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Thèse Et Mémoire Université de Montréal Systématique, biogéographie et diversification du genre Crudia (Leguminosae, Detarioideae) par Boris Domenech Département de Sciences Biologiques Centre sur la Biodiversité Institut de Recherche en Biologie Végétale Faculté des Arts et des Sciences Thèse présentée en vue de l’obtention du grade de Philosophiae Doctor en Sciences Biologiques Août 2018 © Boris Domenech, 2018 Résumé Le genre Crudia Schreb. présente une distribution pantropicale et une richesse spécifique élevée, inhabituelles pour un genre appartenant à la sous famille des Detarioideae (Leguminosae). Les espèces de Crudia, réparties en Amérique du Sud, en Afrique de l’Ouest et en Asie du Sud Est, ont fait l’objet de plusieurs études de taxonomie indépendantes, réalisées par plusieurs auteurs successifs. En revanche, l’évolution et l’histoire biogéographique du genre sont inconnues à ce jour. Afin de mieux comprendre l’histoire évolutive de Crudia, nous proposons une approche pluridisciplinaire visant à mettre à jour les connaissances à propos de ce genre méconnu. La première partie de cette étude a pour objectif de réaliser une révision taxonomique des espèces asiatiques du genre Crudia, les espèces africaines et américaines ayant déjà été traitées par d’autres auteurs. Nous avons pour cela utilisé des méthodes de taxonomie traditionnelle en compilant des données morphologiques sur un grand nombre de spécimens d’herbier. Sur les trente-cinq espèces initiales décrites en Asie, nous en avons retenu quatorze et avons ajouté une nouvelle espèce. Les autres espèces ont été mises en synonymie pour la plupart, exceptée l’une d’entre elle qui est à présent considérée comme douteuse. Suite à ces réassignations taxonomiques, les distributions géographiques respectives des espèces ont été réévaluées et des nouveaux statuts de conservation ont été proposés. La seconde partie de cette étude a pour objectif de poser un cadre conceptuel afin d’étudier dans le détail l’évolution de ce genre, son histoire biogéographique et les relations entre espèces. Nous avons pour cela séquencé cinq régions nucléaires (ITS, ETS, AGT1, CALTL, AIGP) pour de nombreux spécimens, principalement prélevés sur des échantillons d’herbiers (K, US, P, L, WAG, U). Les phylogénies réalisées montrent que Crudia est monophylétique et possède une structure interne bien définie, avec un clade regroupant toutes les espèces asiatiques et un autre regroupant les espèces africaines et américaines, ces dernières formant elles-mêmes un clade clairement identifiable. La reconstruction de l’histoire biogéographique, associée à la datation à l’aide d’un macrofossile, montre que Crudia trouve son origine en Afrique au cours de l’Éocène, puis subit deux évènements indépendants de dispersion vers l’Amérique du Sud et vers l’Asie au cours de l’Éocène moyen. i La troisième partie de cette étude a pour objectif d’identifier si la richesse spécifique du genre Crudia pouvait être associée à un évènement de changement des taux de diversification au cours du temps, mais également savoir si les niches écologiques des différentes espèces étaient semblables à travers l’aire de distribution du genre au complet. Nous avons utilisé pour cela des données d’occurrences des espèces, ainsi que des données reliées au régime de précipitations et à la température. Parallèlement, les taux de diversification ont été étudiés à l’échelle du genre et à l’échelle des Detarioideae. Au final, il s’est avéré que les niches écologiques différaient d’un continent à l’autre, et qu’il n’existait pas de changement des taux de diversification dans le genre Crudia pouvant être relié précisément à la richesse spécifique. Le nombre élevé d’espèces au sein du genre Crudia pourrait en revanche être lié à un âge relativement plus vieux de ce genre, comparé aux autres genres évolutivement proches. Mots-clés : Crudia, Detarioideae, révision taxonomique, phylogénie, évolution, biogéographie, datation, systématique, niche écologique, diversification ii Abstract In the subfamily Detarioideae (Leguminosae), the genus Crudia Schreb. shows an unusual pantropical distribution and high species richness compared to closely related genera. Crudia species, spread throughout South America, West Africa and Southeastern Asia, have been the focus of independent taxonomic studies conducted by several consecutive authors. To date, however, the evolution and biogeographic history of this genus remain poorly understood. We propose a multidisciplinary approach to study this poorly known genus and to improve our understanding of its evolutionary history. First, we conducted a taxonomic revision of Asian species within the genus Crudia, in accordance with the recent revisions of African and American species. We used traditional taxonomic methods by compiling morphological data based on the study of herbarium specimens. From an initial description of thirty five species from the literature, we retained fourteen species and synonymized the others except for one we consider as a doubtful species. A newly described species was also added. Species geographic distributions were reevaluated and new conservation statuses were suggested. Second, we established a conceptual framework to study the evolution, biogeographic history, and relationship between species of this genus. We sequenced five nuclear regions (ITS, ETS, AGT1, CALTL, and AIGP) on numerous sampled herbarium specimens (K, US, P, L, WAG, U). The phylogenetic analyses resolve Crudia as monophyletic with a well- identified internal structure composed of one clade grouping all Asian species and one clade grouping both African and American species, with the American species grouped in a single clade. Reconstructions of biogeographic history and an associated divergence time analysis calibrated with macrofossils show Crudia originated in Africa during the Eocene and underwent two independent dispersal events during mid-Eocene: from Africa to South America and from Africa to Southeastern Asia. Third, we tested if species richness in the genus Crudia is associated with changes in diversification rates through time and with ecological niche shifts throughout its global distribution. We used species occurrence data, carefully selected to avoid identification errors, associated with environmental data retrieved from the literature. Diversification rates were iii studied both at the scale of the genus Crudia and the Detarioideae subfamily. We conclude that ecological niches differ from one continent to another and no diversification rates changes were detected in the genus Crudia. Our finding suggest that the greater species richness in Crudia compared to sister genera may be the consequence of relatively older age of this genus. Keywords: Crudia, Detarioideae, taxonomic revision, phylogeny, evolution, biogeography, divergence time, systematic, ecological niche, diversification iv Table des matières Résumé ......................................................................................................................................... i Abstract ...................................................................................................................................... iii Table des matières....................................................................................................................... v Liste des tableaux ....................................................................................................................... ix Liste des figures .......................................................................................................................... x Liste des abréviations et sigles ................................................................................................... xi Remerciements .......................................................................................................................... xv Introduction ............................................................................................................................... 16 La diversité biologique n’est pas homogène à l’échelle de la planète .................................. 16 L’unité de base pour étudier la diversité biologique : l’espèce ............................................ 16 Étudier la diversité des espèces d’un point de vue taxonomique et systématique ................ 18 La taxonomie : des méthodes pour délimiter les espèces ................................................. 18 La systématique phylogénétique : mettre de l’ordre dans le chaos biologique ................ 19 Étudier les patrons de diversité à l’aide de la biogéographie historique ............................... 20 Une dimension écologique de la diversité biologique .......................................................... 22 La famille des Légumineuses ................................................................................................ 23 Le genre Crudia Schreb. ....................................................................................................... 24 Révision taxonomique des espèces asiatiques du genre Crudia ........................................... 25 Systématique et biogéographie historique du genre Crudia ................................................. 27 Interprétation des patrons de diversité du genre Crudia : changement de taux de diversification et/ou influence des paramètres environnementaux ? .................................... 28 Chapitre I : Taxonomic revision of the Asian species of Crudia Schreb. (Leguminosae, Detarioideae) ............................................................................................................................
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