Field and Genetic Methodologies for the Study of Felids in the Selva Lacandona, Chiapas Mexico: A Noninvasive Approach by Nashieli Garcia Alaniz Thesis presented as a partial requirement in the Doctor of Philosophy (Ph.D) in Biomolecular Sciences School of Graduate Studies Laurentian University Sudbury, Ontario Canada © Nashieli Garcia Alaniz, 2009 Library and Archives Biblioth&que et 1*1 Canada Archives Canada Published Heritage Direction du Branch Patrimoine de I'edition 395 Wellington Street 395, rue Wellington Ottawa ON K1A 0N4 Ottawa ON K1A 0N4 Canada Canada Your file Votre reference ISBN: 978-0-494-57677-9 Our file Notre reference ISBN: 978-0-494-57677-9 NOTICE: AVIS: The author has granted a non- L'auteur a accorde une licence non exclusive exclusive license allowing Library and permettant a la Bibliotheque et Archives Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par telecommunication ou par I'lnternet, preter, telecommunication or on the Internet, distribuer et vendre des theses partout dans le loan, distribute and sell theses monde, a des fins commerciales ou autres, sur worldwide, for commercial or non- support microforme, papier, electronique et/ou commercial purposes, in microform, autres formats. paper, electronic and/or any other formats. The author retains copyright L'auteur conserve la propriete du droit d'auteur ownership and moral rights in this et des droits moraux qui protege cette these. Ni thesis. Neither the thesis nor la these ni des extraits substantiels de celle-ci substantial extracts from it may be ne doivent etre imprimes ou autrement printed or otherwise reproduced reproduits sans son autorisation. without the author's permission. In compliance with the Canadian Conformement a la loi canadienne sur la Privacy Act some supporting forms protection de la vie privee, quelques may have been removed from this formulaires secondaires ont ete enleves de thesis. cette these. While these forms may be included Bien que ces formulaires aient inclus dans in the document page count, their la pagination, il n'y aura aucun contenu removal does not represent any loss manquant. of content from the thesis. 1*1 Canada Previous work has shown that in most ecosystems, the first species to disappear due to anthropogenic activity are the large predators and specialists. In tropical ecosystems, the felids represent this guild. Five species of felids have been reported for the Selva Lacandona, Mexico: jaguar {Panthera oncd), puma {Puma concolor), ocelot {Leopardus pardalis), jaguarundi {Puma yagouaroundi) and margay {Leopardus wiedii). Currently all these species are threaten by habitat loss, fragmentation and human persecution and are listed in Appendix I and II by CITES (Convention on International Trade of endangered Species of Wild Fauna and Flora). Also they are listed by IUCN (International Union for the Conservation of Nature) that monitors and protects endangered species, since evidence indicates that all populations of these felids are in decline. Therefore, it is necessary to generate information on these wild populations that eventually will lead to the development of appropriate management strategies. The primary objectives of this study were: (1) to generate information on the population of the five species of felids present in the Selva Lacandona, Chiapas, Mexico, (2) to develop and test field and genetic techniques for the study of the populations of felids present in the Selva Lacandona, and (3) to identify management strategies that will sustain felid populations in Neotropical ecosystems and prevent extirpation and extinction. Scale and medullar patterns of the guard hair of each terrestrial mammalian species of Chiapas were photographed and described and a hair catalogue and a dichotomous key were developed. The scale and medullar patterns of 79 species of terrestrial mammals are presented and described in this work including 22 Families (100% of the Families) and 10 Orders (100% of the Orders). This thesis evaluates the utility of hair-snares to collect mammalian samples with a specific goal of assessing felid populations. We recorded 389 hits on 888 hair-snare stations over the two years of the study which represents a hit rate of 43%. A total of 240 hits over 560 hair-snare stations (42%) were reported the undisturbed areas and a total of 100 hits over 328 hair-snares stations (30%) were reported in the disturbed agricultural areas. From the hair samples obtained using the hair-snare method, we identified margay (Leopardus wiedii, n=2), ocelot (Leopardus pardalis, n=l) and jaguarundi (Puma yaguarundi, n=l). In addition, primers for species-specific partial sequences of cytochrome b were developed to identify each of the five felid species found in this area. Primers were tested on blood samples obtained from zoo specimens and on hair samples obtained from the field. Successful amplification was obtained when tested on all blood samples from zoo specimens from the Chiapas region and 3 out of 5 of the target species were identified from field samples. The primers were especially useful when used on samples with low-yield and degraded DNA and the species-specific sequences allowed for discrimination among species. The deficit of information on carnivore populations and specifically felids in tropical ecosystems is partially due to the lack of reliable cost effective methodologies and techniques that allow managers to obtain data that will eventually lead to the development of appropriate management strategies. The hair-snare method and results presented in this study in combination molecular markers developed here have a great potential for studying felids in tropical ecosystems. These techniques are valuable for monitoring species of mammalian carnivores and can be used on projects that specifically aim to conserve felid species by supporting ecological research. iv Dedication Este trabajo esta dedicado a mis padres Chelo y Fernando y a mi hermano Rafael, con quienes comparti cada momento de esta etapa. Su incansable apoyo y confianza hicieron que pudiera alcanzar este sueno. v Acknowledgments I want to express my gratitude to my co-supervisors, Dr. F.F. Mallory and Dr. A. Omri, who provided me with much support and guidance throughout this project. I would also like to thank my Research Advisory Committee members, Dr. E.J. Naranjo and Dr. K. Nkongolo for their constant support, pointed suggestions and comments, which enhanced the writing of this thesis. I would also like to thank to Dr. F.V. Clulow for being my internal examiner and Dr. J. Schaefer (Trent University, Peterborough) for being my external examiner. A very special thank to Dr. A. Kumar, Director of the Biomolecular Sciences Doctoral Program for his direction and support. Financial support was provided by The Mexican National Council for Science and Technology (CONACYT) (Graduate Scholarship 167825 to NGA), Laurentian University (Waiver of International Tuition), NSERC for the Research Capacity Development Award and the Chair in Cancer Research Stipend. El Colegio de la Frontera Sur, Unidad San Cristobal, Chiapas, Mexico, provided logistic support. I would also like to thank the people of the local communities in Chiapas, where this study took place; their hospitality was a key element. To my colleagues at Ecosur; Carlos, Emilio, Elena, Fatima and Salvador, who helped me during the field work and showing me unconditional support. To Fernando Garcia, who helped me to build all the hair traps and Elsy Cabrera at Zoologico Miguel Alvarez del Toro and Dr. P. J. Wilson and the people at the Natural Resources DNA Profiling and Forensic Centre, Peterborough for their help with the DNA analysis. I also want to thank to my friends at Laurentian University, Kelly, Ashley, Paul, Curtis, Jesse, Becky and Melanie who were always willing to help me as friends and colleagues. vi Agradezco a toda mi familia y amigos en Mexico y varias partes del mundo que me expresaron su apoyo continuamente y creyeron en mi. Su confianza y constante presencia me mantuvieron cerca de pesar de la distancia. Quiero agradecer a la familia Gordillo Alaniz, por su apoyo incondicional especialmente durante el transcurso de mi trabajo de campo. A Pablo, Sofia, Carlos, Elisa, Isaias, Wendy, Ivan, la familia Figueroa y toda esa gente que me ayudo cuando mas lo necesite. vii List of Abbreviations Pon Panthera onca Pco Puma concolor Lpa Leopardus pardalis Pya Puma yagouaroundi Lwi Leopardus wiedii cyt b cytochrome b MABR Montes Azules Biosphere Reserve UNESCO United Nations, Educational, Scientific and Cultural Organization IUCN International Union for Conservation of Nature CITES Convention of International Trade of endangered Species of Wild Fauna and Flora UNAM Universidad Nacional Autonoma de Mexico ECOSUR Colegio de la Frontera Sur CONACYT Mexico's National Council of Science and Technology NRDPFC Natural Resources DNA Profiling and Forensic Centre DNA Deoxyribonucleic acid PCR Polymerase chain reaction viii Table of Contents Abstract iii Dedication v Acknowledgments vi List of Abbreviations viii Table of Contents ix List of Figures and Tables xi Chapter 1. General Introduction 1 1.1 General Introduction 1 Chapter 2. Taxonomic Guide to the Guard Hairs of Terrestrial Mammals from Chiapas, Mexico 13 2.1 Abstract 13 2.2. Resumen 14 2.3 Introduction 15 2.4 Study Area 16 2.5 Materials and Methods 17 2.6 Results and Discussion 18 2.7 Acknowledgments 23 Chapter 3. Key for the Identification of Guard Hairs of the Terrestrial Mammals from Chiapas, Mexico 25 3.1 Terms of Reference 25 3.2 Key for the Identification of Guard Hairs of the Terrestrial Mammals from Chiapas, Mexico v. 29 Chapter 4. Atlas of the Scale and Medullar Patterns of the Guard Hairs of Terrestrial Mammals from Chiapas, Mexico 47 Chapter 5. Hair-snares: A Noninvasive Method for Monitoring Felid Populations in the Selva Lacandona, Mexico 69 5.1 Abstract 69 5.2 Resumen 70 5.3 Introduction 71 5.4 Study Area 73 5.5 Hair-Snare Surveys 73 5.6 Results 78 5.7 Discussion 79 5.8 Implications for Felid Conservation 82 5.9 Acknowledgments 82 Chapter 6.