Traditionally, the study of biodiversity has focused on quantifying patterns of species diversity, or species richness, by simply counting the number of species across environmental gradients. This approach has been fundamental to ecological investigations and thinking with regards to identifying patterns of biodiversity. Although species diversity is the most commonly used dimension of biodiversity, species diversity alone does not provide a mechanistic understanding of biodiversity gradients. By also quantifying the genetic and phylogenetic diversity of a population, community or ecosystem, ecologists can become more informed on the relationships organisms have with one another, as well as their potential to adapt to changes in their environment. While each of these approaches provides methods for characterizing biodiversity, they do not offer direct insight into what species do, how they function, or how they will respond to changes in their environment. Functional, or trait-based ecology, provides an informative alternative to species-centric approaches that seeks to understand patterns of biodiversity in terms of functional traits. Functional traits capture fundamental tradeoffs in life history strategies that can be used to determine species ecological roles and can be used to scale from organisms to ecosystems to ask broad ecological questions. The overarching goal of my dissertation is to add additional links to trait-based ecology by identifying potential sources of trait variation across different spatial and temporal gradients between varying levels of biological organization. By assessing variation across spatial-temporal scales, I tested two prominent assumptions of trait-based ecology. First, I tested the trait-environment assumption wherein traits affect ecosystem processes. Therefore, there should be a predictable relationship between traits, their environment, and ecosystem function across large ecological gradients and between broad taxonomic groups. Second, I tested the assumption that interspecific trait variation exceeds intraspecific trait variation; thus, the species mean trait value captures much of the variation for a given trait. My study systems include the latitudinal diversity gradient of North America, forests of varying successional age in the tropical dry forests of Costa Rica, and a subalpine meadow of Colorado. First, we collected leaf trait data and soil microbial data at six sites across the latitudinal diversity gradient to test a central hypothesis of trait-based ecology, primarily that shifts in plant traits associated with decomposition and nutrient availability ramify to influence microbial functioning. We found that changes in plant traits not only reflect nutrient limitation across broad ecological gradients, but also have important regional effects on biogeochemical processes, microclimates, and energy fluxes that influence microbial diversity. Furthermore, changes in plant function correspond to changes in bacterial functional traits related to carbon, nitrogen, and phosphorus cycling, although only fungal functional traits related to nitrogen cycling change across the gradient. Our results represent one of the first comparisons of functional diversity within and across bacterial, fungal, and plant communities across a latitudinal gradient. Next, we collected leaf functional trait and abiotic data across a 110-year chronosequence within a tropical dry forest in Costa Rica. We focused on six leaf functional traits for woody plants within 14 plots that have varying times since disturbance in the tropical dry forests of Guanacaste, Costa Rica. When we compare species composition and community function, we find that older tropical dry forest communities differ significantly from younger forests in species composition, above ground biomass, and functional traits. Species in younger forests have traits better adapted to hotter temperatures and increased drought. For example, young forests are characterized by thicker leaves with higher water use efficiency. In contrast, older forests have thinner broader leaves more susceptible to desiccation. Interestingly, in contrast to expectations, variation in these functional traits does not generally change through succession. This means that the different species within each community are converging on similar functional strategies. Our results also suggest that regenerating tropical dry forests are resilient and can be restored within a human lifetime. Finally, we evaluated patterns of trait variation within and between three years to understand the widely-ignored source of temporal variation associated with seasonality and test the assumption that interspecific trait variation exceeds intraspecific variation and the species means account for the overall variation of a trait. To do this, we collected leaf data from eight species at a local site in Colorado throughout the growing season, over three years, as well as extracted data from a global database and made comparisons to assess sources trait variation. We found that, although the timing of collection influences one’s ability to capture fine-scale processes occurring on short time scales, collecting data locally throughout the growing season and across multiple years does not significantly influence species ranking. However, species ranking is not conserved for comparisons between local and global databases. This suggests that extra care should be taken when applying global data for species-specific studies and that ‘snap-shot’ sampling designs may over- or underestimate community trait distributions, reducing predictability. Overall, this body of work extends beyond understanding patterns of species diversity through the inclusion of species function. It contributes to our understanding of variation in biodiversity across broad ecological gradients and between diverse taxonomic groups, how communities assemble via functional traits, and the importance of temporal variation on functional traits for detecting fine-scale patterns.

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Although a common plant response to environmental gradients, leaf trait plasticity is often uncharted in agroforestry systems. The objective of this study was to examine the effect of a i) local-scale gradient (light, nutrients) induced by shade tree diversity and ii) large-scale gradient (climato-edaphic) induced by altitude on coffee plant response on multiple agroforestry research farms in Costa Rica. Results show large variability of coffee traits: leaf photosynthetic rates, specific leaf area (SLA) and number of fruiting nodes deviate along both gradients. Mean SLA increased with increasing shade tree diversity. However, with increasing altitude, full sun coffee photosynthesized at higher rates than shaded coffee. Concurrently, other coffee leaf physiological and morphological traits differentiated between full sun and shaded coffee with increasing altitude. Results suggest soil moisture and light availability dominate environmental correlates to intraspecific coffee trait plasticity, providing insight to sources of coffee performance variability in monoculture and agroforestry systems.

Although a common plant response to environmental gradients, leaf trait plasticity is often uncharted in agroforestry systems. The objective of this study was to examine the effect of a i) local-scale gradient (light, nutrients) induced by shade tree diversity and ii) large-scale gradient (climato-edaphic) induced by altitude on coffee plant response on multiple agroforestry research farms in Costa Rica. Results show large variability of coffee traits: leaf photosynthetic rates, specific leaf area (SLA) and number of fruiting nodes deviate along both gradients. Mean SLA increased with increasing shade tree diversity. However, with increasing altitude, full sun coffee photosynthesized at higher rates than shaded coffee. Concurrently, other coffee leaf physiological and morphological traits differentiated between full sun and shaded coffee with increasing altitude. Results suggest soil moisture and light availability dominate environmental correlates to intraspecific coffee trait plasticity, providing insight to sources of coffee performance variability in monoculture and agroforestry systems.

Les modèles d'occupation de niche au sein des communautés locales, la variabilité spatiale de la biodiversité le long des gradients environnementaux du stress et des perturbations, et les processus de succession végétale sont plusieurs sujets fondamentaux en écologie. Récemment, l'approche basée sur les traits est apparue comme un moyen prometteur de comprendre les processus structurant les communautés végétales et cette approche a même été proposée comme méthode pour reconstruire l'écologie communautaire en fonction des traits fonctionnels. Par conséquent, lier ces thèmes fondamentaux en utilisant une lentille fonctionnelle devrait nous donner un aperçu de certaines questions fondamentales en écologie et sera l'objectif principal de ma thèse. En général, mon projet de doctorat vise à étudier les structures de l'occupation de l'espace fonctionnel dans les gradients spatio-temporels. Plus précisément, l'objectif du chapitre 2 est (i) d'étudier les modèles d'occupation de la niche fonctionnelle en calculant trois métriques clés de niche (le volume total de niche fonctionnelle , le chevauchement des niches fonctionnelles et le volume de niche fonctionnel moyen) des communautés pauvres en espèces aux communautés riches en espèces et (ii) de déterminer le principal facteur de la structure observée de l'occupation de la niche fonctionnelle dans les communautés végétales du monde entier. Dans le chapitre 3, je vise à prédire et à expliquer la variation de la richesse en espèces selon les gradients de stress et de perturbation, en reliant le modèle d'équilibre dynamique et l'occupation de la niche fonctionnelle en fonction du cadre développé au chapitre 2. L'objectif du chapitre 4 est de tester expérimentalement l’application d'une méthode d'ordination CSR évaluée globalement en fonction de trois traits de feuilles (surface foliaire, teneur en matière sèche des feuilles et surface foliaire spécifique) dans les études locales. Enfin, l'objectif du chapitre 5 est de tester expérimentalement les hypothèses qui concilient les points de vue déterministes et historiquement contingents de la succession végétale, en étudiant la variation des divergences taxonomiques et fonctionnelles entre les communautés selon des gradients de stress et de perturbation. L'étude globale (chapitre 2) est basée sur une collection de 21 jeux de données, couvrant les biomes tropicaux et tempérés, et se compose de 313 communautés végétales représentant différentes formes de croissance. Les études locales (chapitre 3, 4 et 5) sont basées sur le même système expérimental constitué de 24 mésocosmes présentant différents niveaux de stress et de perturbation. L'expérience a commencé en 2009 avec le même mélange de graines de 30 espèces herbacées semées sur les 24 mésocosmes et s'est terminée en 2016. Nous avons permis la colonisation naturelle de graines de la banque commune de graines de sol et de l'environnement pendant la succession de sept ans. Dix traits ont été mesurés sur cinq individus (échantillonnés directement à partir des mésocosmes) par espèce par mésocosme en 2014 (chapitre 3 et 4). Un autre ensemble de traits (16 traits, y compris certains traits qui ne pouvaient pas être mesurés directement dans les mésocosmes), ont été mesurés au niveau de l'espèce (valeurs moyennes des traits) pour les 34 espèces les plus abondantes (certaines espèces disparues dans les mésocosmes) au cours des sept Ans, en les regroupant séparément pour une saison de croissance. Au chapitre 2, nous avons constaté que les communautés étaient plus diverses en termes fonctionnels (une augmentation du volume fonctionnel total) dans les communautés riches en espèces et que les espèces se chevauchaient davantage au sein de la communauté (augmentation du chevauchement fonctionnel), mais ne divisaient pas plus finement l'espace fonctionnel (aucune réduction du volume fonctionnel moyen). En outre, le filtrage de l'habitat est un processus répandu qui conduit à la caractérisation de l'occupation de niche fonctionnelle dans les communautés végétales. Dans le chapitre 3, nous avons trouvé un modèle similaire d'occupation de niche fonctionnelle sur un système expérimental avec une taille spatiale communautaire constante et un effort d'échantillonnage des traits, qui, avec le chapitre 2, nous a fourni une image plus complète et plus solide de l'occupation de niche fonctionnelle dans les communautés végétales. De plus, nous avons réussi à relier le modèle de l'occupation de la niche fonctionnelle et le modèle d'équilibre dynamique et avons constaté que le filtrage concurrentiel était le processus dominant qui détermine le mode d'occupation de la niche fonctionnelle et la richesse des espèces le long du stress et de la perturbation des gradients. Au chapitre 4, nous fournissons un soutien empirique à une méthode d'ordination CSR calibrée globalement en montrant une relation entre l'abondance relative d'espèces en croissance dans les mésocosmes ayant différents niveaux de fertilité du sol et mortalité indépendante de la densité et leur classification CSR. Au chapitre 5, nous avons montré que la succession d'installations au cours de sept ans dans ces mésocosmes était plus déterministe d'un point de vue fonctionnel, mais plus historiquement contingent d'un point de vue taxonomique et que l'importance relative de la contingence historique a diminué à mesure que l'environnement devenait plus stressé ou perturbé. En conclusion, les structures de l'occupation de l'espace fonctionnel dans (le volume fonctionnel total, le chevauchement fonctionnel et le volume fonctionnel moyen, les Chapitre 2 et 3) ou entre les communautés locales (dissimilarité fonctionnelle, chapitre 5) sont déterministes plutôt que neutres (ou contingence historique ). Les espèces tolératrices de stress sont plus avantagées dans les mésocosmes moins fertiles tandis que les espèces rudérales sont plus avantagées dans les mésocosmes avec plus de mortalité indépendante de la densité. / Abstract : The patterns of niche occupancy within local communities, the spatial variability of biodiversity along environmental gradients of stress and disturbance, and the processes of plant succession are several fundamental topics in ecology. Recently, the trait-based approach has emerged as a promising way to understand the processes structuring plant communities and has even been proposed as a method to rebuild community ecology based on functional traits. Therefore, linking these fundamental themes through a functional lens should give us more insight into some basic questions in ecology and will be the main objective of my thesis. Generally, my PhD project is to investigate the structures of functional space occupancy along both spatial and temporal gradients. Specifically, the objective of Chapter 2 is to investigate the patterns of functional niche occupancy by calculating three key niche metrics (the total functional niche volume, the functional niche overlap and the average functional niche volume) from speciespoor communities to species-rich communities and to determine the main driver of the observed pattern of functional niche occupancy across plant communities worldwide. In Chapter 3, I aim to predict and explain the variation of species richness along gradients of stress and disturbance, by linking the dynamic equilibrium model and functional niche occupancy based on the framework developed in Chapter 2. The objective of Chapter 4 is to experimentally test the application of a globally calibrated CSR ordination method based on three leaf traits (leaf area, leaf dry matter content and specific leaf area) in local studies. Finally, the aim of Chapter 5 is to experimentally test the hypotheses reconciling the deterministic and historically contingent views of plant succession, by investigating the variation of taxonomic and functional dissimilarities between communities along gradients of stress and disturbance. The global study (Chapter 2) is based on a collection 21 trait datasets, spanning tropical to temperate biomes, and consisting of 313 plant communities representing different growth forms. The local studies (Chapter 3, 4 and 5) are based on the same experimental system consisting of 24 mesocosms experiencing different levels of stress and disturbance. The experiment started in 2009 with the same seed mixture of 30 herbaceous species broadcast over the 24 mesocosms and ended in 2016. We allowed natural colonization of seeds from the common soil seed bank and from the surroundings during the seven-year succession. Ten traits were measured on five individuals (sampled directly from the mesocosms) per species per mesocosms in 2014 (Chapter 3 and 4). Another set of traits (16 traits including some traits that were not able to measured directly in the mesocosms) were measured at the species level (species mean traits values) for the 34 most abundant species (some species disappeared in the mesocosms) over the seven years, by regrowing them separately for one growing season. In Chapter 2, we found communities were more functionally diverse (an increase in total functional volume) in species-rich communities, and species overlapped more within the community (an increase in functional overlap) but did not more finely divide the functional space (no decline in average functional volume). Moreover, habitat filtering is a widespread process driving the pattern of functional niche occupancy across plant communities. In Chapter 3, we found a similar pattern of functional niche occupancy on an experimental system with a constant community spatial size and trait-sampling effort, which together with Chapter 2 provided us a more comprehensive and robust picture of functional niche occupancy across plant communities. In addition, we succeeded in linking the pattern of functional niche occupancy and the dynamic equilibrium model and found that habitat filtering was the dominant process determining the pattern of functional niche occupancy and species richness along the gradients stress and disturbance. In Chapter 4, we provide empirical support for a globally calibrated CSR ordination method by showing a relationship between the relative abundance of species growing in mesocosms having different levels of soil fertility and density-independent mortality and their CSR classification. In Chapter 5, we showed that plant succession over seven years in these mesocosms was more deterministic from a functional perspective but more historically contingent from a taxonomic perspective, and that the relative importance of historical contingency decreased as the environment became more stressed or disturbed. In conclusion, the structures of functional space occupancy within (the total functional volume, the functional overlap and the average functional volume; Chapter 2 and 3) or between local communities (functional dissimilarity, Chapter 5) are deterministic rather than neutral (or historical contingency). Stress-tolerators were more favored in high stress communities, while ruderals are more favored in high disturbed mesocosms (Chapter 4).