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Phylogeography and Systematics of the Mesalina Olivieri Species Complex (Squamata: Lacertidae) from North-West Africa

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Phylogeography and Systematics of the Mesalina Olivieri Species Complex (Squamata: Lacertidae) from North-West Africa Phylogeography and systematics of the Mesalina olivieri species complex (Squamata: Lacertidae) from North-West Africa Cristian Pizzigalli Master in Biodiversity, Genetics and Evolution Department of Biology of the Faculty of Sciences of the University of Porto 2019 Orientador José Carlos Alcobia Rogado de Brito, Principal Researcher, CIBIO- InBIO/FCUP Co-orientador Guillermo Velo-Antón, Auxiliary Researcher, CIBIO-InBIO Fernando Martínez-Freiría Post-Doctoral Researcher, CIBIO-InBIO FCUP 1 Phylogeography and systematics of the Mesalina olivieri species complex (Squamata: Lacertidae) from North-West Africa 2 FCUP 2 Phylogeography and systematics of the Mesalina olivieri species complex (Squamata: Lacertidae) from North-West Africa Todas as correções determinadas pelo júri, e só essas, foram efetuadas. O Presidente do Júri, Porto, ______/______/_________ FCUP 3 Phylogeography and systematics of the Mesalina olivieri species complex (Squamata: Lacertidae) from North-West Africa 4 FCUP 4 Phylogeography and systematics of the Mesalina olivieri species complex (Squamata: Lacertidae) from North-West Africa To my parents FCUP 5 Phylogeography and systematics of the Mesalina olivieri species complex (Squamata: Lacertidae) from North-West Africa 6 FCUP 6 Phylogeography and systematics of the Mesalina olivieri species complex (Squamata: Lacertidae) from North-West Africa 1 Acknowledgments/Agradecimentos 2 I would like to thank BIODESERTS group members for their assistance during fieldwork 3 and the CTM technical staff that patiently thought me everything I know about lab work. My 4 main supervisor José Carlos Brito that gave me the possibility to work on this stimulating 5 thesis and helped me until the end of it. My co-supervisors Guillermo Velo-Antón that 6 helped me during the lab work and the genetic analysis. Pierre-André Crochet and 7 Philippe Geniez for the warm hospitality at the CERN in Montpellier and for their 8 availability in transmitting me useful knowledges. Antigoni Kaliontzopoulou and Fernando 9 Martínez-Freiría that introduced me to CIBIO and to the University of Porto and without 10 whom I wouldn’t never come to Portugal. Andres Pagan, Inês Dinis de Freitas, Silvia 11 Chemello, Orlando Gallo that helped me when I was lost and together with my flatmates 12 Luca, Clara, Aina and Fulvio supported me during this journey. 13 I would also love to thank my parents, my sister Maddalena, my uncle and aunt Giuseppe 14 and Cecilia, my friends Alberto, Dario, Francesco and Roberto for the love and support 15 they gave me that always made me feel home. Thank you. 16 This work was funded by National Geographic Society (CRE 7629-04/8412-08), Mohamed 17 bin Zayed Species Conservation Fund (11052709, 11052707, 11052499), Fundacão para 18 a Ciência e a Tecnologia (PTDC/BIA-BEC/099934/2008 and PTDC/ BIA-BIC/2903/2012), 19 FEDER funds through the Operational Programme for Competitiveness Factors - 20 COMPETE (FCOMP-01- 0124-FEDER-008917/028276), and by AGRIGEN–NORTE-01- 21 0145-FEDER-000007, supported by Norte Portugal Regional Operational Programme 22 (NORTE2020), under the PORTUGAL 2020 Partnership Agreement, through the 23 European Regional Development Fund (ERDF). F.M.F., G.V.A. and J.C.B. were supported 24 by FCT (FCT-DL57, IF/01425/2014, and FCT-DL57, respectively). Capture permits were 25 issued by the Haut Comissaire aux Eaux et Forets (278/2012 and 26 20/2013/HCEFLCD/DLCDPN/DPRN/CFF) and Ministére de l’Environnement et du 27 Développement Durable of Mauritania (460/MDE/PNBA). Logistic support for fieldwork 28 was given by Pedro Santos Lda (Trimble GPS), Off Road Power Shop, P.N. Banc d’Arguin 29 (Mauritania), Association Nature Initiative (Morocco), and Université des Sciences, de 30 Technologie et de Médecine de Nouakchott. 31 FCUP 7 Phylogeography and systematics of the Mesalina olivieri species complex (Squamata: Lacertidae) from North-West Africa 32 8 FCUP 8 Phylogeography and systematics of the Mesalina olivieri species complex (Squamata: Lacertidae) from North-West Africa 33 INDEX 34 ACKNOWLEGMENTS/AGRADECIMENTOS .............................................................................................. 6 35 INDEX ...................................................................................................................................................... 8 36 ABSTRACT .............................................................................................................................................. 10 37 KEYWORDS ............................................................................................................................................ 10 38 RESUMO ................................................................................................................................................ 12 39 PALAVRAS-CHAVE ................................................................................................................................. 12 40 LIST OF TABLES ...................................................................................................................................... 14 41 LIST OF FIGURES ................................................................................................................................... 16 42 LIST OF ABBREVIATIONS ....................................................................................................................... 18 43 1. INTRODUCTION ................................................................................................................................. 20 44 1.1 GLOBAL BIODIVERSITY DECLINE ......................................................................................................................... 20 45 1.2 INTEGRATIVE TAXONOMY ................................................................................................................................. 21 46 1.3 BIOGEOGRAPHY OF NORTH AFRICA ................................................................................................................... 24 47 1.4 THE LIZARDS OF GENUS MESALINA .................................................................................................................... 26 48 1.5 OBJECTIVES ........................................................................................................................................................ 28 49 1.6 REFERENCES ...................................................................................................................................................... 30 50 2. PHYLOGEOGRAPHY AND SYSTEMATICS OF THE MESALINA OLIVIERI SPECIES COMPLEX 51 (SQUAMATA: LACERTIDAE) FROM NORTH-WEST AFRICA WITH THE DESCRIPTION OF A NEW SPECIES 52 AND SUBSPECIES ................................................................................................................................... 39 53 2.1. INTRODUCTION ................................................................................................................................................ 39 54 2.2. MATERIALS AND METHODS .............................................................................................................................. 41 55 2.2.1 Sampling and study area ................................................................................................................................ 41 56 2.2.2. Genetic analyses ................................................................................................................................................ 41 57 2.2.2.1 DNA extraction and amplification ............................................................................................................... 41 58 2.2.2.2 Phylogenetic analyses and haplotype networks ......................................................................................... 43 59 2.2.2.3. Species-tree ............................................................................................................................................... 44 60 2.2.2.4. Time of divergence .................................................................................................................................... 45 FCUP 9 Phylogeography and systematics of the Mesalina olivieri species complex (Squamata: Lacertidae) from North-West Africa 61 2.2.2.5. Genetic distances ....................................................................................................................................... 45 62 2.2.2.6. Historical demography ............................................................................................................................... 45 63 2.2.3 Morphological analyses .......................................................................................... Error! Bookmark not defined. 64 2.2.3.1 Morphological dataset .................................................................................... Error! Bookmark not defined. 65 2.2.3.2 Morphological variation .................................................................................. Error! Bookmark not defined. 66 2.2.4 Distribution modelling of the new species ............................................................. Error! Bookmark not defined. 67 2.3. RESULTS ............................................................................................................................................................ 46 68 2.3.1 Phylogenetic analyses ......................................................................................................................................... 49 69 2.3.2
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