Jorgensen, StacyBolick, Holly2016-03-092016-03-092011-12http://hdl.handle.net/10125/101369MA University of Hawaii at Manoa 2011Includes bibliographical references (leaves 37–47).Heterocentrotus mammillatus, the red pencil sea urchin, is a mass spawning benthic marine species with a large tropical Pacific distribution that is native to the State of Hawaii, which includes one of the largest marine protected areas in the world. Geographic patterns of genetic diversity in the red pencil urchin were investigated within its northeastern range in order to help understand dispersal patterns of marine species throughout the area, and to provide additional (species genetic population structure and distribution) information to assist with coral reef management in and around Hawaii's extensive marine protected areas. Two genetic techniques were used for this study: the mitochondrial DNA region cytochrome oxidase subunit I (COI) and genome-wide amplified fragment length polymorphism (AFLP) markers. Seven populations were sampled within the study area: three populations each from the main and northwest Hawaiian Islands, and an additional population from Kingman Reef (Line Islands) located approximately 1500 km south of the main Hawaiian islands. Both analyses produced concordant results and found that the vast majority of genetic diversity was within populations (99% for COI and 96% for AFLP). Of the 42 total COI haplotypes identified, 28 were found in a single population, three of the most common haplotypes were shared by all populations, and no strong geographic trends were observed in the haplotype network. Average COI haplotype diversity was high at 0.85 and nucleotide diversity was relatively low at 0.01. Of the 146 AFLP loci, 121 were polymorphic in at least one population, and the average expected heterozygosity for all seven populations together was 0.418 (with a range from 0.256 to 0.428). While an analysis of molecular variance (AMOVA) of the COI data identified significant genetic structure between Hawaiian populations and Kingman Reef (3% total variation), the AMOVA of the AFLP data was able to identify significant genetic substructuring at three spatial scales: among populations within the main and northwestern Hawaiian islands (3% total variation), between the main and northwestern islands (1.2% variation), and between Hawaii and Kingman Reef (5% total variation). Within the Hawaiian Archipelago, however, there was no evidence of isolation-by-distance for either analysis, indicating a chaotic or patchy pattern of gene flow among populations.viii, 47 leavesengAll UHM dissertations and theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission from the copyright owner.red pencil sea urchinHeterocentrotus mammillatusbenthic marine speciesHawaiimarine protected areasHawaiian IslandsKingman ReefLine IslandsThesis