Data from: Insights into the genetic architecture of morphological traits in two passerine bird species

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.

要理解并预测表型性状的演化动态，需先掌握其潜在遗传结构相关知识。然而，因果位点的数量、效应大小及其在基因组中的位置，目前仍大多未知。本研究利用两份针对家麻雀与领姬鹟的大型数据集的全基因组单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据，探究了多种形态性状的遗传结构，包括跗跖长度、翅长、体质量、喙深、喙长、总饰斑大小与可见饰斑大小以及白色翼斑。研究人员基于SNP计算的亲缘关系，估算了基因组遗传力。正如标记密度所预期的那样，家麻雀的SNP捕获的方差比例（即基于SNP的遗传力）低于领姬鹟——家麻雀的SNP数量为6348个，领姬鹟为38689个。确实，当将数据下采样至相近的SNP密度与样本量后，两个物种间的该估算值不再存在显著差异。染色体分区分析结果显示，部分性状的每条染色体解释的方差比例与染色体大小呈显著正相关；总体而言，较大的染色体比较小的染色体能解释比例更高的变异。最后，本研究发现了两个全基因组显著关联的位点，但其效应量极小：家麻雀20号染色体上的一个SNP与喙长呈显著关联，可解释1.2%的表型变异（VP）；领姬鹟4号染色体上的一个SNP与跗跖长度呈显著关联，可解释3%的表型变异（VP）。尽管本研究无法排除未被检测到的大效应数量性状基因座（Quantitative Trait Locus, QTL）存在的可能性，但研究结果表明，形态性状的遗传基础为多基因调控。