Publication Date



Open access

Embargo Period


Degree Type


Degree Name

Doctor of Philosophy (PHD)


Marine Biology and Fisheries (Marine)

Date of Defense


First Committee Member

Andrew C. Baker

Second Committee Member

Douglas L. Crawford

Third Committee Member

Chris Langdon

Fourth Committee Member

Alex C. Wilson

Fifth Committee Member

Scott C. France


Molecular approaches to the fields of taxonomy, systematics and population genetics are imperative in order to better understand the evolutionary history and ecological interactions among organisms. This dissertation utilized genetic techniques to address evolutionary and ecological questions in corals and octocorals at different levels of resolution, from ancient phylogenetic relationships to the relatively recent population dynamics of individuals within species in both the coral host and its algal endosymbionts (genus Symbiodinium). Collectively, this work: (1) demonstrates a novel use of genes involved in the calcification process to test hypotheses of morphological convergence in scleractinian corals; (2) helps reconcile contrasting morphological and molecular phylogenetic perspectives among closely related species of a gorgonian octocoral; and (3) elucidates the genetic connectivity, dispersal potential, host acquisition, and specificity between a reef coral and its algal symbionts. Results show that the phylogenetic history of two genes involved in calcification in scleractinian corals is complex and consists of species-specific gene duplications and losses. However, in at least some cases, these calcification gene phylogenies agreed with taxonomic hypotheses based on morphology, in contrast to standard molecular phylogenies of neutral genes not involved in calcification. Second, molecular data support calyx morphology as a valid systematic character among species within the gorgonian octocoral genus Pterogorgia, but do not corroborate branch morphology as a useful systematic character. In addition, hybridization and/or morphological plasticity likely play important roles in shaping the morphological species described within this genus. Finally, populations of the gorgonian octocoral Plexaura flexuosa and its algal symbiont, Symbiodinium B1, showed different genetic structure across the Florida reef tract and Caribbean. P. flexuosa displayed high genetic connectivity over distances up to ~1900 km, while Symbiodinium B1 showed clear population subdivisions among sites separated by <100 km, as well as within sites (<100 m). Despite this structure, local environmental pools of Symbiodinium B1 are genetically diverse, and there is evidence for limited dispersal of Symbiodinium vectored by the larval stage of their coral hosts over ecological timescales. Together, data from the host (P. flexuosa) and its symbiont suggest high resilience potential, mediated by a passive process of stochastic host acquisition and dispersal. Additionally, in contrast to the very high specificity previously reported for gorgonian octocorals and Symbiodinium, genotypic clones (and genetically similar genotypes) of P. flexuosa did not show specificity to particular genotypes of Symbiodinium B1, and vice versa. Future work should continue to further integrate molecular techniques to establish a more comprehensive understanding of the ecology and evolution of these important organisms and the ecosystems they build.


molecular systematics; coral reef; octocoral; population genetics; phylogenetics; Symbiodinium