Abstract

This is the online html version of my PhD thesis. The pdf version is available for download with the download button on top of the window.

Tropical forests shelter the highest species diversity worldwide, a fact that remains partly unexplained and the origin of which is subject to debate. Even at the hectare-scale, tropical forests shelter species-rich genera with closely-related tree species coexisting in sympatry. Due to phylogenetic constraints, closely related species are expected to have similar niches and functional strategies, which raises questions on the mechanisms of their local coexistence. Closely related species may form a species complex, defined as morphologically similar species that share large amounts of genetic variation due to recent common ancestry and hybridization, and that can result from ecological adaptive radiation of species segregating along environmental gradients. Despite the key role of species complexes in Neotropical forest ecology, diversification, and evolution, little is known of the eco-evolutionary forces creating and maintaining diversity within Neotropical species complexes. We explored the intraspecific genomic variability as a continuum within structured populations of closely related species, and measured its role on individual tree performance through growth over time, while accounting for effects of a finely-characterized environment at the abiotic and biotic level. Combining tree inventories, LiDAR-derived topographic data, leaf functional traits, and gene capture data in the research station of Paracou, French Guiana, we used population genomics, environmental association analyses, genome-wide association studies and Bayesian modelling on the tree species complexes Symphonia and Eschweilera clade Parvifolia We showed that the species complexes of Neotropical trees cover all local gradients of topography and competition and are therefore widespread in the study site whereas most of the species within them exhibit pervasive niche differentiation along these same gradients. Specifically, in the species complexes Symphonia and Eschweilera clade Parvifolia, the decrease in water availability due to higher topographic position, e.g., from bottomlands to plateaus, has led to a change in leaf functional traits from acquisitive strategies to conservative strategies, both among and within species. Symphonia species are genetically adapted to the distribution of water and nutrients, hence they coexist locally through exploiting a broad gradient of local habitats. Conversely, Eschweilera species are differentially adapted to soil chemistry and avoid the wettest, hydromorphic habitats. Last but not least, individual tree genotypes of Symphonia species are differentially adapted to regenerate and thrive in response to the fine spatio-temporal dynamics of forest gaps with divergent adaptive growth strategies along successional niches. Consequently, topography and the dynamics of forest gaps drive fine-scale spatio-temporal adaptations of individuals within and among distinct but genetically connected species within the species complexes Symphonia and Eschweilera clade Parvifolia Fine-scale topography drives genetic divergence and niche differentiation with genetic adaptations among species, while forest gap dynamics maintains genetic diversity with divergent adaptive strategies within species. I suggest that adaptations of tree species and individuals to topography and dynamics of forest gaps promote coexistence within and among species within species complexes, and perhaps among mature forest tree species outside species complexes. Overall, I defend the primordial role of individuals within species in tropical forest diversity, suggesting that we should develop a theory of community ecology starting with individuals, because interactions with environments happen after all at the individual level.

Ecological niche | Intraspecific variability | Neighbourhood crowding index | Paracou | Species coexistence | Species complex | Species distribution | Syngameon | Topographic wetness index | Tropical forests