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Tsuga Caroliniana Engelm.) Population Genetic Structure and Diversity in the Southern Appalachians Using Microsatellite Markers

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Tsuga Caroliniana Engelm.) Population Genetic Structure and Diversity in the Southern Appalachians Using Microsatellite Markers ABSTRACT CAMPBELL, ANGELIA ROSE. Assessing Carolina Hemlock (Tsuga caroliniana Engelm.) Population Genetic Structure and Diversity in the Southern Appalachians Using Microsatellite Markers. (Under the direction of Robert Jetton). Carolina hemlock (Tsuga caroliniana Engelm.) is a rare conifer species that exists in a few small, isolated populations throughout the southern Appalachian Mountains. There is a need to develop conservation genetics strategies for this species, as it is under threat by the hemlock woolly adelgid (Adelges tsugae Annand), an invasive species that can kill the trees in as little as four years. In order to develop these strategies, more information about the population genetic structure of Carolina hemlock is necessary. In this study, 439 trees from twenty-nine populations of Carolina hemlock were sampled: a range-wide, comprehensive sampling of most of the known populations of Carolina hemlock. Sixteen polymorphic microsatellite loci were amplified in these samples. The results show that the populations of Carolina hemlock are inbred (Overall FIS = 0.464), and highly differentiated from each other with little gene flow (Overall FST = 0.496, Nm = 0.9116). Three genetic clusters were inferred using STRUCTURE, and the genetic makeup of each population was identified. One cluster dominated in the northern populations, one in the southeastern populations, and one in the southwestern populations -- though all three regions had some representation from every cluster. The relationships displayed on the neighbor-joining tree mirror the population structure shown in the STRUCTURE results. The data indicated that the unusual population of Cuyahoga Valley is likely planted rather than natural. Though no correlation between genetic diversity and latitude, longitude or elevation was uncovered, the analysis yielded informative diversity measures for each population. Pockets of diversity were identified. This information will be invaluable in developing conservation strategies for Carolina hemlock. Knowledge about the population genetic structure of Carolina hemlock will inform management efforts, showing which regions and populations to prioritize for protection and conservation. © Copyright 2014 by Angelia Campbell All Rights Reserved Assessing Carolina Hemlock (Tsuga caroliniana Engelm.) Population Genetic Structure and Diversity in the Southern Appalachians Using Microsatellite Markers by Angelia Rose Campbell A thesis submitted to the Graduate Faculty of North Carolina State University in partial fulfillment of the requirements for the degree of Master of Science Forestry and Environmental Resources Raleigh, North Carolina 2014 APPROVED BY: _______________________________ ______________________________ Robert M. Jetton Kevin M. Potter Committee Chair ________________________________ ________________________________ Fred Gould Jenny Xiang Minor Representative ii BIOGRAPHY Angelia Campbell has been interested in science and the natural world for as long as she can remember. She spent a significant part of her childhood in the mountains of North Carolina, exploring the forests and trails armed with field guides and binoculars. This interest developed into a desire to pursue a career in a field related to plant sciences. From August 2008-May 2011 she pursued a degree in biology at Furman University. She enjoyed the study of botany and worked with Dr. Joe Pollard on an undergraduate research project studying Psychotria grandis, a plant with an unusual ability to take up heavy metals from the soil. This research project resulted in her first scientific publication: Facultative Hyperaccumulation of Nickel in Psychotria grandis (Rubiaceae). Angelia graduated from Furman University with her B.S. in Biology in 2011. In August 2012, Angelia began working on her M.S. in Forestry and Environmental Resources with a minor in Plant Biology at NC State University. Under the direction of Robert Jetton, she studied the population genetic structure and diversity of Carolina hemlock. She sampled most of the known populations across the range of Carolina hemlock, and travelled to the Southern Institute of Forest Genetics in Saucier, Mississippi to analyze the samples using microsatellite markers. The findings are presented in this thesis. iii ACKNOWLEDGMENTS I am grateful to the many people who provided help, support, and advice throughout my research. Foremost, I would like to thank my committee members: Robert Jetton, Kevin Potter, Fred Gould, and Jenny Xiang. Their feedback, expertise, and help throughout my project was invaluable. I would especially like to thank Robert Jetton, my advisor, who guided me through every aspect of the project. Kevin Potter was also very helpful, especially during the data analysis process. Both of them were always available to answer my frequent questions and point me in the right direction. I would like to thank Sedley Josserand, Craig Echt, and Dana Nelson from the Southern Institute of Forest Genetics, who were involved with the lab work portion of the project. SIFG hosted me for months while I completed my lab work for the project. I would especially like to thank Sedley Josserand, who worked closely with me, dedicating much of her time to guiding me through the lab work and helping me resolve any issues that arose. I am also grateful for Andy Whittier's contributions to the project. Andy Whittier was heavily involved with the field work. He put a lot of time and effort into planning and travelling with me to nearly every population that we visited. I owe the success of my project to the many people who helped along the way, and I am grateful to each of them. iv TABLE OF CONTENTS LIST OF TABLES...................................................................................................................v LIST OF FIGURES................................................................................................................vi CHAPTER 1: A Review of the Literature Relevant to Carolina Hemlock and the Hemlock Woolly Adelgid.........................................................................................................1 CHAPTER 2: Assessing Carolina hemlock (Tsuga caroliniana Engelm.) population genetic structure and diversity in the southern Appalachians using microsatellite markers...................................................................................................................................30 INTRODUCTION.................................................................................................................30 MATERIALS AND METHODS..........................................................................................34 RESULTS...............................................................................................................................40 DISCUSSION.........................................................................................................................43 REFERENCES.......................................................................................................................51 TABLES AND FIGURES.....................................................................................................56 v LIST OF TABLES Table 1. Populations of Carolina hemlock from which samples were collected. For each population, location, state, coordinates, elevation (averaged elevation in meters of all samples taken for each population), HWA prevalence (% of sampled trees infested with HWA), date collected and number of samples analyzed from each population are given. The p-value for Hardy Weinberg exact tests for each population is also given. * means that there was a highly significant value for p, and thus that the population was out of Hardy-Weinberg equilibrium...............................................................................................................................56 Table 2. Sixteen loci were utilized in the study. Ho (observed heterozygosity), He (expected heterozygosity), FIS, FST, A (total alleles at each locus), Ae (effective alleles at each locus), and null allele frequency estimates (Brookfield 1996) are given. All loci met the p-value for being out of Hardy Weinberg equilibrium (*=significant p-value).........................................57 Table 3. FSTAT 2.3.9.2 yielded values for the probability that a given pair of loci is in genetic disequilibrium. The adjusted P-value for the 5% nominal level is 0.000417, and all loci that met this significance value for disequilibrium are shown in the table.......................58 Table 4. FSTAT 2.3.9.2 was used to estimate the Weir and Cockerham F-statistics. The table shows FIS and FST. The values given are mean values for each locus, using the jackknifing over populations method..........................................................................................................59 Table 5. Table shows the average Cavalli-Sforza chord distance between the given population and all other populations. Values obtained using FreeNA....................................60 Table 6: Diversity statistics for each population of Carolina hemlock. GenAlEx yielded a list of private alleles per population. Latitude, longitude, elevation (averaged over all trees sampled) are given. Polymorphism (percent of loci that were polymorphic in the population), Ho (observed heterozygosity), and He (expected heterozygosity) values were obtained. A is allelic richness, the number of alleles per locus averaged for each population.......................61 Table 7. R values
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