Date of Award

Fall 2017

Document Type


Degree Name

Master of Science (MS)


Biological Sciences

Committee Director

Kent E. Carpenter

Committee Member

Daniel Barshis

Committee Member

Christopher E. Bird


Southeast Asia includes the Coral Triangle, a marine biodiversity hotspot that supports important fishery resources experiencing varied threats. Patterns of speciation and population structure in the Coral Triangle have been examined to test hypotheses relating to the historical geologic processes that may have influenced this biodiversity phenomenon. This study investigates the genetic population structure of the Pink-ear Emperor Snapper, Lethrinus lentjan (Lacepède, 1802), across the Philippines and the South China Sea. The species is fished throughout the Coral Triangle by subsistence and commercial fishers and their landings have been in decline for several years, which could be indicative of depleted stocks. Six locations were sampled representing the northeastern, southeastern, central, and western Philippines, and central and southern Vietnam. This study used restriction-site associated DNA sequencing (RADSeq) to sample single nucleotide polymorphism markers from throughout the genome. Here, RADseq data is successfully used to detect structuring within the Philippines where a previous study of L. lentjan mitochondrial control region sequences did not. Genetic structure analyses revealed significant divergence along the boundaries of repeatedly isolated ocean basins, as observed in several Indo-Pacific species. Pleistocene vicariance is a suspected driving factor in lineage diversification for this species, supporting the hypothesis that the Coral Triangle is a center of origin. Before management or conservation strategies can be implemented, a stock assessment should be completed for L. lentjan, including research on its life history, ecosystem services, and metapopulation dynamics. This study also used STRUCTURE analysis to detect a strong Illumina sequencer lane effect, where the genotype of a fish is associated with the sequencer lane used to generate the data. To control and remove this lane effect, the data was parsed into two clusters, a new method for salvaging lane-affected data. It is recognized that RADSeq is prone to lane effects that can result in erroneous conclusions, and several strategies are outlined for identifying, mitigating, and avoiding them in future high-throughput RADSeq studies.


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