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Abstract Clark, Catherine Margaret ABSTRACT CLARK, CATHERINE MARGARET. Genetic diversity and phylogeography in a Tasmanian rainforest conifer (Lagarostrobos franklinii (Hook f.) Quinn Podocarpaceae. (Under the direction of Dr. Ronald Sederoff and Dr. Thomas Wentworth). Genetic variation in Huon pine (Lagarostrobos franklinii), a Tasmanian rainforest conifer, was estimated using several marker systems and two spatial scales. Genealogy based methods were used to infer population history of eight Huon pine stands based on chloroplast DNA variation. Chloroplast nucleotide diversity (π) was low (0.00093± 0.00006) in a multilocus haplotype generated by three universal chloroplast primers (trnS-trnT, trnD-trnT, psbC-trnS). Five haplotypes were identified; two were€ widely distributed but the most frequently occurring haplotype was found only in trees in the western portion of the range. Genetic differentiation among populations was significant and showed a high degree of structure (GST = 0.26077 p ≤ 0.00001). Pairwise comparisons between populations revealed significant structure between the southeastern and northwestern watersheds and significant isolation€ by distance€ ( p ≤ 0.0220). Nucleotide variation was also assessed in segments of three nuclear genes, 4Cl (4- € coumarate: coenzyme A ligase), ITS2 (intergenic spacer region of ribosomal DNA) and G3pdh (glyceraldehyde 3-phosphate dehydrogenase). A total of 1,154 base pairs were sequenced from 79 individuals (158 alleles) representing seven geographic locations. Estimates of nucleotide diversity (π = 0.00089 ± 0.00007) and theta (θ) (0.00061 ± 0.00031) were low for the combined loci and similar to chloroplast estimates. There was a higher level of variation at the 4Cl locus (π = 0.00167 ± 0.00014) associated with recombination. Nucleotide diversity for nuclear loci was highest in the subalpine Mt. Read population, previously described as a putative clonal stand. Population differentiation (FST = 0.0130) was lower than estimated in chloroplast DNA, or in a previous allozyme investigation (FST = 0.095). Multilocus genotypes based on RAPD markers (random amplified polymorphic DNA) were generated to further investigate genetic diversity in the Huon pine stand at Mt. Read. DNA was analyzed from 63 trees from Mt. Read and genetic diversity compared to 33 Huon pine samples from a wide geographic range. Twelve random decanucleotide primers amplified a total of 35 alleles. Only three of the alleles (8.6%) from the Mt. Read population were polymorphic in contrast to 18 (51.4%) polymorphic alleles in the reference population. Gene diversity at Mt. Read (0.0316 ± 0.1061) was six-fold lower than that found in the reference sample (0.1973 ± 0.2112). Only four unique DNA fingerprints were revealed at Mt. Read and these were spatially clustered in the stand. Each of the 33 isolates in the wide geographic sample exhibited a unique genotype. The three marker systems of this study, along with a previous allozyme survey, are concordant in indications of a low level of diversity in a Southern Hemisphere conifer. The low level of nucleotide diversity, star-like phylogeny and haplotype distribution of chloroplast DNA suggest that Huon pine has experienced a series of population bottlenecks and colonization events from refugial areas. This is congruent with paleoecological data that suggest that there were major refugial areas on the western coast of Tasmania in addition to small, isolated refugia in other portions of the current range. The low level of variation found in nuclear loci is also compatible with a history of demographic events related to Pleistocene and Holocene environmental variability and long-term range reduction. The limited genetic variation in the Mt. Read population may be related to minimal gene flow into this stand due to geographic isolation, and extensive vegetative reproduction in a harsh environment. For my mother, Jo Graham Clark Herlinger, and for Ernie Retzel and Ken Garrard ii BIOGRAPHY Catherine M. Clark was born in Pasadena, Texas and grew up and attended school in Houston, Texas. After graduating from Daeflower Free School, she left Houston on a bicycle and ended up in the Santa Cruz Mountains of California. After several cross-country moves, Catherine moved to Boone, North Carolina in 1978 to attend Appalachian State University and received a B.S. in 1984 from the Biology Naturalist program. After completing course work at Appalachian State University, she took an extended trip to Mexico. Some of the experiences of this trip led to a decision to pursue an education in the health care field. After graduating from Wake Technical College with an Associate Degree in Nursing in 1985 she worked as a Registered Nurse for ten years in gerontology, student health, chemical dependency treatment and for the American Red Cross. Catherine then decided to return to studying plant biology and returned to school at North Carolina State University. She received a Master’s degree in Botany from North Carolina State University in 1998, based on the study of chloroplast microsatellite variation in North American Abies. She then continued her graduate education in a Ph.D. program, co-majoring in Botany and Forestry at North Carolina State University. iii ACKNOWLEDGEMENTS It is a great privilege to pursue an extended educational program. The support, guidance and friendship of family, friends and professional colleagues have made it possible for me to complete this degree. I would like to first thank the members of my committee for their examples of scholarship, education and leadership: Dr. Ron Sederoff, Dr. Tom Wentworth, Dr. Henry Amerson and Dr. Bruce Weir. A number of sources of financial support and recognition have made my graduate program possible including; an EPA STAR Graduate Fellowship, Department of Forestry Fellowship, Preparing the Professoriate Fellowship, Namkoong Family Graduate Fellowship, The American Chestnut Foundation and a National Science Foundation Small Grant for Exploratory Research. Members of the Forest Biotechnology Group provided technical assistance with molecular markers. In particular, I am grateful to Dr. Henry Amerson, Saul Garcia, Dr. Arthur Johnson, Dr. David Remington, Dr. Alexander Myburg, and Dr. Ying-Hsuan Sun. Jerri Johnson, secretary for the Forest Biotechnology Group and Sue Vitello, Graduate Program secretary for the Botany Department, provided administrative assistance. Thanks to Dr. Ignazio Carbone of the NCSU Plant Pathology Department who provided assistance with data analysis. The people and agencies of Tasmania were very gracious in facilitating my field collections. Mick Brown of Forestry Tasmania provided assistance with field collections. Tasmanian Parks and Wildlife provided information on location of Huon pine populations and facilitated the issuance of sample permits. Dr. Greg Jordan of the Plant Biology iv Department, University of Tasmania assisted with information on the paleohistory of Huon pine and in finding a field assistant for sample collection. Penny Brodrib was a wonderful, resourceful and knowledgeable field assistant. Georgina Davies was my initial contact in Tasmania and provided names of several contacts that were vital to the success of the field collections. Dr. Alison Shapcott shared her knowledge of her previous population genetic survey of Huon pine. Dr. Rosanne D’Arrigo of the Tree Ring Laboratory at Lamont-Doherty Earth Observatory first approached members of the Forest Biotechnology Group about working with Huon pine. She and Dr. Ed Cook, also of the Tree Ring Laboratory, collaborated on a subsequent grant proposal involving this species and I am grateful for their assistance with the project. I am also grateful to Dr. Remy Petit and Dr. Antoine Kremer of INRA for hosting me in their lab at Pierroton, France to study DNA extraction from wood specimens. Finally, I owe very special thanks to both Ernie Retzel and Ken Garrard, two people that have had an extraordinary impact on my life. They provided exceptional support that made it possible for me to complete this program. v TABLE OF CONTENTS LIST OF TABLES...............................................................................................................ix LIST OF FIGURES .............................................................................................................xi PREFACE.............................................................................................................................1 Literature Cited.....................................................................................................................9 CHAPTER 1: CHLOROPLAST DNA PHYLOGEOGRAPHY IN A TASMANIAN ENDEMIC CONIFER (LAGAROSTROBOS FRANKLINII (HOOK F.) QUINN) PODOCARPACEAE ..........................................................................................................20 Abstract ..............................................................................................................................21 Introduction ........................................................................................................................23 Study species...........................................................................................................26 Materials and Methods........................................................................................................29 Sample collection ....................................................................................................29 DNA extraction, PCR amplification and sequencing................................................29
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