RAD genotyping reveals fine-scale population structure and provides evidence for adaptive divergence in a commercially important fish from the northwestern Pacific Ocean
RAD genotyping reveals fine-scale population structure and provides evidence for adaptive divergence in a commercially important fish from the northwestern Pacific Ocean
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RAD 基因分型揭示了精细的种群结构，并为西北太平洋一种具有重要商业价值的鱼类的适应性分化提供了证据
DOI：
10.7717/peerj.7242
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发表时间：
2019-07
期刊：
影响因子：
2.7
通讯作者：
Jin-Xian Liu
中科院分区：
文献类型：
--
作者：
Bai-Dong Zhang;Dong-Xiu Xue;Yu-Long Li;Jin-Xian Liu
由于海洋中基因流动的障碍较少，探索影响海洋鱼类遗传结构的因素具有挑战性。然而，全基因组序列数据可以极大地增强我们描绘以前未识别的种群结构以及潜在的适应性分歧的能力。小黄鱼(Larimichthys Polyactis)是一种重要的商业鱼类，具有较高的基因流，其越冬种群经历了异质性的环境，可能存在种群分化和适应性分化。为了描述种群结构的模式和测试局部适应的特征，利用限制性内切酶位点相关DNA测序(RAD-SEQ)从4个越冬种群中鉴定了80个个体的68666个筛选出的SNP标记。黄海中部、黄海南部和中国海东北部越冬种群间存在显著的遗传分化(成对FST：0.00036~0.00390)，这与传统生态学方法得出的越冬种群划分一致。此外，共检测到126个与环境参数(温度、盐度和浊度)显著相关的独特SNPs。这些候选SNP参与了能量代谢和吞噬等多种途径，表明它们可能在生长和先天免疫中发挥关键作用。我们的结果表明，在这种高基因流动的海水鱼中，存在着迄今未被认识的隐蔽种群结构和局部适应，从而为管理策略的设计提供了新的见解。
Exploring factors shaping genetic structure of marine fish is challenging due to fewer barriers to gene flow in the ocean. However, genome-wide sequence data can greatly enhance our ability to delineate previously unidentified population structure as well as potential adaptive divergence. The small yellow croaker (Larimichthys polyactis) is a commercially important fish species with high gene flow and its overwintering populations experience heterogeneous environment, suggesting possible population differentiation and adaptive divergence. To delineate patterns of population structure as well as test for signatures of local adaptation, a total of 68,666 quality filtered SNP markers were identified for 80 individuals from four overwintering populations by using restriction site-associated DNA sequencing (RAD-seq). Significant genetic differentiation among overwintering populations from the Central Yellow Sea, the South Yellow Sea and the North East China Sea were detected (Pair-wise FST: 0.00036–0.00390), which were consistent with population division of overwintering groups inferred from traditional ecological approaches. In addition, a total of 126 unique SNPs were detected to be significantly associated with environmental parameters (temperature, salinity and turbidity). These candidate SNPs were involved in multiple pathways such as energy metabolism and phagocytosis, suggesting they may play key roles in growth and innate immunity. Our results suggested the existence of hitherto unrecognized cryptic population structure and local adaptation in this high gene flow marine fish and thus gain new insights into the design of management strategies.
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影响因子：
2.8
作者：
Xian-shi Jin
通讯作者：
Xian-shi Jin
影响因子：
3.3
作者：
Babin C;Gagnaire PA;Pavey SA;Bernatchez L
通讯作者：
Bernatchez L
影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
DOI：
10.1016/s0084-3741(09)79294-7
发表时间：
2009
期刊：
Yearbook of Endocrinology
影响因子：
--
作者：
S. Schinner
通讯作者：
S. Schinner
一种对来自多个个体的重叠双端 RAD 读数进行本地从头组装的优化方法
影响因子：
3.5
作者：
Li YL;Xue DX;Zhang BD;Liu JX
通讯作者：
Liu JX