Data from: Comparative population genetic analysis of bocaccio rockfish Sebastes paucispinis using anonymous and gene-associated simple sequence repeat loci

Comparative population genetic analyses of traditional and emergent molecular markers aid in determining appropriate use of new technologies. The bocaccio rockfish Sebastes paucispinis is a high-gene-flow marine species off the west coast of North America that experienced strong population decline over the past three decades. We used 18 anonymous and 13 gene associated simple sequence repeat loci (EST-SSRs) to characterize range-wide population structure with temporal replicates. No FST-outliers were detected using the LOSITAN program, suggesting that neither balancing nor divergent selection affected the loci surveyed. Consistent hierarchical structuring of populations by geography or year class was not detected regardless of marker class. The EST-SSRs were less variable than the anonymous SSRs, but no correlation between FST and variation or marker class was observed. General Linear Model analysis showed that low EST-SSR variation was attributable to low mean repeat number. Comparative genomic analysis with Gasterosteus aculeatus, Takifugu rubripes, and Oryzias latipes showed consistently lower repeat number in EST-SSRs than SSR loci that were not in ESTs. Purifying selection likely imposed functional constraints on EST-SSRs resulting in low repeat numbers that affected diversity estimates, but did not affect the observed pattern of population structure.

传统与新兴分子标记的群体遗传学比较分析，有助于确定新技术的合理应用场景。博氏岩鲈（Bocaccio rockfish, *Sebastes paucispinis*）是北美西海岸海域的高基因流海洋物种，过去三十年间种群数量出现了显著衰退。本研究采用18个匿名简单序列重复（simple sequence repeat, SSR）位点与13个基因关联型简单序列重复位点（表达序列标签-简单序列重复，EST-SSRs），结合时间重复采样对该物种的全分布区群体结构进行解析。通过LOSITAN程序未检测到FST离群位点，表明本次分析所涉及的位点未受平衡选择或歧化选择的影响。无论采用哪一类标记，均未检测到基于地理分区或年龄组的稳定群体层级结构。EST-SSRs的多态性低于匿名SSR位点，但未观测到FST值与多态性水平或标记类型之间存在相关性。广义线性模型（General Linear Model, GLM）分析显示，EST-SSRs较低的多态性源于其平均重复序列数偏低。通过与三刺鱼（*Gasterosteus aculeatus*）、红鳍东方鲀（*Takifugu rubripes*）及青鳉（*Oryzias latipes*）进行比较基因组分析，发现EST-SSRs的重复序列数始终低于非表达序列标签区的SSR位点。净化选择可能对EST-SSRs施加了功能约束，导致其重复序列数偏低，进而影响了多态性评估结果，但并未改变观测到的群体结构模式。