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Genetic Differentiation Among Florida Populations of Diadema Antillarum

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Genetic Differentiation Among Florida Populations of Diadema Antillarum University of Central Florida STARS Honors Undergraduate Theses UCF Theses and Dissertations 2016 Genetic Differentiation Among Florida Populations of Diadema antillarum Luke M. Chandler University of Central Florida Part of the Other Ecology and Evolutionary Biology Commons, and the Population Biology Commons Find similar works at: https://stars.library.ucf.edu/honorstheses University of Central Florida Libraries http://library.ucf.edu This Open Access is brought to you for free and open access by the UCF Theses and Dissertations at STARS. It has been accepted for inclusion in Honors Undergraduate Theses by an authorized administrator of STARS. For more information, please contact [email protected]. Recommended Citation Chandler, Luke M., "Genetic Differentiation Among Florida Populations of Diadema antillarum" (2016). Honors Undergraduate Theses. 44. https://stars.library.ucf.edu/honorstheses/44 GENETIC DIFFERENTIATION AMONG FLORIDA POPULATIONS OF DIADEMA ANTILLARUM by LUKE MILO CHANDLER A thesis submitted in partial fulfillment of the requirements for the Honors in the Major Program in Biology in the College of Sciences and in the Burnett Honors College at the University of Central Florida Orlando, Florida Spring Term 2016 Thesis Chair: Eric Hoffman, PhD. ii ABSTRACT This project used molecular genetic markers (microsatellites) to determine the amount of genetic diversity within populations and whether significant differentiation exists among Florida populations of the long-spined sea urchin, Diadema antillarum. Specifically, this project aimed to (1) compare genetic diversity of D. antillarum from six populations in south Florida ranging from Biscayne Bay, the Florida Keys, and Dry Tortugas, and (2) determine whether two broodstock populations of D. antillarum contain variation indicative of native Florida populations. Together, these questions can address whether broodstock populations contain the genetic variation necessary to meet the Florida Fish and Wildlife Conservation Commission’s (FWC’s) genetic policies for reintroduction throughout south Florida. Global FST among native populations was 0.0004 with a highest pairwise FST of 0.0025 between the Upper Keys and the area west of Key West, showing an overall trend of little natural differentiation between populations. Global FST for all populations inclusive of the broodstock samples was 0.0019 with a highest pairwise FST between a native population and broodstock of 0.0066 between Dry Tortuga and Mote’s broodstock, indicating little differentiation resulting from captive breeding. Average allelic richness and heterozygosity ranged from 22.6–24.4 and 0.937–0.956, respectively, for each population. Two-way ANOVAs comparing genetic diversity between native and broodstock populations showed no statistical difference in allelic richness (F= 3.892, p= 0.0535) or heterozygosity (F=1.43, p=0.237). The computer program STRUCTURE estimated the most likely number of genetic clusters to be k=1, inclusive of broodstock populations, further indicating a lack of differentiation either among native populations or between native and broodstock iii populations. These data suggest that captive-bred individuals of D. antillarum could be used for reintroduction as part of a plan to re-establish healthy urchin populations throughout the Florida Keys. iv Acknowledgements This research was funded by the Florida Fish and Wildlife Conservation Commission, grant 2403-7036. I would like to thank the UCF Office of Undergraduate Research, the Hoffman Lab, the PHaSeD Lab, Dr. Eric Hoffman, Dr. Linda Walters, Dr. William C. Sharp, and all the people who helped collect the sea urchins. v Table of Contents Introduction ..................................................................................................................... 1 Methods .......................................................................................................................... 6 Sampling ...................................................................................................................... 6 Molecular methods ....................................................................................................... 6 Statistical analysis ........................................................................................................ 7 Results ............................................................................................................................ 9 Discussion ..................................................................................................................... 11 Appendix A: Figures ...................................................................................................... 16 Appendix B: Tables ....................................................................................................... 23 Literature Cited .............................................................................................................. 28 vi List of Figures Figure 1: Map of Florida showing the native populations used in this study ................. 18 Figure 2:Two-way ANOVA box-plot for differences in average allelic richness between native and broodstock populations ................................................................................ 19 Figure 3: Two-way ANOVA box-plot for differences in average heterozygosity between native and broodstock populations ................................................................................ 20 Figure 4: Output of STRUCTURE analysis for clusters a) K=2, b) K=6, c) K=8. No clear assignment per population is seen and thus no genetic differentiation exists ............... 21 Figure 5: Mean likelihood scores for values of K (clusters) from Structure Harvester .. 22 vii List of Tables Table 1: Forward and Reverse primers used for amplification of microsatellites in PCR ...................................................................................................................................... 24 Table 2: Allelic richness across loci and averaged per population. ............................... 25 Table 3: Heterozygosity across all loci and averaged per population ........................... 26 Table 4: Evanno table from Structure Harvester showing the likelihood of each value of K (clusters). The largest Delta K generally corresponds with the true value of K. ......... 27 viii Introduction Between 1977 and 2001, coral cover declined by 80% throughout the Caribbean (Gardner et al. 2003; Bellwood et al. 2004). During the past few decades, coral reefs have been increasingly threatened by overfishing and other human activities that cause excess pollution (Lessios 1988a; Brown 1987; Done 1992). Outside of human influence, hurricanes and competition have also caused significant declines in coral abundance (Hughes 1989). There is direct evidence that certain species of macroalgae significantly reduced the survival and recruitment of coral larvae (Kuffner et al. 2006; Paul et al. 2011). This negative relationship between macroalgae and corals suggests that coral recovery may not be possible until macroalgal biomass is reduced on reefs (Hughes & Connell 1999). In order to restore coral reef systems in this sense, the trophic structure and associated keystone species that have been lost due to anthropogenic or catastrophic causes may need to be reestablished (Hughes 1994). When population restoration is considered, three basic criteria must be met. The first two are fundamental for the survival of the population; sufficient habitat protection (Soule & Gilpin 1986; Armstrong & Seddon 2008) and awareness of life history stages critical for survival and reproduction (Marcot & Holthausen 1987; Lande 1988). The third requirement of instating a restoration policy is to determine how the genetic variation of the reintroduced population compares to the population being supplemented (Bowles & Whelan 1994). 1 In recent times, the steepest decline of coral in the Caribbean occurred in 1983-1984 and coincided with the massive die-off of a dominant herbivore, the long-spined sea urchin Diadema antillarum (Gardner et al. 2003). Mature D. antillarum can reach up to 500 mm in diameter with their spines ranging another 300-400 mm. They have been seen to gather in groups around the base of coral reefs for protection from their few predators, the queen triggerfish, two species of toadfish, and a couple shellfish species. With a typical lifespan from 4 to 8 years, this external fertilizer is seen to have a long pelagic larval duration of 30-60 days, giving the sea urchin a wide dispersal rate, especially when strong ocean currents are present (Karlson & Levitan, 1990; Lessios 1988b; White et al. 2010).The D. antillarum die-off expedited the coral’s decline by allowing macroalgae to flourish (Hughes et al. 1987; Lessios 1988a, b; Levitan 1988; Carpenter 1990; Gardner et al. 2003). Diadema antillarum was well documented in tropical systems as an indiscriminate grazer of macroalgae due to its ability to consume large amounts of algal biomass on coral reef ecosystems (Sammarco et al. 1974; Carpenter 1986; Morrison 1988; Carpenter 1990). Carpenter (1990) estimated that D. antillarum consumed 60 - 97% of all macroalgae in St. Croix before the 1980s die-off. In 1983, when this unidentified waterborne pathogen caused the mass mortality of 97% of the D. antillarum population, macroalgae proliferated over the coral reefs (Lessios 2001a; Lessios 2005). Within 16 months of the die-off, macroalgal biomass had increased 439% (Carpenter 1990).
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