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Reconstructing the Demographic History of the Critically Endangered Black-And-White Ruffed Lemur (Varecia Variegata) in Ranomafana National Park

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Reconstructing the Demographic History of the Critically Endangered Black-And-White Ruffed Lemur (Varecia Variegata) in Ranomafana National Park City University of New York (CUNY) CUNY Academic Works School of Arts & Sciences Theses Hunter College Fall 1-3-2019 Reconstructing the demographic history of the critically endangered black-and-white ruffed lemur (Varecia variegata) in Ranomafana National Park Aparna Chandrashekar CUNY Hunter College How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/hc_sas_etds/374 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] Reconstructing the demographic history of the critically endangered black-and-white ruffed lemur (Varecia variegata) in Ranomafana National Park, Madagascar By Aparna Chandrashekar Submitted in partial fulfillment of the requirements for the degree of Master of Arts in Anthropology, Hunter College The City University of New York 2018 Thesis Sponsor: December 13, 2018 Dr. Andrea L. Baden Date Signature of First Reader December 13, 2018 Dr. Carlo Pacioni Date Signature of Second Reader Table of Contents ACKNOWLEDGEMENTS ........................................................................................................................ii LIST OF FIGURES ................................................................................................................................... iii LIST OF TABLES ...................................................................................................................................... iv ABSTRACT.................................................................................................................................................. 1 INTRODUCTION ....................................................................................................................................... 2 NATURAL HISTORY OF MADAGASCAR ................................................................................................... 2 VARECIA VARIEGATA ECOLOGY AND CONSERVATION........................................................................... 7 DEMOGRAPHY AND CONSERVATION ...................................................................................................... 9 SPECIFIC AIMS ....................................................................................................................................... 11 METHODS ................................................................................................................................................. 11 STUDY SITE AND SAMPLE COLLECTION............................................................................................... 11 Study Site ............................................................................................................................................. 11 Sample Collection. .............................................................................................................................. 12 DNA EXTRACTION AND MICROSATELLITE GENOTYPING ................................................................. 13 DNA Extraction and Microsatellite Genotyping. ................................................................................ 13 POPULATION GENETIC ANALYSIS ........................................................................................................ 13 Summary statistics............................................................................................................................... 13 Population genetic structure. .............................................................................................................. 14 POPULATION DIVERGENCE AND DEMOGRAPHY INFERENCE ............................................................. 14 Population Divergence. ...................................................................................................................... 14 Population Demography. .................................................................................................................... 15 RESULTS ................................................................................................................................................... 17 SUMMARY STATISTICS ........................................................................................................................... 17 POPULATION GENETIC STRUCTURE ..................................................................................................... 18 DIVERGENCE TIME ................................................................................................................................ 20 POPULATION DEMOGRAPHY INFERENCE ............................................................................................. 21 DISCUSSION ............................................................................................................................................. 22 DEMOGRAPHIC HISTORY OF V. VARIEGATA IN RANOMAFANA NATIONAL PARK ............................. 22 CONSERVATION AND MANAGEMENT .................................................................................................... 25 FUTURE DIRECTIONS ............................................................................................................................. 27 CONCLUSION .......................................................................................................................................... 28 LITERATURE CITED ............................................................................................................................. 30 APPENDIX ................................................................................................................................................. 37 i ACKNOWLEDGEMENTS I would like to thank my advisor Dr. Andrea Baden for her unending support and guidance throughout my Master’s program. She has been instrumental in helping me cultivate my skills as a budding conservation geneticist and in developing this project. In addition, I would like to thank Dr. Carlo Pacioni for his expertise and assistance for running these analyses. His knowledge regarding conservation management has truly made this project excel. I would like to thank my lab mates in the Primate Molecular Ecology Lab, who helped me keep sane through the ups and downs and to Amanda Mancini who was gracious enough to let me help on her project. Lastly, I’d like to express my gratitude towards my family and Louis Thompson. They have supported and encouraged me throughout my academic career. ii LIST OF FIGURES Figure 1. Madagascar ecological zone map………………………………………………………6 Figure 2. Ranomafana National Park with sampling localities…………………………………12 Figure 3. STRUCTURE analysis mean L(K) graph…………………………………………………18 Figure 4. Ultrametric tree………………………………….…………………………………….19 Figure 5. Extended Bayesian Skyline Plots……………………………………………………21 iii LIST OF TABLES Table 1. Sampling localities, geographic coordinates, sample size..............................................13 Table 2. Models of microsatellite evolution..................................................................................16 Table 3. Characteristics of 10 microsatellite loci..........................................................................17 Table 4. Population genetic parameters at sampling localities.....................................................17 Table 5. Genetic differentiation between sampling sites………………………………......……18 iv ABSTRACT Madagascar’s moist forests have undergone extensive habitat modification within the last century, with deforestation rates progressively increasing in the last few years. Due to heavy fragmentation of their remaining range, the Critically Endangered black-and-white ruffed lemur (Varecia variegata) is facing catastrophic population declines, especially in the southern extent of its range, where genetic diversity is low and gene flow is almost absent. To understand the effects of large-scale landscape change and its influence on the genetic stability of endangered mammalian populations it is fundamental to determine the historical demography of a population. Here, I use microsatellite genotypes from V. variegata individuals in Ranomafana National Park to reconstruct their population history. Four sites were sampled within the park’s boundaries and a total of 38 adult individuals were identified. Pairwise comparisons of the sampling sites indicated each locality as a distinct population (except for Vatorahanana and Mangevo); however, a Bayesian clustering method suggested evidence for one genetic cluster within the park. Extended Bayesian skyline analyses show that the ancestral effective population was stable during Madagascar’s Late Pleistocene and Early Holocene’s drastic climatic transformations. Mean ancestral effective population size was estimated to be ~4,000 before declining by 84% starting around 1,500 years ago. Though human arrival happened as early as 10,000 years ago, extensive settling may have begun around 2,300 years ago on the coasts of Madagascar. While archaeological data for the eastern humid rainforest region are sparse, evidence from charcoal abundance and linguistic data indicate that the interior regions of Madagascar were some of the last areas to be settled and this event may have taken up to seven centuries. The emergence of anthropogenic fire in this region, coupled with annual intense 1 cyclones, may have resulted in habitat modification too great for V. variegata to cope with, leading to population declines
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