for SNP typing was taken.
LundreganEtAl_PhenosAge1.txt
.map file for Helgeland individuals
PLINK .map file containing marker information for Helgeland individuals. File contains information on chromosome, marker id, and bp position within chromosome.
LundreganEtAl_HelgelandBillData.map
.ped file for Helgeland individuals
PLINK .ped file containing genotype information for all Helgeland individuals used in analysis.
LundreganEtAl_HelgelandBillData.ped