Data from: The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

Ecological adaptation is of major relevance to speciation and sustainable population management, but the underlying genetic factors are typically hard to study in natural populations due to genetic differentiation caused by natural selection being confounded with genetic drift in subdivided populations. Here, we use whole genome population sequencing of Atlantic and Baltic herring to reveal the underlying genetic architecture at an unprecedented detailed resolution for both adaptation to a new niche environment and timing of reproduction. We identify almost 500 independent loci associated with a recent niche expansion from marine (Atlantic Ocean) to brackish waters (Baltic Sea), and more than 100 independent loci showing genetic differentiation between spring- and autumn-spawning populations irrespective of geographic origin. Our results show that both coding and non-coding changes contribute to adaptation. Haplotype blocks, often spanning multiple genes and maintained by selection, are associated with genetic differentiation.生态适应与物种形成及种群可持续管理息息相关，但解析其背后的遗传机制在自然种群中往往极具挑战：在被分割为多个亚种群的群体中，自然选择引发的遗传分化常会与遗传漂变相互混淆，二者难以区分。本研究通过对大西洋鲱与波罗的海鲱开展全基因组群体测序（whole genome population sequencing），以前所未有的高分辨率揭示了该类群在适应新生态位环境以及繁殖时序方面的潜在遗传架构。我们共鉴定出近500个独立基因座（locus，复数形式loci），与该类群从海洋（大西洋）向咸淡水水域（波罗的海）的近期生态位扩张相关；同时还鉴定出超100个独立基因座，其所在位点的遗传分化在春季产卵与秋季产卵种群间存在显著差异，且不受地理起源的影响。本研究结果表明，编码区与非编码区的变异均对生态适应具有贡献。通常跨越多个基因且受选择作用维持的单倍型区块（haplotype block），与遗传分化存在显著关联。