Thesis Phylogeography of Myotis, Miniopterus and Emballonura bats from the Comoros and Madagascar WEYENETH, Nicole Abstract Using genetic markers, we reconstructed biogeographic origins, dispersal and diversification patterns of bats endemic to Madagascar and the Comoro islands. Our results give insight on when and how diversification was initiated in these western Indian Ocean bats: (1) populations of the Malagasy bat Myotis goudoti diverged into a southern and a northern component during the Pleistocene, with subsequent expansion and adaptation to all biomes, (2) Malagasy Miniopterus bats colonized the Comoros during the Pleistocene, favored by prevailing winds, yet recent inter-island gene flow is restricted to few individuals flying against winds but a notably shorter distance within the Comoros, (3) Emballonura lineages diverged during the Oligocene into two monophyletic groups, one represented by Malagasy members, the other by Indo-Pacific members, and (4) bioclimatic disparities between the humid east and dry west promoted the rather recent divergence of these emballonurid bats on Madagascar. Reference WEYENETH, Nicole. Phylogeography of Myotis, Miniopterus and Emballonura bats from the Comoros and Madagascar. Thèse de doctorat : Univ. Genève, 2010, no. Sc. 4267 URN : urn:nbn:ch:unige-130947 DOI : 10.13097/archive-ouverte/unige:13094 Available at: http://archive-ouverte.unige.ch/unige:13094 Disclaimer: layout of this document may differ from the published version. 1 / 1 UNIVERSITÉ DE GENÈVE FACULTÉ DES SCIENCES Département de zoologie et Professeur Jean Mariaux biologie animale Département de mammalogie MUSÉUM D’HISTOIRE et d’ornithologie NATURELLE DE GENÈVE Docteur Manuel Ruedi Phylogeography of Myotis, Miniopterus and Emballonura bats from the Comoros and Madagascar THÈSE Présentée à la Faculté des Sciences de l’Université de Genève pour obtenir le grade de Docteur ès sciences, mention biologie par Nicole Weyeneth de Soleure (Suisse) Thèse N° 4267 GENÈVE 2010 TABLE OF CONTENTS REMERCIEMENTS................................................................................................................ 7 RÉSUMÉ................................................................................................................................... 9 ABSTRACT ............................................................................................................................ 11 CHAPTER 1: GENERAL INTRODUCTION .................................................................... 13 1. Biodiversity hotspot in the western Indian Ocean .......................................................... 14 2. Phylogeography of species and populations: the choice of genetic markers ................ 16 3. Bats, the model organisms for this study ......................................................................... 19 4. The aims of this thesis ........................................................................................................ 22 CHAPTER 2: Biogeography of Myotis bats (Chiroptera: Vespertilionidae) in Madagascar............................................................................................................................. 25 Abstract................................................................................................................................... 26 1. Introduction ........................................................................................................................ 27 2. Materials and Methods ...................................................................................................... 30 2.1 Sampling......................................................................................................................... 30 2.2 Sequencing ..................................................................................................................... 30 2.3 Genetic diversity ............................................................................................................ 31 2.4 Phylogenetic analyses .................................................................................................... 32 2.5 Population structure analyses ......................................................................................... 32 2.6 Demographic history analyses ....................................................................................... 34 2.7 Dating analyses .............................................................................................................. 34 3. Results ................................................................................................................................. 35 3.1 Haplotype diversity and relationships ............................................................................ 35 3.2 Population structure........................................................................................................ 39 4. Discussion............................................................................................................................ 42 1 4.1 Do island-wide diversification mechanisms explain the population structure of Myotis goudoti?................................................................................................................................ 43 4.2 Phylogeography of Myotis goudoti ................................................................................ 45 5. Conclusion........................................................................................................................... 46 Acknowledgements................................................................................................................. 47 Supplementary Data .............................................................................................................. 48 CHAPTER 3: Biogeography of Miniopterus bats (Chiroptera: Miniopteridae) from the Comoros .................................................................................................................................. 57 Abstract................................................................................................................................... 58 1. Introduction ........................................................................................................................ 59 2. Materials and Methods ...................................................................................................... 62 2.1 Sampling......................................................................................................................... 62 2.2 Sequence data................................................................................................................. 62 2.3 Cyt-b analyses ................................................................................................................ 64 2.4 D-loop analyses .............................................................................................................. 65 2.5 Phylogenetic and taxonomic analyses............................................................................ 65 2.6 Network analyses ........................................................................................................... 66 2.7 Population genetic analyses ........................................................................................... 66 2.8 Migration analyses ......................................................................................................... 67 3. Results ................................................................................................................................. 69 3.1 Cyt-b analyses ................................................................................................................ 69 3.2 D-loop analyses .............................................................................................................. 71 4. Discussion............................................................................................................................ 79 4.1 Phylogeny and taxonomy............................................................................................... 79 4.2 Population structure and history..................................................................................... 80 2 4.3 Biogeographic origins .................................................................................................... 82 5. Conclusion........................................................................................................................... 84 Supplementary Data .............................................................................................................. 86 CHAPTER 4: Bat migration in a stepping-stone archipelago ........................................... 93 Abstract................................................................................................................................... 94 1. Introduction ........................................................................................................................ 95 2. Materials and methods....................................................................................................... 97 2.1 Sampling......................................................................................................................... 97 2.2 DNA amplification and sequencing ............................................................................... 97 2.3 Genetic diversity ...........................................................................................................