Date of Award

Fall 2017

Document Type


Degree Name

Doctor of Philosophy (PhD)


Biological Sciences

Committee Director

Kent E. Carpenter

Committee Member

Daniel Barshis

Committee Member

David Gauthier

Committee Member

Christopher Bird


Overfishing is one of the most pervasive threats to coral reef ecosystems, and management of these multi-species resources is hampered by limited species-specific population level information. The reefs in the western tropical Pacific Ocean, including the Coral Triangle, are the most bio-diverse in the world. Home to more than 400 million people, this region contains some of the most threatened coral reef ecosystems. Presented here is the first comprehensive analysis of the genetic structure of Caesio cuning, planktivorous fish inhabiting reefs in the Coral Triangle and western Pacific Ocean. Data from both classical Sanger and next-generation sequencing were analyzed across multiple spatial scales to test hypotheses regarding the biogeography, ecology, and population connectivity of this important food fish.

Across the Coral Triangle, mitochondrial DNA sequencing was used to examine broad-scale genetic patterns from 33 locations. Results show the presence of two clades found on either side of the Sunda Shelf, a biogeographic pattern attributed to vicariant isolation during low sea level stands during the Pleistocene Epoch. No evidence for isolation-by-distance across the sampling region was found, however, within the clade associated with the Pacific Ocean, AMOVA and BARRIER analyses indicate significant genetic differences between central Indonesia and the Philippines relative to eastern Indonesia.

Restriction site-associated DNA (RAD) sequencing data from five sites along the Kuroshio Current were used to examine fine-scale gene flow from the core to the northern limit of the species range. Results indicate that C. cuning in this region conform to the predictions of the central-peripheral population model described by Mayr (1963). Edge effects were found in peripheral populations including decreasing effective sample size, increased relatedness, and disjunct peripheral populations.

Finally, since management of reef fish resources occurs at the country-level, RAD sequencing data from seven sites were used to examine fine-scale patterns of population structure within the Philippines. Results suggest that C. cuning from Palawan are genetically distinct from all other sites in the north, central, and eastern Philippines. Excluding Palawan, no isolation-by-distance was found despite significant genetic structure between many sites, indicating that gene flow within the Philippines is largely impacted by regional oceanographic features.