PhD Student EPHE - PSL / SPYGEN
Floor 1 - Wing C - Office 114
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ORCID – ResearchGate – Google Scholar
Main supervisor: Stéphanie Manel (CEFE, EPHE - PSL)
Co-supervisor: Erwan Delrieu-Trottin (CEFE, EPHE - PSL)
Co-supervisor: Alice Valentini (SPYGEN)
Thesis project: Urban imprint on marine biodiversity: an environmental DNA-based approach in the French Mediterranean
Coastal ecosystems, true mosaics of habitats, are major reservoirs of biodiversity, home to numerous species and supporting a wide range of ecological functions. However, anthropogenic pressures on these ecosystems are intensifying, particularly due to human population growth and its concentration on coastal areas. These pressures pose various threats to marine biodiversity, including pollution (chemical, plastic, noise, etc.), overexploitation of fishery resources, introduction of non-native species, and coastal artificialization. The replacement of natural substrates with artificial structures profoundly alters the heterogeneity of habitats, fragmenting and isolating them. Urbanization, defined as the transformation of space for the benefit of a single species, Homo sapiens, therefore does not spare the marine environment. While the same eco-evolutionary processes occur in “natural” and urban environments, certain phenomena are amplified or altered in an urban context, while others are more specific to it, due to the new interactions that arise when species that would not necessarily meet in their original habitat come into contact. Urbanization most often favors generalist species that are “pre-adapted” to disturbances, to the detriment of specialist species, leading to a change in the composition of communities along the urbanization gradient. At the regional or global level, these changes can be so marked that communities become more similar between urban areas, reflecting a phenomenon of biotic homogenization. Urbanization thus leads to a profound reorganization of assemblages and also has consequences at the intraspecific level: urban centers, often isolated from one another, generally exhibit strong genetic differentiation between populations and lower genetic diversity than external habitats. However, the increased connectivity of artificial marine areas via maritime transport can reverse these effects, promoting genetic circulation between populations. Nevertheless, most urban ecology research focuses on terrestrial environments. The marine biodiversity of artificial coastal areas, such as ports, remains largely unknown, and the ecological processes associated with urbanization in the marine environment have been little studied. One of the main obstacles to understanding these ecosystems is the lack of standardized, non-invasive methods capable of providing a comprehensive inventory of biodiversity. Environmental DNA (eDNA) metabarcoding is now a promising solution. This thesis therefore aims to fill the gaps in our knowledge of biodiversity in urbanized coastal areas, particularly ports, by using eDNA. It is based on data collected in the French Mediterranean – a region where artificialization has stabilized since the 1980s – and targets a wide variety of organisms, with a particular focus on fish communities. The thesis combines an assessment of the local effects of urbanization on assemblages, an analysis of biotic homogenization processes at the regional scale, an exploration of genetic variations within populations, and the development of methodological tools to model species occurrence and detectability. It thus makes it possible to characterize the impact of urbanization on marine biodiversity and to better understand the ecological processes that shape coastal communities in artificial environments.
Publications
Macé, B., Manel, S., Valentini, A., Rocle, M., Roset, N., & Delrieu-Trottin, E. (2025). NeMO: a flexible R package for nested multi-species occupancy modelling and eDNA study optimisation. bioRxiv, 2025.05.23.655794. https://doi.org/10.1101/2025.05.23.655794
Manel, S., Gauthier, J., Benestan, L., Dubois, M.-P., Romant, L., Macé, B., Bruno, M., Arnal, V., Testud, G., Garcia, M., Carrasquer Puyal, I., Bilat, J., Miaud, C., & Alvarez, N. (2025). An enrichment-based capture method from nuclear environmental DNA presents new opportunities for population genomics: A case study on the common frog. Methods in Ecology and Evolution, 16, 1106-1115. https://doi.org/10.1111/2041-210X.70039
Macé, B., Mouillot, D., Dalongeville, A., Bruno, M., Deter, J., Varenne, A., Gudefin, A., Boissery, P., & Manel, S. (2024). The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves. Molecular Ecology, 33(12), e17373. https://doi.org/10.1111/mec.17373
Faure, N., Manel, S., Macé, B., Arnal, V., Guellati, N., Holon, F., Barroil, A., Pichot, F., Riutort, J.-J., Insacco, G., Zava, B., Mouillot, D., & Deter, J. (2023). An environmental DNA assay for the detection of Critically Endangered angel sharks (Squatina spp.). Aquatic Conservation: Marine and Freshwater Ecosystems, 33(10), 1088–1097. https://doi.org/10.1002/aqc.3954
Macé, B., Hocdé, R., Marques, V., Guerin, P.-E., Valentini, A., Arnal, V., Pellissier, L., & Manel, S. (2022). Evaluating bioinformatics pipelines for population-level inference using environmental DNA. Environmental DNA, 4(3), 674–686. https://doi.org/10.1002/edn3.269
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