UNIVERSIDADE FEDERAL DE PERNAMBUCO CENTRO DE TECNOLOGIA E GEOCIÊNCIAS DEPARTAMENTO DE OCEANOGRAFIA PROGRAMA DE PÓS-GRADUAÇÃO EM OCEANOGRAFIA Population genetics and conservation strategies for the West Indian manatee (Trichechus manatus Linnaeus, 1758) in Brazil FÁBIA DE OLIVEIRA LUNA RECIFE, PE May, 2013 UNIVERSIDADE FEDERAL DE PERNAMBUCO CENTRO DE TECNOLOGIA E GEOCIÊNCIAS DEPARTAMENTO DE OCEANOGRAFIA PROGRAMA DE PÓS-GRADUAÇÃO EM OCEANOGRAFIA Population genetics and conservation strategies for the West Indian manatee (Trichechus manatus Linnaeus, 1758) in Brazil Presented by Fábia de Oliveira Luna A thesis approved for the degree of Doctor of Science in Oceanography 2013 2 Catalogação na fonte Bibliotecária Maria Luiza de Moura Ferreira, CRB-4 / 1469 L961p Luna, Fábia de Oliveira. Population genetics and conservation strategies for the West Indian manatee (Trichechus manatus Linnaeaus,1758) in Brazil / Fábia de Oliveira Luna. - Recife: O Autor, 2013. 236 folhas; il., tabs. Orientador: Prof. Dr. José Zanon de Oliveira Passavante. Co-Orientador: Dr. Robert K. Bonde. Co-Orientadora: Drª. Margaret Hunter. Tese (Doutorado) – Universidade Federal de Pernambuco. CTG. Programa de Pós-Graduação em Oceanografia, 2013. Inclui Referências. 1. Oceanografia. 2. Genética populacional de peixe-boi. 3. Conservação de mamíferos aquáticos. 4. Hibridização entre duas espécies de Sirênios. 5. Endogamia de peixe-boi em cativeiro. I. Passavante, José Zanon de Oliveira. (Orientador). II. Bonde, Robert K. (Co-Orientador). III. Hunter, Margaret. (Co-Orientadora). IV. Título. 551.46 CDD (22. ed.) UFPE/BCTG/2013-096 Advisers: Dr. José Zanon de Oliveira Passavante UFPE - Brazil Dr. Robert K. Bonde USGS - USA Dr. Margaret Hunter USGS - USA Jury composed by: Dr. José Zanon de Oliveira Passavante – UFPE Dr. Coralie Nourisson – GEOMARE-México Dr. Danielle Sequeira Garcez – LABOMAR-UFC Dr. Jean Carlos Ramos da Silva – UFRPE Dr. Rodrigo Augusto Torres – UFPE Substitutes: Dr. Fernando Antônio do Nascimento Feitosa – UFPE Dr. Flávio José de Lima Silva – UERN 3 Population genetics and conservation strategies for the West Indian manatee (Trichechus manatus Linnaeus, 1758) in Brazil Fábia de Oliveira Luna Tese aprovada pela banca examinadora: ______________________________________________________________________ Dr. José Zanon de Oliveira Passavante ______________________________________________________________________ Dr. Coralie Nourisson ______________________________________________________________________ Dr. Danielle Sequeira Garcez – LABOMAR-UFC ______________________________________________________________________ Dr. Jean Carlos Ramos da Silva – UFRPE ______________________________________________________________________ Dr. Rodrigo Augusto Torres – UFPE 4 This thesis is dedicated to: My beloved daughter, that even wanting more time devoted to her, is always understanding about my time dedicated to manatees, and is always by my side, what gives me courage and determination to always seek more the preservation of these docile animals. Dedico a minha amada filhinha, que mesmo querendo mais tempo dedicado a ela, é sempre compreensiva quanto ao meu tempo dedicado aos peixes-bois, e está sempre ao meu lado, o que me dá coragem e determinação para sempre buscar mais a conservação desses dóceis animais. The one process now going on that will take millions of years to correct is the loss of genetic and species diversity by the destruction of natural habitats. Edward. O. Wilson 5 Table of contents List of Tables ............................................................................................................................................. 11 List of Figures ........................................................................................................................................... 14 ACKNOWLEDGEMENTS ....................................................................................................................... 17 LIST OF ABBREVIATIONS .................................................................................................................... 22 ABSTRACT ............................................................................................................................................... 28 RESUMO ................................................................................................................................................... 30 Chapter I - General Introduction ............................................................................................................ 32 I.I - INTRODUCTION ........................................................................................................................... 32 I.I.1 - The Order Sirenia ................................................................................................................... 32 I.I.2 - Manatee biology ..................................................................................................................... 36 I.I.3 - Threats to manatees .............................................................................................................. 38 I.I.4 - Conservation genetics ........................................................................................................... 40 I.I.5 - Genetic studies of sirenians ................................................................................................. 40 I.I.6 - Sirenia conservation in Brazil ............................................................................................... 44 I.II - OBJECTIVES ................................................................................................................................ 46 I.II.1 - General objectives of the thesis .......................................................................................... 46 I.II.2 - Specific objectives and description of the chapters ......................................................... 46 I.IV - BACKGROUND GENETIC RESEARCH ................................................................................ 48 6 I.V - DESCRIPTION OF THE AREA ................................................................................................. 49 Chapter II - Phylogeographic implications for release of critically endangered manatee calves rescued in Northeast Brazil ..................................................................................................................... 52 II.I - INTRODUCTION .......................................................................................................................... 52 II.II - MATERIALS AND METHODS .................................................................................................. 57 II.II.1 - Sample collection and DNA extraction ............................................................................. 57 II.II.2 - Mitochondrial DNA analysis ............................................................................................... 58 II.II.3 - Mitochondrial statistical analysis ....................................................................................... 58 II.III – RESULTS ................................................................................................................................... 59 II.III.1 - Northeast Brazilian manatee populations exhibit strong phylogeographic division and low haplotype diversity ............................................................................................................. 59 II.III.2 - Rescue, rehabilitation and release of manatee calves from 1989-2011 .................... 61 II.IV - DISCUSSION ............................................................................................................................. 62 II.IV.1 - Considering genetic information in the release of rehabilitated and captive-born manatees ........................................................................................................................................... 62 II.IV.2 - Inbreeding depression in isolated Brazilian manatee populations.............................. 63 II.IV.3 - Genetic swamping and outbreeding depression ........................................................... 64 II.IV.4 - Conservation of West Indian manatees in Northeastern Brazil .................................. 65 Chapter III - Nuclear genetic diversity and population structure of the West Indian manatee (Trichechus manatus) in Brazil. ............................................................................................................. 67 III.I - INTRODUCTION ......................................................................................................................... 67 III.II – MATERIALS AND METHODS ................................................................................................ 69 7 III.II.1 - Microsatellite DNA amplification and fragment analysis ............................................... 69 III.II.2 - Data analysis ....................................................................................................................... 72 III.III - RESULTS ................................................................................................................................... 74 III.III.1 - Population structure .......................................................................................................... 74 III.III.2 - Population structure analyses within the Northeast coast of Brazil ........................... 78 III.III.3 - Genetic diversity within the subclusters