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Lopes-Lima M, Geist J, Egg S, Beran L, Bikashvili A, Van Bocxlaer B, Bogan AE, Bolotov IN, Chelpanovskaya OA, Douda K, Fernandes V, Gomes-Dos-Santos A, Gonçalves DV, Gürlek ME, Johnson NA, Karaouzas I, Kebapçı Ü, Kondakov AV, Kuehn R, Lajtner J, Mumladze L, Nagel KO, Neubert E, Österling M, Pfeiffer J, Prié V, Riccardi N, Sell J, Schneider LD, Shumka S, Sîrbu I, Skujienė G, Smith CH, Sousa R, Stöckl K, Taskinen J, Teixeira A, Todorov M, Trichkova T, Urbańska M, Välilä S, Varandas S, Veríssimo J, Vikhrev IV, Woschitz G, Zając K, Zając T, Zanatta D, Zieritz A, Zogaris S, Froufe E. Integrative phylogenetic, phylogeographic and morphological characterisation of the Unio crassus species complex reveals cryptic diversity with important conservation implications. Mol Phylogenet Evol 2024; 195:108046. [PMID: 38447924 DOI: 10.1016/j.ympev.2024.108046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 02/16/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
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.
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Affiliation(s)
- M Lopes-Lima
- 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.
| | - J Geist
- Aquatic Systems Biology, Technical University of Munich, TUM School of Life Sciences, Mühlenweg 22, 85354 Freising, Germany
| | - S Egg
- 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
| | - L Beran
- Regional Office Kokořínsko - Máchův kraj Protected Landscape Area Administration, Nature Conservation Agency of the Czech Republic, Česká 149, CZ-27601 Mělnik, Czech Republic
| | - A Bikashvili
- Institute of Zoology, Ilia State University, Cholokashvili ave. 3/5, 0162 Tbilisi, Georgia
| | - B Van Bocxlaer
- CNRS, Univ. Lille, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - A E Bogan
- North Carolina Museum of Natural Sciences, 11 West Jones Street, Raleigh, NC 27601 USA
| | - I N Bolotov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Nikolsky Av. 20, 163020 Arkhangelsk, Russia
| | - O A Chelpanovskaya
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Nikolsky Av. 20, 163020 Arkhangelsk, Russia
| | - K Douda
- Department of Zoology and Fisheries, FAFNR, Czech University of Life Sciences Prague, Kamýcká 129, CZ-16500 Prague, Czech Republic
| | - V Fernandes
- 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
| | - A Gomes-Dos-Santos
- 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
| | - D V Gonçalves
- 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
| | - M E Gürlek
- Burdur Vocational School of Food Agriculture and Livestock, Mehmet Akif Ersoy University, 15100 Burdur, Türkiye
| | - N A Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, USA
| | - I Karaouzas
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, 46.7 km Athens-Sounio Av., Anavyssos 19013, Greece
| | - Ü Kebapçı
- Biology Department, Faculty of Science and Arts, Burdur Mehmet Akif Ersoy University, Burdur, Türkiye
| | - A V Kondakov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Nikolsky Av. 20, 163020 Arkhangelsk, Russia
| | - R Kuehn
- Molecular Zoology, Technical University of Munich, TUM School of Life Sciences, Hans-Carl-von-Carlowitz-Platz 2, Freising, Germany
| | - J Lajtner
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - L Mumladze
- Institute of Zoology, Ilia State University, Cholokashvili ave. 3/5, 0162 Tbilisi, Georgia
| | - K-O Nagel
- Malacological Section, Senckenberg Research Institute and Natural History Museum Frankfurt/M., Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - E Neubert
- Natural History Museum, 3005 Bern, Switzerland; Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - M Österling
- Institution of Environmental and Life Sciences, Karlstad University, Biology, 65188 Karlstad, Sweden
| | - J Pfeiffer
- National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue, Washington, DC, USA
| | - V Prié
- 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 (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75005 Paris, France
| | - N Riccardi
- CNR Water Research Institute, Largo Tonolli 50, 28922 Verbania, Italy
| | - J Sell
- Department of Genetics and Biosystematics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - L D Schneider
- The Rural Economy and Agricultural Society, 305 96 Eldsberga, Sweden
| | - S Shumka
- Faculty Of Biotechnology and Food, Agricultural University of Tirana, Koder Kamez, Tirana 2029, Albania
| | - I Sîrbu
- Lucian Blaga University of Sibiu, Faculty of Sciences, 5-7 Dr. I. Rațiu St., 550012 Sibiu, Romania
| | - G Skujienė
- Department of Zoology, Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10223 Vilnius, Lithuania
| | - C H Smith
- Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - R Sousa
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - K Stöckl
- Bavarian Academy for Nature Conservation and Landscape Management, Seethalerstrasse 6, 83410 Laufen, Germany
| | - J Taskinen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - A Teixeira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - M Todorov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
| | - T Trichkova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
| | - M Urbańska
- Department of Zoology, Poznań University of Life Sciences, ul. Wojska Polskiego 28, 60-637 Poznań, Poland
| | - S Välilä
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - S Varandas
- 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
| | - J Veríssimo
- 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
| | - I V Vikhrev
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Nikolsky Av. 20, 163020 Arkhangelsk, Russia
| | - G Woschitz
- IFIS - Ichthyological Research Initiative Styria, 1160 Vienna, Austria
| | - K Zając
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Adama Mickiewicza 33, 31-120 Kraków, Poland
| | - T Zając
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Adama Mickiewicza 33, 31-120 Kraków, Poland
| | - D Zanatta
- Biology Department, Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - A Zieritz
- School of Geography, University of Nottingham, University Park, Sir Clive Granger Building, Nottingham NG7 2RD, United Kingdom
| | - S Zogaris
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, 46.7 km Athens-Sounio Av., Anavyssos 19013, Greece
| | - E Froufe
- 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
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Hofman S, A D Cameron R, Proćków M, Sîrbu I, Osikowski A, Rysiewska A, Sokół M, Falniowski A. Two new pseudocryptic species in the medium-sized common European land snails, Fruticicola Held, 1838; as a result of phylogeographic analysis of Fruticicola fruticum (O. F. Müller, 1774) (Gastropoda: Helicoidea: Camaenidae). Mol Phylogenet Evol 2022; 168:107402. [PMID: 35031469 DOI: 10.1016/j.ympev.2022.107402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 12/27/2021] [Accepted: 01/01/2022] [Indexed: 11/16/2022]
Abstract
Fruticicola fruticum (O. F. Müller, 1774), a medium-sized helicoid snail in the Bradybaenidae, has a wide range in Europe, reaching from the Urals and the Caucasus to the Balkans, and from the southern part of Scandinavia, through Central Europe to eastern and central France and northern Italy. There are numerous studies on its distribution, biology, life cycle, etc., but little is known about the genetic diversity of this taxon. Here, we studied the phylogeny and phylogeography of F. fruticum using two mitochondrial markers: cytochrome oxidase subunit I (COI) and 16S ribosomal RNA (16S); and four nuclear markers: 18S ribosomal RNA (18S), 28S ribosomal RNA (28S), internal transcribed spacer (ITS-2), and histone 3 (H3). The study was based on 59 populations sampled across the range. Whereas nuclear markers showed little differentiation, phylogenetic analysis of COI sequences clearly confirmed the distinctness of the European Fruticicola and Asian Bradybaena (p-distance 0.229). Within Fruticicola 54 haplotypes were detected, haplotype diversity (Hd) = 0.973±0.006, nucleotide diversity (π) = 0.137±0.005. ABGD and PTP delimitation analyzes distinguished eight mOTUs. Two sequences (our mOTU C) from Russia were published in the GenBank as two distinct species: F. schrenckii and F. transbaicalia. Seven further mOTUs identified in our study formed three distinct lineages, regarded as species. The first (mOTU A and mOTU B), represented by 40 populations, occupies a wide range across northern and central Europe, extending east to Ukraine and south to northern Croatia (mOTU B). It encompasses the type locality of F. fruticum, and can be recognized as F. fruticum sensu stricto. Another lineage (mOTU D and mOTU E), represented by six populations in central Romania, appears to form another species. Both mOTUs were found together in one population. A third lineage, containing mOTUs F, G and H, represented by 14 populations, was distributed across the Balkans from N.E. Croatia to Bulgaria. p-distances between the three species ranged from 0.172 to 0.219, and between all the mOTUs, pooled together, from 0.172 to 0.258. The highest genetic diversity was found in species 3 (0.112) and the lowest in species 1 (0.025), despite its largest geographic distribution. Pairwise p-distances, Tamura 3-parameter distances, composite likelihood distances, as well as the coancestry coefficient FST, calculated for all populations pooled together were significantly associated with geographic distance, but this was not the case within each of these three species. The significant association for all populations reflected high diversity between the species coupled with high geographic distances between their populations, not the character of intraspecies diversity. With a few exceptions, there hold a rather infinite island model with low migration. AMOVA detected 78% of the variance between the three species, 18% among populations within the species, and only 3.6% within the populations. The low genetic diversity of widespread F. fruticum s. stricto, compared with much higher diversity of two narrowly distributed newly found species of Fruticicola, may reflect the rapid spread of the former into previously uninhabitable regions, while the latter were able to maintain populations in glacial refugia. The estimated time of divergence between the three species, 1.7-2.19 mya, suggests their ancestors' isolation in southern European refugia during the lower Pleistocene, the Gelasian/Calabrian. There was no clear association of variation in shell morphology and lineage or mOTU identity; on external characters, these species are semicryptic, subtle differences in reproductive anatomy among them were found.
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Affiliation(s)
- Sebastian Hofman
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland.
| | - Robert A D Cameron
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom, and Department of Zoology, Natural History Museum, London SW7 5BD, United Kingdom.
| | - Małgorzata Proćków
- Museum of Natural History, University of Wrocław, Sienkiewicza 21, 50-335 Wrocław, Poland.
| | - Ioan Sîrbu
- Lucian Blaga University of Sibiu, Faculty of Sciences, 5-7 Dr. I. Rațiu St., 550012 Sibiu, Romania.
| | - Artur Osikowski
- Department of Animal Reproduction, Anatomy and Genomics, University of Agriculture in Krakow, Mickiewicza 24/28, 30-059 Kraków, Poland.
| | - Aleksandra Rysiewska
- Department of Malacology, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland.
| | - Magdalena Sokół
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland
| | - Andrzej Falniowski
- Department of Malacology, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland.
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