SPATIAL AND TEMPORAL PATTERNS OF GENETIC VARIATION IN SCARLET MACAWS (ARA MACAO): IMPLICATIONS FOR POPULATION MANAGEMENT IN LA SELVA MAYA, CENTRAL AMERICA Kari Lynn Schmidt Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2013 © 2013 Kari Lynn Schmidt All Rights Reserved ABSTRACT SPATIAL AND TEMPORAL PATTERNS OF GENETIC VARIATION IN SCARLET MACAWS (ARA MACAO): IMPLICATIONS FOR POPULATION MANAGEMENT IN LA SELVA MAYA, CENTRAL AMERICA Kari Lynn Schmidt Advances in technology and molecular methodologies now provide an unprecedented view into the complex realm of natural populations by elucidating the degree and distribution of genetic variation, historical and contemporary processes driving differentiation, and individual behavior patterns. These critical biological parameters create a framework to enhance wildlife management initiatives, as illustrated here through the implementation of a model approach for the systematic genetic assessment of a group of scarlet macaws (Ara macao) under threat in La Selva Maya, a tri-national system of protected areas in Mexico, Guatemala, and Belize. A total of 2172 base pairs across four mitochondrial data partitions were employed to test the current hypothesis of subspecific diversification. Phylogenetic reconstruction uncovered two phylogeographic units exhibiting distinct and complex evolutionary histories, emphasizing the importance of Central American populations to intraspecific diversity. Focusing on A. m. cyanoptera, mitochondrial control region sequences of 850 base pairs were examined within a hierarchical context to investigate patterns of genetic substructure at varying spatial scales (i.e. subspecific, regional, local) and extent of molecular variation, including potential temporal shifts in response to anthropogenic pressures. Population-level statistical tests detected evidence of recently restricted gene flow among nest sites in La Selva Maya, a stark contrast to the historical state of panmixia across the region; although overall levels of genetic variation remain high, a decrease in diversity was noted among modern samples originating in the Chiquibul Forest Reserve, Belize. Multilocus genotypes based on eight microsatellite markers were combined with haplotypic data to evaluate whether focal nest sites in the Maya Biosphere Reserve, Guatemala represent distinct genetic clusters. Results from population genetic analyses argue against the presence of site fidelity at fine geographic scales. Examination of pairwise relative relatedness indices supports the observation of genetic connectivity across local breeding areas, while also revealing important insights into recent demographic trends, movement patterns, and breeding behaviors. In summary, this work demonstrates the continuity of biological and ecological influences across individual, local, regional, and continental scales, thus creating an empirical framework to refine population management goals and prioritize mitigation strategies in order to maximize conservation outcomes and foster long-term survival of wild scarlet macaws in La Selva Maya. TABLE OF CONTENTS LIST OF TABLES ii LIST OF FIGURES iv ACKNOWLEDGEMENTS vi DEDICATION ix PREFACE x CHAPTER 1: MODEL APPROACH FOR INTEGRATING GENETIC CONSIDERATIONS IN THE DESIGN AND IMPLEMENTATION OF POPULATION MANAGEMENT PROGRAMS MOLECULAR GENETICS AND CONSERVATION BIOLOGY 1 MODEL APPROACH FOR GENETIC EVALUATION 5 CASE STUDY: SCARLET MACAW 9 REFERENCES 23 CHAPTER 2: PHYLOGEOGRAPHIC ASSESSMENT OF SCARLET MACAWS (ARA MACAO): PATTERNS OF INTRASPECIFIC DIVERSITY AND IMPLICATIONS FOR CONSERVATION MANAGEMENT ABSTRACT 39 INTRODUCTION 40 MATERIALS AND METHODS 43 RESULTS 48 DISCUSSION 52 REFERENCES 76 CHAPTER 3: POPULATION DYNAMICS, GENETIC DIVERSITY AND DEMOGRAPHY OF SCARLET MACAWS (ARA MACAO CYANOPTERA) IN LA SELVA MAYA, CENTRAL AMERICA ABSTRACT 93 INTRODUCTION 94 MATERIALS AND METHODS 100 RESULTS 110 DISCUSSION 119 REFERENCES 144 CHAPTER 4: MAJOR CONCLUSIONS AND RECOMMENDATIONS FOR SCARLET MACAW (ARA MACAO CYANOPTERA) CONSERVATION MANAGEMENT IN LA SELVA MAYA, CENTRAL AMERICA SYNTHESIS OF GENETIC INSIGHTS INTO SPECIES BIOLOGY 175 EVALUATION OF CONSERVATION NEEDS 178 i LIST OF TABLES TABLE 2.1 85 Primers for PCR amplification and sequencing. TABLE 2.2 89 Genetic variation within scarlet macaw subspecies and haplogroups. TABLE 2.3 89 Indicators of demographic change in scarlet macaw subspecies. APPENDIX I 90 List of museum specimens included in phylogeographic analyses. TABLE 3.1 158 Primers for PCR amplification and sequencing. TABLE 3.2 158 Indices of genetic variation for mitochondrial haplotypes and microsatellite genotypes in A. m. cyanoptera. TABLE 3.3 159 AMOVA and global tests of differentiation for putative populations and sampling localities in La Selva Maya (LSM), Central America based on haplotypic data. TABLE 3.4 160 Pairwise fixation indices for putative populations and sampling localities in LSM, Central America based on mitochondrial haplotypes. TABLE 3.5 161 Indicators of demographic change in LSM, Central America. TABLE 3.6 161 Genetic divergence among nest sites in the Maya Biosphere Reserve (MBR), Guatemala. TABLE 3.7 163 Mitochondrial haplotype distribution across sampling years for nest sites in the MBR, Guatemala. ii TABLE 3.8 163 Mitochondrial haplotype distribution for reoccupied nest cavities in the MBR, Guatemala across sampling years. TABLE 3.9 164 Mean relatedness ± variance for 1000 simulated pairs of known relationship category based empirical allele frequencies based on allele frequencies sampled in the MBR, Guatemala. TABLE 3.10 164 Rate of misclassification based on the midpoint method of Blouin et al. (1996). TABLE 3.11 166 Evaluation of mean relatedness across nest sites in the MBR, Guatemala. TABLE 3.12 167 Influence of shared haplotype and/or nest cavity on mean relatedness for scarlet macaws in the MBR, Guatemala. TABLE 3.13 168 Pairs of putative relatives sampled in the MBR, Guatemala based on rxyLR and rxyML. TABLE 3.14 169 Sex ratio for nestlings in the MBR, Guatemala. APPENDIX II 169 List of museum specimens included in population genetic analyses. iii LIST OF FIGURES FIGURE 1.1 37 Map illustrating recent changes in the geographic range of scarlet macaw (Ara macao) subspecies. FIGURE 1.2 38 Map depicting the distribution of scarlet macaws in La Selva Maya (LSM), Central America. FIGURE 2.1 86 Map showing sampling effort and geographic distribution of seven haplogroups detected across Central and South America. FIGURE 2.2 87 Maximum likelihood and strict consensus Bayesian inference trees from concatenated data partitions. FIGURE 3.1 156 Map depicting sampling localities for historical A. m. cyanoptera specimens. FIGURE 3.2 157 Map illustrating modern sampling localities in LSM, Central America. FIGURE 3.3 159 Median-joining network showing relationships among historical A. m. cyanoptera haplotypes. FIGURE 3.4 160 Median-joining networks showing relationships among historical and modern haplotypes recovered in LSM, Central America. FIGURE 3.5 162 Individual population membership demonstrating the relative contribution of putative genetic clusters for individuals sampled in the MBR, Guatemala. FIGURE 3.6 165 Distribution of observed relatedness values recovered within the MBR, Guatemala overlaid with simulation distributions for 1000 simulated dyads of known relatedness categories. iv FIGURE 3.7 166 Pairwise rxy plot showing mean ± variance, maximum and minimum values within the total sample and at focal nest sites in the MBR, Guatemala. FIGURE 3.8 167 Pairwise rxy plot showing mean ± variance, maximum and minimum values showing relative influence of shared mitochondrial haplotypes and/or nest cavity. v ACKNOWLEDGEMENTS My tenure as a graduate student has been an adventure like no other, taking me from the cornfields of the Midwest to the concrete jungle of New York City and lowland tropical forests of Central America. This journey would not have been possible without the companionship, encouragement, and assistance from a host of family, friends, and collaborators. First and foremost I must thank my advisor, George Amato, for graciously taking me under his auspices, introducing me to the multidimensional world of conservation management, and sharing his passion for Neotropical psittacines. Admittedly it has been a long and winding road, with each experiencing their share of speed bumps along the way, but somehow we made it. I am extremely grateful for his patience and support throughout the dissertation. I offer my gratitude to the other members of my committee for their participation in the project. Many thanks to Michael Russello for providing valuable advice in regard to manipulation of historical tissues and data analysis, and creating opportunities for outside collaborations. I also acknowledge Rob DeSalle, George Barrowclough, and Shahid Naeem for their helpful suggestions and contributions. It was a privilege to work alongside a group of dedicated and talented graduate students and post-docs in the Ecology, Evolution, and Environmental Biology Department at Columbia University and the Sackler Institute for Comparative Genomics at the American Museum of Natural History. I want to thank Martin Mendez, Oscar Pineda, Charles Yackulic, Nicole Mihnovets, Matt Leslie, Ines Carvalho, Isabela Dias-Freedman, and Anna Philips for their companionship, technical assistance, and support at various stages throughout the graduate student experience.