Rodrigo Barban Zucoloto Patricia Susana Amavet Luciano Martins Verdade Izeni Pires Farias  Editors Conservation Genetics of New World Crocodilians Conservation Genetics of New World Crocodilians Rodrigo Barban Zucoloto Patricia Susana Amavet Luciano Martins Verdade • Izeni Pires Farias Editors Conservation Genetics of New World Crocodilians Editors Rodrigo Barban Zucoloto Patricia Susana Amavet Laboratório de Genética de Populações e Laboratorio de Genética, Departamento Evolução Molecular (GENEV), de Ciencias Naturales, Facultad de Instituto de Biologia, Humanidades y Ciencias, Universidad Universidade Federal da Bahia, Nacional del Litoral, Consejo Nacional Salvador, Bahia, Brasil de Investigaciones Científicas y Técnicas (CONICET), Luciano Martins Verdade Santa Fe, Argentina Universidade de São Paulo CENA/LE²Ave Izeni Pires Farias Piracicaba, São Paulo, Brasil Laboratório de Evolução e Genética Animal Departamento de Genética Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brasil ISBN 978-3-030-56382-0 ISBN 978-3-030-56383-7 (eBook) https://doi.org/10.1007/978-3-030-56383-7 © Springer Nature Switzerland AG 2021 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors, and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. This Springer imprint is published by the registered company Springer Nature Switzerland AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland Foreword Since decades, information on crocodilians in the Americas has been available. The champions of crocodilian conservation were Eduard Mc Ilhenny in the USA, Miguel Alvarez del Toro in México, Federico Medem in Colombia, and Angel Gallardo in Argentina, just to mention a few, with obviously many unfair omissions. These examples, in my opinion, somehow describe what it was like to do science at that time in our region, when solitary naturalists with or without a budget invested their best to search, investigate, and communicate their findings mainly on the natural history of our crocodiles. Not so long ago, the Group of Crocodile Specialists with its meetings around the world, especially on this continent, with the USA, Venezuela, Ecuador, and Argentina being the first to participate, launched a process of consolidation of a network of American crocodile specialists. In this way, the first volume on the con- servation and management of Latin American alligators and crocodiles was pro- duced in 1995, and from there, an increasing number of publications referring to crocodiles were developed in different peer-reviewed journals. These publications were characterized by multi-thematic content but with single authorship in most cases. Right now, with a thematic specialization and globalized world, and with easy and cheap communication between researchers, more and more research is being generated by multiple authors, very often belonging not only to different institutions but also to different continents, as can be seen in this book. In my opinion, this gen- erates more and better information on the one hand, but also favors its dissemination at the local, regional, and international levels. We were used to seeing in the old days that the information in South America referred mainly to individual descriptions about a nesting female, the size of an individual, or the finding of a crocodile in a place that allowed to determine the approximate geographic distribution of that species. Despite the fact that the situa- tion in North America was different, the publications referred to only one or two species, which was totally useless for a conservation strategy at the regional level. Globalization has many pros and cons, but from a scientific point of view, bene- fits are almost the rule. In this context, we are also involved in a kind of v vi Foreword “continentalization” process, and this book is an excellent example of this. The synergy between authors from all over the Americas (and also from other conti- nents) is generating high-quality results in topics such as hybridization, genetic diversity, genetics and evolution, multi-paternity, and molecular phylogenetics, among other topics, allowing the joint use of the best available technology no matter the boundaries between countries. I used to say many years ago that conservation programs for crocodiles must be developed on a regional basis, because the species has no nationality and distribu- tion area has no political boundaries, well, it seems that now this is also valid for science and scientists. I cannot wait to see how things evolve in the near future. In the meantime, I’m sure you’ll enjoy this book very much. Departamento de Ciencias Naturales, Facultad de Alejandro Larriera Humanidades y Ciencias Universidad Nacional del Litoral Santa Fe, Argentina Proyecto Yacaré, Laboratorio de Zoología Aplicada: Anexo Vertebrados (FHUC-UNL/MAyCC) Santa Fe, Argentina Acknowledgments We thank all contributors of this book for working together to organize these texts carefully and sharing decades of research effort in conservation genetics studies on crocodilians. vii Contents 1 Geographic Distribution, Habitat, Reproduction, and Conservation Status of Crocodilians in the Americas . . . . . . . . . 1 Francisco Villamarín, Armando H. Escobedo-Galván, Pablo Siroski, and William E. Magnusson 2 Molecular Markers Applied to Conservation Genetics of American Crocodilians . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 Rodrigo Barban Zucoloto, Izeni Pires Farias, and Patricia Susana Amavet 3 Molecular Phylogenetics of the New-World Crocodylia . . . . . . . . . . . 79 Llewellyn D. Densmore III and Tomas Hrbek 4 Biogeography and Comparative Phylogeography of New-World Crocodylians . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95 Fábio de Lima Muniz, Pedro Senna Bittencourt, Sandra Marcela Hernández-R angel, Igor Joventino Roberto, Izeni Pires Farias, and Tomas Hrbek 5 Genetic Diversity of New World Crocodilians . . . . . . . . . . . . . . . . . . . 123 Patricia Susana Amavet, Rodrigo Barban Zucoloto, Tomas Hrbek, and Izeni Pires Farias 6 Crocodilians Are Promiscuous But Not to the Benefit of Heterozygosity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153 Sally R. Isberg 7 Hybridization and Speciation Among New- World Crocodilian Species . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171 Gualberto Pacheco-Sierra and Patricia Susana Amavet 8 Crocodilian Genome Advances . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185 Katherine Brittain, David A. Ray, and Jaime Gongora ix x Contents 9 How Genetic Tools Can Help Crocodilians’ Management and Governance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203 Luciano M. Verdade, Carlos I. Piña, Melina Simoncini, and Karina L. Silva-Brandão 10 Perspectives and Final Considerations About the Molecular Ecology of New-W orld Crocodilians . . . . . . . . . . . . . . . . . . . . . . . . . . . 215 Patricia Susana Amavet and Rodrigo Barban Zucoloto Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223 Contributors Patricia Susana Amavet Laboratorio de Genética, Departamento de Ciencias Naturales, Facultad de Humanidades y Ciencias, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina Pedro Senna Bittencourt Universidade Federal do Amazonas. Departamento de Genética, Manaus, Amazonas, Brasil Katherine Brittain Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, Australia Fábio  de Lima  Muniz Departamento de Genética, Universidade Federal do Amazonas, Manaus, Amazonas, Brasil Llewellyn D. Densmore III Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA Armando H. Escobedo-Galván Centro Universitario de la Costa, Universidad de Guadalajara, Puerto Vallarta, Jalisco, México Izeni Pires Farias Laboratório de Evolução e Genética Animal, Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brasil Jaime  Gongora Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, Australia Sandra Marcela Hernández-Rangel Departamento de Genética, Universidade Federal do Amazonas, Manaus, Amazonas, Brasil Tomas Hrbek Departamento de Genética, Universidade Federal do Amazonas, Manaus, Amazonas, Brasil Sally R. Isberg Centre for Crocodile Research, Noonamah, Northern Territory, Australia xi