Molecular Population Genetics And Systematics Of Alaska Brown Bear (Ursus Arctos L.) Item Type Thesis Authors Talbot, Sandra Looman Download date 06/10/2021 20:14:11 Link to Item http://hdl.handle.net/11122/8899 MOLECULAR POPULATION GENETICS AND SYSTEMATICS OF ALASKA BROWN BEAR (URSUS ARCTOS L.) A THESIS Presented to the Faculty of the University of Alaska Fairbanks in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY By Sandra Looman Talbot, B.S., M.S. Fairbanks, Alaska May 2006 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. UMI Number: 3229743 INFORMATION TO USERS The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleed-through, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. ® UMI UMI Microform 3229743 Copyright 2006 by ProQuest Information and Learning Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. ProQuest Information and Learning Company 300 North Zeeb Road P.O. Box 1346 Ann Arbor, Ml 48106-1346 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. MOLECULAR POPULATION GENETICS AND SYSTEMATICS OF ALASKA BROWN BEAR (URSUS ARCTOS L.) By Sandra Looman Talbot RECOMMENDED: Advisory Committee Co-Chair €UX. r "' Advisory Committee Co-Chair er'C I Assistant Chair, Department of Biology,and\ Wildlife APPROVED: v Dean, College of Natural Science and Mathematics . c M - d t * - . Dean of the Graduate School Date Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. ABSTRACT Complete nucleotide sequences of the mitochondrial cytochrome b, tRNApmline and tRNA!/'re0"",e genes of the eight extant species of ursids, as well as 166 brown bears (Ursus arctos L.) from 10 geographic regions of Alaska and elsewhere, are used to generate hypotheses about phylogenetic relationships among ursids and phylogeographic relationships among brown bears. Additional data were obtained from mitochondrial DNA control region from over 200 brown bears among 14 populations in Alaska, to assess structuring among brown bears. Phylogenetic analyses indicate the giant panda (Ailuropoda melanoleuca ) and spectacled bear ( Tremarctos ornata) represent basal extant taxa. Ursines, including the sun bear ( Helarctos malayanus), sloth bear (Melursus ursinus), Asiatic and American black bears ( Ursus thibetanus and U. americanus), brown bear, and polar bear (U. maritimus) apparently experienced rapid radiation during the mid-Pliocene to early Pleistocene. The two black bears appear to be sister taxa; brown and polar bear are the most recently derived of the ursines. Polar bears apparently arose during the Pleistocene from within a clade of brown bears ancestral to populations currently inhabiting islands of the Alexander Archipelago of southeastern Alaska. Thus, brown bears are paraphyletic with respect to polar bears. Parsimony and distance analyses suggest two distinct clades of mtDNA: one (Clade I) composed only of Alexander Archipelago bears, and the other clade comprised of bears inhabiting all other regions of Alaska (Clade II). This latter clade represents bears inhabiting eastern (Clade Ha) and western (Clade lib) Alaska. Mismatch analysis uncovered a pattern suggestive of recent expansion among some populations comprising Clade lib. Over 90% of populations in Alaska were significantly differentiated as measured by variance in haplotype frequencies, suggesting limited contemporary female-mediated gene flow and/or shifts in gene frequency through genetic drift. The degree of population genetic differentiation revealed using mtDNA, as well as limited information from comparisons of multilocus microsatellite genotypes from bears representing four Alaska populations, suggests many Alaskan populations are evolving independently. Analyses of molecular Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. variance gave little support for currently accepted subspecies hypotheses. This research has provided new perspectives on processes that drive population structure of brown bears of Alaska and worldwide. Reproduced with permission of the copyright owner. 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Table of Contents Page Signature Page .......................................................................................................................i Title Page.............................................................................................................................. ii Abstract ................................................................................................................................iii Table of Contents .................................................................................................................v List of Figures .....................................................................................................................vii List of Tables .......................................................................................................................xi List of Appendices ........................................................................................................... xiii Preface................................................................................................................................xiv Introduction ........................................................................................................................... 1 Background...................................................................................................................... 1 Choice of Model...............................................................................................................2 Choice of Tool and Molecule........................................................................................3 Specific Aims..................................................................................................................10 Models, Hypotheses and Predictions.........................................................................12 Insularization in Fragmented Populations .............................................................12 Congruence of Morphological and Genetic Differentiation .............................. 14 Comparison Between Nuclear and MtDNA Differentiation: Dispersal 17 Insular Bear Populations and Conservation Biology........................................... 18 Phylogenetics and Conservation Biology.................................................................21 References....................................................................................................................... 22 Chapter 1. A Phylogeny of the Bears (Ursidae) Inferred from Complete Sequences of Three Mitochondrial Genes..................................................................40 1.1 Abstract ...................................................................................................................... 40 1.2 Introduction ............................................................................................................... 41 1.3 Materials and Methods ............................................................................................. 42 1.4 Results and Discussion .............................................................................................44 1.5 Acknowledgments .....................................................................................................53 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. VI 1.6 References ................................................................................................................. 53 Chapter 2. Phylogeography of Brown Bears (Ursus arctos) of Alaska and Paraphyly Within the Ursidae...............................................................................65 2.1 Abstract ......................................................................................................................65 2.2 Introduction ...............................................................................................................66 2.3 Materials and Methods .............................................................................................69 2.4 Results........................................................................................................................72 2.5 Discussion ................................................................................................................. 80 2.6 Acknowledgments .................................................................................................... 89 2.7 References ................................................................................................................. 89 Chapter 3. Population Genetic Structure and Population History of Ursus arctos in Alaska: Evidence for Female Philopatry and Male-biased Gene Flow................................................................................................ 115 3.1 Abstract