In Belize, shallow populations (10 and 16 m) of the coral species Montastraea cavernosa from the back reef and reef crest are genetically differentiated from deeper populations on the fore reef and reef wall (25 and 35 m). Like many species of scleractinian corals, M. cavernosa has an obligate symbiosis with dinoflagellate microalgae from the family Symbiodiniaceae. Here, we describe the Symbiodiniaceae taxa found within previously sampled and genotyped M. cavernosa populations along a depth gradient on the Belize Barrier Reef by implementing high-throughput sequencing of the ITS2 region of Symbiodiniaceae ribosomal DNA and the SymPortal analysis framework. While Symbiodiniaceae ITS2 type profiles across all sampling depths were almost entirely (99.99%) from the genus Cladocopium (formerly Symbiodinium Clade C), shallow (10 and 16 m) populations had a greater diversity of ITS2 type profiles in comparison to deeper (25 and 35 m) populations. Permutational multivariate analysis of variance (PERMANOVA) confirmed significant differences in ITS2 type profiles between shallow and deep sample populations. Overall Symbiodiniaceae communities changed significantly with depth, following patterns similar to the coral host's population genetic structure. Though physiological differences among species in the cosmopolitan genus Cladocopium are not well-described, our results suggest that although some members of Cladocopium are depth-generalists, shallow M. cavernosa populations in Belize may harbor shallow-specialized Symbiodiniaceae not found in deeper populations.

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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.