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 desectusstat. rev., Unio gontieriistat. rev., Unio mardinensisstat. rev., Unio nanusstat. rev., and Unio vicariusstat. 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.

Aquatic Systems Biology Technical University of Munich TUM School of Life Sciences Mühlenweg 22 85354 Freising Germany

Aquatic Systems Biology Technical University of Munich TUM School of Life Sciences Mühlenweg 22 85354 Freising Germany; Molecular Zoology Technical University of Munich TUM School of Life Sciences Hans Carl von Carlowitz Platz 2 Freising Germany

Bavarian Academy for Nature Conservation and Landscape Management Seethalerstrasse 6 83410 Laufen Germany

Biology Department Faculty of Science and Arts Burdur Mehmet Akif Ersoy University Burdur Türkiye

Biology Department Institute for Great Lakes Research Central Michigan University Mount Pleasant MI 48859 USA

Burdur Vocational School of Food Agriculture and Livestock Mehmet Akif Ersoy University 15100 Burdur Türkiye

CBMA Centre of Molecular and Environmental Biology Department of Biology University of Minho Campus Gualtar 4710 057 Braga Portugal

Centro de Investigação de Montanha Instituto Politécnico de Bragança Campus de Santa Apolónia 5300 253 Bragança Portugal

CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Campus de Vairão Universidade do Porto 4485 661 Vairão Portugal; BIOPOLIS Program in Genomics Biodiversity and Land Planning CIBIO Campus de Vairão 4485 661 Vairão Portugal

CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Campus de Vairão Universidade do Porto 4485 661 Vairão Portugal; BIOPOLIS Program in Genomics Biodiversity and Land Planning CIBIO Campus de Vairão 4485 661 Vairão Portugal; CIIMAR CIMAR Interdisciplinary Centre of Marine and Environmental Research University of Porto Terminal de Cruzeiros do Porto de Leixões Av General Norton de Matos s n 4450 208 Matosinhos Portugal

CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Campus de Vairão Universidade do Porto 4485 661 Vairão Portugal; BIOPOLIS Program in Genomics Biodiversity and Land Planning CIBIO Campus de Vairão 4485 661 Vairão Portugal; Institut Systématique Evolution Biodiversité Muséum national d'Histoire naturelle CNRS Sorbonne Université EPHE Université des Antilles 57 rue Cuvier CP 51 75005 Paris France

CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Campus de Vairão Universidade do Porto 4485 661 Vairão Portugal; CITAB UTAD Centre for Research and Technology of Agro Environment and Biological Sciences University of Trás os Montes and Alto Douro Forestry Department Vila Real Portugal

CIIMAR CIMAR Interdisciplinary Centre of Marine and Environmental Research University of Porto Terminal de Cruzeiros do Porto de Leixões Av General Norton de Matos s n 4450 208 Matosinhos Portugal

CNR Water Research Institute Largo Tonolli 50 28922 Verbania Italy

CNRS Univ Lille UMR 8198 Evo Eco Paleo F 59000 Lille France

Department of Biological and Environmental Science University of Jyväskylä P O Box 35 40014 University of Jyväskylä Finland

Department of Biology Faculty of Science University of Zagreb Horvatovac 102a 10000 Zagreb Croatia

Department of Genetics and Biosystematics Faculty of Biology University of Gdańsk Wita Stwosza 59 80 308 Gdańsk Poland

Department of Integrative Biology University of Texas Austin TX USA

Department of Zoology and Fisheries FAFNR Czech University of Life Sciences Prague Kamýcká 129 CZ 16500 Prague Czech Republic

Department of Zoology Institute of Biosciences Life Sciences Center Vilnius University Saulėtekio av 7 LT 10223 Vilnius Lithuania

Department of Zoology Poznań University of Life Sciences ul Wojska Polskiego 28 60 637 Poznań Poland

Faculty Of Biotechnology and Food Agricultural University of Tirana Koder Kamez Tirana 2029 Albania

Hellenic Centre for Marine Research Institute of Marine Biological Resources and Inland Waters 46 7 km Athens Sounio Av Anavyssos 19013 Greece

IFIS Ichthyological Research Initiative Styria 1160 Vienna Austria

Institute of Biodiversity and Ecosystem Research Bulgarian Academy of Sciences 1 Tsar Osvoboditel Blvd 1000 Sofia Bulgaria

Institute of Nature Conservation Polish Academy of Sciences Al Adama Mickiewicza 33 31 120 Kraków Poland

Institute of Zoology Ilia State University Cholokashvili ave 3 5 0162 Tbilisi Georgia

Institution of Environmental and Life Sciences Karlstad University Biology 65188 Karlstad Sweden

Lucian Blaga University of Sibiu Faculty of Sciences 5 7 Dr 1 Rațiu St 550012 Sibiu Romania

Malacological Section Senckenberg Research Institute and Natural History Museum Frankfurt M Senckenberganlage 25 60325 Frankfurt am Main Germany

Molecular Zoology Technical University of Munich TUM School of Life Sciences Hans Carl von Carlowitz Platz 2 Freising Germany

N Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences Nikolsky Av 20 163020 Arkhangelsk Russia

National Museum of Natural History Smithsonian Institution 10th and Constitution Avenue Washington DC USA

Natural History Museum 3005 Bern Switzerland; Institute of Ecology and Evolution University of Bern 3012 Bern Switzerland

North Carolina Museum of Natural Sciences 11 West Jones Street Raleigh NC 27601 USA

Regional Office Kokořínsko Máchův kraj Protected Landscape Area Administration Nature Conservation Agency of the Czech Republic Česká 149 CZ 27601 Mělnik Czech Republic

School of Geography University of Nottingham University Park Sir Clive Granger Building Nottingham NG7 2RD United Kingdom

The Rural Economy and Agricultural Society 305 96 Eldsberga Sweden

U S Geological Survey Wetland and Aquatic Research Center Gainesville FL USA

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