DOI: 10.5061/dryad.786m4
title: Data from: Insights into the genetic architecture of morphological traits in two passerine bird species

description: Knowledge about the underlying genetic architecture of phenotypic traits
 is needed to understand and predict their evolutionary dynamics. The
 number of causal loci, magnitude of their effects and location in the
 genome is however still largely unknown. Here we use genome-wide SNP data
 from two large-scale datasets on house sparrows and collared flycatchers
 to examine the genetic architecture of different morphological traits
 (tarsus length, wing length, body mass, bill depth, bill length, total and
 visible badge size and white wing patches). Genomic heritabilities were
 estimated using relatedness calculated from SNPs. The proportion of
 variance captured by the SNPs (SNP-based heritability) was lower in house
 sparrows compared to collared flycatchers, as expected given marker
 density (6,348 SNPs in house sparrows versus 38,689 SNPs in collared
 flycatchers). Indeed, after down-sampling to similar SNP density and
 sample size this estimate was no longer markedly different between
 species. Chromosome partitioning analyses demonstrated that the proportion
 of variance explained by each chromosome was significantly positively
 related to the chromosome size for some traits, and, generally, that
 larger chromosomes tended to explain proportionally more variation than
 smaller chromosomes. Finally, we found two genome-wide significant
 associations with very small effect sizes. One SNP on chromosome 20 was
 associated with bill length in house sparrows and explained 1.2% of
 phenotypic variation (VP) and one SNP on chromosome 4 was associated with
 tarsus length in collared flycatchers (3% of VP). Although we cannot
 exclude the possibility of undetected large-effect QTL, our results
 indicate a polygenic basis for morphological traits.
description: collareds_morphofile containing information about the position of the markers (.map file) for flycatcherscollareds_morphofiles contain the genotype data (.ped file) for flycatchersmeanphenos_flycatchersPhenotype mean values for flycatchersRepeatABEL_sesR script for RepeatABEL analyses (repeated phenotype values) for flycatchersrepeatedmeasuresphenotypes_flycatchersPhenotype values (repeated values) for flycatchersFlycatchers GCTA scriptscript for GCTA analyses of FlycatchersSilva et al. Flycatcher GCTA codeFlycatcher GenABEL-RepeatABEL codeR script for GenABEL and RepeatABEL analyses of flycatchersSilva et al. Flycatcher GenABEL-RepeatABEL code.RGCTA script SparrowsCommand line script for GCTA analyses (heritability estimates and chromosome partitioning analyses) for sparrowsGWAS RepeatAbel_SparrowsR script for RepeatABEL analyses (repeated phenotype values) for sparrowsh2SE_GenABELR script for estimating Standard Errors of heritability values from genABELmap_Sparrowsfile containing information about the position of the markers (.map file) for sparrowsped_Sparrows.pedfiles contain the genotype data (.ped) for sparrowspheno_mean_SparrowsPhenotype mean values for sparrowspheno_rep_SparrowsPhenotype values (repeated values) for sparrowsQC and GWAS mean_SparrowsR script for quality control and GenABEL analyses (mean phenotype values) for sparrows