Data from: Population genomics reveals multiple drivers of population differentiation in a sex-role-reversed pipefish

A major goal of molecular ecology is to identify the causes of genetic and phenotypic differentiation among populations. Population genomics is suitably poised to tackle these key questions by diagnosing the evolutionary mechanisms driving divergence in nature. Here, we set out to investigate the evolutionary processes underlying population differentiation in the Gulf pipefish, Syngnathus scovelli. We sampled approximately 50 fish from each of 12 populations distributed from the Gulf Coast of Texas to the Atlantic Coast of Florida and performed restriction-site-associated DNA sequencing (RAD-seq) to identify SNPs throughout the genome. After imposing quality and stringency filters, we selected a panel of 6,348 SNPs present in all 12 populations, 1,753 of which were not physically linked. We identified a genome-wide pattern of isolation by distance, in addition to a more substantial genetic break separating populations in the Gulf of Mexico from those in the Atlantic. We also used several divergence outlier approaches and tests for genotype-environment correlation to identify 400 SNPs putatively involved in local adaptation. Patterns of phenotypic differentiation and variation diverged from the overall genomic pattern, suggesting that selection, phenotypic plasticity or demographic factors may be shaping phenotypes in distinct populations. Overall, our results suggest that population divergence is driven by a variety of factors in S. scovelli, including neutral processes and selection on multiple traits.

分子生态学的核心目标之一，是解析种群间遗传与表型分化的成因。种群基因组学恰好能够通过甄别自然界中驱动分化的进化机制，攻克此类关键科学问题。本研究以海湾海马（Syngnathus scovelli）为研究对象，旨在解析其种群分化背后的进化过程。我们从分布于德克萨斯州墨西哥湾沿岸至佛罗里达州大西洋沿岸的12个种群中，每个种群采集约50尾个体，并通过限制性酶切位点相关DNA测序（RAD-seq）对全基因组范围内的单核苷酸多态性（SNPs）进行分型。经过质量控制与严格过滤流程后，我们筛选出在全部12个种群中均存在的6348个SNPs，其中1753个不存在物理连锁关系。我们检测到全基因组范围内的距离隔离效应，同时发现墨西哥湾沿岸种群与大西洋沿岸种群之间存在更为显著的遗传断点。此外，我们采用多种分化离群位点分析方法与基因型-环境关联检验，筛选出400个可能参与本地适应的SNPs。表型分化与变异模式与整体基因组模式存在显著差异，这提示选择作用、表型可塑性或种群历史动态因素，可能在不同种群中对表型塑造产生独特影响。综上，本研究结果表明，海湾海马（S. scovelli）的种群分化由多种因素共同驱动，包括中性进化过程与多性状选择作用。