Data from: Genetic differences between willow warbler migratory phenotypes are few and cluster in large haplotype blocks

It is well established that differences in migratory behavior between populations of songbirds have a genetic basis but the actual genes underlying these traits remains largely unknown. In an attempt to identify such candidate genes we de novo assembled the genome of the willow warbler Phylloscopus trochilus, and used whole-genome resequencing and a SNP array to associate genomic variation with migratory phenotypes across two migratory divides around the Baltic Sea that separate SW migrating P. t. trochilus wintering in western Africa and SSE migrating P. t. acredula wintering in eastern and southern Africa. We found that the genomes of the two migratory phenotypes lack clear differences except for three highly differentiated regions located on chromosomes 1, 3, and 5 (containing 146, 135, and 53 genes, respectively). Within each migratory phenotype we found virtually no differences in allele frequencies for thousands of SNPs, even when comparing geographically distant populations breeding in Scandinavia and Far East Russia (>6000 km). In each of the three differentiated regions, multidimensional scaling-based clustering of SNP genotypes from more than 1100 individuals demonstrates the presence of distinct haplotype clusters that are associated with each migratory phenotype. In turn, this suggests that recombination is absent or rare between haplotypes, which could be explained by inversion polymorphisms. Whereas SNP alleles on chromosome 3 correlate with breeding altitude and latitude, the allele distribution within the regions on chromosomes 1 and 5 perfectly matches the geographical distribution of the migratory phenotypes. The most differentiated 10 kb windows and missense mutations within these differentiated regions are associated with genes involved in fatty acid synthesis, possibly representing physiological adaptations to the different migratory strategies. The ∼200 genes in these regions, of which several lack described function, will direct future experimental and comparative studies in the search for genes that underlie important migratory traits.现已明确，鸣禽不同种群间的迁徙行为差异具有遗传基础，但支撑这些性状的具体基因在很大程度上仍未被探明。为鉴定此类候选基因，我们对柳莺（willow warbler，Phylloscopus trochilus）的基因组进行了从头组装（de novo assembly），并利用全基因组重测序与单核苷酸多态性（SNP）芯片，对波罗的海周边两条迁徙分界区的基因组变异与迁徙表型开展关联分析——这两条分界区分隔了迁徙方向为西南、越冬于西非的P. t. trochilus亚种，与迁徙方向为南东南、越冬于非洲东部与南部的P. t. acredula亚种。研究发现，两种迁徙表型的基因组除三处高度分化的区域外，其余区域无清晰差异；这三处区域分别位于1号、3号和5号染色体上，各自包含146、135和53个基因。在每种迁徙表型内部，我们对数千个SNP位点的等位基因频率进行比较，即便对比了繁殖地横跨斯堪的纳维亚与俄罗斯远东地区（直线距离超6000公里）的种群，也几乎未发现差异。在这三处高度分化的区域中，基于超过1100个个体的SNP基因型进行的多维标度聚类分析显示，存在与两种迁徙表型分别对应的不同单倍型簇。这一结果提示，不同单倍型之间几乎不存在重组或重组率极低，该现象可由倒位多态性（inversion polymorphism）予以解释。3号染色体上的SNP等位基因与繁殖海拔及纬度相关，而1号与5号染色体上的区域内等位基因分布，则与迁徙表型的地理分布完全吻合。这些分化区域中，分化程度最高的10kb窗口区域与错义突变（missense mutation），均与参与脂肪酸合成的基因相关，这可能代表了对不同迁徙策略的生理适应性。上述区域中约有200个基因，其中部分基因尚未明确功能，这些基因将为未来探索支撑重要迁徙性状的基因提供实验与比较研究的方向。