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Wang Y, Yang Y, Kong L, Sasaki T, Li Q. Phylogenomic resolution of Imparidentia (Mollusca: Bivalvia) diversification through mitochondrial genomes. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:326-336. [PMID: 37637250 PMCID: PMC10449738 DOI: 10.1007/s42995-023-00178-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 04/25/2023] [Indexed: 08/29/2023]
Abstract
Despite significant advances in the phylogenomics of bivalves over the past decade, the higher-level phylogeny of Imparidentia (a superorder of Heterodonta) remains elusive. Here, a total of five new mitochondrial sequences (Chama asperella, Chama limbula, Chama dunkeri, Barnea manilensis and Ctena divergens) was added to provide resolution in nodes that required additional study. Although the monophyly of Lucinida remains less clear, the results revealed the overall backbone of the Imparidentia tree and the monophyly of Imparidentia. Likewise, most relationships among the five major Imparidentia lineages-Lucinida, Cardiida, Adapedonta, Myida and Venerida-were addressed with a well-supported topology. Basal relationships of Imparidentia recovered Lucinidae as the sister group to all remaining imparidentian taxa. Thyasiridae is a sister group to other imparidentian bivalves (except Lucinidae species) which is split into Cardiida, Adapedonta and the divergent clade of Neoheterodontei. Neoheterodontei was comprised of Venerida and Myida, the former of which now also contains Chamidae as the sister group to all the remaining venerid taxa. Moreover, molecular divergence times were inferred by calibrating nine nodes in the Imparidentia tree of life by extinct taxa. The origin of these major clades ranged from Ordovician to Permian with the diversification through the Palaeozoic to Mesozoic. Overall, the results obtained in this study demonstrate a better-resolved Imparidentia phylogeny based on mitochondrial genomes. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00178-x.
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Affiliation(s)
- Yu Wang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003 China
| | - Yi Yang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003 China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003 China
| | - Takenori Sasaki
- The University Museum, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, 266237 China
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2
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An Authentication Survey on Retail Seafood Products Sold on the Bulgarian Market Underlines the Need for Upgrading the Traceability System. Foods 2023; 12:foods12051070. [PMID: 36900583 PMCID: PMC10000581 DOI: 10.3390/foods12051070] [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: 01/26/2023] [Revised: 02/13/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Economically motivated or accidental species substitutions lead to economic and potential health damage to consumers with a loss of confidence in the fishery supply chain. In the present study, a three-year survey on 199 retail seafood products sold on the Bulgarian market was addressed to assess: (1) product authenticity by molecular identification; (2) trade name compliance to the list of official trade names accepted in the territory; (3) adherence of the list in force to the market supply. DNA barcoding on mitochondrial and nuclear genes was applied for the identification of whitefish (WF), crustaceans (C) and mollusks (cephalopods-MC; gastropods-MG; bivalves-MB) except for Mytilus sp. products for which the analysis was conducted with a previously validated RFLP PCR protocol. Identification at the species level was obtained for 94.5% of the products. Failures in species allocation were reconducted due to low resolution and reliability or the absence of reference sequences. The study highlighted an overall mislabeling rate of 11%. WF showed the highest mislabeling rate (14%), followed by MB (12.5%), MC (10%) and C (7.9%). This evidence emphasized the use of DNA-based methods as tools for seafood authentication. The presence of non-compliant trade names and the ineffectiveness of the list to describe the market species varieties attested to the need to improve seafood labeling and traceability at the national level.
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Harbuzov Z, Farberova V, Tom M, Pallavicini A, Stanković D, Lotan T, Lubinevsky H. Amplicon sequence variant-based meiofaunal community composition revealed by DADA2 tool is compatible with species composition. Mar Genomics 2022; 65:100980. [PMID: 35963148 DOI: 10.1016/j.margen.2022.100980] [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: 06/12/2022] [Revised: 07/15/2022] [Accepted: 07/15/2022] [Indexed: 11/16/2022]
Abstract
The present study is aimed at implementing the morphological identification-free amplicon sequence variant (ASV) concept for describing meiofaunal species composition, while strongly indicating reasonable compatibility with the underlying species. A primer pair was constructed and demonstrated to PCR amplify a 470-490 bp 18S barcode from a variety of meiofaunal taxa, high throughput sequenced using the Illumina 300 × 2 bps platform. Sixteen 18S multi-species HTS assemblies were created from meiofaunal samples and merged to one assembly of ~2,150,000 reads. Five quality scores (q = 35, 30, 25, 20, 15) were implemented to filter five 18S barcode assemblies, which served as inputs for the DADA2 software, ending with five reference ASV libraries. Each of these libraries was clustered, applying 3% dissimilarity threshold, revealed an average number of 1.38 ± 0.078 ASVs / cluster. Hence, demonstrating high level of ASV uniqueness. The libraries which were based on q ≤ 25 reached a near-asymptote number of ASVs which together with the low average number of ASVs / cluster, strongly indicated fair representation of the actual number of the underlying species. Hence, the q = 25 library was selected to be used as metabarcoding reference library. It contained 461 ASVs and 342-3% clusters with average number of 1.34 ± 1.036 ASV / cluster and their BLASTN annotation elucidated a variety of expected meiofaunal taxa. The sixteen assemblies of sample-specific paired reads were mapped to this reference library and sample ASV profiles, namely the list of ASVs and their proportional copy numbers were created and clustered.
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Affiliation(s)
- Zoya Harbuzov
- National Institute of Oceanography, Department of Biology and Biotechnology, Israel Oceanographic & Limnological Research, P.O.B 9753, Haifa 3109701, Israel; Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, 199 Aba Koushy Ave., Mount Carmel, Haifa 3498838, Israel.
| | - Valeria Farberova
- National Institute of Oceanography, Department of Biology and Biotechnology, Israel Oceanographic & Limnological Research, P.O.B 9753, Haifa 3109701, Israel; Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, 199 Aba Koushy Ave., Mount Carmel, Haifa 3498838, Israel
| | - Moshe Tom
- National Institute of Oceanography, Department of Biology and Biotechnology, Israel Oceanographic & Limnological Research, P.O.B 9753, Haifa 3109701, Israel
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - David Stanković
- National institute of Biology, Department of Organisms and Ecosystems Research, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Tamar Lotan
- Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, 199 Aba Koushy Ave., Mount Carmel, Haifa 3498838, Israel
| | - Hadas Lubinevsky
- National Institute of Oceanography, Department of Biology and Biotechnology, Israel Oceanographic & Limnological Research, P.O.B 9753, Haifa 3109701, Israel
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Edie SM, Collins KS, Jablonski D. Specimen alignment with limited point-based homology: 3D morphometrics of disparate bivalve shells (Mollusca: Bivalvia). PeerJ 2022; 10:e13617. [PMID: 35769136 PMCID: PMC9235814 DOI: 10.7717/peerj.13617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/01/2022] [Indexed: 01/17/2023] Open
Abstract
Background Comparative morphology fundamentally relies on the orientation and alignment of specimens. In the era of geometric morphometrics, point-based homologies are commonly deployed to register specimens and their landmarks in a shared coordinate system. However, the number of point-based homologies commonly diminishes with increasing phylogenetic breadth. These situations invite alternative, often conflicting, approaches to alignment. The bivalve shell (Mollusca: Bivalvia) exemplifies a homologous structure with few universally homologous points-only one can be identified across the Class, the shell 'beak'. Here, we develop an axis-based framework, grounded in the homology of shell features, to orient shells for landmark-based, comparative morphology. Methods Using 3D scans of species that span the disparity of shell morphology across the Class, multiple modes of scaling, translation, and rotation were applied to test for differences in shell shape. Point-based homologies were used to define body axes, which were then standardized to facilitate specimen alignment via rotation. Resulting alignments were compared using pairwise distances between specimen shapes as defined by surface semilandmarks. Results Analysis of 45 possible alignment schemes finds general conformity among the shape differences of 'typical' equilateral shells, but the shape differences among atypical shells can change considerably, particularly those with distinctive modes of growth. Each alignment corresponds to a hypothesis about the ecological, developmental, or evolutionary basis of morphological differences, but we suggest orientation via the hinge line for many analyses of shell shape across the Class, a formalization of the most common approach to morphometrics of shell form. This axis-based approach to aligning specimens facilitates the comparison of approximately continuous differences in shape among phylogenetically broad and morphologically disparate samples, not only within bivalves but across many other clades.
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Affiliation(s)
- Stewart M. Edie
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Katie S. Collins
- Department of Earth Sciences, Invertebrates and Plants Palaeobiology Division, Natural History Museum, London, United Kingdom
| | - David Jablonski
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, United States,Committee on Evolutionary Biology, University of Chicago, Chicago, IL, United States
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Li H, Yu R, Ma P, Li C. Complete mitochondrial genome of Cultellus attenuatus and its phylogenetic implications. Mol Biol Rep 2022; 49:8163-8168. [PMID: 35716283 DOI: 10.1007/s11033-022-07276-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND The mitochondrial genomes of three species in Solenoidea of Heterodonta have been reported, but the mitochondrial genes and phylogenetic relationships of Cultellus attenuatus, which also belongs to this superfamily and has high economic value, are unknown. METHODS AND RESULTS The complete mitochondrial genome of C. attenuatus was sequenced and compared with mitogenomes of seven species of Heterodonta bivalve mollusks in GenBank. The mitochondrial genome of C. attenuatus has a length of 16,888 bp and contains 36 genes, including 12 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNAs. In comparison with C. attenuates, the mitochondrial genes of Sinonovacula constricta from the same family were not rearranged, but those of six other species from different families were rearranged to different degrees. The location, size, and composition of the largest noncoding regions in eight species suggested a closer relationship between C. attenuatus and S. constricta. The phylogenetic analysis showed that C. attenuatus and S. constricta belonging to Cultellidae cluster into one branch and that two species of Solenidae (Solen grandis and Solen strictus) clustered as their sister taxa. CONCLUSIONS Overall, we used mitochondrial genome data to demonstrate that C. attenuatus and S. constricta exhibit the closest relationship in Heterodonta. These data and analyses provide new insights into the phylogenetic relationships in Heterodonta.
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Affiliation(s)
- Haikun Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, 5 Yushan Road, 266003, Qingdao, China
| | - Ruihai Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, 5 Yushan Road, 266003, Qingdao, China.
| | - Peizhen Ma
- Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, 266071, Qingdao, China
| | - Chunhua Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, 5 Yushan Road, 266003, Qingdao, China
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Edie SM, Khouja SC, Collins KS, Crouch NMA, Jablonski D. Evolutionary modularity, integration and disparity in an accretionary skeleton: analysis of venerid Bivalvia. Proc Biol Sci 2022; 289:20211199. [PMID: 35042422 PMCID: PMC8767195 DOI: 10.1098/rspb.2021.1199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Modular evolution, the relatively independent evolution of body parts, may promote high morphological disparity in a clade. Conversely, integrated evolution via stronger covariation of parts may limit disparity. However, integration can also promote high disparity by channelling morphological evolution along lines of least resistance-a process that may be particularly important in the accumulation of disparity in the many invertebrate systems having accretionary growth. We use a time-calibrated phylogenetic hypothesis and high-density, three-dimensional semilandmarking to analyse the relationship between modularity, integration and disparity in the most diverse extant bivalve family: the Veneridae. In general, venerids have a simple, two-module parcellation of their body that is divided into features of the calcium carbonate shell and features of the internal soft anatomy. This division falls more along developmental than functional lines when placed in the context of bivalve anatomy and biomechanics. The venerid body is tightly integrated in absolute terms, but disparity appears to increase with modularity strength among subclades and ecologies. Thus, shifts towards more mosaic evolution beget higher morphological variance in this speciose family.
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Affiliation(s)
- Stewart M. Edie
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Safia C. Khouja
- Department of the Geophysical Sciences, University of Chicago, 5734 South Ellis Ave, Chicago, IL 60637, USA
| | - Katie S. Collins
- Department of Earth Sciences, Invertebrates and Plants Palaeobiology Division, Natural History Museum, London SW7 5BD, UK
| | - Nicholas M. A. Crouch
- Department of the Geophysical Sciences, University of Chicago, 5734 South Ellis Ave, Chicago, IL 60637, USA
| | - David Jablonski
- Department of the Geophysical Sciences, University of Chicago, 5734 South Ellis Ave, Chicago, IL 60637, USA,Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Chetoui I, Baraket G, Tir M, Lekired A, Boussaid M, Cafsi ME, Denis F. Molecular signature of phylogenetic relationships and demographic history of Tunisian Mactra stultorum: Evidence from mitochondrial and nuclear DNA data. ZOOLOGY 2021; 151:125989. [PMID: 35007841 DOI: 10.1016/j.zool.2021.125989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 11/25/2022]
Abstract
The genetic structure of Mactra stultorum is inferred from partial sequence of a mitochondrial cox1gene and of the internal transcribed spacer region ITS1. The samples with two colors of shell (white and brown) were collected from three sites belonging to the Tunisian coasts: Kalaât El Andalous (KA) and Soliman (SM) and Gabes (GM)). The phylogenetic trees obtained from the 2 markers are similar and subdivided samples into 3 distinct clades; clade (1) regrouped GM, clade (2) regrouped KS (KS contains samples from SM and KAa) and clade (3) is formed by KAb. Using the external sequences from genbank, it can be suggested that M. stultorum from the three clades KS, GM and KAb are three subspecies. The two sympatric M. stultorum from KA (KAa and KAb) appear to be genetically isolated showing a high genetic distance and no common haplotypes where the shell color serves for segregating marker. A total of 29 and 18 haplotypes were detected in the examined cox1 and ITS1 regions, respectively. Our study revealed higher levels of genetic diversity for ITS1 compared to cox1. For both markers, significant clinal changes in haplotypes frequencies between the north and the south populations supported by the absence of common haplotypes were observed. The demographic history of M. stultorum populations has been assessed using neutral tests and mismatch distribution for cox1 marker. A unimodal curve of the Mismatch's distribution and negative significant neutral tests suggested a recent sudden demographic expansion for GM.
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Affiliation(s)
- Imene Chetoui
- Laboratoire d'Ecologie, Biologie et Physiologie des Organismes Aquatiques, Département de Biologie, Faculté des Sciences de Tunis El Manar, Université de Tunis El Manar.Farhat Hached Tunis, B.P. n° 94 - ROMMANA 1068, Tunisie.
| | - Ghada Baraket
- Faculté des Sciences de Tunis El Manar, Université de Tunis El Manar. Farhat Hached Tunis, B.P. n° 94 - ROMMANA 1068, Tunisie
| | - Mariem Tir
- Laboratoire d'Ecologie, Biologie et Physiologie des Organismes Aquatiques, Département de Biologie, Faculté des Sciences de Tunis El Manar, Université de Tunis El Manar.Farhat Hached Tunis, B.P. n° 94 - ROMMANA 1068, Tunisie
| | - Abdelmalek Lekired
- Laboratory of Microorganisms and Active Biomolecules, MBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Farhat Hached Tunis, B.P. n° 94 - ROMMANA 1068, Tunisia
| | - Mohamed Boussaid
- Laboratoire de biotechnologie Végétale, Institut National des Sciences Appliquées de Technologie, centre urbain Nord B.PN°676, 1080, Tunis cedex, Tunisie
| | - M'hamed El Cafsi
- Laboratoire d'Ecologie, Biologie et Physiologie des Organismes Aquatiques, Département de Biologie, Faculté des Sciences de Tunis El Manar, Université de Tunis El Manar.Farhat Hached Tunis, B.P. n° 94 - ROMMANA 1068, Tunisie
| | - Francoise Denis
- FRE BOREA, Muséum National d'Histoire Naturelle, Place de la Croix, Concarneau, 29900, France; Laboratoire Mer Molécule Santé, EA 2160, Le Mans Université, avenue O.-Messiaen, 72085, Le Mans Cedex 9, France
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Gwo JC, Kuo TY, Huang YS. Sperm ultrastructure of Ruditapes variegata and Tapes literatus (Mollusca, Bivalvia, Veneridae, Tapetinae) from Pescadores, Taiwan. Tissue Cell 2021; 71:101575. [PMID: 34130071 DOI: 10.1016/j.tice.2021.101575] [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: 09/21/2020] [Revised: 05/23/2021] [Accepted: 06/07/2021] [Indexed: 10/21/2022]
Abstract
In the present study, we have investigated the ultrastructures of the mature gonadal spermatozoa of R. variegata and T. literatus and presented comparisons with the Manila clam, R. philippinarum, sperm ultrastructure examined. Spermatozoa of R. variegata consist of (in anterior to posterior sequence): an elongate conical, deeply invaginated, acrosomal vesicle (length 1.58 ± 0.06 μm; width 0.99 ± 0.07 μm; invagination occupied by a granular subacrosomal material); a barrel-shaped nucleus (length 1.82 ± 0.06 μm; width 1.50 ± 0.03 μm); a midpiece consisting of two orthogonally arranged centrioles, surrounded by four spherical mitochondria; nine satellite fibers connecting the distal centriole to the plasma membrane; and a flagellum originating from the distal centriole. Contents of the acrosomal vesicle of R. variegata are differentiated into a very electron-dense basal ring and a less electron-dense zone (with seven dense transverse layers structure) on the anterior region of the acrosome. Spermatozoa of T. literatus differ from those of R. variegata and are characterized by a rounded-conical invaginated, acrosomal vesicle (length 0.88 ± 0.08 μm; width 0.77 ± 0.06 μm), with a basal ring; and an anteriorly-tapered, barrel-shaped nucleus (length 1.57 ± 0.04 μm; width 1.60 ± 0.09 μm); a midpiece composed of four mitochondria. Centriolar and flagellar details are essential as for R. variegata. Sperm morphology separating R. variegate, R. philippinarum, and T. literatus in different clades. The anterior region of the acrosomal vesicle in R. variegata sperm had the transverse bands structure whereas the apex of the acrosomal vesicle of T. literatus sperm had no such structure. This difference advocated that acrosomal feature could be an important character for taxonomic distinction. Our data supported the previous studies that the ultrastructure of bivalve sperm is species-specific. This advocates that the phyletic relationships of Tapetinae, commonly based on shell morphology, should also add additional and newer approaches.
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Affiliation(s)
- Jin-Chywan Gwo
- Department of Aquaculture, Taiwan National Ocean University, Keelung 20224, Taiwan.
| | - Ting-Yung Kuo
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Hsinhua, Tainan, 71246, Taiwan
| | - Yung-Sen Huang
- Department of Life Science, National University of Kaohsiung, Kaohsiung, Taiwan
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McCartney MA. Structure, function and parallel evolution of the bivalve byssus, with insights from proteomes and the zebra mussel genome. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200155. [PMID: 33813897 DOI: 10.1098/rstb.2020.0155] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The byssus is a structure unique to bivalves. Byssal threads composed of many proteins extend like tendons from muscle cells, ending in adhesive pads that attach underwater. Crucial to settlement and metamorphosis, larvae of virtually all species are byssate. By contrast, in adults, the byssus is scattered throughout bivalves, where it has had profound effects on morphological evolution and been key to adaptive radiations of epifaunal species. I compare byssus structure and proteins in blue mussels (Mytilus), by far the best characterized, to zebra mussels (Dreissena polymorpha), in which several byssal proteins have been isolated and sequenced. By mapping the adult byssus onto a recent phylogenomic tree, I confirm its independent evolution in these and other lineages, likely parallelisms with common origins in development. While the byssus is superficially similar in Dreissena and Mytilus, in finer detail it is not, and byssal proteins are dramatically different. I used the chromosome-scale D. polymorpha genome we recently assembled to search for byssal genes and found 37 byssal loci on 10 of the 16 chromosomes. Most byssal genes are in small families, with several amino acid substitutions between paralogs. Byssal proteins of zebra mussels and related quagga mussels (D. rostriformis) are divergent, suggesting rapid evolution typical of proteins with repetitive low complexity domains. Opportunities abound for proteomic and genomic work to further our understanding of this textbook example of a marine natural material. A priority should be invasive bivalves, given the role of byssal attachment in the spread of, and ecological and economic damage caused by zebra mussels, quagga mussels and others. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Zhong S, Jiang Y, Liu Y, Huang G, Chen X. The first complete mitochondrial genome of Antigona lamellaris (Schumacher, 1817) (Veneroida: Veneridae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1212-1213. [PMID: 33796786 PMCID: PMC7995898 DOI: 10.1080/23802359.2021.1902406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Venus clams (Veneridae) including Antigona lamellaris are commercially important fishery resources by their dominance in local benthic communities. However, despite their great diversity, the phylogenetic and taxonomic relationships in venus clams remain poorly understood. In this study, we report the first complete mitochondrial genome of A. lamellaris. The mitogenome has 17,532 base pairs (67.9% A + T content) and is made up of a total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), plus a putative control region. This study will provide useful molecular resources for clarifying taxonomic and phylogenetic confusion in venus clams.
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Affiliation(s)
- Shengping Zhong
- Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd, Beihai, China.,Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Yan Jiang
- Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd, Beihai, China
| | - Yonghong Liu
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Guoqiang Huang
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
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12
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Wang Y, Yang Y, Liu H, Kong L, Yu H, Liu S, Li Q. Phylogeny of Veneridae (Bivalvia) based on mitochondrial genomes. ZOOL SCR 2020. [DOI: 10.1111/zsc.12454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu Wang
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Yi Yang
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Hongyue Liu
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
- Laboratory for Marine Fisheries Science and Food Production Processes Qingdao National Laboratory for Marine Science and Technology Qingdao China
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Mitogenomic architecture of the multivalent endemic black clam (Villorita cyprinoides) and its phylogenetic implications. Sci Rep 2020; 10:15438. [PMID: 32963308 PMCID: PMC7508841 DOI: 10.1038/s41598-020-72194-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 08/03/2020] [Indexed: 11/24/2022] Open
Abstract
The Indian black clam Villorita cyprinoides (Family: Cyrenidae), an extractive commercially exploited species with aquaculture importance contributing more than 70% of clam fishery in India, is endemic to the Indian peninsula. Currently, there is very sparse information, especially on the molecular data of Villorita. The present study aims to provide a comprehensive knowledge of mitogenome architecture and assess the phylogenetic status of Cyrenidae. This has resulted in reporting the first complete mitogenome of V. cyprinoides using next-generation sequencing technology. The A+T circular mitogenome was 15,880 bp long, exhibiting 13 protein-coding genes (PCGs) including ATP8 (absent in several bivalves), 22 transfer RNA, and two ribosomal RNA genes residing in the heavy strand in a clockwise orientation and a gene order akin to Corbicula fluminea. The molecular phylogeny inferred from a concatenated multi-gene sequence [14 mitochondrial (12 PCGs, rrnS and rrnL) and two nuclear genes (Histone H3, 18S rRNA)] from 47 representative species of superorder Imparidentia, clustered V. cyprinoides and Cyrenid clams to a single clade supporting the monophyly of Cyrenidae. The subsequent mitochondrial gene order analysis substantiates the close relationship of V. cyprinoides and C. fluminea, analogous to phylogenetic output. The multilocus tree topology calibrated with verified fossil data deciphered the origin and diversification of Cyrenid clams during late Triassic-early Jurassic. The data derived from this study shall contribute remarkably for further insights on cryptic species identification, molecular characterization of bivalve mitogenomes and mitochondrial evolutionary history of genus Villorita. Moreover, complete mitogenome can aid in potential marker development for assessing the genetic health of black clam populations.
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Lucentini L, Plazzi F, Sfriso AA, Pizzirani C, Sfriso A, Chiesa S. Additional taxonomic coverage of the doubly uniparental inheritance in bivalves: Evidence of sex‐linked heteroplasmy in the razor clam
Solen marginatus
Pulteney, 1799, but not in the lagoon cockle
Cerastoderma glaucum
(Bruguière, 1789). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Livia Lucentini
- Department of Chemistry, Biology and Biotechnologies University of Perugia Perugia Italy
| | - Federico Plazzi
- Department of Biological, Geological and Environmental Sciences University of Bologna Bologna Italy
| | - Andrea Augusto Sfriso
- Department of Chemical and Pharmaceuticals Sciences University of Ferrara Ferrara Italy
| | - Claudia Pizzirani
- Department of Chemistry, Biology and Biotechnologies University of Perugia Perugia Italy
| | - Adriano Sfriso
- Department of Environmental Sciences, Informatics and Statistics Ca' Foscari University of Venice Venice Italy
| | - Stefania Chiesa
- Department of Molecular Sciences and Nanosystems Ca' Foscari University of Venice Venice Italy
- ISPRA Institute for Environmental Protection and Research Rome Italy
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15
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Zelaya DG, Güller M, Ituarte C. Filling a blank in bivalve taxonomy: an integrative analysis of Cyamioidea (Mollusca: Bivalvia). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Abstract
This contribution provides the first integrative study of Cyamioidea, a group of bivalves largely neglected in the past. By combining information obtained from shell morphology, gross anatomy, histology, reproductive biology and DNA sequencing, the distinctive characters of Cyamioidea are determined, and the taxa belonging to this superfamily are revised. Gaimardioidea, previously considered as a distinct superfamily, is reduced to family level (Gaimardiidae), which, along with Cyamiidae, are assigned to Cyamioidea. All studied cyamioideans share a common reproductive character: the presence of a true follicular epithelium surrounding each developing oocyte, which persists after spawning, surrounding the developing embryos and participating in their anchorage to the gill filaments. Several morphological and anatomical characters support the distinction of Gaimardiidae and Cyamiidae. Based on that information, the placement of Gaimardia and Kidderia in Gaimardiidae, and that of Cyamiocardium, Cyamiomactra, Cyamium, Heteromactra, Pseudokelly, Ptychocardia and Reloncavia in Cyamiidae, is confirmed. Jukesena, historically placed in Veneroidea, is here allocated to Cyamiidae. Neoleptonidae, previously also attributed to Cyamioidea, are reallocated to Veneroidea.
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Affiliation(s)
- Diego G Zelaya
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Biodiversidad y Biología Experimental, Ciudad Universitaria, Piso, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Marina Güller
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Biodiversidad y Biología Experimental, Ciudad Universitaria, Piso, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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16
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Hu Z, Song H, Zhou C, Yu ZL, Yang MJ, Zhang T. Complete mitochondrial genome of the hard clam ( Mercenaria mercenaria). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:3738-3739. [PMID: 33366167 PMCID: PMC7707499 DOI: 10.1080/23802359.2019.1681306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The hard clam (Mercenaria mercenaria) is an important economic and ecological bivalve. In this study, the mitochondrial genome was sequenced. The sequenced genome size was 18,360 bp. The nucleotide composition was asymmetric with a AT bias. Mitogenome contained 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes. Of 13 PCGs, 3 genes (cox3, nad3, and cox2) had incomplete stop codons. Furthermore, phylogenetic analysis using 12 PCGs (except atp8) figured out that M. mercenaria was closely related to genus Dosinia. The complete mitogenome of M. mercenaria provides essential information for further phylogenetic and evolutionary analysis in Veneridae.
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Affiliation(s)
- Zhi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao, Shandong, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hao Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
| | - Cong Zhou
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao, Shandong, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zheng-Lin Yu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
| | - Mei-Jie Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao, Shandong, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Tao Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao, Shandong, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
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17
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Takeuchi S, Honma K, Hirasaka K. Byssus production ability and degree of byssal‐gland development in the infaunal clam
Ruditapes philippinarum. ACTA ZOOL-STOCKHOLM 2019. [DOI: 10.1111/azo.12307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Seiji Takeuchi
- Graduate School of Fisheries and Environmental Sciences Nagasaki University Nagasaki Japan
| | - Kohei Honma
- Faculty of Fisheries Nagasaki University Nagasaki Japan
| | - Katsuya Hirasaka
- Graduate School of Fisheries and Environmental Sciences Nagasaki University Nagasaki Japan
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18
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McElwain A, Warren MB, Pereira FB, Ksepka SP, Bullard SA. Pathobiology and first report of larval nematodes (Ascaridomorpha sp.) infecting freshwater mussels ( Villosa nebulosa, Unionidae), including an inventory of nematode infections in freshwater and marine bivalves. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2019; 10:41-58. [PMID: 31372335 PMCID: PMC6658933 DOI: 10.1016/j.ijppaw.2019.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 11/17/2022]
Abstract
Little information is available on host-parasite relationships between bivalves and larval nematodes. Herein, we describe nematode larvae (likely stage 2) in the infraorder Ascaridomorpha infecting the foot, intestine, and mantle of a freshwater mussel (Alabama rainbow, Villosa nebulosa [Conrad, 1834]) and detail histopathological changes to infected tissues. A total of 43 live mussels from the South Fork of Terrapin Creek, Alabama, were collected between 2010 and 2014, with 14 sectioned for histopathology and 29 dissected. Of the 14 sectioned mussels, 5 appeared to be uninfected, and 7, 1, and 1 had histozoic infections observed in the foot and intestine, intestine only, and mantle edge and foot, respectively. Twenty-three of 29 (79%) of the mussels dissected were infected by live nematodes, and mean nematode abundance was 8.3 (CL = 5.23–13), with 2 mussels infected with >100 nematodes each. Thus, with a total of 32 of the 43 collected mussels observed with nematodes, overall infection prevalence was 74.4% (CL = 0.594–0.855). The 18S rDNA of this nematode was 99% similar to that of several ascaridids (species of Kathlaniidae Lane, 1914 and Quimperiidae Baylis, 1930) that mature in aquatic/semi-aquatic vertebrates; the recovered 18S phylogenetic tree indicated this nematode from V. nebulosa shares a recent common ancestor with Ichthyobronema hamulatum (Ascaridomorpha: Quimperiidae; GenBank Accession Number KY476351). Pathological changes to tissue associated with these infections comprised focal tissue damage, but a cellular response was not evident. The Alabama rainbow possibly represents an intermediate or paratenic host. Given these results, the nematode is likely not pathogenic under normal stream conditions; however, high intensity infections in the foot could inhibit pedal extension and retraction; which would have demonstrable health consequences to a freshwater mussel. Based on our review of the bivalve mollusc parasite literature, a collective biodiversity of 61 nematodes reportedly exhibit some degree of symbiosis (from commensal to parasitic) with 21 bivalves (28 nematode spp. from 17 marine bivalve spp.; 33 nematode spp. from 4 freshwater bivalve spp.); only four records exist of putatively parasitic nematodes from Unionida. The present study represents the first description of a nematode species that invades the tissues of a Unionidae species. Pathological changes comprised focal tissue damage but a cellular response to the parasites was not evident. Nematodes from infected tissues appear to be second stage larvae of Ascaridomorpha. The small subunit rDNA sequence of this nematode was 99% similar to species of Kathlaniidae and Quimperiidae. The nematode is likely not pathogenic under normal stream conditions.
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Affiliation(s)
- Andrew McElwain
- Department of Biological Sciences, College of Liberal Arts and Sciences, State University of New York (SUNY) at Oswego, 30 Centennial Drive, Oswego, NY 13126, USA
| | - Micah B Warren
- Aquatic Parasitology Laboratory, School of Fisheries Aquaculture and Aquatic Sciences, College of Agriculture, Auburn University, 203 Swingle Hall, Auburn, AL, 36849, USA
| | - Felipe B Pereira
- Programa de Pós-Graduação em Biologia Animal, Instituto de Biociências, Universidade Federal de Mato Grossodo Sul, Av. Costa e Silva s/n°, CEP 79070-900, Campo Grande, MS, Brazil
| | - Steven P Ksepka
- Aquatic Parasitology Laboratory, School of Fisheries Aquaculture and Aquatic Sciences, College of Agriculture, Auburn University, 203 Swingle Hall, Auburn, AL, 36849, USA
| | - Stephen A Bullard
- Aquatic Parasitology Laboratory, School of Fisheries Aquaculture and Aquatic Sciences, College of Agriculture, Auburn University, 203 Swingle Hall, Auburn, AL, 36849, USA
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19
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Chacón GM, Arias‐Pérez A, Freire R, Martínez L, Nóvoa S, Naveira H, Insua A. Evidence of doubly uniparental inheritance of the mitochondrial
DNA
in
Polititapes rhomboides
(Bivalvia, Veneridae): Evolutionary and population genetic analysis of F and M mitotypes. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Ginna M. Chacón
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
| | - Alberto Arias‐Pérez
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
| | - Ruth Freire
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
| | - Luisa Martínez
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
| | - Susana Nóvoa
- Centro de Cultivos Marinos de Ribadeo‐CIMAXunta de Galicia Ribadeo (Lugo) Spain
| | - Horacio Naveira
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
| | - Ana Insua
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
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20
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Marín A, Serna J, Robles C, Ramírez B, Reyes-Flores LE, Zelada-Mázmela E, Sotil G, Alfaro R. A glimpse into the genetic diversity of the Peruvian seafood sector: Unveiling species substitution, mislabeling and trade of threatened species. PLoS One 2018; 13:e0206596. [PMID: 30444869 PMCID: PMC6239289 DOI: 10.1371/journal.pone.0206596] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/16/2018] [Indexed: 01/07/2023] Open
Abstract
Peru is one of the world's leading fishing nations and its seafood industry relies on the trade of a vast variety of aquatic resources, playing a key role in the country's socio-economic development. DNA barcoding has become of paramount importance for systematics, conservation, and seafood traceability, complementing or even surpassing conventional identification methods when target organisms show similar morphology during the early life stages, have recently diverged, or have undergone processing. Aiming to increase our knowledge of the species diversity available across the Peruvian supply chain (from fish landing sites to markets and restaurants), we applied full and mini-barcoding approaches targeting three mitochondrial genes (COI, 16S, and 12S) and the control region to identify samples purchased at retailers from six departments along the north-central Peruvian coast. DNA barcodes from 131 samples were assigned to 55 species (plus five genus-level taxa) comprising 47 families, 24 orders, and six classes including Actinopterygii (45.03%), Chondrichthyes (36.64%), Bivalvia (6.87%), Cephalopoda (6.11%), Malacostraca (3.82%), and Gastropoda (1.53%). The identified samples included commercially important pelagic (anchovy, bonito, dolphinfish) and demersal (hake, smooth-hound, Peruvian rock seabass, croaker) fish species. Our results unveiled the marketing of protected and threatened species such as whale shark, Atlantic white marlin, smooth hammerhead (some specimens collected during closed season), shortfin mako, and pelagic thresher sharks. A total of 35 samples (26.72%) were mislabeled, including tilapia labeled as wild marine fish, dolphinfish and hake labeled as grouper, and different shark species sold as "smooth-hounds". The present study highlights the necessity of implementing traceability and monitoring programs along the entire seafood supply chain using molecular tools to enhance sustainability efforts and ensure consumer choice.
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Affiliation(s)
- Alan Marín
- Biodes Laboratorios Soluciones Integrales S.C.R.L., Tumbes, Perú
- * E-mail:
| | - José Serna
- Biodes Laboratorios Soluciones Integrales S.C.R.L., Tumbes, Perú
| | - Christian Robles
- Biodes Laboratorios Soluciones Integrales S.C.R.L., Tumbes, Perú
| | - Beder Ramírez
- Laboratorio Costero de Tumbes, Instituto del Mar del Perú-IMARPE, Tumbes, Perú
| | - Lorenzo E. Reyes-Flores
- Laboratorio de Genética, Fisiología y Reproducción, Facultad de Ciencias, Universidad Nacional del Santa, Chimbote, Perú
| | - Eliana Zelada-Mázmela
- Laboratorio de Genética, Fisiología y Reproducción, Facultad de Ciencias, Universidad Nacional del Santa, Chimbote, Perú
| | - Giovanna Sotil
- Laboratorio de Genética Molecular, Instituto del Mar del Perú-IMARPE, Lima, Perú
| | - Ruben Alfaro
- Laboratorio de Biología Molecular, Facultad de Ciencias de la Salud, Universidad Nacional de Tumbes, Tumbes, Perú
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22
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23
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Liu J, Zhang H. DNA barcoding for species identification in deep-sea clams (Mollusca: Bivalvia: Vesicomyidae). Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:1165-1173. [PMID: 29334293 DOI: 10.1080/24701394.2018.1424843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Deep-sea clams (Bivalvia: Vesicomyidae) have been found in reduced environments over the world oceans, but taxonomy of this group remains confusing at species and supraspecific levels due to their high-morphological similarity and plasticity. In the present study, we collected mitochondrial COI sequences to evaluate the utility of DNA barcoding on identifying vesicomyid species. COI dataset identified 56 well-supported putative species/operational taxonomic units (OTUs), approximately covering half of the extant vesicomyid species. One species (OTU2) was first detected, and may represent a new species. Average distances between species ranged from 1.65 to 29.64%, generally higher than average intraspecific distances (0-1.41%) when excluding Pliocardia sp.10 cf. venusta (average intraspecific distance 1.91%). Local barcoding gap existed in 33 of the 35 species when comparing distances of maximum interspecific and minimum interspecific distances with two exceptions (Abyssogena southwardae and Calyptogena rectimargo-starobogatovi). The barcode index number (BIN) system determined 41 of the 56 species/OTUs, each with a unique BIN, indicating their validity. Three species were found to have two BINs, together with their high level of intraspecific variation, implying cryptic diversity within them. Although fewer 16 S sequences were collected, similar results were obtained. Nineteen putative species were determined and no overlap observed between intra- and inter-specific variation. Implications of DNA barcoding for the Vesicomyidae taxonomy were then discussed. Findings of this study will provide important evidence for taxonomic revision in this problematic clam group, and accelerate the discovery of new vesicomyid species in the future.
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Affiliation(s)
- Jun Liu
- a Institute of Deep-Sea Science and Engineering , Chinese Academy of Sciences , Sanya, China
| | - Haibin Zhang
- a Institute of Deep-Sea Science and Engineering , Chinese Academy of Sciences , Sanya, China
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DNA barcoding as a tool for detecting mislabeling of fishery products imported from third countries: An official survey conducted at the Border Inspection Post of Livorno-Pisa (Italy). Food Control 2017. [DOI: 10.1016/j.foodcont.2017.03.056] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Armani A, Tinacci L, Lorenzetti R, Benvenuti A, Susini F, Gasperetti L, Ricci E, Guarducci M, Guidi A. Is raw better? A multiple DNA barcoding approach (full and mini) based on mitochondrial and nuclear markers reveals low rates of misdescription in sushi products sold on the Italian market. Food Control 2017. [DOI: 10.1016/j.foodcont.2017.03.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Resolving the Taxonomic Status of Chamelea gallina and C. striatula (Veneridae, Bivalvia): A Combined Molecular Cytogenetic and Phylogenetic Approach. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7638790. [PMID: 28555195 PMCID: PMC5438835 DOI: 10.1155/2017/7638790] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/27/2017] [Accepted: 04/03/2017] [Indexed: 12/26/2022]
Abstract
The striped venus clams Chamelea gallina and C. striatula are commercially important bivalves inhabiting European and North African coastal waters. The taxonomic status of these taxa has been the subject of debate for decades. In order to elucidate this issue, we generated 5S and 28S ribosomal RNA and H3 histone gene probes and mapped them by fluorescent in situ hybridization to the chromosomes of morphologically identified striped venus clams, collected from four geographically distant Atlantic and Mediterranean populations. The nucleotide variation at the three DNA markers, that is, the nuclear internal transcribed spacer 2 (ITS2), the mitochondrial cytochrome c oxidase subunit I (COI), and the large ribosomal subunit rRNA (16S) fragments, was also studied and the resultant phylogenetic trees were evaluated. Striking differences in both the chromosome distribution of these genes and the clustering of the samples on the phylogenetic trees observed provide clear evidence that C. gallina and C. striatula are separated species.
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Giusti A, Tinacci L, Sotelo CG, Marchetti M, Guidi A, Zheng W, Armani A. Seafood Identification in Multispecies Products: Assessment of 16SrRNA, cytb, and COI Universal Primers' Efficiency as a Preliminary Analytical Step for Setting up Metabarcoding Next-Generation Sequencing Techniques. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:2902-2912. [PMID: 28290697 DOI: 10.1021/acs.jafc.6b05802] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Few studies applying NGS have been conducted in the food inspection field, particularly on multispecies seafood products. A preliminary study screening the performance and the potential application in NGS analysis of 14 "universal primers" amplifying 16SrRNA, cytb, and COI genes in fish and cephalopods was performed. Species used in surimi preparation were chosen as target. An in silico analysis was conducted to test primers' coverage capacity by assessing mismatches (number and position) with the target sequences. The 9 pairs showing the best coverage capacity were tested in PCR on DNA samples of 53 collected species to assess their amplification performance (amplification rate and amplicon concentration). The results confirm that primers designed for the 16SrRNA gene amplification are the most suitable for NGS analysis also for identification of multispecies seafood products. In particular, the primer pair of Chapela et al. (2002) is the best candidate.
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Affiliation(s)
- Alice Giusti
- FishLab, Department of Veterinary Sciences, University of Pisa , Via delle Piagge 2, 56124 Pisa, Italy
| | - Lara Tinacci
- FishLab, Department of Veterinary Sciences, University of Pisa , Via delle Piagge 2, 56124 Pisa, Italy
| | - Carmen G Sotelo
- Instituto de Investigaciones Marinas (IIM-CSIC) , Eduardo Cabello 6, 36208 Vigo, Spain
| | - Martina Marchetti
- FishLab, Department of Veterinary Sciences, University of Pisa , Via delle Piagge 2, 56124 Pisa, Italy
| | - Alessandra Guidi
- FishLab, Department of Veterinary Sciences, University of Pisa , Via delle Piagge 2, 56124 Pisa, Italy
| | - Wenjie Zheng
- Tianjin Entry-Exit Inspection and Quarantine Bureau of the People's Republic of China , Jingmen Road 158, Free trade Zone, Tianjin Port, 300461 Tianjin, China
| | - Andrea Armani
- FishLab, Department of Veterinary Sciences, University of Pisa , Via delle Piagge 2, 56124 Pisa, Italy
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Next generation sequencing of gonadal transcriptome suggests standard maternal inheritance of mitochondrial DNA in Eurhomalea rufa (Veneridae). Mar Genomics 2017. [DOI: 10.1016/j.margen.2016.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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29
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Combosch DJ, Collins TM, Glover EA, Graf DL, Harper EM, Healy JM, Kawauchi GY, Lemer S, McIntyre E, Strong EE, Taylor JD, Zardus JD, Mikkelsen PM, Giribet G, Bieler R. A family-level Tree of Life for bivalves based on a Sanger-sequencing approach. Mol Phylogenet Evol 2016; 107:191-208. [PMID: 27840226 DOI: 10.1016/j.ympev.2016.11.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 10/28/2016] [Accepted: 11/03/2016] [Indexed: 12/12/2022]
Abstract
The systematics of the molluscan class Bivalvia are explored using a 5-gene Sanger-based approach including the largest taxon sampling to date, encompassing 219 ingroup species spanning 93 (or 82%) of the 113 currently accepted bivalve families. This study was designed to populate the bivalve Tree of Life at the family level and to place many genera into a clear phylogenetic context, but also pointing to several major clades where taxonomic work is sorely needed. Despite not recovering monophyly of Bivalvia or Protobranchia-as in most previous Sanger-based approaches to bivalve phylogeny-our study provides increased resolution in many higher-level clades, and supports the monophyly of Autobranchia, Pteriomorphia, Heteroconchia, Palaeoheterodonta, Heterodonta, Archiheterodonta, Euheterodonta, Anomalodesmata, Imparidentia, and Neoheterodontei, in addition to many other lower clades. However, deep nodes within some of these clades, especially Pteriomorphia and Imparidentia, could not be resolved with confidence. In addition, many families are not supported, and several are supported as non-monophyletic, including Malletiidae, Nuculanidae, Yoldiidae, Malleidae, Pteriidae, Arcidae, Propeamussiidae, Iridinidae, Carditidae, Myochamidae, Lyonsiidae, Pandoridae, Montacutidae, Galeommatidae, Tellinidae, Semelidae, Psammobiidae, Donacidae, Mactridae, and Cyrenidae; Veneridae is paraphyletic with respect to Chamidae, although this result appears to be an artifact. The denser sampling however allowed testing specific placement of species, showing, for example, that the unusual Australian Plebidonax deltoides is not a member of Donacidae and instead nests within Psammobiidae, suggesting that major revision of Tellinoidea may be required. We also showed that Cleidothaerus is sister group to the cementing member of Myochamidae, suggesting that Cleidothaeridae may not be a valid family and that cementation in Cleidothaerus and Myochama may have had a single origin. These results highlight the need for an integrative approach including as many genera as possible, and that the monophyly and relationships of many families require detailed reassessment. NGS approaches may be able to resolve the most recalcitrant nodes in the near future.
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Affiliation(s)
- David J Combosch
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Timothy M Collins
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
| | - Emily A Glover
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Daniel L Graf
- Biology Department, University of Wisconsin-Stevens Point, 800 Reserve Street, Stevens Point, Wisconsin 54481, USA
| | - Elizabeth M Harper
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, UK
| | - John M Healy
- Queensland Museum, PO Box 3300, South Brisbane, Queensland 4101, Australia
| | - Gisele Y Kawauchi
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; Zoology Department, Universidade Federal de Minas Gerais, Brazil
| | - Sarah Lemer
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Erin McIntyre
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Ellen E Strong
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, MRC 163, Washington, DC 20013, USA
| | - John D Taylor
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - John D Zardus
- Department of Biology, The Citadel, 171 Moultrie Street, Charleston, SC 29409, USA
| | - Paula M Mikkelsen
- Integrative Research Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Integrative Research Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA.
| | - Rüdiger Bieler
- Integrative Research Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
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Armani A, Guardone L, La Castellana R, Gianfaldoni D, Guidi A, Castigliego L. DNA barcoding reveals commercial and health issues in ethnic seafood sold on the Italian market. Food Control 2015. [DOI: 10.1016/j.foodcont.2015.02.030] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Armani A, Giusti A, Guardone L, Castigliego L, Gianfaldoni D, Guidi A. Universal Primers Used for Species Identification of Foodstuff of Animal Origin: Effects of Oligonucleotide Tails on PCR Amplification and Sequencing Performance. FOOD ANAL METHOD 2015. [DOI: 10.1007/s12161-015-0301-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Herrera ND, Ter Poorten JJ, Bieler R, Mikkelsen PM, Strong EE, Jablonski D, Steppan SJ. Molecular phylogenetics and historical biogeography amid shifting continents in the cockles and giant clams (Bivalvia: Cardiidae). Mol Phylogenet Evol 2015; 93:94-106. [PMID: 26234273 DOI: 10.1016/j.ympev.2015.07.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 07/02/2015] [Accepted: 07/18/2015] [Indexed: 10/23/2022]
Abstract
Reconstructing historical biogeography of the marine realm is complicated by indistinct barriers and, over deeper time scales, a dynamic landscape shaped by plate tectonics. Here we present the most extensive examination of model-based historical biogeography among marine invertebrates to date. We conducted the largest phylogenetic and molecular clock analyses to date for the bivalve family Cardiidae (cockles and giant clams) with three unlinked loci for 110 species representing 37 of the 50 genera. Ancestral ranges were reconstructed using the dispersal-extinction-cladogenesis (DEC) method with a time-stratified paleogeographic model wherein dispersal rates varied with shifting tectonics. Results were compared to previous classifications and the extensive paleontological record. Six of the eight prior subfamily groupings were found to be para- or polyphyletic. Cardiidae originated and subsequently diversified in the tropical Indo-Pacific starting in the Late Triassic. Eastern Atlantic species were mainly derived from the tropical Indo-Mediterranean region via the Tethys Sea. In contrast, the western Atlantic fauna was derived from Indo-Pacific clades. Our phylogenetic results demonstrated greater concordance with geography than did previous phylogenies based on morphology. Time-stratifying the DEC reconstruction improved the fit and was highly consistent with paleo-ocean currents and paleogeography. Lastly, combining molecular phylogenetics with a rich and well-documented fossil record allowed us to test the accuracy and precision of biogeographic range reconstructions.
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Affiliation(s)
- Nathanael D Herrera
- Department of Biological Science, Florida State University, Tallahassee, FL 32304, United States.
| | - Jan Johan Ter Poorten
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, Netherlands; Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, United States.
| | - Rüdiger Bieler
- Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, United States.
| | - Paula M Mikkelsen
- Paleontological Research Institution, and Department of Earth and Atmospheric Sciences, Cornell University, Ithaca, NY 14850, United States.
| | - Ellen E Strong
- Smithsonian Institution, National Museum of Natural History, Washington, DC 20013, United States.
| | - David Jablonski
- Department of Geophysical Sciences, University of Chicago, Chicago, IL 60637, United States.
| | - Scott J Steppan
- Department of Biological Science, Florida State University, Tallahassee, FL 32304, United States
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García-Souto D, Pérez-García C, Morán P, Pasantes JJ. Divergent evolutionary behavior of H3 histone gene and rDNA clusters in venerid clams. Mol Cytogenet 2015; 8:40. [PMID: 26106449 PMCID: PMC4477615 DOI: 10.1186/s13039-015-0150-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/09/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Histone H3 gene clusters have been described as highly conserved chromosomal markers in invertebrates. Surprisingly, in bivalves remarkable interspecific differences were found among the eight mussels and between the two clams in which histone H3 gene clusters have already been located. Although the family Veneridae comprises 10 % of the species of marine bivalves, their chromosomes are poorly studied. The clams belonging to this family present 2n = 38 chromosomes and similar karyotypes showing chromosome pairs gradually decreasing in length. In order to assess the evolutionary behavior of histone and rRNA multigene families in bivalves, we mapped histone H3 and ribosomal RNA probes to chromosomes of ten species of venerid clams. RESULTS In contrast with the reported conservation of histone H3 gene clusters and their intercalary location in invertebrates, these loci varied in number and were mostly subterminal in venerid clams. On the other hand, while a single 45S rDNA cluster, highly variable in location, was found in these organisms, 5S rDNA clusters showed interspecific differences in both number and location. The distribution patterns of these sequences were species-specific and mapped to different chromosomal positions in all clams but Ruditapes decussatus, in which one of the minor rDNA clusters and the major rDNA cluster co-located. CONCLUSION The diversity in the distribution patterns of histone H3 gene, 5S rDNA and 28S rDNA clusters found in venerid clams, together with their different evolutionary behaviors in other invertebrate taxa, strongly suggest that the control of the spreading of these multigene families in a group of organisms relies upon a combination of evolutionary forces that operate differently depending not only on the specific multigene family but also on the particular taxa. Our data also showed that H3 histone gene and rDNA clusters are useful landmarks to integrate nex-generation sequencing (NGS) and evolutionary genomic data in non-model species.
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Affiliation(s)
- Daniel García-Souto
- Departamento Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain
| | | | - Paloma Morán
- Departamento Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain
| | - Juan J Pasantes
- Departamento Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain
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de Freitas Tallarico L, Orlandi Introíni G, Bonini A, Dias Passos F, Marcondes Machado F, Pintor de Arruda E, Recco-Pimentel SM. Spermatozoan ultrastructure and mitochondrial gene sequence ofCaryocorbula caribaea(d'Orbigny, 1853) (Corbulidae: Bivalvia), a species with plasticity in shell morphology. MOLLUSCAN RESEARCH 2015. [DOI: 10.1080/13235818.2015.1052127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Pfeiffer JM, Graf DL. Evolution of bilaterally asymmetrical larvae in freshwater mussels (Bivalvia: Unionoida: Unionidae). Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12282] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- John M. Pfeiffer
- Department of Biological Sciences; University of Alabama; Tuscaloosa AL 35487 USA
- Florida Museum of Natural History; University of Florida; Gainesville FL 32611 USA
| | - Daniel L. Graf
- Department of Biology; University of Wisconsin-Stevens Point; Stevens Point WI 54481 USA
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Signorelli J, Pastorino G. A New Species ofLaubiericoncha(Bivalvia: Vesicomyidae) from Deep Waters Off Argentina. MALACOLOGIA 2015. [DOI: 10.4002/040.058.0213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Chiesa S, Lucentini L, Freitas R, Nonnis Marzano F, Minello F, Ferrari C, Filonzi L, Figueira E, Breda S, Baccarani G, Argese E. Genetic diversity of introduced Manila clam Ruditapes philippinarum populations inferred by 16S rDNA. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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38
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Yu Z, Li Q, Kong L. New insight into the phylogeny of Sinonovacula (Bivalvia: Solecurtidae) revealed by comprehensive DNA barcoding analyses of two mitochondrial genes. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1554-7. [PMID: 25186335 DOI: 10.3109/19401736.2014.953135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The present study was undertaken to clarify the genetic relationships of Sinonovacula through comprehensive DNA barcoding analyses of COI and 16S rRNA genes. For both genes, the K2P distances between individuals of Sinonovacula and individuals of other genera belonging to Tellinoidea were much bigger than those between Sinonovacula and genera of Solenoidea. On the Bayesian tree of combined data, Sinonovacula and Cultellus formed a well supports monophylic clade. An extremely high matching rate of CAs between Sinonovacula and the reference family Cultellidae was found. Thus, we suggest transferring Sinonovacula from Solecurtidae to Cultellidae, as a sister group of Cultellus.
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Affiliation(s)
- Zhenzhen Yu
- a Key Laboratory of Mariculture , Ministry of Education, Ocean University of China , Qingdao , China
| | - Qi Li
- a Key Laboratory of Mariculture , Ministry of Education, Ocean University of China , Qingdao , China
| | - Lingfeng Kong
- a Key Laboratory of Mariculture , Ministry of Education, Ocean University of China , Qingdao , China
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Bressan M, Chinellato A, Munari M, Matozzo V, Manci A, Marčeta T, Finos L, Moro I, Pastore P, Badocco D, Marin MG. Does seawater acidification affect survival, growth and shell integrity in bivalve juveniles? MARINE ENVIRONMENTAL RESEARCH 2014; 99:136-148. [PMID: 24836120 DOI: 10.1016/j.marenvres.2014.04.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 04/08/2014] [Accepted: 04/18/2014] [Indexed: 06/03/2023]
Abstract
Anthropogenic emissions of carbon dioxide are leading to decreases in pH and changes in the carbonate chemistry of seawater. Ocean acidification may negatively affect the ability of marine organisms to produce calcareous structures while also influencing their physiological responses and growth. The aim of this study was to evaluate the effects of reduced pH on the survival, growth and shell integrity of juveniles of two marine bivalves from the Northern Adriatic sea: the Mediterranean mussel Mytilus galloprovincialis and the striped venus clam Chamelea gallina. An outdoor flow-through plant was set up and two pH levels (natural seawater pH as a control, pH 7.4 as the treatment) were tested in long-term experiments. Mortality was low throughout the first experiment for both mussels and clams, but a significant increase, which was sensibly higher in clams, was observed at the end of the experiment (6 months). Significant decreases in the live weight (-26%) and, surprisingly, in the shell length (-5%) were observed in treated clams, but not in mussels. In the controls of both species, no shell damage was ever recorded; in the treated mussels and clams, damage proceeded via different modes and to different extents. The severity of shell injuries was maximal in the mussels after just 3 months of exposure to a reduced pH, whereas it progressively increased in clams until the end of the experiment. In shells of both species, the damaged area increased throughout the experiment, peaking at 35% in mussels and 11% in clams. The shell thickness of the treated and control animals significantly decreased after 3 months in clams and after 6 months in mussels. In the second experiment (3 months), only juvenile mussels were exposed to a reduced pH. After 3 months, the mussels at a natural pH level or pH 7.4 did not differ in their survival, shell length or live weight. Conversely, shell damage was clearly visible in the treated mussels from the 1st month onward. Monitoring the chemistry of seawater carbonates always showed aragonite undersaturation at 7.4 pH, whereas calcite undersaturation occurred in only 37% of the measurements. The present study highlighted the contrasting effects of acidification in two bivalve species living in the same region, although not exactly in the same habitat.
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Affiliation(s)
- M Bressan
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy.
| | - A Chinellato
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - M Munari
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - V Matozzo
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - A Manci
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - T Marčeta
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - L Finos
- Department of Statistical Sciences, University of Padova, Via C. Battisti 241, 35121 Padova, Italy
| | - I Moro
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - P Pastore
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - D Badocco
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - M G Marin
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
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Golding RE, Bieler R, Rawlings TA, Collins TM. DeconstructingDendropoma: A Systematic Revision of a World-Wide Worm-Snail Group, with Descriptions of New Genera (Caenogastropoda: Vermetidae). MALACOLOGIA 2014. [DOI: 10.4002/040.057.0103] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Evolutionary dynamics of rDNA clusters in chromosomes of five clam species belonging to the family Veneridae (Mollusca, Bivalvia). BIOMED RESEARCH INTERNATIONAL 2014; 2014:754012. [PMID: 24967400 PMCID: PMC4054880 DOI: 10.1155/2014/754012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 04/23/2014] [Accepted: 04/25/2014] [Indexed: 11/26/2022]
Abstract
The chromosomal changes accompanying bivalve evolution are an area about which few reports have been published. To improve our understanding on chromosome evolution in Veneridae, ribosomal RNA gene clusters were mapped by fluorescent in situ hybridization (FISH) to chromosomes of five species of venerid clams (Venerupis corrugata, Ruditapes philippinarum, Ruditapes decussatus, Dosinia exoleta, and Venus verrucosa). The results were anchored to the most comprehensive molecular phylogenetic tree currently available for Veneridae. While a single major rDNA cluster was found in each of the five species, the number of 5S rDNA clusters showed high interspecies variation. Major rDNA was either subterminal to the short arms or intercalary to the long arms of metacentric or submetacentric chromosomes, whereas minor rDNA signals showed higher variability. Major and minor rDNAs map to different chromosome pairs in all species, but in R. decussatus one of the minor rDNA gene clusters and the major rDNA cluster were located in the same position on a single chromosome pair. This interspersion of both sequences was confirmed by fiber FISH. Telomeric signals appeared at both ends of every chromosome in all species. FISH mapping data are discussed in relation to the molecular phylogenetic trees currently available for Veneridae.
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42
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Zhang H, Geller JB, Vrijenhoek RC. Genetic diversity in native and introduced populations of the amethyst gem clam Gemma gemma (Totten, 1834) from the U.S. east and west coasts. Biol Invasions 2014. [DOI: 10.1007/s10530-014-0699-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Habitat preferences and growth of Ruditapes bruguieri (Bivalvia: Veneridae) at the northern boundary of its range. ScientificWorldJournal 2014; 2014:235416. [PMID: 24526886 PMCID: PMC3914519 DOI: 10.1155/2014/235416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 10/27/2013] [Indexed: 11/17/2022] Open
Abstract
This work is the first attempt to study growth and some morphological parameters of the clam Ruditapes bruguieri, as well as its habitat preferences. It is found that R. bruguieri lives on bottom sediments including pebble and coarse- and medium-grained sand with a slight admixture of silt. At the study area, this bivalve inhabits sea waters with good aeration, stable oceanic water salinity, and a high oxygen concentration. The annual fluctuations of the water temperature from 13-14°C (in winter) to 22–29°C (in summer) are close to the threshold temperature values, within which the species can exist. Near the boundary of the species range, along the Jeju Island coasts, south of Republic of Korea, 83.8% of all clams die during the coldest period of the year. Here, annual rings are formed on R. bruguieri shells during winter. The maximum age of R. bruguieri, determined during the study, is 6.5 years, but the clam samples contain mainly individuals at 3.0–3.5 years of age (34%). The largest clam dimensions are 36.0 × 26.5 mm (length × height of shell). At the study area, a usual shell length is 20.0–32.0 mm (75% of all the collected individuals).
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Bieler R, Mikkelsen PM, Collins TM, Glover EA, González VL, Graf DL, Harper EM, Healy J, Kawauchi GY, Sharma PP, Staubach S, Strong EE, Taylor JD, Tëmkin I, Zardus JD, Clark S, Guzmán A, McIntyre E, Sharp P, Giribet G. Investigating the Bivalve Tree of Life – an exemplar-based approach combining molecular and novel morphological characters. INVERTEBR SYST 2014. [DOI: 10.1071/is13010] [Citation(s) in RCA: 165] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
To re-evaluate the relationships of the major bivalve lineages, we amassed detailed morpho-anatomical, ultrastructural and molecular sequence data for a targeted selection of exemplar bivalves spanning the phylogenetic diversity of the class. We included molecular data for 103 bivalve species (up to five markers) and also analysed a subset of taxa with four additional nuclear protein-encoding genes. Novel as well as historically employed morphological characters were explored, and we systematically disassembled widely used descriptors such as gill and stomach ‘types’. Phylogenetic analyses, conducted using parsimony direct optimisation and probabilistic methods on static alignments (maximum likelihood and Bayesian inference) of the molecular data, both alone and in combination with morphological characters, offer a robust test of bivalve relationships. A calibrated phylogeny also provided insights into the tempo of bivalve evolution. Finally, an analysis of the informativeness of morphological characters showed that sperm ultrastructure characters are among the best morphological features to diagnose bivalve clades, followed by characters of the shell, including its microstructure. Our study found support for monophyly of most broadly recognised higher bivalve taxa, although support was not uniform for Protobranchia. However, monophyly of the bivalves with protobranchiate gills was the best-supported hypothesis with incremental morphological and/or molecular sequence data. Autobranchia, Pteriomorphia, Heteroconchia, Palaeoheterodonta, Archiheterodonta, Euheterodonta, Anomalodesmata and Imparidentia new clade ( = Euheterodonta excluding Anomalodesmata) were recovered across analyses, irrespective of data treatment or analytical framework. Another clade supported by our analyses but not formally recognised in the literature includes Palaeoheterodonta and Archiheterodonta, which emerged under multiple analytical conditions. The origin and diversification of each of these major clades is Cambrian or Ordovician, except for Archiheterodonta, which diverged from Palaeoheterodonta during the Cambrian, but diversified during the Mesozoic. Although the radiation of some lineages was shifted towards the Palaeozoic (Pteriomorphia, Anomalodesmata), or presented a gap between origin and diversification (Archiheterodonta, Unionida), Imparidentia showed steady diversification through the Palaeozoic and Mesozoic. Finally, a classification system with six major monophyletic lineages is proposed to comprise modern Bivalvia: Protobranchia, Pteriomorphia, Palaeoheterodonta, Archiheterodonta, Anomalodesmata and Imparidentia.
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Into the deep: a phylogenetic approach to the bivalve subclass Protobranchia. Mol Phylogenet Evol 2013; 69:188-204. [PMID: 23742885 DOI: 10.1016/j.ympev.2013.05.018] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 05/14/2013] [Accepted: 05/21/2013] [Indexed: 01/19/2023]
Abstract
A molecular phylogeny of Protobranchia, the subclass of bivalve mollusks sister to the remaining Bivalvia, has long proven elusive, because many constituent lineages are deep-sea endemics, which creates methodological challenges for collecting and preserving genetic material. We obtained 74 representatives of all 12 extant protobranch families and investigated the internal phylogeny of this group using sequence data from five molecular loci (16S rRNA, 18S rRNA, 28S rRNA, cytochrome c oxidase subunit I, and histone H3). Model-based and dynamic homology parsimony approaches to phylogenetic reconstruction unanimously supported four major clades of Protobranchia, irrespective of treatment of hypervariable regions in the nuclear ribosomal genes 18S rRNA and 28S rRNA. These four clades correspond to the superfamilies Nuculoidea (excluding Sareptidae), Nuculanoidea (including Sareptidae), Solemyoidea, and Manzanelloidea. Salient aspects of the phylogeny include (1) support for the placement of the family Sareptidae with Nuculanoidea; (2) the non-monophyly of the order Solemyida (Solemyidae+Nucinellidae); (3) and the non-monophyly of most nuculoid and nuculanoid genera and families. In light of this first family-level phylogeny of Protobranchia, we present a revised classification of the group. Estimation of divergence times in concert with analyses of diversification rates demonstrate the signature of the end-Permian mass extinction in the phylogeny of extant protobranchs.
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Corse E, Rampal J, Cuoc C, Pech N, Perez Y, Gilles A. Phylogenetic analysis of Thecosomata Blainville, 1824 (holoplanktonic opisthobranchia) using morphological and molecular data. PLoS One 2013; 8:e59439. [PMID: 23593138 PMCID: PMC3625178 DOI: 10.1371/journal.pone.0059439] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 02/14/2013] [Indexed: 11/18/2022] Open
Abstract
Thecosomata is a marine zooplankton group, which played an important role in the carbonate cycle in oceans due to their shell composition. So far, there is important discrepancy between the previous morphological-based taxonomies, and subsequently the evolutionary history of Thecosomata. In this study, the remarkable planktonic sampling of TARA Oceans expedition associated with a set of various other missions allowed us to assess the phylogenetic relationships of Thecosomata using morphological and molecular data (28 S and COI genes). The two gene trees showed incongruities (e.g. Hyalocylis, Cavolinia), and high congruence between morphological and 28S trees (e.g. monophyly of Euthecosomata). The monophyly of straight shell species led us to reviving the Orthoconcha, and the split of Limacinidae led us to the revival of Embolus inflata replacing Limacina inflata. The results also jeopardized the Euthecosomata families that are based on plesiomorphic character state as in the case for Creseidae which was not a monophyletic group. Divergence times were also estimated, and suggested that the evolutionary history of Thecosomata was characterized by four major diversifying events. By bringing the knowledge of palaeontology, we propose a new evolutionary scenario for which macro-evolution implying morphological innovations were rhythmed by climatic changes and associated species turn-over that spread from the Eocene to Miocene, and were shaped principally by predation and shell buoyancy.
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Affiliation(s)
- Emmanuel Corse
- IMBE (UMR CNRS 7263, IRD 237) Evolution Génome Environnement, Aix-Marseille Université, Marseille, France.
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Kitada S, Fujikake C, Asakura Y, Yuki H, Nakajima K, Vargas KM, Kawashima S, Hamasaki K, Kishino H. Molecular and morphological evidence of hybridization between native Ruditapes philippinarum and the introduced Ruditapes form in Japan. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0467-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Abstract
Marine aquaculture and stock enhancement are major causes of the introduction of alien species. A good example of such an introduction is the Japanese shortneck clam Ruditapes philippinarum, one of the most important fishery resources in the world. To meet the domestic shortage of R. philippinarum caused by depleted catches, clams were imported to Japan from China and the Korean peninsula. The imported clam is an alien species that has a very similar morphology, and was misidentified as R. philippinarum (hereafter, Ruditapes form). We genotyped 1,186 clams of R. philippinarum and R. form at four microsatellite loci, sequenced mitochondrial DNA (COI gene fragment) of 485 clams, 34 of which were R. variegatus, and measured morphometric and meristic characters of 754 clams from 12 populations in Japan and China, including the Ariake Sea and Tokyo Bay, where large numbers of R. form were released. Our analyses confirmed that R. form was from the genus Ruditapes, and the genetic differentiation between R. philippinarum and R. form was distinct, but small, compared with five bivalve outgroups. However, R. form had distinct shell morphology, especially larger numbers of radial ribs on the shell surface, suggesting that R. form might be a new Ruditapes species or a variation of R. philippinarum that originated from southern China. A genetic affinity of the sample from the Ariake Sea to R. form was found with the intermediate shell morphology and number of radial ribs, and the hybrid proportion was estimated at 51.3 ± 4.6 % in the Ariake Sea.
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Marshall BA, Spencer HG. Comments on some taxonomic changes affecting marine Bivalvia of the New Zealand region recently introduced in Huber'sCompendium of bivalves, with some additional taxonomic changes. MOLLUSCAN RESEARCH 2013. [DOI: 10.1080/13235818.2012.754147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Salvi D, Mariottini P. Molecular phylogenetics in 2D: ITS2 rRNA evolution and sequence-structure barcode from Veneridae to Bivalvia. Mol Phylogenet Evol 2012; 65:792-8. [DOI: 10.1016/j.ympev.2012.07.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 07/11/2012] [Accepted: 07/19/2012] [Indexed: 11/30/2022]
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Phylogenetic analysis of four nuclear protein-encoding genes largely corroborates the traditional classification of Bivalvia (Mollusca). Mol Phylogenet Evol 2012; 65:64-74. [PMID: 22659514 DOI: 10.1016/j.ympev.2012.05.025] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 05/16/2012] [Accepted: 05/22/2012] [Indexed: 11/21/2022]
Abstract
Revived interest in molluscan phylogeny has resulted in a torrent of molecular sequence data from phylogenetic, mitogenomic, and phylogenomic studies. Despite recent progress, basal relationships of the class Bivalvia remain contentious, owing to conflicting morphological and molecular hypotheses. Marked incongruity of phylogenetic signal in datasets heavily represented by nuclear ribosomal genes versus mitochondrial genes has also impeded consensus on the type of molecular data best suited for investigating bivalve relationships. To arbitrate conflicting phylogenetic hypotheses, we evaluated the utility of four nuclear protein-encoding genes-ATP synthase β, elongation factor-1α, myosin heavy chain type II, and RNA polymerase II-for resolving the basal relationships of Bivalvia. We sampled all five major lineages of bivalves (Archiheterodonta, Euheterodonta [including Anomalodesmata], Palaeoheterodonta, Protobranchia, and Pteriomorphia) and inferred relationships using maximum likelihood and Bayesian approaches. To investigate the robustness of the phylogenetic signal embedded in the data, we implemented additional datasets wherein length variability and/or third codon positions were eliminated. Results obtained include (a) the clade (Nuculanida+Opponobranchia), i.e., the traditionally defined Protobranchia; (b) the monophyly of Pteriomorphia; (c) the clade (Archiheterodonta+Palaeoheterodonta); (d) the monophyly of the traditionally defined Euheterodonta (including Anomalodesmata); and (e) the monophyly of Heteroconchia, i.e., (Palaeoheterodonta+Archiheterodonta+Euheterodonta). The stability of the basal tree topology to dataset manipulation is indicative of signal robustness in these four genes. The inferred tree topology corresponds closely to those obtained by datasets dominated by nuclear ribosomal genes (18S rRNA and 28S rRNA), controverting recent taxonomic actions based solely upon mitochondrial gene phylogenies.
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