Data from: From refugia to rookeries: phylogeography of Atlantic green turtles

Investigating species’ distribution and abundance over time is central to evolutionary biology, and provides important context for conservation and management. With respect to population genetic structure in green sea turtles (Chelonia mydas), certain processes such as female philopatry to natal rookeries are well understood, while others, such as male philopatry and historical changes in distribution and abundance, remain relatively understudied. Further, although inferences from mitochondrial DNA and nuclear microsatellites have both been critical in identifying management units, comparisons of these units based on both markers are still rare. Here we analyzed novel data from fifteen microsatellite markers gathered at six green turtle rookeries in the western Atlantic as well as previously published mitochondrial sequences from 13 regional rookeries. We detected low, but significant, population structure at microsatellite loci, which coincides with previous delineations of local and regional management units as well as reports of male philopatry. However, we also detected a discord between nuclear and mitochondrial data, in which two tropical rookeries (Aves Island, Venezuela; and Matapica, Surinam) clustered with the Caribbean and Mediterranean based on microsatellite data, but displayed a mitochondrial lineage characteristic of the southern Atlantic and Africa. To investigate the possible causes of this discord, we used both classical and Bayesian methods to estimate historical migration rates and the timing and magnitude of changes in population size. We detected a strong barrier to dispersal between the northern and southern Atlantic, as well as an expansion in the southern mitochondrial lineage during the Wisconsin glacial period and a later expansion in the northern lineage following the Last Glacial Maximum. We propose that the Aves and Surinam rookeries were colonized by females from a southern glacial refugium, after which they experienced gene flow from the Caribbean. This study highlights the utility of incorporating data from multiple types of molecular markers in accurately identifying conservation units and in elucidating the complex historical and contemporary processes underlying population genetic structure in marine species.长期探究物种的分布格局与种群丰度，是进化生物学的核心研究内容，同时可为物种保护与管理工作提供重要的理论支撑与实践依据。就绿海龟（Chelonia mydas）的种群遗传结构而言，雌性返回出生地产卵滩的归巢行为已得到充分研究，而雄性归巢行为、分布与丰度的历史变化等议题，目前仍相对缺乏深入探究。此外，尽管线粒体DNA（mitochondrial DNA）与核微卫星（nuclear microsatellites）的推导结果均对管理单元的划定起到了关键作用，但同时基于两类标记开展的管理单元对比研究仍较为少见。本研究分析了西大西洋6处绿海龟产卵滩的15个微卫星标记的全新测序数据，以及13个区域产卵滩的已发表线粒体DNA序列。研究在微卫星位点上检测到了程度较低但显著的种群遗传结构，这与此前划定的局域与区域管理单元，以及雄性归巢行为的相关报道相一致。但本研究同时发现核基因与线粒体数据之间存在不一致性：基于微卫星数据，两处热带产卵滩——委内瑞拉阿韦斯岛（Aves Island）与苏里南马塔皮卡滩（Matapica）——与加勒比海及地中海种群聚为一类，但其线粒体谱系却呈现南大西洋与非洲种群的特征。为探究该数据不一致性的潜在成因，本研究同时采用经典统计方法与贝叶斯（Bayesian）方法，对历史迁移率、种群规模变化的时间节点与变化幅度进行了估算。研究发现北大西洋与南大西洋之间存在显著的扩散障碍；同时，南大西洋线粒体谱系在威斯康星冰期（Wisconsin glacial period）发生种群扩张，而北部线粒体谱系则在末次冰盛期（Last Glacial Maximum）之后出现扩张。本研究推测，阿韦斯岛与苏里南产卵滩的种群最初由来自南部冰期避难所的雌性绿海龟奠基，随后该种群与加勒比海种群发生了基因交流。本研究凸显了整合多类型分子标记数据的重要价值，这有助于精准划定保护单元，并阐明海洋物种种群遗传结构背后复杂的历史与当代演化过程。