DOI: 10.5061/dryad.hp758sn
title: Data from: Inferences of genetic architecture of bill morphology in house sparrow using a high‐density SNP array point to a polygenic basis

description: 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.
description: All phenotypic
 measurements for Helgeland house sparrowsFile 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.txtSingle phenotypic measurements for Helgeland house sparrows adjusted to May 2CYFile 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 &lt; 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 individualsPLINK .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 individualsPLINK .ped file containing genotype information for all Helgeland individuals used in analysis.LundreganEtAl_HelgelandBillData.ped