Prioritizing Regions for the Conservation of Amphibians With

PRIORITIZING REGIONS FOR THE CONSERVATION OF AMPHIBIANS WITH SPECIAL EMPHASIS ON THE RED HILLS SALAMANDER (PHAEOGNATHUS HUBRICHTI) by JOSEPH J. APODACA A DISSERTATION Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Biological Sciences in the Graduate School of The University of Alabama TUSCALOOSA, ALABAMA 2010 Copyright Joseph J. Apodaca 2010 ALL RIGHTS RESERVED ABSTRACT Amphibians are the most threatened vertebrate group in the world, and are experiencing rapid species declines and numerous extinctions. The most effective way to stem these losses is through the establishment of protected areas. The limited amount of funding available to such efforts requires that conservation agencies and biologists must find a way to properly focus their efforts and resources. Yet, there is no clear-cut method to prioritize areas for biological reserves. In fact, the identification of biologically important regions is one of the most debated topics in the field of conservation biology. As this debate wages on and as species continue to decline at an unprecedented rate, conservation biologists have come to rely on increasingly sophisticated methods for the identification of these areas. In this dissertation I focus on recently developed techniques for prioritizing reserve selection from macro to micro-scales for amphibians in the southeastern United States. For chapters one and two I focus on broad scale issues for wide taxonomic groups. Chapter one focuses on testing whether using environmental niche models rather than extent of occurrence maps to create richness patterns is a valid approach. I found that environmental niche models could be useful for generating richness patterns for understudied regions or taxa if proper precautions are taken. Chapter two focuses on implementing evolutionary data into richness and endemism patterns using all members of the family Plethodontidae found in the southeastern United States. I found that using evolutionary data in conjunction with traditional biodiversity metrics provides a unique and valuable perspective. Chapters three and four narrow the focus to a single taxon, the Red Hills salamander (Phaeognathus hubrichti). The Red Hills salamander is a federally threatened species whose ii conservation has been hampered by their secretive and fossorial nature. To circumvent this problem, I conduct a conservation genetics study in chapter three and combine the data with spatial and life history data in order to make habitat acquisition recommendations in chapter four. I found that there are five distinct and well supported populations of P. hubrichti. Additionally, each population has extremely low levels of gene flow and high levels of inbreeding. I recommend that 21 sites are acquired and that attempts are made to restore habitat in-between known populations. iii DEDICATION This dissertation is dedicated to Sharon and John Watson, who have provided an incredible amount of support throughout the years and who never stopped believing in me. iv LIST OF ABBREVIATIONS AND SYMBOLS U.S. United States km2 square kilometers km Kilometer IUCN International Union for Conservation of Nature PAs Protected Areas EOO Extent of Occurrence ENM Environmental Niche Modeling GBIF Global Biodiversity Information Facility ROC Receiver Operating Characteristic AUC Area Under the Curve LPT Least Point Threshold OLS Ordinary Least Squares AIC Akaike Information Criterion SAR Simultaneous AutoRegression SAM Spatial Analysis in Macroecology v. Version r Correlation coefficient P Probability associated with the occurrence under the null hypothesis of a value as extreme or more extreme than the observed value. v % Percent = Equals > Greater than < Less than & And e.g. Exempli gratia (for example) i.e. id est (that is) et al. et alii (and others) - Negative PD Phylogenetic Diversity PE Phylogenetic Endemism WE Weighted Endemism EDGE Evolutionary Distinctive and Globally Endangered Cyt b Cytochrome b POMC Pro-opiomelanocortin ND2 Nicotinamide adenine dinucleotide subunit 2 ND4 Nicotinamide adenine dinucleotide subunit 4 RAG-1 Recombination Activating Gene 1 BDNF Brain-derived Neurotrophic Factor Fig. Figure ° Degree vi λ Lambda FST Fixation Index FIS Inbreeding coefficient of an individual relative to the population m migration rate ESU Evolutionarily Significant Unit USGS United States Geological Society DNA Deoxyribonucleic acid PCR Polymerase Chain Reaction MCMC Markov Chain Monte Carlo AMOVA Analysis of Molecular Variance HO Observed heterozygosity HE Expected heterozygosity µ Mutation rate Ne Effective population size IAM Infinite alleles model TPM Two phase model SMM Stepwise mutation model AL-GAP Alabama Gap Analysis Project ETM+ Enhanced Thermatic Mapper Plus HWE Hardy Weinberg Equilibrium vii t-test a statistical test in which the test statistic follows a Student’s t distribution if the null hypothesis is true. Θ 4 times the effective population size times the mutation rate USFWS United States Fish and Wildlife Service HCP Habitat Conservation Plan Pers. Comm. Personal Communication NED National Elevational Dataset ALNHP Alabama Natural Heritage Program Etc. et cetera (and other things) viii ACKNOWLEDGMENTS This dissertation would not be possible without the support and effort of several people. First off I would like to thank the members of my dissertation committee: Drs. Leslie Rissler, Joseph Travis, Jonathan Benstead, Phil Harris, and Katrina Ramonell. Their advice and expertise over the years are greatly appreciated. I am especially grateful to my advisor, Dr. Leslie Rissler. Without her advice, support, and knowledge this project would not have been possible. I would also like to thank Christina Anderson, who has done more for me than she will ever realize. J Gailbreath has always supported me and has been a huge influence throughout my life. I owe tremendous gratitude to Jim Godwin, who provided an incredible amount of effort and knowledge on the Red Hills salamander. Heather Cunningham has been an integral part of my graduate school career and provided an infinite amount of support. Walter Smith has provided a great deal of fieldwork help and support. Christoph Thawley, Horace Downer, and Nicole Mattheus provided a lot of useful feedback on my writings. Shannon Hoss, Michael Wines, and Will Callans provided much needed help in the field. Rachel Crawford, Jessica Mitchell, Catherine Tucker, and Alicia Waggoner provided assistance in the lab. Piper Apodaca has provided an enormous amount of support and has been an incredible friend throughout my graduate school experience. Financial support was provided by the University of Alabama Department of Biological Sciences and by the State of Alabama Division of Wildlife & Freshwater Fisheries. ix CONTENTS ABSTRACT............................................................................................. ...ii DEDICATION........................................................................................... iv LIST OF ABBREVIATIONS AND SYMBOLS ........................................v ACKNOWLEDGMENTS ......................................................................... ix LIST OF TABLES..................................................................................... xi LIST OF FIGURES ................................................................................. xiv 1. CHAPTER 1: INTRODUCTION............................................................1 2. CHAPTER 2: CHAPTER TWO: USING ENVIRONMENTAL NICHE MODELING TO REFINE SPECIES RICHNESS MAPS FOR AMPHIBIANS IN THE SOUTHEASTERN U.S…………………6 3. CHAPTER 3: COMPARING APPROACHES FOR IDENTIFYING BIODIVERSITY HOTSPOTS: A CASE STUDY FEATURING PLETHODONTIDS IN THE SOUTHEASTERN UNITED STATES........................................................................32 4. CHAPTER 4: ESTIMATING THE EFFECTS OF HABITAT MODIFICATION ON GENETIC PATTERNS AND POPULATION CONNECTIVITY; A CASE STUDY USING THE FEDERALLY THREATENED RED HILLS SALAMANDER (PHAEOGNATHUS HUBRICHTI)………………………………59 5. CHAPTER 5: RECOMMENDATIONS FOR THE RECOVERY OF THE THREATENED RED HILLS SALAMANDER (PHAEOGNATHUS HUBRICHTI): INCLUDING HABITAT-PURCHASING GUIDELINES, A PROPOSAL FOR HABITAT RECOVERY, AND IDENTIFYING LOCATIONS OF UNKNOWN POPULATIONS……………………………………………….....92 6. CHAPTER 6: OVERALL CONCLUSION.........................................122 7. LITERATURE CITED .......................................................................126 x LIST OF TABLES TABLE 2.1 Regression models evaluating the ability of Anuran environmental niche models to predict extent of occurrence richness values…………………………………25 TABLE 2.2 Regression models evaluating the ability of Caudata environmental niche models to predict extent of occurrence richness values…………………………………26 TABLE 3.1 Covariance and correlation between biodiversity metrics for southeastern U.S. plethodontids. Covariance values are in the upper diagonal. Correlation values are in the lower diagonal. PE = Phylogenetic endemism, PD= Phylogenetic diversity, WE= weighted endemism………………………………………………………..48 TABLE 3.2 Null model regression analysis between non-genetic metrics (WE & Richness) and genetic metrics (PE & PD) for southeastern U.S. plethodontids. PE = Phylogenetic endemism, PD= Phylogenetic diversity, WE= weighted endemism. ……………………………………………………………………………………49 TABLE 3.3 Three Highest contribution index values for range size in southeastern U.S. plethodontids…………………………………………………………….……….50 xi TABLE 4.1 Results of the Analysis of Molecular Variance

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