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，需掌握其潜在遗传结构相关知识。然而，目前其因果位点的数量、效应大小以及在基因组中的定位仍未得到充分解析。本研究采用针对家麻雀与领姬鹟的两个大型数据集的全基因组单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据，对多项形态性状的遗传结构展开探究，涵盖跗跖长度、翅长、体重、喙深、喙长、羽饰总面积与可见羽饰面积以及白色翼斑。研究通过基于SNP计算的亲缘关系估算基因组遗传力（genomic heritability）。结果显示，家麻雀中由SNP捕获的方差比例（即基于SNP的遗传力）低于领姬鹟，这与标记密度差异的预期相符：家麻雀的SNP标记数为6348个，而领姬鹟为38689个。事实上，当将数据下采样至相近的SNP密度与样本量后，两物种间的该估计值不再存在显著差异。染色体分区分析结果表明，针对部分性状而言，每条染色体解释的方差比例与其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更多比例的表型变异。最后，本研究发现2个全基因组水平显著的关联位点，但其效应量极小：家麻雀中20号染色体上的1个SNP与喙长显著相关，可解释1.2%的表型变异（VP）；领姬鹟中4号染色体上的1个SNP与跗跖长度显著相关，可解释3%的表型变异（VP）。尽管我们无法排除存在未被检测到的大效应数量性状位点（Quantitative Trait Locus, QTL）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。