Within-species Individual Trait Variation (ITV) is now recognised as an important source of variability in ecological communities. Individual variation in trophic niche traits (i.e. individual niche width and between-individual variation) can greatly modify top-down and/or competitive interactions. Trophic traits vary according to variation in ecological opportunity, which represents the range of exploitable resources. While the role of prey availability in driving trophic traits is well-established, abiotic drivers (e.g. habitat structure) are rarely accounted for, or are solely considered via their effect on the prey community. We aimed to disentangle prey-mediated from direct habitat effects on trophic ITV in a critically endangered riverine fish, the Rhone streber (Zingel asper). We quantified individual trophic traits using high-resolution diet data obtained from faeces metabarcoding, and quantified prey availability and habitat structure using a fine-scale sampling protocol. Trophic traits were driven by distinct mechanisms: the individual niche width was driven by prey availability, while between-individual variation was largely driven by habitat conditions. Habitat conditions acted both directly on trophic traits and indirectly via their effect on the prey community. By simultaneously accounting for biotic and abiotic drivers of trophic ITV, we obtained a more complete understanding of how prey availability and habitat structure jointly determine ecological opportunity. Furthermore, by accounting for fine-scale variation in prey community and habitat conditions, the importance of spatial heterogeneity factors was highlighted. This study demonstrates how robust metabarcoding data, combined with detailed prey community and habitat information can be used to reveal the mechanistic pathways that drive trophic traits.

The intra- and interspecific facets of biodiversity have traditionally been quantified and analysed separately, limiting our understanding of how evolution has shaped biodiversity, how biodiversity (as a whole) alters ecological dynamics, and hence eco-evolutionary feedbacks at the community scale. Here, we propose using candidate genes phylogenetically-conserved across species and sustaining functional traits as an inclusive biodiversity unit transcending the intra- and interspecific boundaries. This framework merges knowledge from functional genomics and functional ecology, and we first provide conceptual and technical guidelines for identifying phylogenetically-conserved candidate genes (PCCGs) within communities, and for measuring inclusive biodiversity from PCCGs. We then explain how biodiversity measured at PCCGs can be linked to ecosystem functions, which may unify recent observations that both intra- and interspecific biodiversity are important for ecosystem functions. We then highlight the eco-evolutionary processes shaping PCCGs diversity patterns, and argue that their respective role can be inferred from concepts derived from population genetics. Finally, we explain how PCCGs may shift the field of eco-evolutionary dynamics from a focal-species approach to a more realistic focal-community approach. This framework provides a novel perspective to investigate the global ecosystem consequences of diversity loss across biological scales, and how these ecological changes further alter biodiversity evolution.

Recent studies have highlighted associations between diseases and host microbiota. However, the role of microbe in infection process is yet to be clarified between host microbiota promoting future infections, or changes in host microbiota resulting from infections. We longitudinally surveyed, in the wild, the microbiota of individual fish hosts (Leuciscus burdigalensis) both before and after infection by a crustacean ectoparasite (Tracheliastes polycolpus). We found a striking association between parasite infection and the host microbiota composition restricted to the fins the parasite anchored. We clearly demonstrated that infections by the parasite induced a shift in (and did not result from) the host fin microbiota. Fin microbiota further got similar to that of the adult stage, and the free-living infective stage of the parasite during infection with a predominance of the Burkholderiaceae bacteria family. This suggests that Burkholderiaceae bacteria is involved in a co-infection process and possibly facilitate T. polycolpus infection.

Invasive species are significant contributors to global changes and constitute a severe threat to biodiversity. Yet invasions offer an incredible framework to understand how small and low-diverse introduced populations adapt to novel environmental conditions and succeed in colonizing large areas. However, due to the insufficient data on the origin of the first introduced propagule and the first stage of invasion, reconstructing a species’ invasion history is challenging. Here, we applied genetic clustering methods and explicit admixture tests combined with ABC models and Machine Learning algorithms to describe the phylogeography of native and invasive populations and infer the most probable demographic invasion scenarios of Pseudorasbora parva, a highly invasive freshwater fish and the healthy carrier of a novel lethal fungi-like pathogen (Sphaerothecum destruens), which is responsible for the decline of several fish species in Europe. We found that the current genetic structuring of the native P. parva range has been shaped by waves of gene flow originating from southern and northern Chinese populations. Furthermore, our results strongly suggest that the invasive genetic diversity is the outcome of past recurrent global invasion pathways of admixed native populations. Our study also illustrates how the combination of admixture tests, ABC, Machine Learning can be used to detect high-resolution demographic signatures and reconstruct an integrative biological invasion history.