Data from: Molecular signatures of lineage-specific adaptive evolution in a unique sea basin: the example of an anadromous goby Leucopsarion petersii

Climate changes on various time scales often shape genetic novelty and adaptive variation in many biotas. We explored molecular signatures of directional selection in populations of the ice goby Leucopsarion petersii inhabiting a unique sea basin, the Sea of Japan, where a wide variety of environments existed in the Pleistocene in relation to shifts in sea level by repeated glaciations. This species consisted of two historically allopatric lineages, the Japan Sea (JS) and Pacific Ocean (PO) lineages, and these have lived under contrasting marine environments that are expected to have imposed different selection regimes caused by past climatic and current oceanographic factors. We applied a limited genome-scan approach using seven candidate genes for phenotypic differences between two lineages in combination with 100 anonymous microsatellite loci. Neuropeptide Y (NPY) gene, which is an important regulator of food intake and potent orexigenic agent, and three anonymous microsatellites were identified as robust outliers, that is, candidate loci potentially under directional selection, by multiple divergence- and diversity-based outlier tests in comparisons focused on multiple populations of the JS vs. PO lineages. For these outlier loci, populations of the JS lineage had putative signals of selective sweeps. Additionally, real-time quantitative PCR analysis using fish reared in a common environment showed a higher expression level for NPY gene in the JS lineage. Thus, this study succeeded in identifying candidate genomic regions under selection across populations of the JS lineage and provided evidence for lineage-specific adaptive evolution in this unique sea basin.

不同时间尺度下的气候变化，往往塑造了众多生物类群的遗传新奇性与适应性变异。本研究针对栖息于独特海盆——日本海的冰𫚥虎鱼（Leucopsarion petersii）的多个种群，探索其定向选择的分子特征；该海域在更新世时期因反复冰川作用引发海平面变化，形成了多样的环境条件。该物种存在两个历史异域支系：日本海支系（JS）与太平洋支系（PO），二者分别栖息于截然不同的海洋环境中，过往气候与当前海洋学因素所造成的选择压力模式存在显著差异。本研究采用受限基因组扫描策略，选取7个与两支系表型差异相关的候选基因，结合100个匿名微卫星位点开展分析。通过针对JS与PO支系多个种群的多组比较，结合多种基于分化与多样性的离群位点检测方法，本研究鉴定出神经肽Y（Neuropeptide Y, NPY）基因——一种重要的进食调控因子与强效促食因子——以及3个匿名微卫星位点作为稳健离群位点，即潜在处于定向选择下的候选位点。针对这些离群位点，JS支系的种群呈现出选择性清除的推定信号。此外，对共同饲养环境下的冰𫚥虎鱼开展实时荧光定量PCR分析，结果显示JS支系的NPY基因表达水平更高。综上，本研究成功鉴定出JS支系种群中受选择作用的候选基因组区域，并为该独特海盆内支系特异性适应性演化提供了实证依据。