Coral reef habitats surrounding Cuba include relatively healthy, well-developed shallow and mesophotic (30–150 m) scleractinian communities at the cross-currents of the Tropical Western Atlantic (TWA). However, Cuba’s coral communities are not immune to the declines observed throughout the TWA, and there is limited information available regarding genetic connectivity, diversity, and structure among these populations. This represents an immense gap in our understanding of coral ecology and population dynamics at both local and regional scales. To address this gap, we evaluated the population genetic structure of the coral Montastraea cavernosa across eight reef sites surrounding Cuba. Colonies were genotyped using nine microsatellite markers and > 9,000 single nucleotide polymorphism (SNP) markers generated using the 2bRAD approach to assess fine-scale genetic structure across these sites. Both the microsatellite and SNP analyses identified patterns of genetic differentiation among sample populations. While the microsatellite analyses did not identify significant genetic structure across the seven shallow M. cavernosa sampling sites, the SNP analyses revealed significant pairwise population differentiation, suggesting that differentiation is greater between eastern and western sites. This study provides insight into methodological differences between microsatellite and SNP markers including potential trade-offs between marker-specific biases, sample size, sequencing costs, and the ability to resolve subtle patterns of population genetic structure. Furthermore, this study suggests that locations in western Cuba may play important roles in this species’ regional metapopulation dynamics and therefore may merit incorporation into developing international management efforts in addition to the local management the sites receive.

古巴周围的珊瑚礁栖息地包括相对健康、发育良好的浅层和中光层 (30-150 m) 石珊瑚群落，位于热带西大西洋 (TWA) 的横流处。然而，古巴的珊瑚群落并不能幸免于整个 TWA 观察到的下降，并且关于这些种群之间的遗传连通性、多样性和结构的可用信息有限。这代表了我们对当地和区域尺度的珊瑚生态和种群动态的理解存在巨大差距。为了解决这一差距，我们评估了珊瑚Montastraea cabernosa的种群遗传结构横跨古巴周围的八个珊瑚礁遗址。使用 9 个微卫星标记和使用 2bRAD 方法生成的 > 9,000 个单核苷酸多态性 (SNP) 标记对菌落进行基因分型，以评估这些位点的精细遗传结构。微卫星和 SNP 分析都确定了样本群体之间的遗传分化模式。虽然微卫星分析没有识别出七个浅层海绵状海绵体的显着遗传结构采样点，SNP 分析揭示了显着的成对种群分化，表明东部和西部站点之间的分化更大。这项研究提供了对微卫星和 SNP 标记之间方法学差异的洞察，包括标记特异性偏差、样本大小、测序成本以及解决群体遗传结构细微模式的能力之间的潜在权衡。此外，这项研究表明，古巴西部的地点可能在该物种的区域复合种群动态中发挥重要作用，因此除了这些地点接受的当地管理外，可能值得纳入发展国际管理工作。