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Historical and Contemporary Genetic Perspectives on New World Monk Seals (Genus Neomonachus)

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Historical and Contemporary Genetic Perspectives on New World Monk Seals (Genus Neomonachus) Historical and Contemporary Genetic Perspectives on New World Monk Seals (Genus Neomonachus) Alicia Nicole Mihnovets Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2017 © 2017 Alicia Nicole Mihnovets All Rights Reserved ABSTRACT Historical and Contemporary Genetic Perspectives on New World Monk Seals (Genus Neomonachus) Alicia Nicole Mihnovets Through common descent, closely-related taxa share many life history traits, some of which can influence extinction-proneness. Thus, examining historical and contemporary genetic patterns is valuable in accounting for evolutionary and ecological processes that may be critical to the successful conservation of threatened species. Unsustainable harvesting of monk seals (tribe Monachini) until the late nineteenth century caused the recent extinction of Caribbean monk seals (Neomonachus tropicalis) and critically low population sizes for Hawaiian and Mediterranean monk seals (Neomonachus schauinslandi and Monachus monachus, respectively). Having lost one branch of its evolutionary lineage, and with a second branch threatened by extinction, the genus Neomonachus can serve as a valuable case for examining evolutionary and ecological linkages that are sensitive to non-random anthropogenic selection pressure. An important foundation for such pursuits is the understanding of evolutionary sequences of speciation and diversification that gave rise to common traits shared by extinct and vulnerable species. Further consideration of the phylogenetic non- randomness of species vulnerability requires examination of genetic variation at the population level to infer the presence of fundamental processes (e.g., migration and reproduction) that directly influence population viability. This dissertation includes three individual studies that make use of molecular systematic and population genetic techniques to address these topics. First, a complete mitochondrial genome sequence of the extinct Caribbean monk seal (N. tropicalis) was assembled and used to resolve long-standing phylogenetic questions regarding the sequence of divergence among monk seal species and sister taxa. Second, novel microsatellite marker assays were developed and used to characterize the extent of population-level variation across 24 polymorphic microsatellite loci of 1192 endangered Hawaiian monk seals (N. schauinslandi) that were sampled during a longitudinal study spanning three decades. Third, resulting genotypes from a subset of individuals (N= 785) were integrated with previously reported genotypes consisting of 18 other loci for the largest ever population-level assessment of N. schauinslandi genetic diversity and population differentiation throughout the Hawaiian archipelago. The new microsatellite data will be of particular value for future individual-level assessment of parentage and relatedness in N. schauinslandi, which will help managers better infer the reproductive mechanisms that factor into population persistence and recovery. Results of this study expand understanding of the evolutionary and conservation genetic status of monk seals, as well as molecular genetic capacity, for future research regarding a unique and highly imperiled New World pinniped lineage. TABLE OF CONTENTS List of Figures ......................................................................................................................v List of Tables .................................................................................................................... vii List of Abbreviations ......................................................................................................... ix iv Acknowledgements ............................................................................................................ xi vi Dedication ........................................................................................................................ xiv ix CHAPTER 1. INTRODUCTION .....................................................................................1 The Phylogenetic Relationships of Monk Seals ................................................................3 The Population Status of Monk Seals ..................................................................................3 The Conservation Genetics of Monk Seals ..........................................................................7 Research Focus ...................................................................................................................8 References .........................................................................................................................10 CHAPTER 2. A RECONSTRUCTION OF THE MITOCHONDRIAL GENOME OF THE CARRIBEAN MONK SEAL ..........................................................................14 Abstract ..............................................................................................................................15 Introduction ........................................................................................................................17 Materials and Methods .......................................................................................................20 Tissue sampling and aDNA extraction ..............................................................................20 Mitochondrial genome sequencing and assembly .............................................................20 Mitochondrial genome annotation and sequence analysis ................................................21 Phylogenetic analysis.........................................................................................................21 Results and Discussion ......................................................................................................23 Mitochondrial genome sequencing and assembly ............................................................23 Genome organization and nucleotide composition ...........................................................23 i Protein coding regions .......................................................................................................24 tRNA and rRNA genes ........................................................................................................24 Non-coding regions ............................................................................................................25 Phylogenetic analysis.........................................................................................................26 Conclusion .........................................................................................................................27 Acknowledgements ............................................................................................................28 References ..........................................................................................................................29 Supplementary Information ...............................................................................................48 Ancient DNA extraction methods .......................................................................................48 CHAPTER 3. A NOVEL MICROSATELLITE MULTIPLEX ASSAY FOR THE ENDANGERED HAWAIIAN MONK SEAL......................................................49 Abstract ..............................................................................................................................50 Introduction ........................................................................................................................51 Methods and Results ..........................................................................................................52 Acknowledgements ............................................................................................................54 Author’s Contributions ......................................................................................................54 References ..........................................................................................................................56 Supplementary Material .....................................................................................................61 CHAPTER 4. REVISITING THE GENETIC DIVERSITY AND CONNECTIVITY OF THE ENDANGERED HAWAIIAN MONK SEAL ...............................................63 Abstract ..............................................................................................................................64 Introduction ........................................................................................................................67 ii Methods and Materials .......................................................................................................69 Study system .......................................................................................................................69 Sample collection, DNA extraction, and microsatellite genotyping ..................................70 Study design .......................................................................................................................71 Data analysis .....................................................................................................................72 Results ................................................................................................................................75 DNA sample summary........................................................................................................75
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