Integrative phylogenetic, phylogeographic and morphological characterisation of the Unio crassus species complex reveals cryptic diversity with important conservation implications

The global decline of freshwater mussels and their crucial ecological services highlight the need to understand their phylogeny, phylogeography and patterns of genetic diversity to guide conservation efforts. Such knowledge is urgently needed for Unio crassus, a highly imperilled species originally widespread throughout Europe and southwest Asia. Recent studies have resurrected several species from synonymy based on mitochondrial data, revealing U. crassus to be a complex of cryptic species. To address long-standing taxonomic uncertainties hindering effective conservation, we integrate morphometric, phylogenetic, and phylogeographic analyses to examine species diversity within the U. crassus complex across its entire range. Phylogenetic analyses were performed using cytochrome c oxidase subunit I (815 specimens from 182 populations) and, for selected specimens, whole mitogenome sequences and Anchored Hybrid Enrichment (AHE) data on ∼ 600 nuclear loci. Mito-nuclear discordance was detected, consistent with mitochondrial DNA gene flow between some species during the Pliocene and Pleistocene. Fossil-calibrated phylogenies based on AHE data support a Mediterranean origin for the U. crassus complex in the Early Miocene. The results of our integrative approach support 12 species in the group: the previously recognised Unio bruguierianus, Unio carneus, Unio crassus, Unio damascensis, Unio ionicus, Unio sesirmensis, and Unio tumidiformis, and the reinstatement of five nominal taxa: Unio desectus stat. rev., Unio gontierii stat. rev., Unio mardinensis stat. rev., Unio nanus stat. rev., and Unio vicarius stat. rev. Morphometric analyses of shell contours reveal important morphospace overlaps among these species, highlighting cryptic, but geographically structured, diversity. The distribution, taxonomy, phylogeography, and conservation of each species are succinctly described.We thank Ana-Maria Benedek, Monica Sîrbu and Jouni Leinikki for their assistance with the fieldwork, and to Jeroen Goud, Sankurie Pye, Fiona Ware, Emily Mitchell, and Aleksandra Skawina for their assistance with the taxonomic investigation. We would also like to thank the editor, Dr. Guillermo Ortí, and two anonymous reviewers for their time and effort in reviewing our manuscript and for their insightful comments and valuable improvements to our work. This publication is based upon work from COST Action CA18239: CONFREMU - Conservation of freshwater mussels: a pan-European approach, supported by COST (European Cooperation in Science and Technology), including STSMs, the interaction of the authors and the writing of the paper. This work was supported by the project ConBiomics: The Missing Approach for the Conservation of Freshwater Bivalves Project No. POCI-01-0145-FEDER-030286, co-financed by FEDER through POCI and by FCT - Fundaç˜ao para a Ciˆencia e a Tecnologia, through national funds. Strategic funding UIDB/04423/2020 and UIDP/04423/2020 was provided by FCT. FCT also supported DVG (2020.03848.CEECIND), EF (CEECINST/00027/ 2021/CP2789/CT0003) and MLL (2020.03608.CEECIND). INB, AVK and IVV were supported by the Russian Science Foundation under grants (19-14-00066-P), (21-17-00126) and (21-74-10130) respectively. BVB acknowledges the bioinformatics platform of UMR 8198 for the computing resources to perform time-calibrated phylogenetic analyses; this platform is in part funded by CPER research project CLIMIBIO through the French Minist`ere de l’Enseignement Sup´erieur et de la Recherche, the Agence Nationale de la Recherche, the European Fund for Regional Development (FEDER) and the region Hauts-de-France (HdF). Support to KD came from the Czech Science Foundation (19–05510S). TT and MT were supported by the National Science Fund of Bulgaria under the project ‘Conservation of freshwater mussels on the Balkan Peninsula’ (KP-06-COST-9/20.07.2022). Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the United States Government.info:eu-repo/semantics/publishedVersio

Variation in the COI gene of the freshwater pearl mussel Margaritifera margaritifera from River Vuokkijoki

The freshwater pearl mussel Margaritifera margaritifera L. is one of the most endangered freshwater mussels in the world. Effective conservation of threatened species requires not only ecological, but also genetic information from the target species and populations. Since low genetic diversity can reduce the ability of a species to adapt to environmental changes, maintaining genetic diversity has been identified as one of the key elements in successful conservation programs. We examined genetic variation of the freshwater pearl mussel from the River Vuokkijoki, Karelia, Russia. We sequenced a fragment of the cytochrome c oxidase subunit I gene (COI) from 22 individuals and compared the data to 32 previously published COI sequences available in GenBank. We identified 10 different COI haplotypes in the sequenced samples, three of which had not been previously reported. Our results show that the River Vuokkijoki has high genetic diversity and suggest that the colonization of this northern freshwater pearl mussel population might have occurred from multiple and even distant refugia. Therefore, the freshwater pearl mussel population of the River Vuokkijoki is valuable for the conservation of the whole species.peerReviewe