HCNSO Student Theses and Dissertations

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Defense Date


Document Type

Dissertation - NSU Access Only

Degree Name

Ph.D. Oceanography/Marine Biology


Oceanographic Center

First Advisor

Mahmood Shivji

Second Advisor

Bernhard Riegl

Third Advisor

Samuel J. Purkis

Fourth Advisor

George Duncan


Chapter 1

The brittle star Ophiothrix suensonii is a coral reef invertebrate with high dispersal potential (up to 49 days larval duration in culture). Here I utilize COI sequence data from 264 individuals collected from 10 locations throughout the Florida reef tract and Caribbean to investigate dispersal dynamics and demographic history. Locations separated by up to 1,700km lacked genetic differentiation, confirming ability for long-range dispersal. However, significant differentiation was detected among other regions. Honduras showed the greatest subdivision, suggesting that this region may need independent management, and the circulation of the Mesoamerican gyre within the Gulf of Honduras could be a significant factor responsible for this subdivision. Demographic analyses provide strong evidence for an expansion of population size and range, possibly out of Florida, through the Caribbean, and into Honduras, which commenced in the mid-Pleistocene. However, the presence of a clade of rare haplotypes (likely a cryptic species), which split much earlier (late Pliocene), indicates that O. suensonii persisted long before its recent expansion, suggesting a cyclic history of population contraction and expansion. Finally, patterns of gene flow are not concordant with contemporary surface currents; rather, they reflect historical movements possibly linked with changes in circulation during periods of Pleistocene climate change.

Chapter 2

Although over half of all known elasmobranchs are batoids, with many species exploited and several of conservation concern, little is known of their population genetic structure and microevolutionary history. Here I utilized sequence variation in 648bp of the mitochondrial control region to study the phylogeography and microevolution of the southern stingray (Dasyatis americana) throughout the Carolinas, Florida, and the Caribbean. Out of 267 individuals sampled from eight locations, 67 haplotypes were identified with AMOVA results revealing high overall population structure (ST = 0.59; P = 0.0000). However, phylogenetic and statistical parsimony analyses described three lineages that were sufficiently divergent to suggest cryptic speciation. The geographic distribution of haplotypes from these lineages described a complex phylogeographic pattern, which despite some degree of geographic partitioning among the following regions: (i) USA and Belize, (ii) Bahamas and the West Indies, and (iii) Grand Cayman Island, showed many haplotypes from divergent lineages to be sympatric at the same sampling site. The Grand Cayman population showed high genetic partitioning and despite evidence for recent migration, this population should be a conservation concern as the immigrants possessed highly divergent haplotypes and could therefore be reproductively incompatible with individuals of the resident population.

Chapter 3

Sponges are one of the dominant fauna on Florida and Caribbean reefs, with species diversity often exceeding that of scleractinian corals. Despite their importance as structural components and habitat providers on reefs, their dispersal dynamics are little understood. I utilized ten microsatellite markers to study the population structure and dispersal patterns of the giant barrel sponge (Xestospongia muta), a widespread species throughout Florida and the Caribbean. F-statistics, exact tests of population differentiation, and Bayesian multilocus genotype analyses revealed high levels of overall genetic partitioning (FST = 0.12, P = 0.001) and grouped 375 individuals from the Bahamas, Honduras, US Virgin Islands, Key Largo, and the remainder of the Florida reef tract into five genetic clusters (K = 5). Assignment tests showed dispersal over ecological time scales to be limited to relatively short distances, as the only migration among populations detected was within the Florida reef tract. Consequently, populations are largely self-recruiting representing distinct management units. A combination of levels of genetic differentiation, genetic distance, and assignment tests support the important role of the Caribbean and Florida currents in shaping patterns of contemporary and historical gene flow.

Chapter 4

The spotted eagle ray (Aetobatus narinari), a large coral-reef associated batoid of conservation concern, is currently described as a single, circumglobally distributed species. However, geographic differences in its morphology and parasite diversity have raised unconfirmed suspicions that A. narinari may constitute a species complex. I used 1570bp of mitochondrial and nuclear sequence data (cytochrome b, COI, and ITS2) to assess the validity of A. narinari as a single cosmopolitan species and infer its evolutionary history. Specimens from four major geographic regions were examined: the Central Western Atlantic, Eastern Pacific, Western Pacific and Central Pacific. Phylogenies described three distinct, reciprocally monophyletic lineages with no genetic exchange among regions. Based on combined genealogical concordance and genetic distance criteria, I recommend that the Western/Central Pacific lineage be recognized as a distinct species from lineages in the Central Western Atlantic and Eastern Pacific. The latter two lineages, separated by the Isthmus of Panama, are proposed as subspecies. Dramatically higher nucleotide diversity and sequence divergence coupled with a basal position in multiple phylogenetic analyses support an Indo-West Pacific origin for the A. narinari species complex, with subsequent westerly dispersal around the southern tip of Africa into the Atlantic and then into the Eastern Pacific.

Chapter 5

Numerous marine species with seemingly wide geographic ranges have been delineated using molecular and biochemical techniques into cryptic complexes whose component species are distributed over far smaller areas. Accordingly, if cryptic species are a common feature of coral reefs, conservation measures will need to encompass all regions of endemism. I analyzed 414bp of the mitochondrial COI gene from two brooding amphipod species (Leucothoe ashleyae and Leucothoe kensleyi) commensal inside the branching vase sponge Callyspongia vaginalis, sampled throughout Florida and the Caribbean. The level of intraspecific divergence was among the highest reported for any marine crustacean (12.4 – 26.0% uncorrected) and exceeds that of congeners from nine diverse amphipod families. Our findings reveal multiple cryptic species endemic to Caribbean islands that suffer from depressed levels of genetic diversity when compared to mainland Florida. Molecular clock calibration suggests that morphology has remained in stasis for at least 9 million years, and it is proposed that stabilizing selection within a homogeneous sponge environment is responsible. Although lineages have been reproductively isolated since the late Miocene, secondary contact has occurred with cryptic species co-occurring within the same host, compounding the levels of species diversity missed under the morphospecies concept.


Funding provided by the National Coral Reef Institute, the Guy Harvey Research Institute, the US National Park Service, and the Save Our Seas Foundation.

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