par Salussolia, Alice 
Président du jury Mardulyn, Patrick
Promoteur Flot, Jean-François
Co-Promoteur Stoch, Fabio
Publication Non publié, 2026-03-20
Président du jury Mardulyn, Patrick
Promoteur Flot, Jean-François
Co-Promoteur Stoch, Fabio
Publication Non publié, 2026-03-20
Thèse de doctorat
| Résumé : | Subterranean ecosystems host highly specialized and often narrowly distributed organisms, whose evolutionary histories are tightly linked to geological and climatic processes. Among them, the amphipod genus Niphargus represents one of the most diverse and taxonomically challenging lineages of groundwater fauna in the Western Palearctic, owing to widespread cryptic diversity, morphological convergence, and fragmented habitats. The Alpine region, repeatedly reshaped by Pleistocene glacial–interglacial cycles, provides an exceptional natural laboratory for investigating how historical climate fluctuations and habitat fragmentation have shaped subterranean biodiversity. This thesis aims to reconstruct the taxonomy, phylogeny, and evolutionary history of Niphargus in Alpine groundwater using an integrative framework combining morphology, multilocus molecular data, and genomic approaches. Extensive sampling was conducted across caves, springs, and wells throughout the Alpine chain. Species boundaries and cryptic diversity were assessed using mitochondrial and nuclear markers generated through Sanger sequencing and Oxford Nanopore amplicon sequencing, coupled with detailed morphotaxonomic analyses. Phylogenetic relationships and divergence times were inferred using maximum-likelihood and Bayesian methods. To address the long-standing uncertainties in deep phylogenetic nodes, a genome skimming approach based on long-read nanopore sequencing, complemented by Illumina polishing, was applied to generate and annotate the first complete mitochondrial genome for Niphargus. The results revealed a high degree of previously unrecognized diversity, including the presence of cryptic species and polyphyletic species groups, and demonstrated that several widely distributed taxa actually represent complexes of geographically restricted lineages. Time-calibrated phylogenies indicate that major diversification events predated the Pleistocene, while glacial cycles further promoted isolation and regional endemism within the Alpine aquifer systems. Overall, this thesis advances the understanding of the evolutionary history of Niphargus in the Alps, highlights the importance of integrative taxonomy for groundwater biodiversity, and provides a robust evolutionary framework for future ecological studies and conservation strategies in subterranean ecosystems. |
