University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 5-2011 Islands, Metapopulations, and Archipelagos: Genetic Equilibrium and Non-equilibrium Dynamics of Structured Populations in the Context of Conservation Robert Graham Reynolds [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Evolution Commons, and the Population Biology Commons Recommended Citation Reynolds, Robert Graham, "Islands, Metapopulations, and Archipelagos: Genetic Equilibrium and Non- equilibrium Dynamics of Structured Populations in the Context of Conservation. " PhD diss., University of Tennessee, 2011. https://trace.tennessee.edu/utk_graddiss/1016 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Robert Graham Reynolds entitled "Islands, Metapopulations, and Archipelagos: Genetic Equilibrium and Non-equilibrium Dynamics of Structured Populations in the Context of Conservation." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Ecology and Evolutionary Biology. Benjamin M. Fitzpatrick, Major Professor We have read this dissertation and recommend its acceptance: James Fordyce, Graciela Cabana, Daniel Simberloff Accepted for the Council: Carolyn R. Hodges Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) To the Graduate Council: I am submitting herewith a dissertation written by Robert Graham Reynolds entitled “Islands, metapopulations, and archipelagos: genetic equilibrium and non-equilibrium dynamics of structured populations in the context of conservation.” I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the requirements for the degree of Doctor of Philosophy, with a major in Ecology and Evolutionary Biology. Dr. Benjamin Fitzpatrick, Major Professor We have read this dissertation and recommend its acceptance: Dr. James Fordyce Dr. Graciela Cabana Dr. Dan Simberloff Accepted for the Council: Carolyn R. Hodges Vice Provost and Dean of the Graduate School (Original signatures are on file with official student records.) Islands, Metapopulations, and Archipelagos Genetic Equilibrium and Non-equilibrium Dynamics of Structured Populations in the Context of Conservation A Dissertation Presented for The Doctor of Philosophy Degree The University of Tennessee, Knoxville Robert Graham Reynolds May 2011 ii Copyright © 2011 by Robert Graham Reynolds All rights reserved. iii ACKNOWLEDGMENTS Foremost a debt of gratitude is owed to my wife Jennifer for encouraging me to pursue a lifelong desire to become a scientist. Her support of both her husband and her household was essential to my ability to remain a student until completion of a terminal degree, and I will be forever in her debt. I am also indebted to my advisor, Ben Fitzpatrick, for his mountains of patience and assistance that cannot be efficiently communicated for sake of brevity and lexical forfeit. I am especially grateful to my committee: Jim Fordyce, Dan Simberloff, and Graciela Cabana, for their encouragement and sagacious influence on my development as a scientist. Stan Guffey has been a tremendous pedagogical mentor to me, he is a gifted teacher and I have benefited greatly from his instruction and encouragement. Finally, I am grateful to the many members of the Department of Ecology and Evolutionary Biology who have encouraged or assisted me: especially Chris Boake, Gary McCracken, Darrin Hulsey, Sandy Echternacht, Mark Alston, Brian O'Meara, Phyllis Bice, Cheryl Lynn, Kate Weaver (Core Biology), Pearl Kirkland-Smith, Anne Mintz, and Jaime Call; and to the wonderful custodial and maintenance staff in Hesler Hall who kept my office clean and functional for five years. I have many individuals to thank for their assistance (including blood and sweat) in the Turks and Caicos Islands: Kelly Bradley, Joe Burgess, Cory Deal, Matt Emery, Glenn Gerber, T.J. Jett, Chuck Knapp, Brian Naqqi Manco, Lindsay Mensen, Naz Missick, Matt Niemiller, Richard Plate, Tarren Wagner, George Waters, and Matt Wilson. The staff, both current and former, of the Department of Environment and Coastal Resources of the Turks and Caicos Islands Government assisted me with mounds iv of information and permitting, and I am especially grateful to Brain Naqqi Manco, Brian Riggs, Eric Salamanca, Paul Dickenson, and Marlon Hibbert for their assistance. For logistic support in the Turks and Caicos I am grateful to The Turks and Caicos National Trust, and to Blue Horizon Resort for property access. I am especially grateful to the Turks and Caicos Sporting Club at Ambergris Cay for logistical support, property access, use of the Environmental Center, delicious meals, and air transportation over four seasons of field work; and to Lindsay Mensen and Matt Emery for always making me feel welcome on Ambergris. Glenn Gerber is owed special thanks for his unofficial advisor status, encouragement, and huge amount of assistance with funding, logistics, and information; and for letting me complete a book chapter even though he was not able to contribute and the chapter suffered the deficit of his knowledge and experience. Glenn also patiently spent many long hours searching for boas at night on Ambergris, ignoring the peril of wobbly boulders surrounded by lacerating cactus catch-nets. A special thanks is owed to the members of the H.O.F.F. lab group at the University of Tennessee for the years of discussions, manuscript reviews, advice, and encouragement: especially Ben Fitzpatrick, Jim Fordyce, Darrin Hulsey, Brian O’Meara, Matt Niemiller, Stesha Pasachnik, JR Jones, Premal Shah, Philip Hollingsworth, Dylan Dittrich-Reed, Megan Todd-Thompson, Romina Dimarco, Jason Robinson, Amanda Allison, Zach Marion, Barb Banbury, Sharon Clemmensen, and others. Ðenita Hadžiabdić and the Trigiano Lab assisted greatly in teaching me use of the eGene machine for microsatellite analysis and I am grateful for their patience, and I am v appreciative of the assistance and training Joe May provided in the UTK Molecular Biology Resource Facility. My family and friends are owed special thanks for their support and encouragement and for making my time in graduate school a wonderful experience. To my family: Jennifer Reynolds, Bob and Kim Reynolds, Terry Deal, Blair Reynolds, Taylor Reynolds, and Rick and Margaret Gourdin thank you as always for your love and support: to my grandparents Jack and Betty Reynolds for weekly Sunday home cooked meals and many wonderful afternoons spent together; and to my good friends Matt Niemiller, Premal Shah, Stesha Pasachnik, and Dylan Dittrich-Reed for all the good times, assistance, advice, and field excursions. Thanks as well to Darrin Hulsey for the great trip to Honduras and for the invitation to Malawi I grudgingly had to forfeit. Funding for my research in graduate school has been provided by the following: The University of Tennessee Department of Ecology and Evolutionary Biology Summer Research Grant Program, The Sigma Xi Grant-in-Aid of Research, The American Philosophical Society Lewis and Clark Fund for Exploration and Research, The American Museum of Natural History Theodore Roosevelt Memorial Fund Grant in Support of Research, The Mohamed bin Zayed Species Conservation Fund, The University of Tennessee W. K. McClure Scholarship for the Study of World Affairs, The San Diego Zoo Institute for Conservation Research and the Offield Family Foundation, and The American Genetics Association. vi Abstract Understanding complex population dynamics is critical for both basic and applied ecology. Analysis of genetic data has been promoted as a way to reconstruct recent non- equilibrium processes that influence the apportioning of genetic diversity among populations of organisms. In a structured-deme context, where individual populations exist as geographically distinct units, island biogeography theory and metapopulation genetics predict that the demographic processes of extinction, colonization, and migration will affect the magnitude and rate of genetic divergence between demes. New methods have been developed to attempt to detect the influence of non-equilibrium dynamics in structured populations. I challenged two of these methods: decomposed pairwise regression and allele frequency analyses, using simulations of genetic data from structured demes. I found that these methods suffer from a high type II error rate, or failure to reject the null hypothesis of mutation-migration-drift equilibrium for demes experiencing historical demographic events. In addition, island biogeography and metapopulation ecology predict that at equilibrium, some species in a patch will be recent colonists, as equilibrium indicates a balance between colonization of the patch and extinction from the patch. Recent colonists are unlikely to have reached population mutation-migration-drift equilibrium; hence a paradox exists between population and community level equilibrium.