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Hirano T, Saito T, Ito S, Ye B, Linscott TM, Do VT, Dong Z, Chiba S. Phylogenomic analyses reveal incongruences between divergence times and fossil records of freshwater snails in East Asia. Mol Phylogenet Evol 2023; 182:107728. [PMID: 36804427 DOI: 10.1016/j.ympev.2023.107728] [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: 02/15/2022] [Revised: 01/26/2023] [Accepted: 02/05/2023] [Indexed: 02/17/2023]
Abstract
Fossils provide important insight into our understanding of phylogenetic history by serving as calibration points for divergence time estimation. However, uncertainties in the fossil record due to parallel evolution and convergent evolution can critically affect estimates of node ages. Here, we compare and contrast estimates of phylogenetic divergence with geologic and fossil history for two freshwater snail genera of the family Viviparidae in East Asia (Cipangopaludina and Margarya). Cipangopaludina species are commonly widely distributed species in East Asia, but extant Margarya species are endemic to the ancient lakes in Yunnan, China. According to some previous studies, parallel evolution or convergent evolution of shell morphology has occurred in the family several times which may affect divergence time estimation using fossil records. In this study, we used SNP data derived from ddRAD-seq loci to investigate population demographic history of both genera. Our results show a common pattern of lake endemic lineages diversifying from widely distributed lineages in the Miocene, and multiple colonization to a single ancient lake occurred in the Pleistocene. Our results indicate substantial incongruence among estimated phylogenomic divergence times, some fossil records, and formation ages of ancient lakes. These findings suggest some fossil records may be misidentified in these groups and highlight the need to carefully evaluate geological evidence and fossil records when using these for divergence time estimation.
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Affiliation(s)
- Takahiro Hirano
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Graduate School of Life Sciences, Tohoku University, Miyagi, Japan; Biology Program, Faculty of Science, University of the Ryukyus, Okinawa, Japan.
| | - Takumi Saito
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Shun Ito
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan
| | - Bin Ye
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - T Mason Linscott
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, USA
| | - Van Tu Do
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Ha Noi, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Ha Noi, Viet Nam
| | - Zhengzhong Dong
- Agricultural Experiment Station, Zhejiang University, Hangzhou, China
| | - Satoshi Chiba
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
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2
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Ito S, Yamazaki D, Kameda Y, Kagawa O, Ye B, Saito T, Kimura K, Do VT, Chiba S, Hirano T. Taxonomic insights and evolutionary history in East Asian terrestrial slugs of the genus Meghimatium. Mol Phylogenet Evol 2023; 182:107730. [PMID: 36781029 DOI: 10.1016/j.ympev.2023.107730] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 03/26/2021] [Revised: 01/26/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
East Asia, specifically the Japanese Archipelago, is a biodiversity hotspot of both vertebrates and invertebrates. Mollusks represent a burst of species diversity in this region due to the effects of biotic and abiotic factors on their morphological traits, such as shell shape and size. However, the evolutionary history of terrestrial slugs in East Asia remains unknown. In the present study, we investigated the molecular phylogeny of terrestrial slugs of the genus Meghimatium. This genus includes three described and eight undescribed species, and our study used all except for two. Based on phylogeny and the species delimitation tests, the genus Meghimatium was split into many putative species, suggesting higher species diversity than previously thought based on morphological and anatomical studies and that almost undescribed species may be inappropriate. Therefore, morphological traits, such as body size and colour, conventionally considered for classification may easily vary or be similar across geographic region. Moreover, the divergence time of this genus is almost concordant with the geographical time scale of the formation of the Japanese mainland. Our findings suggest that molecular phylogenetics helps classify Japanese Meghimatium slugs, but comprehensive taxonomic revisions using multi-locus analyses are needed.
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Affiliation(s)
- Shun Ito
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Graduate School of Life Science, Tohoku University, Miyagi, Japan.
| | - Daishi Yamazaki
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Faculty of Agriculture and Marine Science, Kochi University, Kochi, Japan
| | - Yuichi Kameda
- Department of Anthropology, National Museum of Nature and Science, Ibaraki, Japan
| | - Osamu Kagawa
- Graduate School of Life Science, Tohoku University, Miyagi, Japan; Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
| | - Bin Ye
- Graduate School of Life Science, Tohoku University, Miyagi, Japan; Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, China
| | - Takumi Saito
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Department of Botany and Zoology, Faculty of Science, Masaryk University, Czech Republic
| | - Kazuki Kimura
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Research Institute for Ulleung-do and Dok-do islands, Department of Biology, Kyungpook National University, Buk-gu, South Korea
| | - Van Tu Do
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Viet Nam
| | - Satoshi Chiba
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Graduate School of Life Science, Tohoku University, Miyagi, Japan
| | - Takahiro Hirano
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan; Graduate School of Life Science, Tohoku University, Miyagi, Japan; Biology Program, Faculty of Science, University of the Ryukyus, Okinawa, Japan
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3
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Gomes-Dos-Santos A, Froufe E, Pfeiffer JM, Johnson NA, Smith CH, Machado AM, C Castro LF, Do VT, Hattori A, Garrison N, Whelan NV, Bolotov IN, Vikhrev IV, Kondakov AV, Ghamizi M, Prié V, Bogan AE, Lopes Lima M. A novel assembly pipeline and functional annotations for targeted sequencing: A case study on the globally threatened Margaritiferidae (Bivalvia: Unionida). Mol Ecol Resour 2023. [PMID: 37092367 DOI: 10.1111/1755-0998.13802] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/10/2023] [Accepted: 04/05/2023] [Indexed: 04/25/2023]
Abstract
The proliferation of genomic sequencing approaches has significantly impacted the field of phylogenetics. Target capture approaches provide a cost-effective, fast and easily applied strategy for phylogenetic inference of non-model organisms. However, several existing target capture processing pipelines are incapable of incorporating whole genome sequencing (WGS). Here, we develop a new pipeline for capture and de novo assembly of the targeted regions using whole genome re-sequencing reads. This new pipeline captured targeted loci accurately, and given its unbiased nature, can be used with any target capture probe set. Moreover, due to its low computational demand, this new pipeline may be ideal for users with limited resources and when high-coverage sequencing outputs are required. We demonstrate the utility of our approach by incorporating WGS data into the first comprehensive phylogenomic reconstruction of the freshwater mussel family Margaritiferidae. We also provide a catalogue of well-curated functional annotations of these previously uncharacterized freshwater mussel-specific target regions, representing a complementary tool for scrutinizing phylogenetic inferences while expanding future applications of the probe set.
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Affiliation(s)
- André Gomes-Dos-Santos
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Elsa Froufe
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - John M Pfeiffer
- National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Nathan A Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, Florida, USA
| | - Chase H Smith
- Department of Integrative Biology, University of Texas, Austin, Texas, USA
| | - André M Machado
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - L Filipe C Castro
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Van Tu Do
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Vietnam
| | | | - Nicole Garrison
- School of Fisheries, Aquaculture, and Aquatic Sciences, College of Agriculture, Auburn University, Auburn, Alabama, USA
| | - Nathan V Whelan
- School of Fisheries, Aquaculture, and Aquatic Sciences, College of Agriculture, Auburn University, Auburn, Alabama, USA
- Southeast Conservation Genetics Lab, Warm Springs Fish Technology Center, U.S. Fish and Wildlife Service, Auburn, Alabama, USA
| | - Ivan N Bolotov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Arkhangelsk, Russia
| | - Ilya V Vikhrev
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Arkhangelsk, Russia
| | - Alexander V Kondakov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Arkhangelsk, Russia
| | - Mohamed Ghamizi
- Department of Biology, Natural History Museum of Marrakech, University of Cadi Ayyad, Marrakech, Morocco
| | - Vincent Prié
- Institute of Systematics, Evolution, Biodiversity (ISYEB), National Museum of Natural History (MNHN), CNRS, SU, EPHE, UA, CP-51, Paris, France
- CIBIO/InBIO-Research Center in Biodiversity and Genetic Resources, Universidade do Porto, Vairão, Portugal
| | - Arthur E Bogan
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina, USA
| | - Manuel Lopes Lima
- CIBIO/InBIO-Research Center in Biodiversity and Genetic Resources, Universidade do Porto, Vairão, Portugal
- IUCN SSC Mollusc Specialist Group, c/o IUCN, Cambridge, UK
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4
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Saito T, Fujimoto K, Uchida S, Yamazaki D, Hirano T, Sano I, Ye B, Kagawa O, Shariar Shovon M, Tu Do V, Morii Y, Prozorova L, Chiba S. Uncovering overlooked diversity using molecular phylogenetic approach: a case of Japanese sphaeriid clams (Sphaeriidae: Bivalvia). Mol Phylogenet Evol 2022; 173:107508. [DOI: 10.1016/j.ympev.2022.107508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 03/29/2022] [Accepted: 04/05/2022] [Indexed: 12/12/2022]
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5
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Maasri A, Jähnig SC, Adamescu MC, Adrian R, Baigun C, Baird DJ, Batista‐Morales A, Bonada N, Brown LE, Cai Q, Campos‐Silva JV, Clausnitzer V, Contreras‐MacBeath T, Cooke SJ, Datry T, Delacámara G, De Meester L, Dijkstra KB, Do VT, Domisch S, Dudgeon D, Erös T, Freitag H, Freyhof J, Friedrich J, Friedrichs‐Manthey M, Geist J, Gessner MO, Goethals P, Gollock M, Gordon C, Grossart H, Gulemvuga G, Gutiérrez‐Fonseca PE, Haase P, Hering D, Hahn HJ, Hawkins CP, He F, Heino J, Hermoso V, Hogan Z, Hölker F, Jeschke JM, Jiang M, Johnson RK, Kalinkat G, Karimov BK, Kasangaki A, Kimirei IA, Kohlmann B, Kuemmerlen M, Kuiper JJ, Kupilas B, Langhans SD, Lansdown R, Leese F, Magbanua FS, Matsuzaki SS, Monaghan MT, Mumladze L, Muzon J, Mvogo Ndongo PA, Nejstgaard JC, Nikitina O, Ochs C, Odume O, Opperman JJ, Patricio H, Pauls S, Raghavan R, Ramírez A, Rashni B, Ross‐Gillespie V, Samways MJ, Schäfer RB, Schmidt‐Kloiber A, Seehausen O, Shah DN, Sharma S, Soininen J, Sommerwerk N, Stockwell JD, Suhling F, Tachamo Shah RD, Tharme RE, Thorp JH, Tickner D, Tockner K, Tonkin JD, Valle M, Vitule J, Volk M, Wang D, Wolter C, Worischka S. Cover Image. Ecol Lett 2022. [DOI: 10.1111/ele.13793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Maasri A, Jähnig SC, Adamescu MC, Adrian R, Baigun C, Baird DJ, Batista-Morales A, Bonada N, Brown LE, Cai Q, Campos-Silva JV, Clausnitzer V, Contreras-MacBeath T, Cooke SJ, Datry T, Delacámara G, De Meester L, Dijkstra KDB, Do VT, Domisch S, Dudgeon D, Erös T, Freitag H, Freyhof J, Friedrich J, Friedrichs-Manthey M, Geist J, Gessner MO, Goethals P, Gollock M, Gordon C, Grossart HP, Gulemvuga G, Gutiérrez-Fonseca PE, Haase P, Hering D, Hahn HJ, Hawkins CP, He F, Heino J, Hermoso V, Hogan Z, Hölker F, Jeschke JM, Jiang M, Johnson RK, Kalinkat G, Karimov BK, Kasangaki A, Kimirei IA, Kohlmann B, Kuemmerlen M, Kuiper JJ, Kupilas B, Langhans SD, Lansdown R, Leese F, Magbanua FS, Matsuzaki SIS, Monaghan MT, Mumladze L, Muzon J, Mvogo Ndongo PA, Nejstgaard JC, Nikitina O, Ochs C, Odume ON, Opperman JJ, Patricio H, Pauls SU, Raghavan R, Ramírez A, Rashni B, Ross-Gillespie V, Samways MJ, Schäfer RB, Schmidt-Kloiber A, Seehausen O, Shah DN, Sharma S, Soininen J, Sommerwerk N, Stockwell JD, Suhling F, Tachamo Shah RD, Tharme RE, Thorp JH, Tickner D, Tockner K, Tonkin JD, Valle M, Vitule J, Volk M, Wang D, Wolter C, Worischka S. A global agenda for advancing freshwater biodiversity research. Ecol Lett 2021; 25:255-263. [PMID: 34854211 DOI: 10.1111/ele.13931] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 03/15/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 12/20/2022]
Abstract
Global freshwater biodiversity is declining dramatically, and meeting the challenges of this crisis requires bold goals and the mobilisation of substantial resources. While the reasons are varied, investments in both research and conservation of freshwater biodiversity lag far behind those in the terrestrial and marine realms. Inspired by a global consultation, we identify 15 pressing priority needs, grouped into five research areas, in an effort to support informed stewardship of freshwater biodiversity. The proposed agenda aims to advance freshwater biodiversity research globally as a critical step in improving coordinated actions towards its sustainable management and conservation.
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Affiliation(s)
- Alain Maasri
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,The Academy of Natural Sciences of Drexel University, Philadelphia, Pennsylvania, USA
| | - Sonja C Jähnig
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mihai C Adamescu
- Research Center in Systems Ecology and Sustainability, University of Bucharest, Bucharest, Romania
| | - Rita Adrian
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Claudio Baigun
- Universidad Nacional de San Martin, San Martin, Argentina
| | - Donald J Baird
- Environment & Climate Change Canada/University of New Brunswick, Fredericton, New Brunswick, Canada
| | | | - Núria Bonada
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Lee E Brown
- School of Geography & water@leeds, University of Leeds, Leeds, UK
| | - Qinghua Cai
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | | | - Viola Clausnitzer
- Senckenberg Research Institute and Natural History Museum, Frankfurt am Main, Germany
| | | | | | | | | | - Luc De Meester
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Institut für Biologie, Freie Universität Berlin, Berlin, Germany.,Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Van Tu Do
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | - Sami Domisch
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | | | - Tibor Erös
- Balaton Limnological Research Institute, Tihany, Hungary
| | | | - Joerg Freyhof
- Museum für Naturkunde-Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | | | - Martin Friedrichs-Manthey
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | | | - Mark O Gessner
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Berlin Institute of Technology, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | | | | | | | - Hans-Peter Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Georges Gulemvuga
- International Commission for Congo-Ubangui-Sangha Basin, Kinshasa, D.R. Congo
| | | | - Peter Haase
- Senckenberg Research Institute and Natural History Museum, Frankfurt am Main, Germany.,University of Duisburg-Essen, Essen, Germany
| | | | - Hans Jürgen Hahn
- University of Koblenz-Landau, Koblenz and Landau, Germany.,Institute for Groundwater Ecology IGÖ GmbH, Landau, Germany
| | | | - Fengzhi He
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Jani Heino
- Finnish Environment Institute, Oulu, Finland
| | - Virgilio Hermoso
- Centre de Ciència i Tecnologia Forestal de Catalunya, Solsona, Spain
| | - Zeb Hogan
- University of Nevada, Reno, Nevada, USA
| | - Franz Hölker
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Jonathan M Jeschke
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Institut für Biologie, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Meilan Jiang
- Chongqing University of Posts and Telecommunications, Chongqing, China
| | | | - Gregor Kalinkat
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Bakhtiyor K Karimov
- Tashkent Institute of Irrigation and Agricultural Mechanization Engineers, Tashkent, Uzbekistan
| | | | | | | | | | - Jan J Kuiper
- Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden
| | - Benjamin Kupilas
- Norwegian Institute for Water Research, Oslo, Norway.,University of Münster, Münster, Germany
| | - Simone D Langhans
- Basque Centre for Climate Change (BC3), Leioa, Spain.,University of Otago, Dunedin, New Zealand
| | | | | | | | | | - Michael T Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Levan Mumladze
- Institute of Zoology, Ilia State University, Tiblis, Georgia
| | - Javier Muzon
- Universidad Nacional de Avellaneda, Avellaneda, Argentina
| | | | - Jens C Nejstgaard
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | | | - Clifford Ochs
- University of Mississippi, University Park, Mississippi, USA
| | | | | | | | - Steffen U Pauls
- Senckenberg Research Institute and Natural History Museum, Frankfurt am Main, Germany.,Justus-Liebig-University, Gießen, Germany
| | - Rajeev Raghavan
- Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Alonso Ramírez
- North Carolina State University, Raleigh, North Carolina, USA
| | - Bindiya Rashni
- Institute of Applied Science, University of the South Pacific, Suva, Fiji
| | | | | | - Ralf B Schäfer
- University of Koblenz-Landau, Koblenz and Landau, Germany
| | | | - Ole Seehausen
- University of Bern, Bern, Switzerland.,Swiss Federal Institute of Aquatic Science and Technology (Eawag), Kastanienbaum, Switzerland
| | | | | | | | - Nike Sommerwerk
- Museum für Naturkunde-Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | | | - Frank Suhling
- Technische Universität Braunschweig, Braunschweig, Germany
| | | | | | | | | | - Klement Tockner
- Senckenberg Society for Nature Research, Frankfurt am Main, Germany.,Goethe University, Frankfurt am Main, Germany
| | - Jonathan D Tonkin
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Mireia Valle
- National Center for Ecological Analysis and Synthesis, University of California, Santa Barbara, California, USA.,AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Jean Vitule
- Federal University of Paraná, Curitiba, Brazil
| | - Martin Volk
- Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Ding Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Christian Wolter
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
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7
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Ye B, Saito T, Hirano T, Dong Z, Do VT, Chiba S. Human-geographic effects on variations in the population genetics of Sinotaia quadrata (Gastropoda: Viviparidae) that historically migrated from continental East Asia to Japan. Ecol Evol 2020; 10:8055-8072. [PMID: 32788961 PMCID: PMC7417235 DOI: 10.1002/ece3.6456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/06/2020] [Accepted: 05/11/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Anthropogenic factors potentially affect observed biogeographical patterns in population genetics, but the effects of ancient human activities on the original patterns created by natural processes are unknown. Sinotaia quadrata, a widely distributed freshwater snail species in East Asia, was used to investigate this issue. It is unclear whether S. quadrata in Japan was introduced from China and how different human uses and varying geographic patterns affect the contemporary population genetics between the two regions. Thus, we investigated the demography of S. quadrata and detected its genetic structure in Japan and continental East Asia. RESULTS Sinotaia quadrata populations first naturally migrated from continental East Asia to Japan, which is associated with the ancient period in Japanese geohistory (about 70,000 years ago). They were then artificially introduced in association with agriculture expansion by human movements in two recent periods (about 8,000 and 1,200 years ago). Populations in different parts of Japan have their own sources. Natural migration in the ancient period and artificial introduction in the recent period suggest that the population distribution is affected by both the geohistory of East Asia and the history of human expansion. In the background of the historical migration and introduction, contemporary populations in the two regions show different genetic patterns. Population divergence levels were significantly correlated with geographical patterns in Japan and significantly correlated with human interventions variables in continental East Asia, suggesting that long-term geographical isolation is likely the major factor that shaped the contemporary population genetics in Japan, while modern human uses are likely the major factor in continental East Asia. CONCLUSIONS Our preliminary results show a complex demography and unusual genetic patterns in the contemporary populations for a common freshwater snail and are of significance to determine the historical formation and contemporary patterns of biogeography in Japan and continental East Asia.
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Affiliation(s)
- Bin Ye
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
| | - Takumi Saito
- Department of BiologyFaculty of ScienceToho UniversityFunabashiJapan
| | - Takahiro Hirano
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
- Center for Northeast Asian StudiesTohoku UniversitySendaiJapan
| | - Zhengzhong Dong
- Agricultural Experiment StationZhejiang UniversityHangzhouChina
| | - Van Tu Do
- Institute of Ecology and Biological ResourcesVietnam Academy of Science and TechnologyHa NoiVietnam
- Graduate University of Science and TechnologyVietnam Academy of Science and TechnologyHa NoiVietnam
| | - Satoshi Chiba
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
- Center for Northeast Asian StudiesTohoku UniversitySendaiJapan
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8
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Hirano T, Saito T, Tsunamoto Y, Koseki J, Prozorova L, Do VT, Matsuoka K, Nakai K, Suyama Y, Chiba S. Role of ancient lakes in genetic and phenotypic diversification of freshwater snails. Mol Ecol 2019; 28:5032-5051. [DOI: 10.1111/mec.15272] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 09/14/2019] [Accepted: 09/16/2019] [Indexed: 01/17/2023]
Affiliation(s)
- Takahiro Hirano
- Department of Biological Sciences University of Idaho Moscow ID USA
| | - Takumi Saito
- Department of Biology Faculty of Science Toho University Funabashi Japan
| | - Yoshihiro Tsunamoto
- Tohoku Research Center Forestry and Forest Products Research Institute Morioka Japan
| | - Joichiro Koseki
- Graduate School of Life Sciences Tohoku University Sendai Japan
| | - Larisa Prozorova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch Russian Academy of Sciences Vladivostok Russia
| | - Van Tu Do
- Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Hanoi Vietnam
- Graduate University of Science and Technology Vietnam Academy of Science and Technology Hanoi Vietnam
| | | | | | - Yoshihisa Suyama
- Kawatabi Field Science Center Graduate School of Agricultural Science Tohoku University Osaki Japan
| | - Satoshi Chiba
- Graduate School of Life Sciences Tohoku University Sendai Japan
- Center for Northeast Asian Studies Tohoku University Sendai Japan
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9
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Hirano T, Saito T, Tsunamoto Y, Koseki J, Ye B, Do VT, Miura O, Suyama Y, Chiba S. Enigmatic incongruence between mtDNA and nDNA revealed by multi-locus phylogenomic analyses in freshwater snails. Sci Rep 2019; 9:6223. [PMID: 30996240 PMCID: PMC6470147 DOI: 10.1038/s41598-019-42682-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 04/05/2019] [Indexed: 02/08/2023] Open
Abstract
Phylogenetic incongruence has frequently been encountered among different molecular markers. Recent progress in molecular phylogenomics has provided detailed and important information for evolutionary biology and taxonomy. Here we focused on the freshwater viviparid snails (Cipangopaludina chinensis chinensis and C. c. laeta) of East Asia. We conducted phylogenetic analyses and divergence time estimation using two mitochondrial markers. We also performed population genetic analyses using genome-wide SNPs. We investigated how and which phylogenetic patterns reflect shell morphology. The results showed these two species could be separated into four major mitochondrial clades, whereas the nuclear clusters supported two groups. The phylogenetic patterns of both mtDNA and nDNA largely reflected the geographical distribution. Shell morphology reflected the phylogenetic clusters based on nDNA. The findings also showed these two species diversified in the Pliocene to early Pleistocene era, and occurred introgressive hybridisation. The results also raise the taxonomic issue of the two species.
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Affiliation(s)
- Takahiro Hirano
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA.
| | - Takumi Saito
- Graduate school of Life Sciences, Tohoku University, Miyagi, Japan
| | - Yoshihiro Tsunamoto
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Joichiro Koseki
- Graduate school of Life Sciences, Tohoku University, Miyagi, Japan
| | - Bin Ye
- Graduate school of Life Sciences, Tohoku University, Miyagi, Japan
- Agricultural Experiment Station, Zhejiang University, Hangzhou, China
| | - Van Tu Do
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Osamu Miura
- Faculty of Agriculture and Marine Science, Kochi University, Kochi, Japan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Satoshi Chiba
- Graduate school of Life Sciences, Tohoku University, Miyagi, Japan
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan
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10
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Lopes-Lima M, Bolotov IN, Do VT, Aldridge DC, Fonseca MM, Gan HM, Gofarov MY, Kondakov AV, Prié V, Sousa R, Varandas S, Vikhrev IV, Teixeira A, Wu RW, Wu X, Zieritz A, Froufe E, Bogan AE. Expansion and systematics redefinition of the most threatened freshwater mussel family, the Margaritiferidae. Mol Phylogenet Evol 2018; 127:98-118. [DOI: 10.1016/j.ympev.2018.04.041] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 04/09/2018] [Accepted: 04/30/2018] [Indexed: 01/10/2023]
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11
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Affiliation(s)
- Van Tu Do
- Institute of Ecology and Biological Resources (IEBR), Vietnam Academy of Science and Technology, 18
| | - Le Quang Tuan
- Institute of Ecology and Biological Resources (IEBR), Vietnam Academy of Science and Technology, 18
| | - Arthur E. Bogan
- North Carolina Museum of Natural Sciences, 11 West Jones Street, Raleigh, NC 27601 USA
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12
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Lopes-Lima M, Froufe E, Do VT, Ghamizi M, Mock KE, Kebapçı Ü, Klishko O, Kovitvadhi S, Kovitvadhi U, Paulo OS, Pfeiffer JM, Raley M, Riccardi N, Şereflişan H, Sousa R, Teixeira A, Varandas S, Wu X, Zanatta DT, Zieritz A, Bogan AE. Phylogeny of the most species-rich freshwater bivalve family (Bivalvia: Unionida: Unionidae): Defining modern subfamilies and tribes. Mol Phylogenet Evol 2016; 106:174-191. [PMID: 27621130 DOI: 10.1016/j.ympev.2016.08.021] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [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: 02/25/2016] [Revised: 06/08/2016] [Accepted: 08/30/2016] [Indexed: 11/15/2022]
Abstract
Freshwater mussels of the order Unionida are key elements of freshwater habitats and are responsible for important ecological functions and services. Unfortunately, these bivalves are among the most threatened freshwater taxa in the world. However, conservation planning and management are hindered by taxonomic problems and a lack of detailed ecological data. This highlights the urgent need for advances in the areas of systematics and evolutionary relationships within the Unionida. This study presents the most comprehensive phylogeny to date of the larger Unionida family, i.e., the Unionidae. The phylogeny is based on a combined dataset of 1032bp (COI+28S) of 70 species in 46 genera, with 7 of this genera being sequenced for the first time. The resulting phylogeny divided the Unionidae into 6 supported subfamilies and 18 tribes, three of which are here named for the first time (i.e., Chamberlainiini nomen novum, Cristariini nomen novum and Lanceolariini nomen novum). Molecular analyses were complemented by investigations of selected morphological, anatomical and behavioral characters used in traditional phylogenetic studies. No single morphological, anatomical or behavioral character was diagnostic at the subfamily level and few were useful at the tribe level. However, within subfamilies, many tribes can be recognized based on a subset of these characters. The geographical distribution of each of the subfamilies and tribes is also presented. The present study provides important advances in the systematics of these extraordinary taxa with implications for future ecological and conservation studies.
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Affiliation(s)
- Manuel Lopes-Lima
- 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.
| | - Elsa 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
| | - Van Tu Do
- Department of Aquatic Ecology, Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi, Viet Nam
| | - Mohamed Ghamizi
- Muséum d'Histoire Naturelle de Marrakech, Université Cadi Ayyad, Faculté des Sciences, Semlalia, B.P. 2390 Marrakech, Morocco
| | - Karen E Mock
- Ecology Center and Department of Wildland Resources, Utah State University, Logan, UT 84322, USA
| | - Ümit Kebapçı
- Department of Biology, Faculty of Arts and Sciences, Mehmet Akif Ersoy University, Burdur, Turkey
| | - Olga Klishko
- Institute of Natural Resources, Ecology and Criology, Russian Academy of Sciences Siberian Branch, Chita 672014, Russia
| | - Satit Kovitvadhi
- Department of Agriculture, Faculty of Science and Technology, Bansomdejchaopraya Rajabhat University, Bangkok 10600, Thailand
| | - Uthaiwan Kovitvadhi
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, cE3c - Centre for Centre for Ecology Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - John M Pfeiffer
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | | | | | - Hülya Şereflişan
- Faculty of Marine Sciences and Technology, İskenderun Technical University, 31200 Iskenderun, Hatay, Turkey
| | - Ronaldo Sousa
- 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; CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - Amílcar Teixeira
- CIMO/ESA/IPB - Mountain Research Centre, School of Agriculture, Polytechnic Institute of Bragança, Campus de Santa Apolónia, Apartado 1172, 5301-854 Bragança, Portugal
| | - Simone Varandas
- CITAB/UTAD - Centre for Research and Technology of Agro-Environment and Biological Sciences, University of Trás-os-Montes and Alto Douro, Forestry Department, 5000-801 Vila Real, Portugal
| | - Xiaoping Wu
- School of Life Sciences, Center for Watershed Ecology, Institute of Life Science, Nanchang University, Nanchang 330031, People's Republic of China
| | - David T Zanatta
- Biology Department, Institute for Great Lakes Research, Central Michigan University, Biosciences Bldg. 2408, Mount Pleasant, MI 48859, USA
| | - Alexandra Zieritz
- School of Geography, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Malaysia
| | - Arthur E Bogan
- Research Laboratory, North Carolina State Museum of Natural Sciences, MSC 1626, Raleigh, NC 27699-1626, USA
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Do VT, Le VT, Phan DD. Binhthuanomon vinhtan, a new genus and new species of semi-terrestrial freshwater crab (Crustacea: Decapoda: Brachyura: Potamidae) from south central Vietnam. Zootaxa 2015; 4052:117-26. [PMID: 26624780 DOI: 10.11646/zootaxa.4052.1.6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 11/04/2022]
Abstract
A new genus and new species of semi-terrestrial crab of the family Potamidae, Binhthuanomon vinhtan n. sp., is described from south central Vietnam. The new genus is morphologically closest to Villopotamon Dang & Ho, 2003, and Balssipotamon Dang & Ho, 2008, in the shapes of the carapace and first gonopod but is easily distinguished by distinct carapace characteristics and gonopod 1 structures, and the habitat occupied.
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Affiliation(s)
- Van Tu Do
- Institute of Ecology and Biological Resources (IEBR), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Ha Noi, Vietnam;
| | - Van Tho Le
- Institute of Tropical Biology (ITB), Vietnam Academy of Science and Technology (VAST), 85 Tran Quoc Toan, District 3, Ho Chi Minh City, Vietnam; unknown
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Shih HT, Do VT. A new species of Tiwaripotamon Bott, 1970, from northern Vietnam, with notes on T. vietnamicum (Dang & Ho, 2002) and T. edostilus Ng & Yeo, 2001 (Crustacea, Brachyura, Potamidae). Zootaxa 2014; 3764:26-38. [PMID: 24870278 DOI: 10.11646/zootaxa.3764.1.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Indexed: 11/04/2022]
Abstract
A new species of potamid freshwater crab, Tiwaripotamon vixuyenense sp. nov., is described from caves in Ha Giang, northern Vietnam. The new species can be distinguished from congeners by a suite of characters, including the relatively small epibranchial tooth, more slender ambulatory legs and a proportionately stout male first gonopod. Molecular data using the mitochondrial cytochrome oxidase subunit I (COI) supports its placement as a new species. The molecular data also supports the inclusion of another species, Geothelphusa vietnamica Dang & Ho, 2002, from Ninh Binh, south of Hanoi, Vietnam in Tiwaripotamon Bott, 1970. The live coloration of T. vietnamicum and T. edostilus Ng & Yeo, 2001 is provided to help field identification.
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Affiliation(s)
- Hsi-Te Shih
- Department of Life Science, National Chung Hsing University, 250, Kuo Kuang Road, Taichung 402, Taiwan;
| | - Van Tu Do
- Institute of Ecology and Biological Resources (IEBR), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Ha Noi, Vietnam; unknown
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15
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Boatright JH, Stodulkova E, Do VT, Padove SA, Nguyen HT, Borst DE, Nickerson JM. The effect of retinoids and butyrate on the expression of CRX and IRBP in retinoblastoma cells. Vision Res 2002; 42:933-8. [PMID: 11934446 DOI: 10.1016/s0042-6989(02)00037-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We sought to determine whether differentiation agents such as retinoids and butyrate regulate transcript levels of interphotoreceptor retinoid binding protein (IRBP) and cone rod homeobox (CRX), a homeodomain transcription factor that regulates IRBP promoter activity. WERI-Rb1 retinoblastoma cells were treated with all-trans retinol, all-trans retinoic acid, or butyrate. IRBP and CRX mRNA levels were determined by quantitative RT-PCR. Butyrate at low concentrations increased both mRNA levels but suppressed them at higher concentrations. Retinoic acid had minimal effects. Retinol increased CRX mRNA over four fold. IRBP and CRX transcript levels are sensitive to butyrate and CRX expression is sensitive to retinol.
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Do VT, Thomas GM, Bjarnason GA. Postoperative concurrent chronomodulated 5-fluorouracil/leucovorin infusion and pelvic radiotherapy for squamous cell carcinoma of the ovary arising from mature cystic teratoma. Int J Gynecol Cancer 2001; 11:418-21. [PMID: 11737476 DOI: 10.1046/j.1525-1438.2001.01044.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Primary squamous cell carcinoma (SCC) of the ovary arising from mature cystic teratoma (MCT) is rare. Survival is very poor. Although different postoperative treatments have been tried, none appears to have influenced outcomes. A 44-year-old patient with FIGO stage IIB SCC of the ovary arising in MCT had exploratory laparotomy and left salpingo-oophorectomy, leaving macroscopic residual pelvic disease. Postoperative treatment consisted of a continuous concurrent chronomodulated infusion of 5-fluorouracil 150 mg/m2/day and leucovorin 10 mg/m2/day with 5 weeks of pelvic radiotherapy. Three years after initial surgery, she remains disease and complication free. Given this patient's unusually long disease-free survival and the efficacy of concurrent chemotherapy and radiotherapy in other SCCs, the concurrent circadian treatment approach used for this patient should be explored in other cases of SCC of the ovary.
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