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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] [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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Johnson NA, Henderson AR, Jones JW, Beaver CE, Ahlstedt SA, Dinkins GR, Eckert NL, Endries MJ, Garner JT, Harris JL, Hartfield PD, Hubbs DW, Lane TW, McGregor MA, Moles KR, Morrison CL, Wagner MD, Williams JD, Smith CH. Glacial vicariance and secondary contact shape demographic histories in a freshwater mussel species complex. J Hered 2024; 115:72-85. [PMID: 38015800 DOI: 10.1093/jhered/esad075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/16/2023] [Accepted: 11/27/2023] [Indexed: 11/30/2023] Open
Abstract
Characterizing the mechanisms influencing the distribution of genetic variation in aquatic species can be difficult due to the dynamic nature of hydrological landscapes. In North America's Central Highlands, a complex history of glacial dynamics, long-term isolation, and secondary contact have shaped genetic variation in aquatic species. Although the effects of glacial history have been demonstrated in many taxa, responses are often lineage- or species-specific and driven by organismal ecology. In this study, we reconstruct the evolutionary history of a freshwater mussel species complex using a suite of mitochondrial and nuclear loci to resolve taxonomic and demographic uncertainties. Our findings do not support Pleurobema rubrum as a valid species, which is proposed for listing as threatened under the U.S. Endangered Species Act. We synonymize P. rubrum under Pleurobema sintoxia-a common and widespread species found throughout the Mississippi River Basin. Further investigation of patterns of genetic variation in P. sintoxia identified a complex demographic history, including ancestral vicariance and secondary contact, within the Eastern Highlands. We hypothesize these patterns were shaped by ancestral vicariance driven by the formation of Lake Green and subsequent secondary contact after the last glacial maximum. Our inference aligns with demographic histories observed in other aquatic taxa in the region and mirrors patterns of genetic variation of a freshwater fish species (Erimystax dissimilis) confirmed to serve as a parasitic larval host for P. sintoxia. Our findings directly link species ecology to observed patterns of genetic variation and may have significant implications for future conservation and recovery actions of freshwater mussels.
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Affiliation(s)
- Nathan A Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, United States
| | - Andrew R Henderson
- U.S. Fish and Wildlife Service, Ecological Services, Asheville, NC, United States
| | - Jess W Jones
- U.S. Fish and Wildlife Service, Virginia Tech University, Blacksburg, VA, United States
| | - Caitlin E Beaver
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, United States
| | - Steven A Ahlstedt
- McClung Museum of Natural History and Culture, University of Tennessee, Knoxville, TN, United States
| | - Gerald R Dinkins
- McClung Museum of Natural History and Culture, University of Tennessee, Knoxville, TN, United States
| | - Nathan L Eckert
- U.S. Fish and Wildlife Service, Neosho National Fish Hatchery, Neosho, MO, United States
| | - Mark J Endries
- U.S. Fish and Wildlife Service, Ecological Services, Asheville, NC, United States
| | - Jeffrey T Garner
- Alabama Division of Wildlife and Freshwater Fisheries, Florence, AL, United States
| | - John L Harris
- Arkansas State University Museum of Zoology, Jonesboro, AR, United States
| | - Paul D Hartfield
- U.S. Fish and Wildlife Service, Ecological Services, Jackson, MS, United States
| | - Don W Hubbs
- DJH Environmental Services, Camden, TN, United States
| | - Timothy W Lane
- Virginia Department of Wildlife Resources, Marion, VA, United States
| | - Monte A McGregor
- Kentucky Department of Fish and Wildlife Resources, Frankfort, KY, United States
| | - Kendall R Moles
- Arkansas Game and Fish Commission, Benton, AR, United States
| | - Cheryl L Morrison
- U.S. Geological Survey, Eastern Ecological Science Center, Kearneysville, WV, United States
| | - Matthew D Wagner
- U.S. Fish and Wildlife Service, Ecological Services, Jackson, MS, United States
| | - James D Williams
- Florida Museum, University of Florida, Gainesville, FL, United States
| | - Chase H Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
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7
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Bolotov IN, Pasupuleti R, Subba Rao NV, Unnikrishnan SK, Chan N, Lunn Z, Win T, Gofarov MY, Kondakov AV, Konopleva ES, Lyubas AA, Tomilova AA, Vikhrev IV, Pfenninger M, Düwel SS, Feldmeyer B, Nesemann HF, Nagel KO. Oriental freshwater mussels arose in East Gondwana and arrived to Asia on the Indian Plate and Burma Terrane. Sci Rep 2022; 12:1518. [PMID: 35087130 PMCID: PMC8795121 DOI: 10.1038/s41598-022-05257-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 01/10/2022] [Indexed: 12/21/2022] Open
Abstract
Freshwater mussels cannot spread through oceanic barriers and represent a suitable model to test the continental drift patterns. Here, we reconstruct the diversification of Oriental freshwater mussels (Unionidae) and revise their taxonomy. We show that the Indian Subcontinent harbors a rather taxonomically poor fauna, containing 25 freshwater mussel species from one subfamily (Parreysiinae). This subfamily most likely originated in East Gondwana in the Jurassic and its representatives arrived to Asia on two Gondwanan fragments (Indian Plate and Burma Terrane). We propose that the Burma Terrane was connected with the Indian Plate through the Greater India up to the terminal Cretaceous. Later on, during the entire Paleogene epoch, these blocks have served as isolated evolutionary hotspots for freshwater mussels. The Burma Terrane collided with mainland Asia in the Late Eocene, leading to the origin of the Mekong’s Indochinellini radiation. Our findings indicate that the Burma Terrane had played a major role as a Gondwanan “biotic ferry” alongside with the Indian Plate.
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Affiliation(s)
- Ivan N Bolotov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia. .,Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russia. .,SSC/IUCN - Mollusc Specialist Group, Species Survival Commission, International Union for Conservation of Nature, Cambridge, CB2 3QZ, UK.
| | - Rajeev Pasupuleti
- Institute of Molecular Biotechnology (IMBT), Technical University of Graz, Petersgasse 14, 8010, Graz, Austria
| | | | - Suresh Kumar Unnikrishnan
- Regional Facility for DNA Fingerprinting (RFDF), Rajiv Gandhi Centre for Biotechnology (RGCB), Trivandrum, 695014, Kerala, India
| | - Nyein Chan
- Fauna & Flora International - Myanmar Programme, 34 D/9 San Yae Twin Street, Kaba Aye Pagoda Road, Bahan Township, 11201, Yangon, Myanmar
| | - Zau Lunn
- Fauna & Flora International - Myanmar Programme, 34 D/9 San Yae Twin Street, Kaba Aye Pagoda Road, Bahan Township, 11201, Yangon, Myanmar.,Biology Department, University of New Brunswick, 100 Tucker Park Road, PO Box 5050, Saint John, NB, E2L 4L5, Canada
| | - Than Win
- Department of Zoology, Dawei University, 14043, Dawei, Tanintharyi Region, Myanmar
| | - Mikhail Y Gofarov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia
| | - Alexander V Kondakov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia.,Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russia
| | - Ekaterina S Konopleva
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia.,Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russia
| | - Artyom A Lyubas
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia
| | - Alena A Tomilova
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia.,Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russia
| | - Ilya V Vikhrev
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia.,Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russia.,SSC/IUCN - Mollusc Specialist Group, Species Survival Commission, International Union for Conservation of Nature, Cambridge, CB2 3QZ, UK
| | - Markus Pfenninger
- Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Sophie S Düwel
- Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Barbara Feldmeyer
- Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | | | - Karl-Otto Nagel
- Malacological Section, Senckenberg Research Institute and Natural History Museum Frankfurt/M., Senckenberganlage 25, 60325, Frankfurt am Main, Germany
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