Semester Award Granted

Summer 2025

Submission Date

July 2025

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Thesis/Dissertation Advisor [Chair]

Joshua D. Voss

Abstract

Population genetic analyses provide critical insights into biodiversity and resilience on coral reefs. This dissertation investigated the genetic connectivity and cryptic diversity of multiple foundational reef species, the corals Stephanocoenia intersepta, Orbicella faveolata, Montastraea cavernosa, and the sponge Xestospongia muta, across shallow and mesophotic reefs in the Flower Garden Banks National Marine Sanctuary (FGBNMS) and across marine protected areas on the Florida Reef Tract. Using a reduced representation genotyping approach, 2bRAD-seq, we generated genome-wide single nucleotide polymorphism (SNP) datasets for each species to assess patterns of population structure across regions and depth zones. Analyses uncovered cryptic lineages within all species, with some species exhibiting distinct depth and regional distributions. Notably, there was strong regional genetic differentiation between FGBNMS and Florida populations in both Stephanocoenia intersepta and Xestospongia muta, suggesting limited contemporary gene flow among these regions. Within regions, depth-associated genetic structure was also detected, particularly among S. intersepta in Florida Keys National Marine Sanctuary as well as O. faveolata and X. muta in FGBNMS. These results highlight that patterns of connectivity and lineage diversity are complex and variable by species and region, and that mesophotic populations do not uniformly serve as refugia for shallow reefs in these areas. Together, these findings emphasize the need to incorporate depth and cryptic genetic diversity into reef management and conservation planning. This work contributes to a growing understanding of how environmental gradients and historical processes influence the genetic structure of coral reef species populations, with important implications for their future persistence under climate change.

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