Data from: Large-scale connectivity, cryptic population structure, and relatedness in Eastern Pacific olive ridley sea turtles (Lepidochelys olivacea)

Endangered species are grouped into genetically discrete populations to direct conservation efforts. Mitochondrial Control Region (mtCR) haplotypes are used to elucidate deep divergences between populations, as compared to nuclear microsatellites that can detect recent structuring. When prior populations are unknown, it is useful to subject microsatellite data to clustering and/or ordination population inference. Olive ridley sea turtles (Lepidochelys olivacea) are the most abundant sea turtle, yet few studies have characterized olive ridley population structure. Recently, clustering results of olive ridleys in the Eastern Tropical Pacific Ocean suggested weak structuring (FST=0.02) between Mexico and Central America. We analyzed mtCR haplotypes, new microsatellite genotypes from Costa Rica, and pre-existing microsatellite genotypes from olive ridleys across the Eastern Tropical Pacific, to further explore population structuring in this region. We subjected inferred populations to multiple analyses to explore the mechanisms behind their structuring. We found 10 mtCR haplotypes from 60 turtles nesting at three sites in Costa Rica, but did not detect divergence between Costa Rican sites, or between Central America and Mexico. In Costa Rica, clustering suggested one population with no structuring, but ordination suggested four cryptic clusters with moderate structuring (FST=0.08, p<0.001). Across the Eastern Tropical Pacific, ordination suggested nine cryptic clusters with moderate structuring (FST=0.103, p<0.001) that largely corresponded to Mexican and Central American populations. All ordination clusters displayed significant internal relatedness relative to global relatedness (p<0.001) and contained numerous sibling pairs. This suggests that broadly dispersed family lineages have proliferated in Eastern Tropical Pacific olive ridleys and corroborates previous work showing basin-wide connectivity and shallow population structure in this region. The existence of broadly dispersed kin in Eastern Tropical Pacific olive ridleys has implications for management of olive ridleys in this region, and adds to our understanding of sea turtle ecology and life-history, particularly in light of the natal-homing paradigm.

为指导物种保护工作，濒危物种会被划分为遗传上独立的种群。线粒体控制区（Mitochondrial Control Region, mtCR）单倍型可用于阐明种群间的深层分化；而核微卫星（nuclear microsatellite）则能够检测近期形成的种群结构分化。当预先未知种群划分情况时，对微卫星数据开展聚类分析或排序种群推断是一种有效的研究策略。太平洋丽龟（Lepidochelys olivacea）是现存数量最多的海龟类群，但目前针对其种群结构的系统性研究仍较为匮乏。此前针对东热带太平洋海域太平洋丽龟的聚类分析结果显示，墨西哥与中美洲种群间仅存在微弱的结构分化（FST=0.02）。本研究整合东热带太平洋海域太平洋丽龟的线粒体控制区单倍型数据、哥斯达黎加地区新增的微卫星基因型数据，以及已公开的该海域太平洋丽龟微卫星基因型数据，以进一步探究该区域的种群结构分化。研究团队通过多种分析手段对推断得到的种群进行解析，以揭示其结构分化的潜在机制。本研究对哥斯达黎加3处筑巢地的60只太平洋丽龟进行分析，共检出10种线粒体控制区单倍型，但未检测到哥斯达黎加各筑巢地间，或是中美洲与墨西哥种群间存在显著分化。在哥斯达黎加区域，聚类分析结果显示存在一个无结构分化的随机交配种群，但排序分析则揭示了4个存在中等程度分化的隐秘种群簇（FST=0.08，p<0.001）。针对整个东热带太平洋海域的分析显示，排序分析共检出9个存在中等程度分化的隐秘种群簇（FST=0.103，p<0.001），其分布大体与墨西哥及中美洲种群相对应。所有排序得到的种群簇均表现出相较于全局亲缘关系的显著内部亲缘聚集现象（p<0.001），且簇内存在大量同胞个体对。该结果表明，东热带太平洋海域的太平洋丽龟种群中存在广泛扩散的家族谱系扩张现象，同时也佐证了此前的研究结论——该海域存在全盆地尺度的种群连通性及较浅的种群结构。东热带太平洋海域太平洋丽龟中广泛存在的亲缘个体扩散现象，对该区域太平洋丽龟的保护管理具有重要指导意义，同时也加深了我们对海龟生态学与生活史特征的认知，尤其是在归巢范式（natal-homing paradigm）的研究框架下。