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Systematic and Phylogeographic Implications of Molecular Variation in the Western North American Roseroot, Rhodiola Integrifolia (Crassulaceae)

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Systematic and Phylogeographic Implications of Molecular Variation in the Western North American Roseroot, Rhodiola Integrifolia (Crassulaceae) Systematic and phylogeographic implications of molecular variation in the western North American roseroot, Rhodiola integrifolia (Crassulaceae). by Heidi J. Guest B.Sc. University of Victoria, 2001 Thesis submitted in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE in the Department of Biology © Heidi J. Guest, 2009 University of Victoria All rights reserved. This thesis may not be reproduced in whole or in part, by photocopying or other means, without the permission of the author. ii Systematic and phylogeographic implications of molecular variation in the western North American roseroot, Rhodiola integrifolia (Crassulaceae). by Heidi J. Guest B.Sc. University of Victoria, 2001 Supervisory Committee Dr. Geraldine A. Allen, Supervisor (Department of Biology) Dr. Barbara Hawkins, Departmental Member (Department of Biology) Dr. John Taylor, Departmental Member (Department of Biology) Dr. Ken Marr, Additional Member (Royal British Columbia Museum) iii Supervisory Committee Dr. Geraldine A. Allen, Supervisor (Department of Biology) Dr. Barbara Hawkins, Departmental Member (Department of Biology) Dr. John Taylor, Departmental Member (Department of Biology) Dr. Ken Marr, Additional Member (Royal British Columbia Museum) Abstract The roseroot genus Rhodiola is widely distributed in arctic and alpine areas of the Northern Hemisphere. It is most speciose in the high mountain ranges of central Asia. Rhodiola integrifolia occurs at high altitudes and high latitudes in western North America and northeastern Asia. During the Pleistocene glaciations the region between Asia and North America known as Beringia was ice free and acted as a glacial refugium for cold- adapted taxa. I surveyed variation in a nuclear (ITS) and chloroplast (psbA-trnH spacer) DNA region in R. integrifolia and its North American relatives, R. rosea and R. rhodantha. Phylogenetic analyses based on ITS showed that (i) the western North American species R. integrifolia and R. rhodantha are distinct but closely related sister taxa; and (ii) these two species and the eastern North American R. rosea belong to separate clades within Rhodiola. Analyses of the plastid region showed that although the iv sister species R. integrifolia and R. rhodantha are distinct, some populations sampled in the southern Rocky Mountains (where the two species overlap) share psbA-trnH haplotypes, suggesting that they hybridized at some time in the past. Within R. integrifolia, both nuclear and plastid DNA regions showed strong north-south patterns of differentiation, a pattern consistent with western North America’s glacial history. Restriction site analysis and sequencing of the plastid psbA-trnH spacer region from samples from 66 populations of R. integrifolia revealed 12 restriction-site haplotypes and 28 sequence haplotypes. A few of the sequence haplotypes were widely distributed, but most were relatively localized. Of the localized haplotypes, 10 were exclusively Beringian and an additional four were found along the northern boundary of glaciation (at the last glacial maximum) in the Yukon and Alaska; two haplotypes were found in northern coastal BC (Queen Charlotte Islands and adjacent mainland), in the vicinity of possible glacial refugia on the Queen Charlotte Islands. Only five haplotypes occurred exclusively south of the glacial maximum. Haplotype diversity in R. integrifolia decreased toward the south. Populations north of 60 N contained 21 (75%) of the 28 sequence haplotypes, and often contained multiple restriction-site haplotypes. Populations south of that latitude contained a total of only 13 restriction haplotypes, and were usually monomorphic for restriction-site haplotypes. Phylogenetic analyses of R. integrifolia plastid DNA sequences supported a hypothesis of southward spread from Alaska, and suggested that two to three clades of R. integrifolia independently migrated southward in western North America. v Table of Contents Supervisory Committee......................................................................................... ii Abstract.................................................................................................................. iii Table of Contents................................................................................................... v List of Tables ......................................................................................................... viii List of Figures ........................................................................................................ ix Acknowledgements ................................................................................................ x Dedication .............................................................................................................. xi Chapter 1: INTRODUCTION 1.1 Climatic and Glacial History of Western North America ....................... 1 1.2 Phylogeography and Plant Molecular Markers....................................... 6 1.3 The Study Species, Rhodiola integrifolia............................................... 8 1.4 Objectives ............................................................................................. 12 Chapter 2: METHODS 2.1 Collection of Plant Material................................................................... 13 2.2 DNA Extraction .................................................................................... 20 2.3 DNA Regions Sampled ......................................................................... 20 2.3.1 Nuclear DNA: ITS ................................................................ 20 2.3.2 CpDNA Markers/Regions ...................................................... 21 2.3.2.1 Screening of Chloroplast DNA Markers/Regions....... 21 2.3.2.2 Amplification and Sequencing of PsbA-trnH Region. 22 2.3.2.3 RFLP Sampling of the PsbA-trnH Region................. 26 2.3.2.4 Restriction Site Haplotype Determination.................. 27 2.4 Data Analyses ....................................................................................... 29 2.4.1 Phylogenetic Analyses ........................................................... 29 2.4.1.1 Sequence Assembly and Alignment........................... 29 2.4.1.2 ITS Analyses............................................................. 29 2.4.1.2.1. Maximum Parsimony and Maximum Likelihood Analyses using PAUP ............ 30 vi 2.4.1.3 Chloroplast DNA Analyses....................................... 32 2.4.2 Haplotype Network Estimation .............................................. 33 2.4.3 Nested Clade Phylogeographic Analysis of RFLP data........... 35 2.4.4 Geographic Mapping of CpDNA Haplotypes ......................... 36 Chapter 3: RESULTS 3.1 ITS Sequence Analyses and Relationships in Rhodiola.......................... 38 3.1.1 Summary of ITS Sequence Variation. .................................... 38 3.1.2 Phylogenetic Analyses of the ITS Region of the Nuclear Genome ................................................................................ 38 3.1.3 Geographic Distributions of ITS Sequence Variants of R. integrifolia and R. rhodantha............................................ 43 3.2 Chloroplast DNA Sequence Analyses and Comparison of Nuclear and Chloroplast Phylogenies............................................................. 43 3.2.1 Summary of PsbA-trnH Sequence Variation.......................... 43 3.2.2 Phylogenetic Analyses of the PsbA-trnH Region of the CpDNA........................................................................... 45 3.2.3 Comparison of Nuclear and Chloroplast Genome Sequences ............................. ............................................... 46 3.3 Chloroplast DNA Patterns and the Phylogeography of R. integrifolia.... 49 3.3.1 Restriction enzyme haplotype diversity and distributions. ..... 49 3.3.2 Sequence haplotype diversity and distributions. .................... 67 3.3.3 Statistical Parsimony and the CpDNA Sequence Haplotype Network................................................................................ 70 3.3.4 Nested Clade Phylogeographic Analyses............................... 70 Chapter 4: DISCUSSION 4.1 Rhodiola Relationships.......................................................................... 74 4.1.1 Similarities and Differences Between R. integrifolia and R. rosea ................................................................................ 75 4.1.1.1 Geographic Relationships.......................................... 76 4.1.1.2 Medicinal Properties.................................................. 77 4.1.2 Rhodiola integrifolia and R. rhodantha: Daughters of an Ancient Colonist? ................................................................. 78 vii 4.2 Hybridization ........................................................................................ 80 4.3 Phylogeography of Rhodiola integrifolia............................................... 82 4.3.1 Colonization and Dispersal ..................................................... 82 4.3.1.1 Causes of Observed Geographic Patterns................... 83 4.3.1.2 Use of NCPA (or not) in the Absence of Other Methods .................................................................... 84 4.3.2 Other Refugia ......................................................................... 86 4.4 Climate Change Implications................................................................. 87 Literature Cited....................................................................................................
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