Hollenbeck Christopher M, Portnoy David S, Gold John R
Marine Genomics Laboratory, Department of Life Sciences Texas A&M University - Corpus Christi Corpus Christi Texas.
Present address: Scottish Oceans Institute University of St. Andrews St. Andrews, Fife UK.
Ecol Evol. 2019 Feb 26;9(6):3141-3152. doi: 10.1002/ece3.4936. eCollection 2019 Mar.
Restriction site-associated DNA (RAD) sequencing was used to characterize neutral and adaptive genetic variation among geographic samples of red drum, , an estuarine-dependent fish found in coastal waters along the southeastern coast of the United States (Atlantic) and the northern Gulf of Mexico (Gulf). Analyses of neutral and outlier loci revealed three genetically distinct regional clusters: one in the Atlantic and two in the northern Gulf. Divergence in neutral loci indicated gradual genetic change and followed a linear pattern of isolation by distance. Divergence in outlier loci was at least an order of magnitude greater than divergence in neutral loci, and divergence between the regions in the Gulf was twice that of divergence between other regions. Discordance in patterns of genetic divergence between outlier and neutral loci is consistent with the hypothesis that the former reflects adaptive responses to environmental factors that vary on regional scales, while the latter largely reflects drift processes. Differences in basic habitat, initiated by glacial retreat and perpetuated by contemporary oceanic and atmospheric forces interacting with the geomorphology of the northern Gulf, followed by selection, appear to have led to reduced gene flow among red drum across the northern Gulf, reinforcing differences accrued during isolation and resulting in continued divergence across the genome. This same dynamic also may pertain to other coastal or nearshore fishes (18 species in 14 families) where genetically or morphologically defined sister taxa occur in the three regions.
限制性内切酶位点相关DNA（RAD）测序被用于表征美国东南沿海（大西洋）和墨西哥湾北部沿海水域中河口依赖型鱼类红鼓的地理样本之间的中性和适应性遗传变异。对中性位点和异常位点的分析揭示了三个遗传上不同的区域集群：一个在大西洋，两个在墨西哥湾北部。中性位点的差异表明遗传变化是渐进的，并遵循距离隔离的线性模式。异常位点的差异至少比中性位点的差异大一个数量级，并且墨西哥湾各区域之间的差异是其他区域之间差异的两倍。异常位点和中性位点的遗传分化模式不一致，这与以下假设一致：前者反映了对区域尺度上变化的环境因素的适应性反应，而后者主要反映了漂变过程。由冰川消退引发、当代海洋和大气力量与墨西哥湾北部地貌相互作用并随后经过选择而导致的基本栖息地差异，似乎导致了红鼓在墨西哥湾北部之间的基因流动减少，强化了隔离期间积累的差异，并导致全基因组的持续分化。同样的动态变化也可能适用于其他沿海或近岸鱼类（14个科的18种），在这三个区域中存在遗传或形态学上定义的姐妹分类群。
