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Integrating Phylogenetic Relationships and Population Structure

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Integrating Phylogenetic Relationships and Population Structure INTEGRATING PHYLOGENETIC RELATIONSHIPS AND POPULATION STRUCTURE FOR CONSERVATION PLANNING IN GALLIFORMES by SOO HYUNG EO (Under the Direction of John P. Carroll) ABSTRACT Genetic components and evolutionary processes are critical to explain variation in both extinction risks among species and population structures within species because they generate and maintain adaptive biological variation. To understand phylogenetic relationships among fowl species, I constructed supertree of orders Galliformes (chicken-like birds) and Anseriformes (duck-like birds). Using formal algorithmic procedures and source trees available, supertree methods are able to represent such a large clade phylogeny, which is almost impossible with conventional approaches using either molecular or non-molecular data. My Galloanserae supertree represents one of the most comprehensive estimates for the group to date, including 376 species (83.2% of all species; all 162 Anseriformes and 214 Galliformes). The use of this phylogenetic supertree enables us to apply comparative analysis, considering phylogenetic independence, to describing their remarkable diversity of life history, morphology, behavioral ecology, conservation biology, and other evolutionary processes across species. Below species level, it is critical that we understand genetic identity as the basis for the conservation and management of the species and surrounding habitat. Using mitochondrial and nuclear microsatellite loci, I investigated intraspecific genetic relationships among northern bobwhites (Colinus virginianus). There was extremely high genetic differentiation between isolated Arizona northern bobwhites (masked bobwhite, C. v. ridgwayi) and the other subspecies (C. v. marilandicus, C. v. virginianus, C. v. floridanus, C. v. mexicanus, C. v. taylori, and C. v. texanus). Based on genetic structure and geographic ranges, my results suggest that each of C. v. ridgwayi and C. v. floridanus should be considered as a distinct unit for conservation or management, supporting current subspecies limits. However, C. v. virginianus, C. v. marilandicus, C. v. mexicanus, and C. v. taylori may be considered a single management unit because levels of genetic divergence among these putative subspecies were quite low. Among all analyzed subspecies, masked bobwhite has the lowest diversity in all genetic information. Therefore, it is highly recommended to set conservation priority to the masked bobwhites as an independent conservation unit. INDEX WORDS: Supertree, Galloanserae, Anseriformes, Galliformes, Colinus virginianus, Population structure, Units for Conservation and management INTEGRATING PHYLOGENETIC RELATIONSHIPS AND POPULATION STRUCTURE FOR CONSERVATION PLANNING IN GALLIFORMES by SOO HYUNG EO B.S., The Seoul National University, South Korea, 1999 M.S., The Seoul National University, South Korea, 2001 A Dissertation Submitted to the Graduate Faculty of The University of Georgia in Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY ATHENS, GEORGIA 2008 © 2008 Soo Hyung Eo All Rights Reserved INTEGRATING PHYLOGENETIC RELATIONSHIPS AND POPULATION STRUCTURE FOR CONSERVATION PLANNING IN GALLIFORMES by SOO HYUNG EO Major Professor: John P. Carroll Committee: Michael J. Conroy Daniel E. L. Promislow John P. Wares Electronic Version Approved: Maureen Grasso Dean of the Graduate School The University of Georgia August 2008 ACKNOWLEDGEMENTS My wife, Eunyoung Cho, has been supportive of every aspect of me through these long years, all while maintaining her job, keeping the household going, and taking care of our daughter, Jadu (Darby). This dissertation would not have been possible without her unconditional love and constant patience. Eunyoung’s and Jadu’s smile has provided motivation to finish this work. I love you, Eunyoung and Jadu. I also thank my mother and parents-in-law for being supportive even though I have stayed in school for much longer time than expected. I would like to acknowledge my committee members for their advice and patience. First, my advisor John P. Carroll took a chance on me as a graduate student and provided a great support and environment for me. His encouragement and laughs kept me on track. John P. Wares was a constant source of information on population genetics and evolutionary biology. He also provided detailed editorial advice on the manuscripts. My other committee members, Michael J. Conroy and Daniel E. L. Promislow, helped me during written and oral exams, and contributed to my dissertation research. For the supertree construction, I would like to thank Olaf, R. P. Bininda-Emonds for assistance and advice during all steps from project design to writing manuscript. I am grateful to Aidan Keane for sharing his idea on comparative analysis and for providing his dataset of Galliformes life history. I would like to thank B. Faircloth, C. J. Nairn, B. Shamblin, and T. Terhune for their assistance in completing molecular work. I am indebted to the following individuals for collecting northern bobwhite samples: R. Aguilar, B. Bass, A. Burnett, R. Chapman, J. Cook, R. Dimmick, B. Faircloth, B. Grossman, R. iv v Hamrick, D. L. Horner, G. Joyner, J. Martin, R. Pierson, L. Potter, B. Robinson, R. Rodgers, C. Sisson, A. Staphenson, R. Stonebraker, S. Taylor, R. Thackston, J. Thompson, M. Travis, T. Valentine, and E. Wehland. Sampling for my population genetics project would not have been possible without their generous cooperation. This dissertation work was funded by many sources: the University of Georgia, Warnell School of Forestry and Natural Resources, MacIntire-Stennis GEO-100 and 136, Bill Terrell Research Grant and Branch Howe Jr. Research Grant of Georgia Ornithological Society, the Northeast Georgia, Augusta, and Albany Chapters of Quail Unlimited, Tall Timbers Research Station, and Land Conservancy, Inc. Thank you all. TABLE OF CONTENTS Page ACKNOWLEDGEMENTS ........................................................................................................... iv LIST OF TABLES ........................................................................................................................ vii LIST OF FIGURES ....................................................................................................................... ix CHAPTER 1 INTRODUCTION AND LITERATURE REVIEW .....................................................1 2 A PHYLOGENETIC SUPERTREE OF THE FOWLS (GALLOANSERAE, AVES)12 3 SUBSPECIES AND UNITS FOR CONSERVATION AND MANAGEMENT OF THE NORTHERN BOBWHITE IN THE EASTERN UNITED STATES ............62 4 EXTREMELY HIGH OR TOO LOW GENETIC DIFFERENTIATION IN HIGHLY POLYTYPIC WIDESPREAD NORTHERN BOBWHITES: CONGRUENT OR CONFLICTING PATTERNS IN MITOCHONDRIAL AND NUCLEAR MICROSATELLITE LOCI ....................................................................................90 5 CONCLUSIONS........................................................................................................138 APPENDICES A The rQS VALUES FOR THE STRICT CONSENSUS SUPERTREE, INDICATING NODAL SUPPORT (± SE) AMONG THE SET OF SOURCE TREES ..............142 B LIST OF ORIGINAL REFERENCES CONTAINING SOURCE TREES USED IN THE GALLOANSERAE SUPERTREE CONSTRUCTION ...............................154 vi LIST OF TABLES Page Table 2.1: Information for major clades of Gallanserae, including number of taxa recognized and covered in this study and summary statistics for the supertrees. ....................................43 Table 3.1: Northern Bobwhite (Colinus virginianus) collection sites (mapped in Figure 4.1), genetic polymorphism, and hypotheses of demographic history for different subspecies or populations, based on mtDNA CR sequences. ...........................................................82 Table 3.2: Pairwise FST (below diagonal) and the significance of Exact tests of differentiation (above diagonal) among the northern bobwhite subspecies in the study area, based on mtDNA control region. ...................................................................................................84 Table 3.3: Analysis of molecular variance in the northern bobwhites with several a priori grouping scenarios, based on putative subspecies. .........................................................85 Table 4.1: Northern Bobwhite (Colinus virginianus) collection sites (mapped in Figure 5.1) and descriptive genetic diversity data of each local populations based on mtDNA control region sequences and 16 multilocus microsatellite loci. Total number of individuals analyzed (NT), number of mtDNA-sequenced individuals (nmt), number of mtDNA haplotypes (nh), haplotype (h) and nucleotide (π) diversities (± standard deviation, SD), number of genotyped individuals (nmic), mean number of alleles per locus (A), allelic richness (AC), observed (HO) and expected (HE) heterozygosities (± SD). ...................125 Table 4.2: Pairwise values of FST (mtDNA; above the diagonal) and RST (microsatellites; below the diagonal) among populations (with seven or more individuals per population) of vii viii northern bobwhites. * indicates significant (P < 0.05) pairwise FST or RST, and values in bold are significant after sequential Bonderroni correction. NA, not available ......127 Table 4.3: Analysis of molecular variance (AMOVA) for the northern bobwhites. Samples were partitioned with several a priori grouping scenarios, based on putative subspecies and/or geographic distribution. .....................................................................................128 Table 4.4: Population
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