Data from: Population genomics meet Lagrangian simulations: oceanographic patterns and long larval duration ensure connectivity among Paracentrotus lividus populations in the Adriatic and Ionian seas

Connectivity between populations is a key factor that influences both their dynamics and the genetic structuring of marine species. In this study, we explored connectivity patterns of a long-dispersing species, the edible common sea urchin Paracentrotus lividus, focusing mainly on the Adriatic-Ionian basins. We applied a multidisciplinary approach integrating population genomics, based on 1122 Single Nucleotide Polymorphisms (SNPs) obtained by 2b-RAD in 275 samples, with Lagrangian simulations performed with a biophysical model of larval dispersal.
We detected genetic homogeneity among eight population samples spanning about 600 km and collected in the focal area (Adriatic-Ionian basins), whereas weak but significant differentiation was found with respect to comparative samples taken from French and Tunisian coasts. Genetic analyses performed separately with putatively neutral and outlier loci confirmed genetic homogeneity within Adriatic-Ionian basins, but showed a much higher differentiation at the large scale. Lagrangian simulations found a significant potential for larval exchange among the eight Adriatic-Ionian locations, supporting the view of strong connectivity of P. lividus populations in this area. A peculiar pattern emerged from the comparison of our results with those obtained from published P. lividus cytochrome b (cytb) sequences, which revealed genetic differentiation in the same area despite a smaller sample size and a lower power to detect differences.
Comparison with studies conducted in the same Adriatic-Ionian locations using nuclear markers on other species having similar pelagic larval durations highlights differences both in realized and potential connectivity patterns, and warns from generalizing single-species results to the entire community of rocky shore habitats.

种群间的连通性是影响海洋物种种群动态与遗传结构的关键因素。本研究聚焦于长扩散性物种——可食用的普通海胆（Paracentrotus lividus），以亚得里亚海-爱奥尼亚海盆为主要研究区域，探讨其种群连通格局。我们采用多学科研究方法，整合了基于275个样本、通过2b-RAD技术获得的1122个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）的群体基因组学分析，以及结合幼虫扩散生物物理模型开展的拉格朗日（Lagrangian）模拟实验。

我们在覆盖约600公里范围的核心研究区域（亚得里亚海-爱奥尼亚海盆）内的8个种群样本中检测到遗传均质性；而相较于采自法国与突尼斯海岸的对照样本，则发现了微弱但显著的遗传分化。分别基于推定中性位点与异常位点开展的遗传分析进一步证实，亚得里亚海-爱奥尼亚海盆内部种群存在遗传均质性，但在大尺度下却表现出更高程度的遗传分化。拉格朗日模拟结果显示，该区域内8个采样点间存在显著的幼虫交换潜力，印证了该区域普通海胆种群连通性较强的观点。将本研究结果与已发表的普通海胆细胞色素b（cytochrome b, cytb）序列分析结果对比后，呈现出一种特殊的格局：尽管后者样本量更小、检测差异的效力更低，却在同一区域内发现了遗传分化。

对比此前针对亚得里亚海-爱奥尼亚海盆同一区域、以具有相似浮游幼虫期的其他物种为研究对象并使用核标记的相关研究，本研究结果在实际连通格局与潜在连通格局两方面均存在差异，这警示我们不可将单物种研究结果泛化至岩岸栖息地的整个群落。