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Dissertation Thesis MASARYK UNIVERSITY Faculty of Science DISSERTATION THESIS Brno 2008 Peter Vallo MASARYK UNIVERSITY Faculty of Science Peter Vallo MOLECULAR GENETIC STUDIES IN AFRICAN LEAF-NOSED BATS (HIPPOSIDERIDAE) Dissertation thesis Supervisor: doc. RNDr. Petr Koubek, CSc. Brno 2008 Bibliographic identification First name and surname of author: Peter Vallo Title of dissertation thesis: Molecular genetic studies in African leaf-nosed bats (Hipposideridae) Title of dissertation thesis in Czech: Molekulárně genetické studie afrických pavrápencovitých (Hipposideridae) Study program: Biology Field of study: Zoology Supervisor: doc. RNDr. Petr Koubek, CSc. Year of defence: 2008 Keywords: mitochondrial DNA, cytochrome b, taxonomy, phylogeny, Hipposideros caffer, Hipposideros ruber, Triaenops persicus Keywords in Czech: mitochondriální DNA, cytochrom b, taxonomie, fylogeneze, Hipposideros caffer, Hipposideros ruber, Triaenops persicus © Peter Vallo, Masaryk University, 2008 Contribution of Ph.D. student Peter Vallo to papers presented in the thesis Paper A Vallo et al. in press. Variation of mitochondrial DNA in the Hipposideros caffer complex (Chiroptera: Hipposideridae) and its taxonomic implications: co-authored the original idea of the paper, took part in field sampling of bats in Senegal and Morocco, processed samples from isolation of DNA to completion of DNA sequences (ca. 50% of samples in the paper), performed molecular phylogenetic analysis, wrote the first version of manuscript and prepared its final version Paper B Vallo et al. manuscript. Genetic structure of H. cf ruber from southeastern Senegal inferred from sequences of the mitochondrial cytochrome b gene: co-authored the original idea of the paper, took part in field sampling of bats in Senegal, processed samples from isolation of DNA to completion of DNA sequences, performed molecular phylogenetic analysis, wrote the first version of manuscript and prepared its final version Paper C Benda and Vallo submitted. Taxonomy of the genus Triaenops (Mammalia: Chiroptera: Hipposideridae) with description of a new species from southern Arabia: processed samples from isolation of DNA to completion of DNA sequences, performed molecular phylogenetic analysis, wrote the molecular phylogenetic parts of manuscript and contributed to its final version doc RNDr. Petr Koubek, CSc. supervisor Acknowledgements I would like thank my supervisor Dr. Petr Koubek for supervising my PhD study and for the opportunity to be a part of the research team investigating the vertebrate fauna of Senegal. Further I would like to thank Dr. Petr Benda for tutoring my existence in the world of bat science and for fruitful cooperation. I cordially thank Dr. Natália Martínková for introducing me into molecular techniques and phylogenetic analysis. I also thank Prof. Jiří Gaisler for provision of bat literature. For opportunities to get experience in non-bat research, I thank Dr.©s Steven Monfort, William McShea, Krzysztof Schmidt and Leandro Silveira. The Foundation Nadání Josefa, Marie a Zdeňky Hlávkových kindly supported my stay in Brazil, the last non-bat experience (so far...). I thank Maťo and Lenka for friendship and social well-being, and Adam for yet another social well-being and friendship. My thanks further go to Jarka and Mirka for five years of inspirative coexistence in one office, and to people from the lab in Studenec for kind attitude. Last but not least, I would like to express thousand thanks to my family and Vlaďka for never-ending support, help and love. Dissertation research was carried out at the Institute of Vertebrate Biology, v.v.i., Academy of Science of the Czech Republic, in Brno. Laboratory work was done at the molecular genetic laboratory of the IVB AS CR, v.v.i., in Studenec. My dissertation related research activities were supported by the grant nr. IAA6093404 by the Grant Agency of the AS CR. Abstract Molecular methods using DNA sequence data have been widely used in solving systematic relationships in bats and have radically changed perception of this mammalian order. The family of leaf-nosed bats (Hipposideridae) has not yet been thoroughly studied by the molecular genetic approach. Suspicion of artificial intrafamilial grouping and proved existence of high cryptic diversity encourage use of this approach. This pays especially for leaf-nosed bats of Afrotropics, as only fragmentary information on their taxonomy and phylogeny has been published to date. This dissertation thesis presents results of analysis of sequences of mitochondrial cytochrome b gene in cryptic forms of Hipposideros caffer complex, and in species Triaenops persicus. Genetic structure revealed within the H. caffer complex challenged a hypothesis of two cryptic species, H. caffer and H. ruber. Six distinct lineages of potentially specific statuses were recovered. Two currently recognised subspecies of H. caffer can be considered two distinct species, H. caffer and H. tephrus. Taxonomic assignation of three lineages of H. ruber and one lineage comprising either H. caffer or H. ruber morphotypes has yet to be confirmed. Two sympatric genetic forms of the West African lineage, originally assigned to H. ruber, were found in southeastern Senegal. Morphological differences between these two forms were slight. A large range of echolocation frequencies detected in a local population, however, had no relevance to this distinction, but was related to sex in the more numerous form. The two Senegalese forms are apparently paraphyletic, because phylogeny revealed sister relationship between the less numerous form and a form from Benin. This indicates that another cryptic species may exist in Senegal. Revision of the Afro-Arabian T. persicus revealed several distinct morphotypes from Africa and the Middle East with significant genetic divergences among most of them. Therefore, a split of the current T. persicus rank into three species was proposed: T. afer in Africa, and T. persicus and T. parvus spec. nov. in the Middle East. Due to considerable genetic and morphologic differences among continental and island forms of Triaenops, two Madagascan species T. furculus and T. auritus were separated into a new genus Paratriaenops gen. nov. Abstrakt Molekulární metody s využitím studia sekvencí DNA jsou velmi často využívány k řešení systematických vztahů u netopýrů a významným způsobem mění pohled na členění tohoto savčího řádu. Pavrápencovití (Hipposideridae) jsou jednou z čeledí, která dosud nebyla těmito metodami komplexně studována. Podezření na umělé vnitřní členění čeledi a prokázaná existence vysoké kryptické diverzity k využití těchto metod přímo vybízí. To platí především o pavrápencovitých ¹Afrotropůº, o jejichž taxonomii i fylogenezi byly dosud publikovány jen dílčí informace. Předložená disertace shrnuje výsledky získané analýzou sekvencí mitochondriálního genu pro cytochrom b u kryptických forem komplexu Hipposideros caffer a druhu Triaenops persicus. Genetická struktura zjištěná v komplexu H. caffer popřela hypotézu dvou kryptických druhů H. caffer a H. ruber. Bylo identifikováno šest rozdílných linií, které mají charakter druhu. Dva dosud platné poddruhy H. caffer je možné považovat za dva odlišné druhy, H. caffer a H. tephrus. Taxonomickou příslušnost tří linií H. ruber a jedné linie obsahující oba morfotypy H. caffer i H. ruber je ještě potřeba potvrdit. Dvě sympatrické genetické formy západoafrické linie původně určené jako H. ruber byly zjištěny v jihovýchodním Senegalu. Morfologicky se lišily jen nepatrně. Poměrně velký rozsah echolokačních frekvencí zjištený u lokální populace však s tímto rozdělením nesouvisel, ale měl vztah k pohlaví u početnejší formy. Senegalské formy jsou zřejmě parafyletické, protože fylogeneze odhalila sesterský vztah mezi méně početnou formou a formou z Beninu. To naznačuje možnost existence dalšího kryptického druhu v Senegalu. Revize afro-arabského druhu T. persicus odhalila několik rozdílných morfotypů z Afriky a Středního Východu s významnými genetickými rozdíly mezi většinou z nich. Proto bylo navrženo rozdělení T. persicus do tří druhů: T. afer v Africe, a T. persicus a T. parvus spec. nov.. na Středním Východě. Kvůli značným genetickým a morfologickým rozdílům mezi kontinentálními a ostrovními formami rodu Triaenops byly madagaskarské druhy T. furculus a T. auritus vyčleněny do rodu Paratriaenops gen. nov. Contents Introduction.....................................................................................9 DNA sequence data.................................................................9 Systematic relationships of Chiroptera.......................................11 Family Hipposideridae............................................................13 Aims of the thesis............................................................................17 Summary of results..........................................................................18 References.....................................................................................22 Paper A.........................................................................................29 Paper B.........................................................................................56 Paper C.........................................................................................77 Curriculum vitae...........................................................................128 Introduction Many generations of naturalists have researched biological forms with the aim of describing and explaining their diversity. Classification of biological
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