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La Genetique Au Service De La Conservation D'une Espece Menacee Endemique a Madagascar, La Tortue Radiee Astrochelys Radiata

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La Genetique Au Service De La Conservation D'une Espece Menacee Endemique a Madagascar, La Tortue Radiee Astrochelys Radiata Universite de Montreal La genetique au service de la conservation d'une espece menacee endemique a Madagascar, la tortue radiee Astrochelys radiata par Sebastien Rioux Paquette Departement de sciences biologiques Faculte des Arts et Sciences These presentee a la Faculte des etudes superieures en vue de l'obtention du grade de Doctorat en Sciences biologiques 19 Septembre, 2008 © Sebastien Rioux Paquette, 2008 Library and Archives Bibliotheque et 1*1 Canada Archives Canada Published Heritage Direction du Branch Patrimoine de I'edition 395 Wellington Street 395, rue Wellington OttawaONK1A0N4 OttawaONK1A0N4 Canada Canada Your file Votre reference ISBN: 978-0-494-53549-3 Our file Notre reference ISBN: 978-0-494-53549-3 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'lntemet, prefer, 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 Universite de Montreal Faculte des etudes superieures Cette these intitulee: La genetique au service de la conservation d'une espece menacee endemique a Madagascar, la tortue radiee As troche lys radiata presentee par: Sebastien Rioux Paquette a ete evaluee par un jury compose des personnes suivantes Bernard Angers, president-rapporteur Franfois-Joseph Lapointe, directeur de recherche Anne bruneau, membre du jury David Green, examinateur externe Paul Comtois, representant du doyen de la FES in Resume Les analyses genetiques peuvent fournir des informations interessantes a propos de la demographie, de l'ecologie ou de revolution des especes, qui a leur tour peuvent jouer un role determinant dans l'elaboration de plans de conservation appropries. Le principal objectif de cette these etait de realiser une analyse detaillee de la genetique des populations d'une espece menacee dans le but d'acquerir des connaissances cruciales a sa conservation. L'espece etudiee etait la tortue radiee, Astrochelys radiata (Chelonia: Testudinidae), endemique a la foret epineuse semi-aride du sud de Madagascar, ou, en plus de la destruction de l'habitat, elle est gravement menacee par la surexploitation pour approvisionner les marches locaux et internationaux. D'un bout a l'autre de cette these, les donnees provenant de treize marqueurs microsatellites ont ete analysees pour repondre a des questions qui concernaient, notamment, la structure genetique de l'espece, l'impact de 1'exploitation et de la fragmentation de l'habitat sur sa diversite genetique, et ridentification d'unites de conservation. Huit de ces marqueurs ont ete specifiquement developpes pour A. radiata pendant cette etude, et plus de 330 echantillons recueillis sur l'ensemble de l'aire de repartition actuelle de l'espece ont ete analyses au total. Les resultats indiquent que la tortue radiee exhibe des niveaux moderes de differentiation, et deux populations genetiquement distinctes ont ete principalement identifiees. Celles-ci compte chacune des sous-populations additionelles peripheriques qui demontrent une differentiation faible mais significative en fonction de leurs frequences alleliques. Une approche statistique basee sur la regression multiple de matrices de distances a mis en evidence le role de quelques fleuves en tant que barrieres au flux genique entre populations de tortues, malgre le fait que ces cours d'eau soient saisonniers et completement asseches plusieurs mois par annee. En combinaison avec des analyses de l'ADNmt, il a ete trouve que le fleuve Menarandra represente la plus importante barriere genetique historique et IV contemporaine chez cette espece. Des analyses de goulots d'etranglement ont suggere que la diversite genetique plus faible des populations exploitees ne pouvait etre attribute a des activites anthropogeniques recentes, et des resultats de l'ADNmt indiquent plutot que ce sont les tailles historiquement plus petites des populations situees a Test du Menarandra, en raison de la nature fragmentee de l'habitat dans cette region, qui sont 1'explication la plus probable. Des analyses morphometriques additionnelles ont trouve des patrons divergents entre les variations genetiques et les variations de la forme de la carapace chez A. radiata, et l'exploitation humaine semble etre le facteur expliquant les differences morphologiques. La methodologie developpee pour realiser les analyses morphometriques pourrait devenir un outil utile pour la gestion des tortues confisquees aupres des braconniers et des trafiquants. Finalement, des analyses genetiques separees pour les males et les femelles ont revele que la dispersion est fortement biaisee en faveur des males chez A. radiata. Cette these fournit un exemple interessant de la panoplie d'applications possibles de la genetique en conservation, et l'interet scientifique qu'a recu la tortue radiee durant cette etude a ete un catalyseur formidable pour amorcer une plus grande conscientisation face au declin dramatique de cette espece emblematique de Madagascar. Mots-cles : barrieres genetiques, dispersion inegale des sexes, differentiation des populations, exploitation, foret epineuse de Madagascar, genetique de la conservation, microsatellites, morphometrie, unites de conservation, Testudinidae V Abstract Genetic analyses can provide insightful information about the demography, ecology and evolution of species, which might in turn be highly relevant to launch appropriate conservation initiatives. The main objective of this thesis was to conduct a thorough population genetics assessment of an endangered species in order to gather crucial knowledge for its conservation. The species under study was the radiated tortoise, Astrochelys radiata (Chelonia: Testudinidae), endemic to the semi-arid spiny forest of southern Madagascar where, in addition to habitat destruction, it is severely threatened by overexploitation for both local and international markets. Throughout this thesis, data from thirteen microsatellite markers were analyzed to answer several questions concerning, among others, the genetic structure of the species, the impact of exploitation and habitat fragmentation on its genetic diversity, and the identification of conservation units. Eight of these markers were specifically developed for A. radiata in the course of this study, and a total of more than 330 samples collected across the extant range of the species were analyzed. Results indicated that the radiated tortoise harbors moderate levels of differentiation, and two major genetically distinct populations were uncovered. Within each of these, additional peripheral subpopulations showed low but significant differentiation based on allele frequencies. A statistical approach based on multiple regression on distance matrices emphasized the role of some rivers as barriers to gene flow between tortoise populations, despite the fact that these are seasonal rivers that are completely dry several months per year. In combination with mtDNA analyses, it was found that the Menarandra River represents the most important historical and contemporary genetic boundary in this species. Bottleneck analyses suggested that the lower genetic diversity in harvested populations may not be attributed to recent exploitation, and mtDNA results pointed towards historically lower sizes of populations located east of the Menarandra, due to the VI fragmented nature of habitat in that region, as the most likely explanation. Additional morphometric analyses found contrasting patterns of genetic and shell shape variation in A. radiata, and human exploitation appears to be the force explaining morphometric differences. The methodology developed to perform morphometric analyses allowed for a high assignment success rate among three geographic groups of tortoise populations, so this method might become a helpful tool for the management of tortoises confiscated from poachers and smugglers. Finally, separate genetic analyses for male and female tortoises revealed that dispersal is strongly male-biased in A. radiata. This thesis provides an interesting example of the array of possible applications of genetics to conservation, and the scientific interest that the radiated
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