12 research outputs found
Ecological constraints coupled with deep-time habitat dynamics predict the latitudinal diversity gradient in reef fishes
We develop a spatially explicit model of diversification based on palaeohabitat to explore the predictions of four major hypotheses potentially explaining the latitudinal diversity gradient (LDG), namely, the âtime-areaâ, âtropical niche conservatismâ, âecological limitsâ and âevolutionary speedâ hypotheses. We compare simulation outputs to observed diversity gradients in the global reef fish fauna. Our simulations show that these hypotheses are non-mutually exclusive and that their relative influence depends on the time scale considered. Simulations suggest that reef habitat dynamics produced the LDG during deep geological time, while ecological constraints shaped the modern LDG, with a strong influence of the reduction in the latitudinal extent of tropical reefs during the Neogene. Overall, this study illustrates how mechanistic models in ecology and evolution can provide a temporal and spatial understanding of the role of speciation, extinction and dispersal in generating biodiversity patterns
Diversité globale des poissons coralliens : histoire évolutive et influence de l'environnement passé
The exceptional diversity of fishes that inhabit coral reefs fascinates researched from all over the world since over 200years. How can those organisms, that only occupy 1% of the surface of the oceans, form one of the richest group of extant vertebrates? The complexity of this question does not only lie in the extraordinary diversity of morphologies, colors and behaviors, but also roots in the heterogeneous repartition of that richness. Explorations of Mayotteâs lagoon, Cuban coasts or the great barrier reef will show different perspectives of coral-reef fishâ diversity. Those pervasive differences are the result of processes that shaped, during millions of years the repartition of coral-reef species, their morphology and their behavior. During those millions of years of evolution, coral-reef fishes along with species that shelter them, faced massive climatic and tectonic changes. During my PhD, I studied the influence of those factors on the repartition and the diversity of coral-reef fishes. Understanding how species and ecosystems responded to important environmental changes can provide essential insights to anticipate future changes of ecosystem composition and functioning under global changesâ pressure. As coral-reefs are under more and more threatening pressures, I particularly focused on the influence of coral habitat availability on extinction, dispersion and speciation processes of coral-reef fishes.To achieve this goal, several methods have been employed. First, a descriptive approach based on sister-species co-occurrence patterns and the comparison between a global reconstruction of coral-reef habitat dynamics from the Cretaceous (â -140 million years) to present and the evolution of several speciose groups of coral-reef fishes permitted to identify a link between diversification rates of several groups of coral-reef fishes and coral habitat fragmentation and to observe the concordance between major earth-history events and biodiversity dynamics of coral-reef fishes.After the identification of a link between habitat fragmentation and coral-reef fishesâ diversification, an important question remains: What are the mechanisms underlying the influence of habitat dynamics on temporal and spatial variations of reef-fish biodiversity? To answer this question a unique approach allowing modeling of species dispersal, extinction and speciation in a gridded space varying in function of habitat dynamics, has been developed and applied to several groups of coastal marine organisms (corals, mangroves, fishes). This approach provided mechanistic insights about how plate movements drove coral reef habitat dynamics and shaped biodiversity gradients of several groups of coastal marine organisms. Finally, the extension of this approach to temperate reefs (rocky reefs), provided mechanistic insights about the interplay between the influence of tectonic events and ecological processes in the formation of present-day latitudinal gradient of biodiversity of reef-fishes.This thesis paves the way towards the use of a new generation of spatialized mechanistic models of macroevolution and the consideration of the influence of past-habitat dynamics in the study of diversification processes.LâĂ©tude de la diversitĂ© des espĂšces de poissons habitant les rĂ©cifs coralliens fascine les chercheurs du monde entier depuis plus de 200ans. Comment ces organismes qui nâoccupent que 1% de la surface des ocĂ©ans du globe ont-ils pu former un des groupes les plus riches des vertĂ©brĂ©s existants ? La complexitĂ© de cette question ne rĂ©side pas seulement dans lâexceptionnelle diversitĂ© de formes, de couleurs et de comportements de ces espĂšces mais aussi dans lâinĂ©gale rĂ©partition de cette richesse. Des explorations du lagon de Mayotte, des cĂŽtes Cubaines ou de la grande barriĂšre de corail donneront des perspectives trĂšs diffĂ©rentes de la diversitĂ© des poissons coralliens. Ces diffĂ©rences trĂšs importantes sont le rĂ©sultat de processus ayant modelĂ©, pendant des millions dâannĂ©es, la rĂ©partition des espĂšces coralliennes, leur morphologie et leur comportement. Pendant ces millions dâannĂ©es dâĂ©volution, les poissons coralliens, ainsi que les espĂšces de coraux qui les abritent, ont Ă©tĂ© confrontĂ©s Ă des changements drastiques des conditions climatiques et Ă la dĂ©rive des continents. Câest lâinfluence de ces facteurs sur la rĂ©partition et la diversitĂ© des poissons coralliens, que jâai Ă©tudiĂ© pendant ma thĂšse. Comprendre comment les espĂšces et les Ă©cosystĂšmes ont rĂ©agi aux changements environnementaux passĂ©s peut nous apporter des clĂ©s essentielles pour anticiper les changements Ă venir des Ă©cosystĂšmes que nous connaissons, sous lâinfluence des changements globaux. Les rĂ©cifs coralliens Ă©tant sous une menace de plus en plus prĂ©sente, je me suis particuliĂšrement intĂ©ressĂ© Ă lâinfluence de la disponibilitĂ© de lâhabitat corallien sur les processus dâextinction, de dispersion et de spĂ©ciation (formation de nouvelles espĂšces par divergence gĂ©nĂ©tique) des poissons coralliens.Afin de rĂ©pondre Ă ces objectifs, plusieurs mĂ©thodes ont Ă©tĂ© employĂ©es. Dans un premier temps, une approche descriptive basĂ©e sur la rĂ©partition de la co-occurrence entre espĂšces sĆurs et une comparaison entre une reconstruction globale de la dynamique des habitats coralliens allant du CrĂ©tacĂ© (â -140 millions dâannĂ©es) et les taux de diversification de plusieurs grands groupes de poissons rĂ©cifaux, ont permis de montrer que les taux de diversification de plusieurs familles de poissons rĂ©cifaux Ă©taient dĂ©pendant de la fragmentation des habitats coralliens, et dâobserver la concordance entre des Ă©vĂšnements climatiques et tectoniques majeurs et lâĂ©volution de la biodiversitĂ© des poissons coralliens.AprĂšs avoir identifiĂ© un lien entre fragmentation de lâhabitat corallien et la diversification des poissons, une grande question demeure : Comment cette dynamique de lâhabitat influence-t-elle dans lâespace et le temps la diversitĂ© des poissons rĂ©cifaux ? Pour rĂ©pondre Ă cette question, une approche unique permettant de modĂ©liser la dispersion, la spĂ©ciation et lâextinction des espĂšces dans un espace formĂ© de grilles dâhabitat dynamique a Ă©tĂ© dĂ©veloppĂ©e et appliquĂ©e Ă plusieurs clades dâorganismes marins cĂŽtiers (coraux, palĂ©tuviers et poissons). Cette approche a permis de dĂ©montrer comment la dĂ©rive des continents a contraint la dynamique de lâhabitat corallien et a façonnĂ© les gradients de diversitĂ© de plusieurs groupes dâorganismes marins cĂŽtiers. Enfin, lâextension de cette approche aux rĂ©cifs tempĂ©rĂ©s, a permis de montrer lâinteraction entre lâinfluence de la dĂ©rive des continents et des processus Ă©cologiques sur la colonisation et le maintien dâespĂšces de poissons rĂ©cifaux dans les milieux tempĂ©rĂ©s, expliquant en partie la formation du gradient latitudinal de diversitĂ© des poissons rĂ©cifaux.Ces travaux ouvrent la voie vers lâutilisation dâune nouvelle gĂ©nĂ©ration de modĂšles spatialisĂ©s de diversification et la prise en compte de la dynamique des habitats passĂ©s dans lâĂ©tude des processus de diversification
Global diversity of coral reef fishes : evolutionnary history and influence of Paleo-environment
LâĂ©tude de la diversitĂ© des espĂšces de poissons habitant les rĂ©cifs coralliens fascine les chercheurs du monde entier depuis plus de 200ans. Comment ces organismes qui nâoccupent que 1% de la surface des ocĂ©ans du globe ont-ils pu former un des groupes les plus riches des vertĂ©brĂ©s existants ? La complexitĂ© de cette question ne rĂ©side pas seulement dans lâexceptionnelle diversitĂ© de formes, de couleurs et de comportements de ces espĂšces mais aussi dans lâinĂ©gale rĂ©partition de cette richesse. Des explorations du lagon de Mayotte, des cĂŽtes Cubaines ou de la grande barriĂšre de corail donneront des perspectives trĂšs diffĂ©rentes de la diversitĂ© des poissons coralliens. Ces diffĂ©rences trĂšs importantes sont le rĂ©sultat de processus ayant modelĂ©, pendant des millions dâannĂ©es, la rĂ©partition des espĂšces coralliennes, leur morphologie et leur comportement. Pendant ces millions dâannĂ©es dâĂ©volution, les poissons coralliens, ainsi que les espĂšces de coraux qui les abritent, ont Ă©tĂ© confrontĂ©s Ă des changements drastiques des conditions climatiques et Ă la dĂ©rive des continents. Câest lâinfluence de ces facteurs sur la rĂ©partition et la diversitĂ© des poissons coralliens, que jâai Ă©tudiĂ© pendant ma thĂšse. Comprendre comment les espĂšces et les Ă©cosystĂšmes ont rĂ©agi aux changements environnementaux passĂ©s peut nous apporter des clĂ©s essentielles pour anticiper les changements Ă venir des Ă©cosystĂšmes que nous connaissons, sous lâinfluence des changements globaux. Les rĂ©cifs coralliens Ă©tant sous une menace de plus en plus prĂ©sente, je me suis particuliĂšrement intĂ©ressĂ© Ă lâinfluence de la disponibilitĂ© de lâhabitat corallien sur les processus dâextinction, de dispersion et de spĂ©ciation (formation de nouvelles espĂšces par divergence gĂ©nĂ©tique) des poissons coralliens.Afin de rĂ©pondre Ă ces objectifs, plusieurs mĂ©thodes ont Ă©tĂ© employĂ©es. Dans un premier temps, une approche descriptive basĂ©e sur la rĂ©partition de la co-occurrence entre espĂšces sĆurs et une comparaison entre une reconstruction globale de la dynamique des habitats coralliens allant du CrĂ©tacĂ© (â -140 millions dâannĂ©es) et les taux de diversification de plusieurs grands groupes de poissons rĂ©cifaux, ont permis de montrer que les taux de diversification de plusieurs familles de poissons rĂ©cifaux Ă©taient dĂ©pendant de la fragmentation des habitats coralliens, et dâobserver la concordance entre des Ă©vĂšnements climatiques et tectoniques majeurs et lâĂ©volution de la biodiversitĂ© des poissons coralliens.AprĂšs avoir identifiĂ© un lien entre fragmentation de lâhabitat corallien et la diversification des poissons, une grande question demeure : Comment cette dynamique de lâhabitat influence-t-elle dans lâespace et le temps la diversitĂ© des poissons rĂ©cifaux ? Pour rĂ©pondre Ă cette question, une approche unique permettant de modĂ©liser la dispersion, la spĂ©ciation et lâextinction des espĂšces dans un espace formĂ© de grilles dâhabitat dynamique a Ă©tĂ© dĂ©veloppĂ©e et appliquĂ©e Ă plusieurs clades dâorganismes marins cĂŽtiers (coraux, palĂ©tuviers et poissons). Cette approche a permis de dĂ©montrer comment la dĂ©rive des continents a contraint la dynamique de lâhabitat corallien et a façonnĂ© les gradients de diversitĂ© de plusieurs groupes dâorganismes marins cĂŽtiers. Enfin, lâextension de cette approche aux rĂ©cifs tempĂ©rĂ©s, a permis de montrer lâinteraction entre lâinfluence de la dĂ©rive des continents et des processus Ă©cologiques sur la colonisation et le maintien dâespĂšces de poissons rĂ©cifaux dans les milieux tempĂ©rĂ©s, expliquant en partie la formation du gradient latitudinal de diversitĂ© des poissons rĂ©cifaux.Ces travaux ouvrent la voie vers lâutilisation dâune nouvelle gĂ©nĂ©ration de modĂšles spatialisĂ©s de diversification et la prise en compte de la dynamique des habitats passĂ©s dans lâĂ©tude des processus de diversification.The exceptional diversity of fishes that inhabit coral reefs fascinates researched from all over the world since over 200years. How can those organisms, that only occupy 1% of the surface of the oceans, form one of the richest group of extant vertebrates? The complexity of this question does not only lie in the extraordinary diversity of morphologies, colors and behaviors, but also roots in the heterogeneous repartition of that richness. Explorations of Mayotteâs lagoon, Cuban coasts or the great barrier reef will show different perspectives of coral-reef fishâ diversity. Those pervasive differences are the result of processes that shaped, during millions of years the repartition of coral-reef species, their morphology and their behavior. During those millions of years of evolution, coral-reef fishes along with species that shelter them, faced massive climatic and tectonic changes. During my PhD, I studied the influence of those factors on the repartition and the diversity of coral-reef fishes. Understanding how species and ecosystems responded to important environmental changes can provide essential insights to anticipate future changes of ecosystem composition and functioning under global changesâ pressure. As coral-reefs are under more and more threatening pressures, I particularly focused on the influence of coral habitat availability on extinction, dispersion and speciation processes of coral-reef fishes.To achieve this goal, several methods have been employed. First, a descriptive approach based on sister-species co-occurrence patterns and the comparison between a global reconstruction of coral-reef habitat dynamics from the Cretaceous (â -140 million years) to present and the evolution of several speciose groups of coral-reef fishes permitted to identify a link between diversification rates of several groups of coral-reef fishes and coral habitat fragmentation and to observe the concordance between major earth-history events and biodiversity dynamics of coral-reef fishes.After the identification of a link between habitat fragmentation and coral-reef fishesâ diversification, an important question remains: What are the mechanisms underlying the influence of habitat dynamics on temporal and spatial variations of reef-fish biodiversity? To answer this question a unique approach allowing modeling of species dispersal, extinction and speciation in a gridded space varying in function of habitat dynamics, has been developed and applied to several groups of coastal marine organisms (corals, mangroves, fishes). This approach provided mechanistic insights about how plate movements drove coral reef habitat dynamics and shaped biodiversity gradients of several groups of coastal marine organisms. Finally, the extension of this approach to temperate reefs (rocky reefs), provided mechanistic insights about the interplay between the influence of tectonic events and ecological processes in the formation of present-day latitudinal gradient of biodiversity of reef-fishes.This thesis paves the way towards the use of a new generation of spatialized mechanistic models of macroevolution and the consideration of the influence of past-habitat dynamics in the study of diversification processes
A multiâplatform package for the analysis of intraâ and interspecific trait evolution
Evolutionary forces affect the distribution of phenotypes both within and among species. Yet, at the macroâevolutionary scale, the evolution of intraspecific variance is rarely considered. Here, we present an r and a BEAST 2 implementation that extends the JIVE (Joint interâ and Intraspecific Variance Evolution) model aimed at the analysis of continuous trait evolution at both interâ and intraspecific level.
Using a hierarchical Bayesian approach, we implemented a range of models for continuous trait evolution that operate independently on species means and variances along a phylogeny. The package uses Markov chain Monte Carlo for the inference of parameters and the evaluation of model fit. JIVE is available in the bite (Bayesian Integrative models of Trait Evolution) r package, as well as in BEAST 2. The two implementations offer the same continuous trait evolutionary models, but differ in their use and types of analyses. The r implementation allows for faster analyses by taking the phylogeny as data, while providing graphical and statistical functions as part of tools for model comparison, result parsing and summary, and plotting. In the BEAST 2 implementation, the species tree is a parameter, and both its topology and divergence times are jointly estimated with trait model parameters.
The bite package and the BEAST 2 implementation introduce new frameworks within comparative phylogenetics that explicitly model intraspecific variance. These tools allow users to tackle longâstanding questions in evolutionary biology, such as the identification of key evolutionary processes determining niche conservatism, niche partitioning, and lifeâhistory strategies
Ecological constraints coupled with deep-time habitat dynamics predict the latitudinal diversity gradient in reef fishes
We develop a spatially explicit model of diversification based on palaeohabitat to explore the predictions of four major hypotheses potentially explaining the latitudinal diversity gradient (LDG), namely, the âtime-areaâ, âtropical niche conservatismâ, âecological limitsâ and âevolutionary speedâ hypotheses. We compare simulation outputs to observed diversity gradients in the global reef fish fauna. Our simulations show that these hypotheses are non-mutually exclusive and that their relative influence depends on the time scale considered. Simulations suggest that reef habitat dynamics produced the LDG during deep geological time, while ecological constraints shaped the modern LDG, with a strong influence of the reduction in the latitudinal extent of tropical reefs during the Neogene. Overall, this study illustrates how mechanistic models in ecology and evolution can provide a temporal and spatial understanding of the role of speciation, extinction and dispersal in generating biodiversity patterns
Presence Absence Matrix of Acanthomorph species
This rdata file contains a matrix of presence/absence within 1° cells. The two first columns are the coordinates and the others are the presence/absence of species
Chronogram of the Labridae family
This file contains the consensus chronogram of the Labridae family in the nexus format
Data from: Ecological constraints coupled with deep-time habitat dynamics predict the latitudinal diversity gradient in reef fishes
We develop a spatially explicit model of diversification based on paleohabitat to explore the predictions of four major hypotheses potentially explaining the latitudinal diversity gradient (LDG), namely, the âtime-areaâ, âtropical niche conservatismâ, âecological limitsâ and âevolutionary speedâ hypotheses. We compare simulation outputs to observed diversity gradients in the global reef fish fauna. Our simulations show that these hypotheses are non-mutually exclusive and that their relative influence depends on the time scale considered. Indeed, simulations suggest that reef habitat dynamics produced the LDG during deep geological time, while ecological constraints shaped the modern LDG, with a strong influence of the reduction in the latitudinal extent of tropical reefs during the Neogene. Overall, this study illustrates how mechanistic models in ecology and evolution can provide a temporal and spatial understanding of the role of speciation, extinction and dispersal in generating contemporary biodiversity patterns
Chronogram of the Chaetodontidae family
This file contains the consensus chronogram of the Chaetodontidae family in the nexus forma
Chronogram of the Pomacentridae familiy
This file contains the consensus chronogram of the Pomacentridae family in the nexus format