Genetic differences between willow warbler migratory phenotypes are few and cluster in large haplotype blocks.
Genetic differences between willow warbler migratory phenotypes are few and cluster in large haplotype blocks.
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DOI：
10.1002/evl3.15
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发表时间：
2017-08
影响因子：
5
通讯作者：
Bensch S
中科院分区：
文献类型：
--
作者：
Lundberg M;Liedvogel M;Larson K;Sigeman H;Grahn M;Wright A;Åkesson S;Bensch S
众所周知，鸣禽种群之间迁徙行为的差异具有遗传基础，但这些特征背后的实际基因仍然很大程度上未知。为了鉴定此类候选基因，我们从头组装了柳莺Phylloscopus trochilus的基因组，并使用全基因组重测序和SNP阵列将基因组变异与波罗的海周围两个迁徙分界线的迁徙表型联系起来，这两个分界线将西南迁徙的柳莺分开。 trochilus 在西非越冬和 SSE 迁徙 P. t. acredula 在非洲东部和南部越冬。我们发现，除了位于1号、3号和5号染色体上的三个高度分化的区域（分别包含146、135和53个基因）之外，两种迁徙表型的基因组缺乏明显的差异。在每个迁徙表型中，我们发现数千个 SNP 的等位基因频率几乎没有差异，即使在比较斯堪的纳维亚半岛和俄罗斯远东地区（> 6000 公里）的地理相距遥远的种群繁殖时也是如此。在这三个差异化区域中的每一个中，来自 1100 多个个体的 SNP 基因型的基于多维标度的聚类表明存在与每个迁移表型相关的不同单倍型簇。反过来，这表明单倍型之间不存在或很少发生重组，这可以通过反转多态性来解释。虽然 3 号染色体上的 SNP 等位基因与繁殖海拔和纬度相关，但 1 号和 5 号染色体区域内的等位基因分布与迁徙表型的地理分布完全匹配。这些分化区域内差异最大的 10 kb 窗口和错义突变与参与脂肪酸合成的基因相关，可能代表对不同迁移策略的生理适应。这些区域的约 200 个基因（其中一些缺乏所描述的功能）将指导未来的实验和比较研究，以寻找重要迁徙性状背后的基因。
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.
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