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Habitat and population structure of the Morelet’s crocodile (Crocodylus moreletii) in Calakmul Biosphere Reserve, Campeche, Mexico José António de Lemos Barão da Nóbrega This thesis is submitted to the School of Science, Engineering and Environment, University of Salford, in fulfilment of the requirements for the degree of Doctor of Philosophy 2021. I dedicate this work to my mother, Maria José Barão, and my late grandfather, José Carlos Barão, as without encouragement and tireless support I would not have had the opportunity to first be a Portuguese in the Amazon and then a Portuguese in Mayan jungles of Mexico. Table of Contents List of Figures .................................................................................................................... IV List of Tables .................................................................................................................... VIII Acknowledgements ........................................................................................................... IX Abstract ............................................................................................................................. XV Chapter 1 – General Introduction ....................................................................................... 1 1.1 Environmental change and herpetofauna .................................................................... 1 1.2 Modern Crocodylians – Crocodiles, Alligators and Gharials ......................................... 3 1.3 Morelet’s crocodile (Crocodylus moreletii, Duméril and Duméril 1851) ........................ 7 1.4 Calakmul Biosphere Reserve (CBR) .......................................................................... 10 1.5 Freshwater habitats in CBR ....................................................................................... 11 1.6 Herpetofauna in Calakmul ......................................................................................... 16 1.7 Crocodylus moreletii in Calakmul ............................................................................... 17 1.8 Project rationale and major aims ............................................................................... 17 1.9 Thesis structure ......................................................................................................... 19 Chapter 2 – Distribution and characterization of aguadas in the Calakmul Biosphere Reserve .............................................................................................................................. 20 2.1 Introduction ................................................................................................................ 20 2.2 Material and Methods ................................................................................................ 24 2.2.1 Surveying for aguada locations ...................................................................................... 24 2.2.2 Aguada general structure characterization................................................................... 25 2.2.4 Aguada water level and vegetation cover analysis ..................................................... 25 2.2.5 Aguada water quality parameters .................................................................................. 26 2.2.3 Setting up an aguada long-term monitoring citizen science project ......................... 26 2.3 Results ...................................................................................................................... 27 2.3.1 Aguada general structure characterization................................................................... 27 2.3.2 Aguada water level and vegetation cover analyses .................................................... 30 2.3.3 Water quality parameter analysis .................................................................................. 34 2.5.2 Long-term aguada monitoring ........................................................................................ 34 I 2.4 Discussion ................................................................................................................. 36 2.4.1 General structure monitoring .......................................................................................... 36 2.4.3 Water quality assessment ............................................................................................... 37 2.4.4 Long-term aguada monitoring ........................................................................................ 39 Chapter 3 – N-mixture models provide informative crocodile (Crocodylus moreletii) abundance estimates in dynamic environments ............................................................ 41 Abstract ........................................................................................................................... 41 3.1 Introduction ................................................................................................................ 42 3.2 Material and Methods ................................................................................................ 43 3.2.1 Study area and data collection ....................................................................................... 43 3.2.2 Abundance estimation ..................................................................................................... 46 3.3 Results ...................................................................................................................... 48 3.4 Discussion ................................................................................................................. 55 3.5 Final Considerations .................................................................................................. 60 Chapter 4 – Screening for evidence of hybridization and assessing genetic structure of Morelet’s crocodile (Crocodylus moreletii) across the region of Calakmul (Campeche, Mexico) using Next Generation Sequencing (dd-RADseq) ............................................ 61 4.1 Introduction ................................................................................................................ 61 4.2 Material and Methods ................................................................................................ 65 4.2.1 Sample collection ............................................................................................................. 65 4.2.2 Double digest RAD Sequencing (dd-RADseq) ............................................................ 68 4.2.3 SNP discovery and genotyping using STACKS .......................................................... 69 4.2.4 Identifying mitochondrial reads ...................................................................................... 70 4.2.5 Genetic structure and introgression .............................................................................. 72 4.2.6 Crocodile relatedness in the region of Calakmul ......................................................... 73 4.3 Results ...................................................................................................................... 74 4.3.1 SNP discovery and genotyping using stacks ............................................................... 74 4.3.2 Genetic structure across Calakmul ................................................................................ 76 4.3.3 Admixture proportions and co-ancestry ........................................................................ 80 4.3.4 Individual relatedness ...................................................................................................... 85 4.4 Discussion ................................................................................................................. 89 4.4.1 Screening for presence of hybrid individuals in Calakmul ......................................... 89 4.4.2 Population structure across Calakmul .......................................................................... 95 II 4.4.3 Relatedness and mating system .................................................................................... 98 4.5 Final Considerations ................................................................................................ 102 Chapter 5 – General discussion and concluding remarks ........................................... 105 5.1 Key Findings ............................................................................................................ 105 5.2 General Discussion ................................................................................................. 106 6. References Cited ......................................................................................................... 114 7. Appendix I – Ethics Approval Letter (University of Salford) .................................... 164 8. Appendix II – Aguadas of Calakmul Database .......................................................... 165 9. Appendix III – Herpetological diversity of Calakmul (Campeche, Mexico): an updated species list with new distribution notes ........................................................................ 167 Abstract ......................................................................................................................... 167 Introduction ................................................................................................................... 168 Material and Methods .................................................................................................... 170 Results .........................................................................................................................
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