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Garcia-Souto D, Bruzos AL, Diaz S, Rocha S, Pequeño-Valtierra A, Roman-Lewis CF, Alonso J, Rodriguez R, Costas D, Rodriguez-Castro J, Villanueva A, Silva L, Valencia JM, Annona G, Tarallo A, Ricardo F, Bratoš Cetinić A, Posada D, Pasantes JJ, Tubio JMC. Mitochondrial genome sequencing of marine leukaemias reveals cancer contagion between clam species in the Seas of Southern Europe. eLife 2022; 11:e66946. [PMID: 35040778 PMCID: PMC8765752 DOI: 10.7554/elife.66946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 12/04/2021] [Indexed: 12/30/2022] Open
Abstract
Clonally transmissible cancers are tumour lineages that are transmitted between individuals via the transfer of living cancer cells. In marine bivalves, leukaemia-like transmissible cancers, called hemic neoplasia (HN), have demonstrated the ability to infect individuals from different species. We performed whole-genome sequencing in eight warty venus clams that were diagnosed with HN, from two sampling points located more than 1000 nautical miles away in the Atlantic Ocean and the Mediterranean Sea Coasts of Spain. Mitochondrial genome sequencing analysis from neoplastic animals revealed the coexistence of haplotypes from two different clam species. Phylogenies estimated from mitochondrial and nuclear markers confirmed this leukaemia originated in striped venus clams and later transmitted to clams of the species warty venus, in which it survives as a contagious cancer. The analysis of mitochondrial and nuclear gene sequences supports all studied tumours belong to a single neoplastic lineage that spreads in the Seas of Southern Europe.
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Affiliation(s)
- Daniel Garcia-Souto
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de CompostelaSantiago de CompostelaSpain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de CompostelaSantiago de CompostelaSpain
- Cancer Ageing and Somatic Mutation Programme, Wellcome Sanger InstituteCambridgeUnited Kingdom
| | - Alicia L Bruzos
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de CompostelaSantiago de CompostelaSpain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de CompostelaSantiago de CompostelaSpain
| | - Seila Diaz
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de CompostelaSantiago de CompostelaSpain
| | - Sara Rocha
- Phylogenomics Lab, Universidade de VigoVigoSpain
| | - Ana Pequeño-Valtierra
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de CompostelaSantiago de CompostelaSpain
| | | | - Juana Alonso
- CINBIO, Universidade de VigoVigoSpain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGOVigoSpain
| | - Rosana Rodriguez
- Centro de Investigación Mariña, Universidade de Vigo, ECIMATVigoSpain
| | - Damian Costas
- Centro de Investigación Mariña, Universidade de Vigo, ECIMATVigoSpain
| | - Jorge Rodriguez-Castro
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de CompostelaSantiago de CompostelaSpain
| | | | - Luis Silva
- Instituto Español de Oceanografía (IEO), Centro Oceanográfico de CádizCádizSpain
| | - Jose Maria Valencia
- Laboratori d’Investigacions Marines i Aqüicultura, (LIMIA) - Govern de les Illes BalearsPort d'Andratx, Balearic IslandsSpain
- Instituto de Investigaciones Agroambientales y de Economía del Agua (INAGEA) (INIA-CAIB-UIB)Palma de Mallorca, Balearic IslandsSpain
| | | | | | - Fernando Ricardo
- ECOMARE, Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Santiago University CampusAveiroPortugal
| | | | - David Posada
- CINBIO, Universidade de VigoVigoSpain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGOVigoSpain
- Department of Biochemistry, Genetics and Immunology, Universidade de VigoVigoSpain
| | - Juan Jose Pasantes
- Department of Biochemistry, Genetics and Immunology, Universidade de VigoVigoSpain
- Centro de Investigación Mariña, Universidade de VigoVigoSpain
| | - Jose MC Tubio
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de CompostelaSantiago de CompostelaSpain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de CompostelaSantiago de CompostelaSpain
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2
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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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3
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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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4
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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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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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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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7
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Xu X, Wu X, Yu Z. Comparative studies of the complete mitochondrial genomes of four Paphia clams and reconsideration of subgenus Neotapes (Bivalvia: Veneridae). Gene 2012; 494:17-23. [DOI: 10.1016/j.gene.2011.12.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Revised: 11/09/2011] [Accepted: 12/02/2011] [Indexed: 10/14/2022]
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8
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Marie B, Trinkler N, Zanella-Cleon I, Guichard N, Becchi M, Paillard C, Marin F. Proteomic identification of novel proteins from the calcifying shell matrix of the Manila clam Venerupis philippinarum. MARINE BIOTECHNOLOGY 2011; 13:955-62. [PMID: 21221694 DOI: 10.1007/s10126-010-9357-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 12/21/2010] [Indexed: 02/05/2023]
Abstract
The shell of the Manila clam Venerupis philippinarum is composed of more than 99% calcium carbonate and of a small amount of organic matrix (around 0.2%). In this study, we developed one of the first proteomic approaches applied to mollusc shell in order to characterise the matrix proteins that are believed to be essential for the formation of the biomineral. The insoluble organic matrix, purified after demineralisation of the shell powder with cold acetic acid (5%), was digested with trypsin enzyme and then separated on nano-LC prior to nanospray/quadrupole time-of-flight analysis. MS/MS spectra were searched against the above 11,000 EST sequences available on the NCBI public database for Venerupis. Using this approach, we were able to identify partial or full-length sequence transcripts that encode for shell matrix proteins. These include three novel shell proteins whose sequences do not present any homologous proteins or already described domains, two putative protease inhibitor proteins containing Kazal-type domains, and a putative Ca(2+)-binding protein containing two EF-hand domains. Biomineral formation and evolutionary implications are discussed.
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Affiliation(s)
- Benjamin Marie
- UMR 5561 CNRS Biogéosciences, Université de Bourgogne, 6 Bd. Gabriel, Dijon, 21000, France.
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9
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Cytogenetic characterization and mapping of rDNAs, core histone genes and telomeric sequences in Venerupis aurea and Tapes rhomboides (Bivalvia: Veneridae). Genetica 2011; 139:823-31. [PMID: 21670988 DOI: 10.1007/s10709-011-9587-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 05/31/2011] [Indexed: 10/18/2022]
Abstract
We describe the chromosomal location of GC-rich regions, 28S and 5S rDNA, core histone genes, and telomeric sequences in the veneroid bivalve species Venerupis aurea and Tapes (Venerupis) rhomboides, using fluorochrome staining with propidium iodide, DAPI and chromomycin A3 (CMA) and fluorescent in situ hybridization (FISH). DAPI dull/CMA bright bands were coincident with the chromosomal location of 28S rDNA in both species. The major rDNA was interstitially clustered at a single locus on the short arms of the metacentric chromosome pair 5 in V. aurea, whereas in T. rhomboides it was subtelomerically clustered on the long arms of the subtelocentric chromosome pair 17. 5S rDNA also was a single subtelomeric cluster on the long arms of subtelocentric pair 17 in V. aurea and on the short arms of the metacentric pair 9 in T. rhomboides. Furthermore, V. aurea showed four telomeric histone gene clusters on three metacentric pairs, at both ends of chromosome 2 and on the long arms of chromosomes 3 and 8, whereas histone genes in T. rhomboides clustered interstitially on the long arms of the metacentric pair 5 and proximally on the long arms of the subtelocentric pair 12. Double and triple FISH experiments demonstrated that rDNA and H3 histone genes localized on different chromosome pairs in the two clam species. Telomeric signals were found at both ends of every single chromosome in both species. Chromosomal location of these three gene families in two species of Veneridae provides a clue to karyotype evolution in this commercially important bivalve family.
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10
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Chen J, Li Q, Kong L, Zheng X. Molecular phylogeny of venus clams (Mollusca, Bivalvia, Veneridae) with emphasis on the systematic position of taxa along the coast of mainland China. ZOOL SCR 2011. [DOI: 10.1111/j.1463-6409.2011.00471.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Genetic variation and population structure of the carpet shell clam Ruditapes decussatus along the Tunisian coast inferred from mtDNA and ITS1 sequence analysis. Biologia (Bratisl) 2010. [DOI: 10.2478/s11756-010-0069-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Ren J, Shen X, Sun M, Jiang F, Yu Y, Chi Z, Liu B. The complete mitochondrial genome of the clamMeretrix petechialis(Mollusca: Bivalvia: Veneridae). ACTA ACUST UNITED AC 2009; 20:78-87. [DOI: 10.1080/19401730902964425] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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13
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Canapa A, Barucca M, Marinelli A, Olmo E. A molecular approach to the systematics of the Antarctic scallopAdamussium colbecki. ACTA ACUST UNITED AC 2009. [DOI: 10.1080/11250009909356281] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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14
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Genetic structure of the endangered species Pinna nobilis (Mollusca: Bivalvia) inferred from mtDNA sequences. Biologia (Bratisl) 2008. [DOI: 10.2478/s11756-008-0061-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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. ABAM, . MAA, . PI, . BM. Molecular Data from the Cytochrome b for the Phylogeny of Channidae (Channa sp.) in Malaysia. ACTA ACUST UNITED AC 2006. [DOI: 10.3923/biotech.2007.22.27] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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16
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MIKKELSEN PAULAM, BIELER RÜDIGER, KAPPNER ISABELLA, RAWLINGS TIMOTHYA. Phylogeny of Veneroidea (Mollusca: Bivalvia) based on morphology and molecules. Zool J Linn Soc 2006. [DOI: 10.1111/j.1096-3642.2006.00262.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Kappner I, Bieler R. Phylogeny of venus clams (Bivalvia: Venerinae) as inferred from nuclear and mitochondrial gene sequences. Mol Phylogenet Evol 2006; 40:317-31. [PMID: 16621616 DOI: 10.1016/j.ympev.2006.02.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Revised: 01/29/2006] [Accepted: 02/09/2006] [Indexed: 11/23/2022]
Abstract
Venerinae (Heterodonta: Veneridae) is a diverse, commercially important, and cosmopolitan marine bivalve subfamily. Recent workers synonymized it with the subfamily Chioninae, due to their overall morphological similarity. The use of traditional shell-based characters alone, however, is questionable for resolving phylogenetic relationships of this group. A phylogenetic study was carried out, based on nucleotide sequences of the mitochondrial large ribosomal subunit (16S), cytochrome oxidase subunit I (COI), and the nuclear protein-coding gene histone 3, to investigate the relationships and circumscription of Venerinae and the phylogenetic pattern of characters in this group. This study consists of a total of 55 taxa: 13 venerine genera, 24 chionine taxa, and 18 taxa of other venerid subfamilies. We analyzed the alignments using a Bayesian approach using Markov Chain Monte Carlo tree sampling and maximum parsimony methods. The resulting phylogenetic hypothesis suggests that Chioninae and Venerinae are actually discrete taxa, but that the circumscription suffered from misplacement of some genera. Our analysis showed that the former chionine genera Chamelea and Clausinella should be placed in Venerinae, as sister taxa to Venus. We re-analyzed morphological and anatomical features in light of the molecular data to describe monophyletic entities. Features of the hinge and internal shell as well as the degree of siphonal fusion are identified as characters to morphologically distinguish the two subfamilies. Of the three genes used in this study, only COI (commonly used as "barcoding" gene) posed substantial problems in obtaining sequence data from older museum material.
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Affiliation(s)
- Isabella Kappner
- Department of Zoology (Invertebrates), Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA.
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18
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Denadai MR, Arruda EP, Domaneschi O, Amaral ACZ. Veneridae (Mollusca, Bivalvia) da costa norte do Estado de São Paulo, Brasil. BIOTA NEOTROPICA 2006. [DOI: 10.1590/s1676-06032006000300011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Coletas intensivas da fauna bentônica marinha da costa norte do Estado de São Paulo, realizadas pelos programas de pesquisa "Fauna de Praia/UNICAMP" de agosto de 1995 a julho de 1997 e "Biota/FAPESP" de março de 2001 a dezembro de 2002 recolheram 2769 exemplares pertencentes a dezesseis espécies, doze gêneros e sete subfamílias. A caracterização de cada espécie foi ampliada com redescrição e ilustrações detalhadas, baseadas nos caracteres da concha. Tabelas comparativas dessas características e uma chave dicotômica de identificação das subfamílias são apresentadas neste estudo.
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19
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Jensen A, Humphreys J, Caldow R, Cesar C. 13. The Manila Clam in Poole Harbour. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s1568-2692(05)80018-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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20
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Barucca M, Olmo E, Schiaparelli S, Canapa A. Molecular phylogeny of the family Pectinidae (Mollusca: Bivalvia) based on mitochondrial 16S and 12S rRNA genes. Mol Phylogenet Evol 2004; 31:89-95. [PMID: 15019610 DOI: 10.1016/j.ympev.2003.07.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2003] [Revised: 07/16/2003] [Indexed: 11/19/2022]
Abstract
Pectinidae is a large bivalve family characterised by almost circular, flat shells. Species are distributed worldwide and fall into three life-styles: swimming, byssally attached to hard substrates, and cemented to rocks with one valve. Despite these very different life strategies, pectinid shells are highly conservative in shape and offer few clues for the unravelling of phylogenetic issues. Consequently, phylogenetic studies based on morphological features have not yielded conclusive results. We thus set out to analyse partial sequences of mitochondrial 12S and 16S rRNA genes from 23 species of 16 genera with molecular techniques. The results are largely in contrast, both at the genus and the subfamily level, with the systematic classifications based on adult morphological characters, whereas they agree with the morphological classifications based on the more conserved non-adaptive features.
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Affiliation(s)
- Marco Barucca
- Istituto di Biologia e Genetica, Facoltà di Scienze, Università Politecnica delle Marche, via Brecce Bianche, I-60131 Ancona, Italy
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21
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Shearer TL, Van Oppen MJH, Romano SL, Wörheide G. Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol Ecol 2002; 11:2475-87. [PMID: 12453233 DOI: 10.1046/j.1365-294x.2002.01652.x] [Citation(s) in RCA: 425] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mitochondrial genes have been used extensively in population genetic and phylogeographical analyses, in part due to a high rate of nucleotide substitution in animal mitochondrial DNA (mtDNA). Nucleotide sequences of anthozoan mitochondrial genes, however, are virtually invariant among conspecifics, even at third codon positions of protein-coding sequences. Hence, mtDNA markers are of limited use for population-level studies in these organisms. Mitochondrial gene sequence divergence among anthozoan species is also low relative to that exhibited in other animals, although higher level relationships can be resolved with these markers. Substitution rates in anthozoan nuclear genes are much higher than in mitochondrial genes, whereas nuclear genes in other metazoans usually evolve more slowly than, or similar to, mitochondrial genes. Although several mechanisms accounting for a slow rate of sequence evolution have been proposed, there is not yet a definitive explanation for this observation. Slow evolution and unique characteristics may be common in primitive metazoans, suggesting that patterns of mtDNA evolution in these organisms differ from that in other animal systems.
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Affiliation(s)
- T L Shearer
- Department of Biological Sciences, 109 Cooke Hall, University at Buffalo, Buffalo, NY 14260, USA.
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22
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Pfenninger M, Reinhardt F, Streit B. Evidence for cryptic hybridization between different evolutionary lineages of the invasive clam genus
Corbicula
(Veneroida, Bivalvia). J Evol Biol 2002. [DOI: 10.1046/j.1420-9101.2002.00440.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- M. Pfenninger
- Abteilung Ökologie & Evolution, J.W. Goethe‐Universität, Frankfurt, Germany
| | - F. Reinhardt
- Abteilung Ökologie & Evolution, J.W. Goethe‐Universität, Frankfurt, Germany
| | - B. Streit
- Abteilung Ökologie & Evolution, J.W. Goethe‐Universität, Frankfurt, Germany
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Fernandez A, García T, Gonzalez I, Asensio L, Rodriguez MA, Hernández PE, Martin R. Polymerase chain reaction-restriction fragment length polymorphism analysis of a 16S rRNA gene fragment for authentication of four clam species. J Food Prot 2002; 65:692-5. [PMID: 11952222 DOI: 10.4315/0362-028x-65.4.692] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Specific identification of four clam species, Ruditapes decussatus (grooved carpet shell), Venerupis pullastra (pullet carpet shell), Ruditapes philippinarum (Japanese carpet shell), and Venerupis rhomboides (yellow carpet shell), was achieved by polymerase chain reaction-restriction fragment length polymorphism analysis of a fragment of the mitochondrial 16S rRNA gene. Amplification of DNA isolated from the foot muscle produced fragments of 511 bp for V. pullastra, 523 bp for R. decussatus, 545 bp for R. philippinarum, and 502 bp for V. rhomboides. The restriction profiles obtained by agarose gel electrophoresis when amplicons were digested with endonucleases BsmAI and BsrI allowed unequivocal identification of the four clam species. This approach would be less costly, simpler, and quicker than conventional sequencing of polymerase chain reaction products followed by detailed comparison of individual sequences, especially when large numbers of samples need to be analyzed.
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Affiliation(s)
- Alicia Fernandez
- Departamento de Nutrición y Bromatología III, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
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Stepien CA, Hubers AN, Skidmore JL. Diagnostic genetic markers and evolutionary relationships among invasive dreissenoid and corbiculoid bivalves in North America: phylogenetic signal from mitochondrial 16S rDNA. Mol Phylogenet Evol 1999; 13:31-49. [PMID: 10508537 DOI: 10.1006/mpev.1999.0666] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Diagnostic genetic markers from 486 aligned nucleotide sequences of mitochondrial 16S ribosomal DNA were developed for the four closely related species of dreissenoid and corbiculoid bivalves that have invaded North America; the zebra mussel Dreissena polymorpha, the quagga mussel D. bugensis, and the dark false mussel Mytilopsis leucophaeata of the superfamily Dreissenoidea, and the Asian clam Corbicula fluminea of the sister superfamily Corbiculoidea. Evolutionary relationships were examined among the four genera and comparisons were made with native Eurasian populations of D. polymorpha and D. bugensis. Tests were conducted for gender-specific mitochondrial lineages, which occur in some other bivalves. Genetic variability and divergence rates were tested between stem (paired) and loop (unpaired) regions of secondary structure. There were 251 variable nucleotide sites, of which 99 were phylogenetically informative. Overall transition to transversion ratio was 0.76:1.00 and both accumulated linearly in stem and loop regions, suggesting appropriate phylogenetic signal. Genetic distance calibration with the fossil record estimated the pairwise sequence divergence as 0. 0057 +/- 0.0004 per million years. Mytilopsis and Dreissena appear to have diverged about 20.7 +/- 2.7 million years ago. D. bugensis and D. polymorpha appear separated by about 13.2 +/- 2.2 million years. No intraspecific variation was found, including between Eurasian and North American populations, among shallow and deep morphotypes of D. bugensis and between the sexes. Restriction endonuclease markers were developed to distinguish among the species at all life history stages, allowing rapid identification in areas of sympatric distribution.
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Affiliation(s)
- C A Stepien
- Department of Biology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106-7080, USA.
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Schmidt W. Phylogenetic analysis of nucleotide sequences: an algebraic approach. Math Biosci 1998; 154:39-55. [PMID: 9990807 DOI: 10.1016/s0025-5564(98)10039-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In a previous paper Schmidt and Mueller [Bull. Math. Biosci. 58 (3) (1996) 449.] proposed a new method for calculating phylogenetic trees from dichotomous (present/absent) properties of the taxonomic units. The proposed method is based on a specified distance measure quantifying the phylogenetic information content of the selected properties with respect to the joint evolutionary history. Formally, the method can be applied to arbitrary property patterns and is not based on restricting evolutionary models and optimization principles looking forward in evolutionary time. Instead, its theoretical foundation is the retrospective postulate that properties which are present in any two (closely related) taxa were also present in their most recent common ancestor. The reliability of the derived trees depends essentially on the phylogenetic relevance of the chosen properties. To apply this method to related nucleotide sequences I have defined a set of biologically meaningful nucleotide properties which separate and evaluate the different substitution events. The proposed algorithm provides additive trees and needs no numerical constraints to avoid negative branch lengths or any other meaningless result. In a series of applications the method has been tested and compared with the outcomes of other established tree reconstruction methods. For demonstration, I report and discuss the results of the reanalysis of two families of genomic sequences. Here and in a series of further applications I obtained trees which are biologically acceptable and in good coincidence with the published trees. Thus, it can be concluded that the proposed method will be a useful alternative for the study of phylogenetic relationships.
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Affiliation(s)
- W Schmidt
- Department of Bioinformatics, Max-Delbrueck-Center for Molecular Medicine, Berlin-Buch, Germany.
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