Data from: Cryptic habitats and cryptic diversity: unexpected patterns of connectivity and phylogeographic breaks in a Mediterranean endemic marine cave mysid

The marine cave-dwelling mysid Hemimysis margalefi is distributed over the whole Mediterranean Sea which contrasts with the poor dispersal capabilities of this brooding species. In addition, underwater marine caves are a highly fragmented habitat which further promotes strong genetic structuring, therefore providing highly informative data on the levels of marine population connectivity across biogeographic regions. This study investigates how habitat and geography have shaped the connectivity network of this poor disperser over the entire Mediterranean Sea through the use of several mitochondrial and nuclear markers. Five deeply divergent lineages were observed among H. margalefi populations resulting from deep phylogeographic breaks, some dating back to the Oligo-Miocene. Whether looking at the intra-lineage or inter-lineage levels, H. margalefi populations present a high genetic diversity and population structuring. This study suggests that the five distinct lineages observed in H. margalefi actually correspond to as many separate cryptic taxa. The nominal species, H. margalefi sensu stricto, corresponds to the westernmost lineage here surveyed from the Alboran Sea to south-eastern Italy. Typical genetic breaks such as the Almeria-Oran Front or the Sicilo-Tunisian Strait do not appear to be influential on the studied loci in H. margalefi sensu stricto. Instead, population structuring appears more complex and subtle than usually found for model species with a pelagic dispersal phase. The remaining four cryptic taxa are all found in the eastern basin, but incomplete lineage sorting is suspected and speciation might still be in process. Present day population structure of the different H. margalefi cryptic species appears to result from past vicariance events started in the Oligo-Miocene and maintained by present day coastal topography, water circulation and habitat fragmentation.

栖息于海洋洞穴的玛氏半糠虾（Hemimysis margalefi）的分布范围覆盖整个地中海，这与该育幼物种有限的扩散能力形成鲜明反差。此外，水下海洋洞穴属于高度破碎化的生境，进一步加剧了显著的种群遗传结构分化，因此该类群可为跨生物地理区域的海洋种群连通性水平研究提供极具信息量的实证数据。本研究借助多套线粒体与核分子标记（mitochondrial and nuclear markers），探究了生境与地理因素如何塑造整个地中海范围内该扩散能力较弱物种的种群连通网络。研究在玛氏半糠虾种群中发现了5个深度分化的支系，这些支系的形成源自古老的系统地理断裂（phylogeographic breaks），部分断裂的形成时间可追溯至渐新世-中新世（Oligo-Miocene）时期。无论是在支系内部还是支系间尺度，玛氏半糠虾种群均表现出较高的遗传多样性与显著的种群结构分化。本研究证实，玛氏半糠虾中发现的5个独立支系实际上分别对应多个独立的隐存分类单元（cryptic taxa）。狭义玛氏半糠虾（H. margalefi sensu stricto）对应本次研究中采样范围最西的支系，其分布区域从阿尔沃兰海延伸至意大利东南部。典型的遗传隔离带如阿尔梅里亚-奥兰锋面（Almeria-Oran Front）与西西里-突尼斯海峡（Sicilo-Tunisian Strait），似乎并未对狭义玛氏半糠虾的研究位点产生显著影响。与之相反，该类群的种群结构分化相较于通常具备远洋扩散阶段的模式物种更为复杂且微妙。剩余的4个隐存分类单元均分布于地中海东部盆地，但研究推测该类群存在不完全谱系分选现象，物种形成过程可能仍在进行中。现今不同玛氏半糠虾隐存物种的种群结构，似乎源自渐新世-中新世时期发生的古代地理隔离事件，并由当前的海岸地形、海水环流系统与生境破碎化所维持。