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Hammel M, Touchard F, Burioli EAV, Paradis L, Cerqueira F, Chailler E, Bernard I, Cochet H, Simon A, Thomas F, Destoumieux-Garzón D, Charrière GM, Bierne N. Marine transmissible cancer navigates urbanized waters, threatening spillover. Proc Biol Sci 2024; 291:20232541. [PMID: 38378149 PMCID: PMC10878816 DOI: 10.1098/rspb.2023.2541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
Inter-individual transmission of cancer cells represents a unique form of microparasites increasingly reported in marine bivalves. In this study, we sought to understand the ecology of the propagation of Mytilus trossulus Bivalve Transmissible Neoplasia 2 (MtrBTN2), a transmissible cancer affecting four Mytilus mussel species worldwide. We investigated the prevalence of MtrBTN2 in the mosaic hybrid zone of M. edulis and M. galloprovincialis along the French Atlantic coast, sampling contrasting natural and anthropogenic habitats. We observed a similar prevalence in both species, probably due to the spatial proximity of the two species in this region. Our results showed that ports had higher prevalence of MtrBTN2, with a possible hotspot observed at a shuttle landing dock. No cancer was found in natural beds except for two sites close to the hotspot, suggesting spillover. Ports may provide favourable conditions for the transmission of MtrBTN2, such as high mussel density, stressful conditions, sheltered and confined shores or buffered temperatures. Ships may also spread the disease through biofouling. Our results suggest ports may serve as epidemiological hubs, with maritime routes providing artificial gateways for MtrBTN2 propagation. This highlights the importance of preventing biofouling on docks and ship hulls to limit the spread of marine pathogens hosted by fouling species.
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Affiliation(s)
- M. Hammel
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, Occitanie, France
- IHPE, Univ Montpellier, CNRS, Ifremer, Univ Perpignan Via Domitia, Montpellier, France
| | - F. Touchard
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, Occitanie, France
| | - E. A. V. Burioli
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, Occitanie, France
- IHPE, Univ Montpellier, CNRS, Ifremer, Univ Perpignan Via Domitia, Montpellier, France
| | - L. Paradis
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, Occitanie, France
| | - F. Cerqueira
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, Occitanie, France
| | - E. Chailler
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, Occitanie, France
| | | | - H. Cochet
- Cochet Environnement, 56550 Locoal, France
| | - A. Simon
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, Occitanie, France
| | - F. Thomas
- CREEC/CANECEV (CREES), MIVEGEC, Unité Mixte de Recherches, IRD 224-CNRS 5290-Université de Montpellier, Montpellier, France
| | - D. Destoumieux-Garzón
- IHPE, Univ Montpellier, CNRS, Ifremer, Univ Perpignan Via Domitia, Montpellier, France
| | - G. M. Charrière
- IHPE, Univ Montpellier, CNRS, Ifremer, Univ Perpignan Via Domitia, Montpellier, France
| | - N. Bierne
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, Occitanie, France
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2
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Burioli EAV, Hammel M, Vignal E, Vidal-Dupiol J, Mitta G, Thomas F, Bierne N, Destoumieux-Garzón D, Charrière GM. Transcriptomics of mussel transmissible cancer MtrBTN2 suggests accumulation of multiple cancer traits and oncogenic pathways shared among bilaterians. Open Biol 2023; 13:230259. [PMID: 37816387 PMCID: PMC10564563 DOI: 10.1098/rsob.230259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023] Open
Abstract
Transmissible cancer cell lines are rare biological entities giving rise to diseases at the crossroads of cancer and parasitic diseases. These malignant cells have acquired the amazing capacity to spread from host to host. They have been described only in dogs, Tasmanian devils and marine bivalves. The Mytilus trossulus bivalve transmissible neoplasia 2 (MtrBTN2) lineage has even acquired the capacity to spread inter-specifically between marine mussels of the Mytilus edulis complex worldwide. To identify the oncogenic processes underpinning the biology of these atypical cancers we performed transcriptomics of MtrBTN2 cells. Differential expression, enrichment, protein-protein interaction network, and targeted analyses were used. Overall, our results suggest the accumulation of multiple cancerous traits that may be linked to the long-term evolution of MtrBTN2. We also highlight that vertebrate and lophotrochozoan cancers could share a large panel of common drivers, which supports the hypothesis of an ancient origin of oncogenic processes in bilaterians.
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Affiliation(s)
- E A V Burioli
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
| | - M Hammel
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - E Vignal
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
| | - J Vidal-Dupiol
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
| | - G Mitta
- IFREMER, UMR 241 Écosystèmes Insulaires Océaniens, Labex Corail, Centre Ifremer du Pacifique, Tahiti, Polynésie française
| | - F Thomas
- CREEC/CANECEV (CREES), MIVEGEC, Unité Mixte de Recherches, IRD 224-CNRS 5290-Université de Montpellier, Montpellier, France
| | - N Bierne
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - D Destoumieux-Garzón
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
| | - G M Charrière
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
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Burioli EAV, Hammel M, Bierne N, Thomas F, Houssin M, Destoumieux-Garzón D, Charrière GM. Traits of a mussel transmissible cancer are reminiscent of a parasitic life style. Sci Rep 2021; 11:24110. [PMID: 34916573 PMCID: PMC8677744 DOI: 10.1038/s41598-021-03598-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 12/03/2021] [Indexed: 12/22/2022] Open
Abstract
Some cancers have evolved the ability to spread from host to host by transmission of cancerous cells. These rare biological entities can be considered parasites with a host-related genome. Still, we know little about their specific adaptation to a parasitic lifestyle. MtrBTN2 is one of the few lineages of transmissible cancers known in the animal kingdom. Reported worldwide, MtrBTN2 infects marine mussels. We isolated MtrBTN2 cells circulating in the hemolymph of cancerous mussels and investigated their phenotypic traits. We found that MtrBTN2 cells had remarkable survival capacities in seawater, much higher than normal hemocytes. With almost 100% cell survival over three days, they increase significantly their chances to infect neighboring hosts. MtrBTN2 also triggered an aggressive cancerous process: proliferation in mussels was ~ 17 times higher than normal hemocytes (mean doubling time of ~ 3 days), thereby favoring a rapid increase of intra-host population size. MtrBTN2 appears to induce host castration, thereby favoring resources re-allocation to the parasites and increasing the host carrying capacity. Altogether, our results highlight a series of traits of MtrBTN2 consistent with a marine parasitic lifestyle that may have contributed to the success of its persistence and dissemination in different mussel populations across the globe.
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Affiliation(s)
- E A V Burioli
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France.
| | - M Hammel
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - N Bierne
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - F Thomas
- CREEC/CANECEV (CREES), MIVEGEC, Unité Mixte de Recherches, IRD 224-CNRS 5290-Université de Montpellier, Montpellier, France
| | - M Houssin
- LABÉO, Caen, France
- Normandie Université, Université de Caen Normandie, FRE BOREA, CNRS-2030, IRD-207, MNHN, UPMC, UCN, Caen, France
| | - D Destoumieux-Garzón
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
| | - G M Charrière
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
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Burioli EAV, Trancart S, Simon A, Bernard I, Charles M, Oden E, Bierne N, Houssin M. Implementation of various approaches to study the prevalence, incidence and progression of disseminated neoplasia in mussel stocks. J Invertebr Pathol 2019; 168:107271. [PMID: 31629707 DOI: 10.1016/j.jip.2019.107271] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 10/12/2019] [Accepted: 10/15/2019] [Indexed: 01/11/2023]
Abstract
Marine mussel production is of substantial economic interest in numerous coastal areas worldwide, making crucial the study of pathologies that affect them. Disseminated neoplasia (DN) has recently been suggested to be linked to blue mussel, Mytilus edulis, mortality outbreaks observed in France since 2014, although the evidence remains indirect. In order to improve DN detection and monitoring, we compared the sensitivity of four diagnostic tools, namely haemocytology, histology, flow cytometry, and genetics. Haemocytological examination gave the best results in sensitivity and had the advantage of being non-invasive, allowing disease progression to be followed in affected mussels. Using this approach, we showed that DN progression is usually slow, and we provide evidence of remission events. We observed a high diversity of forms and mitotic features of neoplastic cells located in the vesicular connective tissue but rarely in the haemolymph. Circulating cells occur as four main types but are homogenous in morphology and DNA content within a single individual. Polyploidy proved very high, from 8 N to 18 N. Genetic analysis of haemolymph DNA showed that a Mytilus trossulus genetic signal was associated with almost all the DN cases here diagnosed by haemocytological examination, regardless of the DN type. This result corroborates DN is a transmissible cancer that first originated in a M. trossulus host and subsequently crossed into M. edulis. No pre-neoplastic conditions were detectable. The prevalence of the disease was quite low, which, together with the low morbidity observed in the lab, suggest DN is unlikely to be the direct cause of mortality outbreaks in France.
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Affiliation(s)
| | - S Trancart
- LABÉO, 1 Route de Rosel, 14280 St Contest, France
| | - A Simon
- ISEM, Univ Montpellier, CNRS-EPHE-IRD, Montpellier, France
| | - I Bernard
- Eurêka Modélisation, 13 rue de Kermarquer, Lézardrieux, France
| | - M Charles
- LABÉO, 1 Route de Rosel, 14280 St Contest, France; Université de Caen Normandie, UMR BOREA, MNHN, UPMC, UCBN, CNRS-7208, IRD-207, Esplanade de la Paix, 14000 Caen, France
| | - E Oden
- LABÉO, 1 Route de Rosel, 14280 St Contest, France
| | - N Bierne
- ISEM, Univ Montpellier, CNRS-EPHE-IRD, Montpellier, France
| | - M Houssin
- LABÉO, 1 Route de Rosel, 14280 St Contest, France; Université de Caen Normandie, UMR BOREA, MNHN, UPMC, UCBN, CNRS-7208, IRD-207, Esplanade de la Paix, 14000 Caen, France
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5
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Ravinet M, Faria R, Butlin RK, Galindo J, Bierne N, Rafajlović M, Noor MAF, Mehlig B, Westram AM. Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow. J Evol Biol 2017; 30:1450-1477. [DOI: 10.1111/jeb.13047] [Citation(s) in RCA: 306] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 12/14/2022]
Affiliation(s)
- M. Ravinet
- Centre for Ecological and Evolutionary Synthesis; University of Oslo; Oslo Norway
- National Institute of Genetics; Mishima Shizuoka Japan
| | - R. Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO, Laboratório Associado; Universidade do Porto; Vairão Portugal
- Department of Experimental and Health Sciences; IBE, Institute of Evolutionary Biology (CSIC-UPF); Pompeu Fabra University; Barcelona Spain
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
| | - R. K. Butlin
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
- Department of Marine Sciences; Centre for Marine Evolutionary Biology; University of Gothenburg; Gothenburg Sweden
| | - J. Galindo
- Department of Biochemistry, Genetics and Immunology; University of Vigo; Vigo Spain
| | - N. Bierne
- CNRS; Université Montpellier; ISEM; Station Marine Sète France
| | - M. Rafajlović
- Department of Physics; University of Gothenburg; Gothenburg Sweden
| | | | - B. Mehlig
- Department of Physics; University of Gothenburg; Gothenburg Sweden
| | - A. M. Westram
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
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6
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Szulkin M, Gagnaire PA, Bierne N, Charmantier A. Population genomic footprints of fine-scale differentiation between habitats in Mediterranean blue tits. Mol Ecol 2016; 25:542-58. [PMID: 26800038 DOI: 10.1111/mec.13486] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 11/13/2015] [Accepted: 11/17/2015] [Indexed: 12/20/2022]
Abstract
Linking population genetic variation to the spatial heterogeneity of the environment is of fundamental interest to evolutionary biology and ecology, in particular when phenotypic differences between populations are observed at biologically small spatial scales. Here, we applied restriction-site associated DNA sequencing (RAD-Seq) to test whether phenotypically differentiated populations of wild blue tits (Cyanistes caeruleus) breeding in a highly heterogeneous environment exhibit genetic structure related to habitat type. Using 12 106 SNPs in 197 individuals from deciduous and evergreen oak woodlands, we applied complementary population genomic analyses, which revealed that genetic variation is influenced by both geographical distance and habitat type. A fine-scale genetic differentiation supported by genome- and transcriptome-wide analyses was found within Corsica, between two adjacent habitats where blue tits exhibit marked differences in breeding time while nesting < 6 km apart. Using redundancy analysis (RDA), we show that genomic variation remains associated with habitat type when controlling for spatial and temporal effects. Finally, our results suggest that the observed patterns of genomic differentiation were not driven by a small proportion of highly differentiated loci, but rather emerged through a process such as habitat choice, which reduces gene flow between habitats across the entire genome. The pattern of genomic isolation-by-environment closely matches differentiation observed at the phenotypic level, thereby offering significant potential for future inference of phenotype-genotype associations in a heterogeneous environment.
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Affiliation(s)
- M Szulkin
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 Campus CNRS, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
| | - P-A Gagnaire
- Université Montpellier 2, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France.,ISEM - CNRS, UMR 5554, SMEL, 2 rue des Chantiers, 34200, Sète, France
| | - N Bierne
- Université Montpellier 2, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France.,ISEM - CNRS, UMR 5554, SMEL, 2 rue des Chantiers, 34200, Sète, France
| | - A Charmantier
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 Campus CNRS, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
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7
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Ament-Velásquez SL, Figuet E, Ballenghien M, Zattara EE, Norenburg JL, Fernández-Álvarez FA, Bierne J, Bierne N, Galtier N. Population genomics of sexual and asexual lineages in fissiparous ribbon worms (Lineus, Nemertea): hybridization, polyploidy and the Meselson effect. Mol Ecol 2016; 25:3356-69. [DOI: 10.1111/mec.13717] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 04/18/2016] [Accepted: 05/02/2016] [Indexed: 12/28/2022]
Affiliation(s)
- S. L. Ament-Velásquez
- Institute of Evolutionary Sciences; University Montpellier; CNRS, IRD, EPHE; Place Eugène Bataillon; 34095 Montpellier France
- Department of Organismal Biology; Systematic Biology; Uppsala University; PO Box 256 SE-751 05 Uppsala Sweden
| | - E. Figuet
- Institute of Evolutionary Sciences; University Montpellier; CNRS, IRD, EPHE; Place Eugène Bataillon; 34095 Montpellier France
| | - M. Ballenghien
- Institute of Evolutionary Sciences; University Montpellier; CNRS, IRD, EPHE; Place Eugène Bataillon; 34095 Montpellier France
| | - E. E. Zattara
- Department of Biology; Indiana University; 107 S Indiana Ave Bloomington IN 47405 USA
- Department of Invertebrate Zoology; National Museum of Natural History; Smithsonian Institution; 10th St. & Constitution Ave. NW Washington DC 20560 USA
| | - J. L. Norenburg
- Department of Invertebrate Zoology; National Museum of Natural History; Smithsonian Institution; 10th St. & Constitution Ave. NW Washington DC 20560 USA
| | | | - J. Bierne
- Laboratoire de Biologie Cellulaire et Moléculaire; Université de Reims Champagne-Ardenne; 9 Boulevard de la Paix 51100 Reims France
| | - N. Bierne
- Institute of Evolutionary Sciences; University Montpellier; CNRS, IRD, EPHE; Place Eugène Bataillon; 34095 Montpellier France
| | - N. Galtier
- Institute of Evolutionary Sciences; University Montpellier; CNRS, IRD, EPHE; Place Eugène Bataillon; 34095 Montpellier France
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8
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Romiguier J, Gayral P, Ballenghien M, Bernard A, Cahais V, Chenuil A, Chiari Y, Dernat R, Duret L, Faivre N, Loire E, Lourenco JM, Nabholz B, Roux C, Tsagkogeorga G, Weber AAT, Weinert LA, Belkhir K, Bierne N, Glémin S, Galtier N. Comparative population genomics in animals uncovers the determinants of genetic diversity. Nature 2014; 515:261-3. [DOI: 10.1038/nature13685] [Citation(s) in RCA: 405] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 07/17/2014] [Indexed: 02/07/2023]
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9
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Roux C, Fraïsse C, Castric V, Vekemans X, Pogson GH, Bierne N. Can we continue to neglect genomic variation in introgression rates when inferring the history of speciation? A case study in a Mytilus hybrid zone. J Evol Biol 2014; 27:1662-75. [PMID: 24913446 DOI: 10.1111/jeb.12425] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/25/2014] [Accepted: 04/25/2014] [Indexed: 11/28/2022]
Abstract
The use of molecular data to reconstruct the history of divergence and gene flow between populations of closely related taxa represents a challenging problem. It has been proposed that the long-standing debate about the geography of speciation can be resolved by comparing the likelihoods of a model of isolation with migration and a model of secondary contact. However, data are commonly only fit to a model of isolation with migration and rarely tested against the secondary contact alternative. Furthermore, most demographic inference methods have neglected variation in introgression rates and assume that the gene flow parameter (Nm) is similar among loci. Here, we show that neglecting this source of variation can give misleading results. We analysed DNA sequences sampled from populations of the marine mussels, Mytilus edulis and M. galloprovincialis, across a well-studied mosaic hybrid zone in Europe and evaluated various scenarios of speciation, with or without variation in introgression rates, using an Approximate Bayesian Computation (ABC) approach. Models with heterogeneous gene flow across loci always outperformed models assuming equal migration rates irrespective of the history of gene flow being considered. By incorporating this heterogeneity, the best-supported scenario was a long period of allopatric isolation during the first three-quarters of the time since divergence followed by secondary contact and introgression during the last quarter. By contrast, constraining migration to be homogeneous failed to discriminate among any of the different models of gene flow tested. Our simulations thus provide statistical support for the secondary contact scenario in the European Mytilus hybrid zone that the standard coalescent approach failed to confirm. Our results demonstrate that genomic variation in introgression rates can have profound impacts on the biological conclusions drawn from inference methods and needs to be incorporated in future studies.
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Affiliation(s)
- C Roux
- Université Montpellier 2, Montpellier, France; CNRS-UMR5554 Institut des Sciences de l'Evolution, Station Méditerranéenne de l'Environnement Littoral, Sète, France; Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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10
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Abbott R, Albach D, Ansell S, Arntzen JW, Baird SJE, Bierne N, Boughman J, Brelsford A, Buerkle CA, Buggs R, Butlin RK, Dieckmann U, Eroukhmanoff F, Grill A, Cahan SH, Hermansen JS, Hewitt G, Hudson AG, Jiggins C, Jones J, Keller B, Marczewski T, Mallet J, Martinez-Rodriguez P, Möst M, Mullen S, Nichols R, Nolte AW, Parisod C, Pfennig K, Rice AM, Ritchie MG, Seifert B, Smadja CM, Stelkens R, Szymura JM, Väinölä R, Wolf JBW, Zinner D. Hybridization and speciation. J Evol Biol 2013; 26:229-46. [DOI: 10.1111/j.1420-9101.2012.02599.x] [Citation(s) in RCA: 1370] [Impact Index Per Article: 124.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 06/25/2012] [Accepted: 07/16/2012] [Indexed: 12/17/2022]
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11
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Affiliation(s)
- C. C. Gosset
- Université Montpellier 2; Montpellier Cedex France
- CNRS; Institut des Sciences de l'Evolution - ISEM UMR 5554; Station Méditerranéenne de l'Environnement Littoral; Sete France
| | - N. Bierne
- Université Montpellier 2; Montpellier Cedex France
- CNRS; Institut des Sciences de l'Evolution - ISEM UMR 5554; Station Méditerranéenne de l'Environnement Littoral; Sete France
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12
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Bonhomme F, Bierne N, Guinand B. Why is it so difficult to delimit reproductive units from genetic data in marine broadcasting species? Comp Biochem Physiol A Mol Integr Physiol 2008. [DOI: 10.1016/j.cbpa.2008.04.567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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13
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Sauvage C, Bierne N, Lapègue S, Boudry P. Single Nucleotide polymorphisms and their relationship to codon usage bias in the Pacific oyster Crassostrea gigas. Gene 2007; 406:13-22. [PMID: 17616269 DOI: 10.1016/j.gene.2007.05.011] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Revised: 05/14/2007] [Accepted: 05/18/2007] [Indexed: 10/23/2022]
Abstract
DNA sequence polymorphism and codon usage bias were investigated in a set of 41 nuclear loci in the Pacific oyster Crassostrea gigas. Our results revealed a very high level of DNA polymorphism in oysters, in the order of magnitude of the highest levels reported in animals to date. A total of 290 single nucleotide polymorphisms (SNPs) were detected, 76 of which being localised in exons and 214 in non-coding regions. Average density of SNPs was estimated to be one SNP every 60 bp in coding regions and one every 40 bp in non-coding regions. Non-synonymous substitutions contributed substantially to the polymorphism observed in coding regions. The non-synonymous to silent diversity ratio was 0.16 on average, which is fairly higher to the ratio reported in other invertebrate species recognised to display large population sizes. Therefore, purifying selection does not appear to be as strong as it could have been expected for a species with a large effective population size. The level of non-synonymous diversity varied greatly from one gene to another, in accordance with varying selective constraints. We examined codon usage bias and its relationship with DNA polymorphism. The table of optimal codons was deduced from the analysis of an EST dataset, using EST counts as a rough assessment of gene expression. As recently observed in some other taxa, we found a strong and significant negative relationship between codon bias and non-synonymous diversity suggesting correlated selective constraints on synonymous and non-synonymous substitutions. Codon bias as measured by the frequency of optimal codons for expression might therefore provide a useful indicator of the level of constraint upon proteins in the oyster genome.
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Affiliation(s)
- C Sauvage
- Laboratoire de Génétique et Pathologie - IFREMER - La Tremblade, France
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14
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Faure B, Bierne N, Tanguy A, Bonhomme F, Jollivet D. Evidence for a slightly deleterious effect of intron polymorphisms at the EF1alpha gene in the deep-sea hydrothermal vent bivalve Bathymodiolus. Gene 2007; 406:99-107. [PMID: 17707599 DOI: 10.1016/j.gene.2007.06.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Revised: 05/26/2007] [Accepted: 06/28/2007] [Indexed: 11/25/2022]
Abstract
A multilocus analysis was initiated in order to infer the general effect of demography and the indirect effect of positive selection on some chromosome segments in Bathymodiolus. Mussels of the genus Bathymodiolus inhabit the very hostile, fragmented and variable environment of deep-sea hydrothermal vents which is thought to cause recurrent population bottlenecks via extinction/colonisation processes and adaptation to new environmental conditions. In the course of this work we discovered that the assumption of neutrality of non-coding polymorphisms usually made in genome scan experiments was likely to be violated at one of the loci we analysed. The direct effect of slight purifying selection on non-coding polymorphisms shares many resemblances with the indirect effect of positive selection through genetic hitchhiking. Combining polymorphism with divergence data for several closely related species allowed us to obtain different expectations for the direct effect of negative selection and the indirect effect of positive selection. We observed a strong excess of rare non-coding polymorphisms at the second intron of the EF1alpha gene in the two species Bathymodiolus azoricus and Bathymodiolus thermophilus, while two other loci, the mitochondrial COI gene and an intron of the Lysozyme gene, did not exhibit such a deviation. In addition, the divergence rate of the EF1alpha intron was estimated to be unexpectedly low when calibrated using the closure of the Panama Isthmus that interrupted gene flow between the two species. The polymorphism to divergence ratio was similar to the one observed for the other two loci, in accordance to the hypothesis of purifying selection. We conclude that slight purifying selection is likely to act on polymorphic intronic mutations of the EF1alpha second intron and discuss the possible relationship with the specific biology of Bathymodiolus mussels.
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Affiliation(s)
- B Faure
- Evolution et Génétique des Populations Marines, UMR 7144, CNRS-UPMC, Station Biologique de Roscoff, Place Georges Teissier, 29682Roscoff, France.
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15
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Abstract
A strong negative correlation between the rate of amino-acid substitution and codon usage bias in Drosophila has been attributed to interference between positive selection at nonsynonymous sites and weak selection on codon usage. To further explore this possibility we have investigated polymorphism and divergence at three kinds of sites: synonymous, nonsynonymous and intronic in relation to codon bias in D. melanogaster and D. simulans. We confirmed that protein evolution is one of the main explicative parameters for interlocus codon bias variation (r(2) approximately 40%). However, intron or synonymous diversities, which could have been expected to be good indicators of local interference [here defined as the additional increase of drift due to selection on tightly linked sites, also called 'genetic draft' by Gillespie (2000)] did not covary significantly with codon bias or with protein evolution. Concurrently, levels of polymorphism were reduced in regions of low recombination rates whereas codon bias was not. Finally, while nonsynonymous diversities were very well correlated between species, neither synonymous nor intron diversities observed in D. melanogaster were correlated with those observed in D. simulans. All together, our results suggest that the selective constraint on the protein is a stable component of gene evolution while local interference is not. The pattern of variation in genetic draft along the genome therefore seems to be instable through evolutionary times and should therefore be considered as a minor determinant of codon bias variance. We argue that selective constraints for optimal codon usage are likely to be correlated with selective constraints on the protein, both between codons within a gene, as previously suggested, and also between genes within a genome.
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Affiliation(s)
- N Bierne
- Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton, UK.
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16
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Bierne N, Daguin C, Bonhomme F, David P, Borsa P. Direct selection on allozymes is not required to explain heterogeneity among marker loci across a Mytilus hybrid zone. Mol Ecol 2003; 12:2505-10. [PMID: 12919488 DOI: 10.1046/j.1365-294x.2003.01936.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Unequal differentiation between two types of loci (allozyme and DNA markers) across a Mytilus hybrid zone has recently been claimed as evidence for direct selection on some allozyme loci. We provide here a counter-example: a noncoding DNA locus that exhibits as much differentiation as the incriminated allozymes do. The levels of genetic differentiation varied widely among both allozymes and noncoding DNA markers and no clear difference emerged between the two types of markers. This suggests that the strong interlocus variance in genetic differentiation has been confounded with a discrepancy between marker types as a result of an insufficient and unbalanced locus sampling. Heterogeneity in differentiation among neutral loci can be created by stochastic variance during the allopatric divergence preceding a secondary contact. In hybrid zones, a further source of variance is differential introgression among chromosomal regions after the secondary contact owing to the local influence of selected genes on more or less distant markers. However, the degree of differentiation alone gives no way to distinguish indirect pseudo-selection (a regular and ubiquitous feature of hybrid zones) from direct selection. More generally, we suggest that comparative neutrality tests based on discrepancies among marker types have to be applied with caution when the presence of semi-permeable genetic barriers to gene exchange is suspected.
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Affiliation(s)
- N Bierne
- Laboratoire Génome, Populations, Interactions, Adaptation, UMR5000 Université Montpellier II--IFREMER--CNRS, Station Méditerranéenne de l'Environnement Littoral, 34200 Sète, France.
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17
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Bierne N, Borsa P, Daguin C, Jollivet D, Viard F, Bonhomme F, David P. Introgression patterns in the mosaic hybrid zone between Mytilus edulis and M. galloprovincialis. Mol Ecol 2003; 12:447-61. [PMID: 12535095 DOI: 10.1046/j.1365-294x.2003.01730.x] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Hybrid zones are fascinating systems to investigate the structure of genetic barriers. Marine hybrid zones deserve more investigation because of the generally high dispersion potential of planktonic larvae which allows migration on scales unrivalled by terrestrial species. Here we analyse the genetic structure of the mosaic hybrid zone between the marine mussels Mytilus edulis and M. galloprovincialis, using three length-polymorphic PCR loci as neutral and diagnostic markers on 32 samples along the Atlantic coast of Europe. Instead of a single genetic gradient from M. galloprovincialis on the Iberian Peninsula to M. edulis populations in the North Sea, three successive transitions were observed in France. From South to North, the frequency of alleles typical of M. galloprovincialis first decreases in the southern Bay of Biscay, remains low in Charente, then increases in South Brittany, remains high in most of Brittany, and finally decreases again in South Normandy. The two enclosed patches observed in the midst of the mosaic hybrid zone in Charente and Brittany, although predominantly M. edulis-like and M. galloprovincialis-like, respectively, are genetically original in two respects. First, considering only the various alleles typical of one species, the patches show differentiated frequencies compared to the reference external populations. Second, each patch is partly introgressed by alleles of the other species. When introgression is taken into account, linkage disequilibria appear close to their maximum possible values, indicating a strong genetic barrier within all transition zones. Some pre- or postzygotic isolation mechanisms (habitat specialization, spawning asynchrony, assortative fertilization and hybrid depression) have been documented in previous studies, although their relative importance remains to be evaluated. We also provided evidence for a recent migratory 'short-cut' connecting M. edulis-like populations of the Charente patch to an external M. edulis population in Normandy and thought to reflect artificial transfer of spat for aquaculture.
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Affiliation(s)
- N Bierne
- Laboratoire Génome, Populations, Interactions, CNRS-UMR5000 - Station Méditerranéenne de l'Environnement Littoral, 1 Quai de la Daurade, 34200 Sète, France.
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Huvet A, Balabaud K, Bierne N, Boudry P. Microsatellite analysis of 6-hour-old embryos reveals no preferential intraspecific fertilization between cupped oysters Crassostrea gigas and Crassostrea angulata. Mar Biotechnol (NY) 2001; 3:448-453. [PMID: 14961337 DOI: 10.1007/s10126-001-0017-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Experimental examination of reproductive isolation is the first step in understanding hybridization processes. Here, we studied preferential fertilization between 2 cupped oyster taxa, Crassostrea angulata and Crassostrea gigas, as a potential prezygotic reproductive isolation. Early examination of sperm competition is now possible by molecular analysis of oyster embryos. This avoids the confounding effect of differential mortality during the larval stage. Six hundred embryos were sampled from 2 crosses. Three microsatellite loci were enough to determine without ambiguity the taxa of contributing sires of embryos. No evidence of preferential fertilization between gametes from the same taxa was shown. A significantly higher contribution of the C. gigas males was revealed with the C. angulata females, but not with the C. gigas females, which might suggest early heterosis or interaction differences between gametes. In the light of these results, natural hybridization between both taxa can be expected in cases of their geographical coexistence, as in the Southern European populations in which both taxa are in contact as a result of aquaculture development.
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Affiliation(s)
- A Huvet
- Laboratoire de Génétique et Pathologie, IFREMER, B.P. 133, 17390 La Tremblade, France
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19
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Abstract
Associative overdominance, the fitness difference between heterozygotes and homozygotes at a neutral locus, is classically described using two categories of models: linkage disequilibrium in small populations or identity disequilibrium in infinite, partially selfing populations. In both cases, only equilibrium situations have been considered. In the present study, associative overdominance is related to the distribution of individual inbreeding levels (i.e., genomic autozygosity). Our model integrates the effects of physical linkage and variation in inbreeding history among individual pedigrees. Hence, linkage and identity disequilibrium, traditionally presented as alternatives, are summarized within a single framework. This allows studying nonequilibrium situations in which both occur simultaneously. The model is applied to the case of an infinite population undergoing a sustained population bottleneck. The effects of bottleneck size, mating system, marker gene diversity, deleterious genomic mutation parameters, and physical linkage are evaluated. Bottlenecks transiently generate much larger associative overdominance than observed in equilibrium finite populations and represent a plausible explanation of empirical results obtained, for instance, in marine species. Moreover, the main origin of associative overdominance is random variation in individual inbreeding whereas physical linkage has little effect.
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Affiliation(s)
- N Bierne
- Laboratoire Génome, Populations, Interactions, Station Méditerranéenne de L'Environnement Littoral, 34200 Sète, France.
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Bierne N, Lehnert SA, Bédier E, Bonhomme F, Moore SS. Screening for intron-length polymorphisms in penaeid shrimps using exon-primed intron-crossing (EPIC)-PCR. Mol Ecol 2000; 9:233-5. [PMID: 10672168 DOI: 10.1046/j.1365-294x.2000.00842.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- N Bierne
- Laboratoire Génome, Populations, Interactions CNRS UPR 9060, SMEL, 1 Quai Daurade 34200 Sète, France.
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21
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Affiliation(s)
- V Vonau
- Laboratoire Génome et Populations, CNRS UPR 9060, Université Montpellier II, France
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Abstract
This paper reports new experimental evidence on the effect of inbreeding on growth and survival in the early developmental phase of a marine bivalve, the flat oyster Ostrea edulis. Two crosses between full sibs were analyzed using four microsatellite markers. Samples of 96 individuals were taken just after spawning (day 1), at the end of the larval stage before metamorphosis (day 10) and at the postlarval stage (day 70). Significant departure from Mendelian expectation was observed at two loci in the first cross and two loci in the second. Departure from 1:1 segregation occurred in one parent of the first cross at three loci and genotypic selection, which resulted in highly significant heterozygote excesses, was recorded at three out of four loci in cross C1 and at two out of three loci in cross C2. Across the four markers, there were similar significant excesses of multilocus heterozygosity, and significant multilocus heterozygosity-growth correlations were recorded for both crosses at all stages. These results suggest that microsatellite markers, often assumed to be neutral, cosegregated with fitness-associated genes, the number of which is estimated to be between 15 and 38 in the whole genome, and that there is a potentially high genetic load in Ostrea edulis genome. This load provides a genetic basis for heterosis in marine bivalves.
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Affiliation(s)
- N Bierne
- Laboratoire Génome et Populations, Centre National de la Recerche Scientifique UPR 9060, Université Montpellier II, France
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