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Wu R, Liu L, Zhang L, Bogan AE, Niu G, Jin D, Wu X, Liu X. Taxonomic revision of two species in the genus Ptychorhynchus Simpson, 1900 (Bivalvia: Unionidae: Gonideinae), with description of a new species. INVERTEBR SYST 2024; 38:IS24014. [PMID: 38963889 DOI: 10.1071/is24014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/04/2024] [Indexed: 07/06/2024]
Abstract
Accurate identification and precise classification of freshwater mussel species that are among the most threatened freshwater taxa in the world, play a crucial role in informing conservation and management efforts for these organisms. However, due to the variability in shell morphology, relying solely on shell characteristics for species taxonomy poses significant challenges, thereby impeding effective conservation planning and management. The freshwater mussel genus Ptychorhynchus Simpson, 1900 is one such group in need of study. We integrate molecular phylogeny, shell morphology and soft-body anatomy to examine the classification of Ptychorhynchus denserugata (Haas, 1910) and Ptychorhynchus resupinatus (von Martens, 1902). The COI barcoding data support the clustering of P. denserugata and Nodularia douglasiae within a single clade, and P. denserugata shares the diagnostic feature of the genus Nodularia , i.e. knobs or bumps on the inner mantle surface in the excurrent aperture. Therefore, by integrating molecular data and anatomical characteristics, we confirm that the nominal species P. denserugata syn. nov. is a new synonym for N. douglasiae . The multi-locus (COI + ND1 + 16S rRNA + 18S rRNA + 28S rRNA ) phylogeny and mitochondrial phylogenomics support the transfer of P. resupinatus from Ptychorhynchus to the newly elevated genus Cosmopseudodon stat. rev., as Cosmopseudodon resupinatus stat. rev. that is still considered the designated type species. We also describe a new species based on integrative taxonomy, i.e. Cosmopseudodon wenshanensis sp. nov. The comprehensive understanding of the taxonomy and diversity of the revised Cosmopseudodon species, and shell heteromorphism of N. douglasiae (=P. denserugata syn. nov.), will serve as a crucial foundation for further scientific assessment and conservation strategies pertaining to these taxa. ZooBank: urn:lsid:zoobank.org:pub:E48968B1-DF0F-42AD-8F31-B8C95F23CE57.
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Affiliation(s)
- Ruiwen Wu
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, PR China
| | - Lili Liu
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, PR China
| | - Liping Zhang
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, PR China
| | - Arthur E Bogan
- North Carolina Museum of Natural Sciences and Department of Applied Ecology, North Carolina State University, Raleigh, NC 27601, USA
| | - Gengyun Niu
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Dandong Jin
- Datian High School, Linhai, 317004, PR China
| | - Xiaoping Wu
- School of Life Sciences, Nanchang University, Nanchang, 330031, PR China
| | - Xiongjun Liu
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, School of Life Sciences, Jiaying University, Meizhou, 514000, PR China
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Grekov AN, Kabanov AA, Vyshkvarkova EV, Trusevich VV. Anomaly Detection in Biological Early Warning Systems Using Unsupervised Machine Learning. SENSORS (BASEL, SWITZERLAND) 2023; 23:2687. [PMID: 36904891 PMCID: PMC10007031 DOI: 10.3390/s23052687] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/15/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
The use of bivalve mollusks as bioindicators in automated monitoring systems can provide real-time detection of emergency situations associated with the pollution of aquatic environments. The behavioral reactions of Unio pictorum (Linnaeus, 1758) were employed in the development of a comprehensive automated monitoring system for aquatic environments by the authors. The study used experimental data obtained by an automated system from the Chernaya River in the Sevastopol region of the Crimean Peninsula. Four traditional unsupervised machine learning techniques were implemented to detect emergency signals in the activity of bivalves: elliptic envelope, isolation forest (iForest), one-class support vector machine (SVM), and local outlier factor (LOF). The results showed that the use of the elliptic envelope, iForest, and LOF methods with proper hyperparameter tuning can detect anomalies in mollusk activity data without false alarms, with an F1 score of 1. A comparison of anomaly detection times revealed that the iForest method is the most efficient. These findings demonstrate the potential of using bivalve mollusks as bioindicators in automated monitoring systems for the early detection of pollution in aquatic environments.
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Affiliation(s)
- Aleksandr N. Grekov
- Institute of Natural and Technical Systems, 299011 Sevastopol, Russia
- Department of Informatics and Control in Technical Systems, Sevastopol State University, 299053 Sevastopol, Russia
| | - Aleksey A. Kabanov
- Department of Informatics and Control in Technical Systems, Sevastopol State University, 299053 Sevastopol, Russia
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Resolving species-level diversity of Beringiana and Sinanodonta mussels (Bivalvia: Unionidae) in the Japanese archipelago using genome-wide data. Mol Phylogenet Evol 2022; 175:107563. [PMID: 35809852 DOI: 10.1016/j.ympev.2022.107563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 06/04/2022] [Accepted: 06/27/2022] [Indexed: 11/22/2022]
Abstract
Accurate species identification is of primary importance in ecology and evolutionary biology. For a long time, the unionid mussels Beringiana and Sinanodonta have puzzled researchers trying to unravel their diversity because of their poorly discernible morphologies. A recent study conducted species delineation of unionid mussels based on mitochondrial DNA variation, opening up a new avenue to grasp species diversity of the mussels. However, mtDNA-based classification may not align with species boundaries because mtDNA is prone to introgression and incomplete lineage sorting that cause discordance between species affiliation and gene phylogeny. In this study, we evaluated the validity of the mtDNA-based classification of unionid mussels Beringiana and Sinanodonta in Japan using mitochondrial sequence data, double digest restriction site-associated DNA library (ddRAD) sequencing, and morphological data. We found significant inconsistencies in the mitochondrial and nuclear DNA phylogenies, casting doubt on the reliability of the mtDNA-based classification in this group. In addition, nuclear DNA phylogeny revealed that there are at least two unionid lineages hidden in the mtDNA phylogeny. Although molecular dating technique indicates that Beringiana and Sinanodonta diverged >35 million years ago, their shell morphologies are often indistinguishable. Specifically, morphological analyses exhibited the parallel appearance of nearly identical ball-like shell forms in the two genera in Lake Biwa, which further complicates species identification and the morphological evolution of unionid mussels. Our study adds to a growing body of literature that accurate species identification of unionid mussels is difficult when using morphological characters alone. Although mtDNA-based classification is a simple and convenient way to classify unionid mussels, considerable caution is warranted for its application in ecological and evolutionary studies.
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Moulpied M, Smith CH, Robertson CR, Johnson NA, Lopez R, Randklev CR. Biogeography of freshwater mussels (Bivalvia: Unionida) in Texas and implications on conservation biology. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Michael Moulpied
- Texas A&M Natural Resources Institute Texas A&M AgriLife Research Center at Dallas Dallas Texas USA
| | - Chase H. Smith
- Department of Integrative Biology University of Texas at Austin Austin Texas USA
| | - Clinton R. Robertson
- Inland Fisheries – Management and Conservation Branch Texas Parks & Wildlife Department San Marcos Texas USA
| | - Nathan A. Johnson
- U.S. Geological Survey Wetland and Aquatic Research Center Florida USA
| | - Roel Lopez
- Texas A&M Natural Resources Institute Texas A&M AgriLife Research Center at Dallas Dallas Texas USA
| | - Charles R. Randklev
- Texas A&M Natural Resources Institute Texas A&M AgriLife Research Center at Dallas Dallas Texas USA
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Klinkenbuß D, Metz O, Reichert J, Hauffe T, Neubauer TA, Wesselingh FP, Wilke T. Performance of 3D Morphological Methods in the Machine Learning Assisted Classification of Closely Related Fossil Bivalve Species of the Genus Dreissena. MALACOLOGIA 2020. [DOI: 10.4002/040.063.0109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Denise Klinkenbuß
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Olivia Metz
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Jessica Reichert
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Torsten Hauffe
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Thomas A. Neubauer
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Frank P. Wesselingh
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - Thomas Wilke
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
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Smith CH, Johnson NA, Havlik K, Doyle RD, Randklev CR. Resolving species boundaries in the critically imperiled freshwater mussel species,
Fusconaia mitchelli
(Bivalvia: Unionidae). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chase H. Smith
- Biology Department Baylor University Waco TX USA
- Texas A&M Natural Resources InstituteTexas A&M AgriLife Research Center at Dallas Dallas TX USA
- Department of Integrative Biology University of Texas Austin TX USA
| | - Nathan A. Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center Gainesville FL USA
| | | | | | - Charles R. Randklev
- Texas A&M Natural Resources InstituteTexas A&M AgriLife Research Center at Dallas Dallas TX USA
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Novel Molecular Resources to Facilitate Future Genetics Research on Freshwater Mussels (Bivalvia: Unionidae). DATA 2020. [DOI: 10.3390/data5030065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Molecular data have been an integral tool in the resolution of the evolutionary relationships and systematics of freshwater mussels, despite the limited number of nuclear markers available for Sanger sequencing. To facilitate future studies, we evaluated the phylogenetic informativeness of loci from the recently published anchored hybrid enrichment (AHE) probe set Unioverse and developed novel Sanger primer sets to amplify two protein-coding nuclear loci with high net phylogenetic informativeness scores: fem-1 homolog C (FEM1) and UbiA prenyltransferase domain-containing protein 1 (UbiA). We report the methods used for marker development, along with the primer sequences and optimized PCR and thermal cycling conditions. To demonstrate the utility of these markers, we provide haplotype networks, DNA alignments, and summary statistics regarding the sequence variation for the two protein-coding nuclear loci (FEM1 and UbiA). Additionally, we compare the DNA sequence variation of FEM1 and UbiA to three loci commonly used in freshwater mussel genetic studies: the mitochondrial genes cytochrome c oxidase subunit 1 (CO1) and NADH dehydrogenase subunit 1 (ND1), and the nuclear internal transcribed spacer 1 (ITS1). All five loci distinguish among the three focal species (Potamilus fragilis, Potamilus inflatus, and Potamilus purpuratus), and the sequence variation was highest for ND1, followed by CO1, ITS1, UbiA, and FEM1, respectively. The newly developed Sanger PCR primers and methodologies for extracting additional loci from AHE probe sets have great potential to facilitate molecular investigations targeting supraspecific relationships in freshwater mussels, but may be of limited utility at shallow taxonomic scales.
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Bolotov IN, Konopleva ES, Vikhrev IV, Gofarov MY, Lopes-Lima M, Bogan AE, Lunn Z, Chan N, Win T, Aksenova OV, Tomilova AA, Tanmuangpak K, Tumpeesuwan S, Kondakov AV. New freshwater mussel taxa discoveries clarify biogeographic division of Southeast Asia. Sci Rep 2020; 10:6616. [PMID: 32313058 PMCID: PMC7171101 DOI: 10.1038/s41598-020-63612-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 03/31/2020] [Indexed: 01/22/2023] Open
Abstract
While a growing body of modern phylogenetic research reveals that the Western Indochina represents a separate biogeographic subregion having a largely endemic freshwater fauna, the boundaries of this subregion are still unclear. We use freshwater mussels (Unionidae) as a model to reconstruct spatial patterns of freshwater biogeographic divides throughout Asia. Here, we present an updated freshwater biogeographic division of mainland Southeast Asia and describe 12 species and 4 genera of freshwater mussels new to science. We show that the Isthmus of Kra represents a significant southern biogeographic barrier between freshwater mussel faunas of the Western Indochina and Sundaland subregions, while the Indian and Western Indochina subregions are separated by the Naga Hills, Chin Hills, and Rakhine Yoma mountain ranges. Our findings highlight that the freshwater bivalve fauna of Southeast Asia primarily originated within three evolutionary hotspots (Western Indochina, Sundaland, and East Asian) supplemented by ancient immigrants from the Indian Subcontinent.
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Affiliation(s)
- Ivan N Bolotov
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation.
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation.
| | - Ekaterina S Konopleva
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| | - Ilya V Vikhrev
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| | - Mikhail Yu Gofarov
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| | - Manuel Lopes-Lima
- CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, University of Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas 7, 4485-661, Vairão, Portugal
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- SSC/IUCN - Mollusc Specialist Group, Species Survival Commission, International Union for Conservation of Nature, c/o The David Attenborough Building, Pembroke Street, CB2 3QZ, Cambridge, United Kingdom
| | - Arthur E Bogan
- North Carolina Museum of Natural Sciences, 11 West Jones St., Raleigh, NC, 27601, USA
| | - Zau Lunn
- Fauna & Flora International - Myanmar Programme, Yangon, Myanmar
| | - Nyein Chan
- Fauna & Flora International - Myanmar Programme, Yangon, Myanmar
| | - Than Win
- Department of Zoology, Dawei University, Dawei, Tanintharyi Region, Myanmar
| | - Olga V Aksenova
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| | - Alena A Tomilova
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| | - Kitti Tanmuangpak
- Department of Science, Faculty of Science and Technology, Loei Rajabhat University, Loei, Thailand
| | - Sakboworn Tumpeesuwan
- Department of Biology, Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand
| | - Alexander V Kondakov
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
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