Data from: Genomic islands of divergence linked to ecotypic variation in sockeye salmon

Regions of the genome displaying elevated differentiation (genomic islands of divergence) are thought to play an important role in local adaptation, especially in populations experiencing high gene flow. However, the characteristics of these islands as well as the functional significance of genes located within them remain largely unknown. Here, we used data from thousands of SNPs aligned to a linkage map to investigate genomic islands of divergence in three ecotypes of sockeye salmon (Oncorhynchus nerka) from a single drainage in southwestern Alaska. We found ten islands displaying high differentiation among ecotypes, contrasting neutral structure throughout the rest of the genome which was low and not partitioned by ecotype. One island on linkage group 13 was particularly large and contained six SNPs with FST > 0.14 (average FST of neutral SNPs = 0.01). Functional annotation revealed that the peak of this island contained a non-synonymous mutation in a gene involved in growth in other species (TULP4). The islands that we discovered were relatively small (80 - 402 Kb), loci found in islands did not show reduced levels of diversity, and loci in islands displayed slightly elevated linkage disequilibrium. These attributes suggest that the islands discovered here were likely generated by divergence hitchhiking, however, we cannot rule out the possibility that other mechanisms may have produced them. Our results suggest that islands of divergence serve an important role in local adaptation with gene flow and represent a significant advance towards understanding the genetic basis of ecotypic differentiation.

基因组中呈现分化水平升高的区域（分化基因组岛，genomic islands of divergence）被认为在局部适应中发挥关键作用，尤其对于经历高基因流的种群而言。然而，此类基因组岛的特征及其内部所包含基因的功能意义，目前尚未得到充分解析。本研究借助比对至连锁图谱的数千个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据，对阿拉斯加西南部单一流域内的三个红大马哈鱼（Oncorhynchus nerka）生态型的分化基因组岛展开探究。我们共发现10个呈现生态型间高分化水平的基因组岛，与之形成鲜明对照的是，基因组其余区域的中性结构水平较低，且未被生态型划分。其中连锁群13上的一个基因组岛规模尤为庞大，包含6个固定指数（Fixation Index, FST）值大于0.14的SNP位点（中性SNP的平均FST值为0.01）。功能注释结果显示，该基因组岛的峰值区域存在一个非同义突变，该突变所在的基因在其他物种中与生长调控相关（TULP4）。本次发现的基因组岛规模相对较小（80-402 kb），位于岛内的位点并未表现出多样性水平降低的特征，反而呈现出轻微升高的连锁不平衡（linkage disequilibrium）水平。上述特征表明，本研究发现的基因组岛大概率由分化搭车效应（divergence hitchhiking）所产生，但我们无法排除其他机制参与形成此类基因组岛的可能性。本研究结果证实，分化基因组岛在存在基因流的局部适应过程中扮演着重要角色，同时为解析生态型分化的遗传基础迈出了重要一步。