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Speciation, Extinction, and Dispersal Processes Related to Fragmentation of Riverine Networks: a Multiscale Approach Using Freshwater Fishes

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Speciation, Extinction, and Dispersal Processes Related to Fragmentation of Riverine Networks: a Multiscale Approach Using Freshwater Fishes MUSEUM NATIONAL D’HISTOIRE NATURELLE Ecole Doctorale Sciences de la Nature et de l’Homme – ED 227 Année 2015 N°attribué par la bibliothèque |_|_|_|_|_|_|_|_|_|_|_|_| THESE Pour obtenir le grade de DOCTEUR DU MUSEUM NATIONAL D’HISTOIRE NATURELLE Spécialité : Ecologie (Macroecologie) Présentée et soutenue publiquement par Murilo Sversut Dias Le 24 juillet 2015 Speciation, extinction, and dispersal processes related to fragmentation of riverine networks: a multiscale approach using freshwater fishes Sous la direction de : Thierry OBERDORFF et Pablo A. TEDESCO JURY : M. Oberdorff, Thierry Directeur de Recherche, IRD Directeur de Thèse M. Tedesco, Pablo A. Chargé de Recherche, IRD Co-Directeur de Thèse Mlle. Felipe, Ana F. Chargé de Recherche, CIBIO/InBIO, Universidade do Porto Examinateur M. Blackburn, Tim Professeur, CBER, University College London Rapporteur M. Floeter, Sergio R. Professeur, Universidade Federal de Santa Catarina Rapporteur Mme. Argillier, Christine Directrice de Recherche, Irstea Président/Examinateur MUSEUM NATIONAL D’HISTOIRE NATURELLE Ecole Doctorale Sciences de la Nature et de l’Homme – ED 227 Année 2015 N°attribué par la bibliothèque |_|_|_|_|_|_|_|_|_|_|_|_| THESE Pour obtenir le grade de DOCTEUR DU MUSEUM NATIONAL D’HISTOIRE NATURELLE Spécialité : Ecologie (Macroecologie) Présentée et soutenue publiquement par Murilo Sversut Dias Le 24 juillet 2015 Speciation, extinction, and dispersal processes related to fragmentation of riverine networks: a multiscale approach using freshwater fishes Sous la direction de : Thierry OBERDORFF et Pablo A. TEDESCO JURY : M. Oberdorff, Thierry Directeur de Recherche, IRD Directeur de Thèse M. Tedesco, Pablo A. Chargé de Recherche, IRD Co-Directeur de Thèse Mlle. Felipe, Ana F. Chargé de Recherche, CIBIO/InBIO, Universidade do Porto Examinateur M. Blackburn, Tim Professeur, CBER, University College London Rapporteur M. Floeter, Sergio R. Professeur, Universidade Federal de Santa Catarina Rapporteur Mme. Argillier, Christine Directrice de Recherche, Irstea Président/Examinateur i Author: Murilo Sversut Dias Title: Speciation, extinction, and dispersal processes related to fragmentation of riverine networks: a multiscale approach using freshwater fishes Supervisors: Thierry Oberdorff and Pablo A. Tedesco Research area: Ecology (Macroecology) Laboratory address: Unité Mixte de Recherche Biologie des Organismes et Écosystèmes Aquatiques (UMR BOREA), MNHN, CNRS 7208, UPMC, IRD 207, UCBN, Partenaire UAG; Département Milieux et Peuplements Aquatiques; Muséum National d'Histoire Naturelle; 43, rue Cuvier, 75005 Paris, France Place and date of oral defense: Paris, 24th July 2015 Abstract: Understanding factors driving the variation of diversity across the Earth is the main goal of ecology and biogeography. To reach this goal one needs to study the drivers of three main processes directly causing variation in diversity: speciation, extinction and dispersal. Speciation increases and extinction decreases diversity levels through time, whereas dispersal has a dual effect: it may increase or decrease diversity depending on the circumstances. Fragmentation, which stands by the emergence of natural or human-driven discontinuities on a given environment, is ubiquitous and has multiple ecological and evolutionary implications for the three diversity processes mentioned above (i.e., speciation, extinction and dispersal). Riverine fishes (i.e., strictly freshwater fishes) naturally experience fragmentation, as natural elements may disrupt connectivity of rivers (e.g., waterfalls) and river basins are separated from one another by barriers (oceans or land) which are insurmountable for these organisms. Riverine fishes thus constitute an ideal model for studying fragmentation effects. Here, I evaluated the effect of fragmentation on freshwater fish diversity by testing its effects on speciation, extinction, and dispersal processes at spatial and temporal scales ranging from a single river basin to worldwide rivers and from decades to million of years. In a first study, by analyzing endemism level of tributaries from the Orinoco river basin, I showed that tributaries highly fragmented by waterfalls have higher speciation probability and higher neo- endemism levels (i.e., species presumably originated by in-situ cladogenetic speciation) than their less fragmented counterparts. In a second study, I tested whether the historical connectivity between basins left an imprint on the global patterns of freshwater fish biodiversity. After controlling for contemporary and past environmental conditions, I found that palaeo-connected basins (those connected during the Last Glacial Maximum; 18-21 kya) displayed greater species richness but lower levels of endemism than did palaeo-disconnected basins. Palaeo-connected basins exhibited shallower distance decay of compositional similarity, suggesting that palaeo-river connections have favored the exchange of fish species. In a third study, I evaluated to what extent, if any, anthropogenic threats related to fragmentation (e.g., damming of rivers, agricultural practices) have been promoting fish extinctions in river basins. Focusing on Western Europe and North America, two strongly impacted regions, I showed that the percentage of cropland in the river basin and river fragmentation by dams are the main causes of present riverine fish species extinction. These extinctions, even if still reduced, correspond to extinction rates 40 times higher than background, natural rates. Overall, my results point for a prominent role of fragmentation as a driver of fish diversity through speciation processes and highlight the strong role played by history in explaining the global contemporary patterns of biodiversity via colonization processes. Moreover, they support the need of maintaining connectivity within river basins where human-made barriers have been created to avoid a substantial increase in species extinction rates. Keywords: speciation; extinction; colonization; freshwater fish; river basins; richness, endemism, beta diversity; history effects; natural barriers, anthropogenic disturbances. ii Résumé: Comprendre les facteurs qui contrôlent les variations de la biodiversité à travers la planète est un objectif central de la macroécologie et de la biogéographie. Pour atteindre cet objectif il est nécessaire d’étudier les facteurs structurant les trois processus qui contrôlent directement les variations de la biodiversité : la spéciation, l'extinction et la dispersion. La spéciation augmente la diversité au cours du temps alors que l'extinction la réduit. La dispersion, quant à elle fait augmenter ou diminuer la biodiversité selon les circonstances. La fragmentation, qui est définie comme l'émergence de discontinuités naturelles ou causées par l'homme sur un environnement donné, est omniprésente et a de multiples implications écologiques et évolutives sur les trois processus mentionnés plus haut (c.-à-d., la spéciation, l'extinction et la dispersion). Les poissons de cours d’eau (strictement d’eau douce) sont naturellement confrontés au phénomène de fragmentation car les bassins versant sont séparés les uns des autres par des barrières (eau de mer ou milieux terrestres) qui sont infranchissables pour ces organismes. Les poissons de cours d’eau constituent donc un modèle idéal pour étudier les effets de la fragmentation. Dans cette thèse, j'ai évalué les effets de la fragmentation sur les processus de spéciation, d’extinction et de colonisation des poissons d'eau douce à des échelles spatiales et temporelles allant du bassin versant à un échantillon représentatif des cours d’eau existantes sur la planète et de plusieurs décennies à quelques millions d'années. Dans une première étude, en analysant les niveaux d'endémisme des affluents du bassin versant de l’Orénoque, j'ai montré que les affluents très fragmentées par des chutes d'eau naturelles ont une probabilité plus élevée de spéciation et des niveaux plus élevés de néo-endémisme (c.-à-d., d’espèces probablement issues de la spéciation cladogénétique in situ) que leurs affluents homologues moins fragmentés. Dans une deuxième étude, j'ai testé si la connectivité historique entre bassins versants a laissé une empreinte sur les patrons mondiaux de biodiversité dans ses bassins. Après avoir contrôlé les conditions environnementales contemporaines et passées, j'ai montré que les bassins palaeo-connectés (ceux étant connectés pendant le dernier Maximum Glaciaire ; 18-21 ka) hébergent une plus grande richesse en espèces, mais des niveaux faibles d'endémisme en comparaison aux bassins palaeo-déconnectés. J’ai également montré que les niveaux de similarités des bassins palaeo-connectés décroissent plus légèrement avec la distance géographique entre bassins que les niveaux de similarités des palaeo-déconnectés, suggérant que les palaeo-connexions des bassins versants ont favorisé la colonisation des espèces. Dans un troisième temps, j'ai évalué dans quelle mesure la fragmentation liée aux activités anthropiques (par exemple la construction de barrages et les pratiques agricoles) a favorisé l’extinction d’espèces dans certains bassins versants. En focalisant sur l'Europe occidentale et l'Amérique du Nord, deux régions fortement touchées par les activités anthropiques, j'ai montré que le pourcentage des terres cultivées dans les bassins et la fragmentation de ces bassins par les barrages sont les principales causes de l'extinction actuelle des poissons d'eau douce. Ces extinctions, même si encore réduites, correspondent à un
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