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Briones C, Nuñez JJ, Pérez M, Garrido O, Campos B, Godoy K, Hartley R, Oyarzún PA, Guiñez R. Linking Acrosome Size and Genetic Divergence in an Inter-Oceanic Mussel from the Pacific and Atlantic Coasts: A Case of Incipient Speciation? Animals (Basel) 2024; 14:674. [PMID: 38473058 DOI: 10.3390/ani14050674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
In recent years, advances in analyses of the sperm morphology and genetics of Perumytilus purpuratus have allowed to two evolutionary scenarios for this mussel to be suggested: (1) the scenario of cryptic species and (2) the scenario of incipient or in progress speciation. For a better understanding of the evolutionary history of P. purpuratus, we performed extensive sampling along a latitudinal gradient of ca. 7180 km of coastline-from the Southern Pacific Ocean to the Atlantic Ocean-and we delved deeper into the sperm morphology of P. purpuratus, exploring its association with the phylogeny and population genetics to determine whether the variability in sperm traits between the northern and southern regions was a signal of cryptic or incipient species. Overall, our results showed that sperm sizes were strongly correlated with the genetic structure in males of P. purpuratus. We identified at 37° S on the Pacific coast a coincident break of both sperm size and genetic disruption that can be explained by historical events and postglacial recolonization as causal phenomena for the observed divergences. Furthermore, evidence of genetic admixture between lineages was found at 38° S, suggesting the presence of an introgressive hybridization zone and incomplete reproductive isolation in an in fraganti or incipient speciation process.
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Affiliation(s)
- Carolina Briones
- Instituto de Ciencias Naturales Alexander von Humbodt, Facultad de Ciencias del Mar y de Recursos Biológicos, Universidad de Antofagasta, Angamos 601, Antofagasta 1270300, Chile
| | - José J Nuñez
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia 5090000, Chile
| | - Montse Pérez
- AquaCOV, Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, Consejo Superior de Investigaciones Científicas (IEO, CSIC), 36390 Vigo, Spain
| | - Orlando Garrido
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia 5090000, Chile
| | | | - Karina Godoy
- Núcleo Científico y Tecnológico de Biorecursos (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile
| | - Ricardo Hartley
- Instituto de Investigación y Postgrado, Facultad de Medicina y Ciencias de la Salud, Universidad Central de Chile, Santiago 8330507, Chile
| | - Pablo A Oyarzún
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay 2340000, Chile
| | - Ricardo Guiñez
- Instituto de Ciencias Naturales Alexander von Humbodt, Facultad de Ciencias del Mar y de Recursos Biológicos, Universidad de Antofagasta, Angamos 601, Antofagasta 1270300, Chile
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Diz AP, Skibinski DOF. Patterns of admixture and introgression in a mosaic Mytilus galloprovincialis and Mytilus edulis hybrid zone in SW England. Mol Ecol 2024; 33:e17233. [PMID: 38063472 DOI: 10.1111/mec.17233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 01/25/2024]
Abstract
The study of hybrid zones offers important insights into speciation. Earlier studies on hybrid populations of the marine mussel species Mytilus edulis and Mytilus galloprovincialis in SW England provided evidence of admixture but were constrained by the limited number of molecular markers available. We use 57 ancestry-informative SNPs, most of which have been mapped genetically, to provide evidence of distinctive differences between admixed populations in SW England and asymmetrical introgression from M. edulis to M. galloprovincialis. We combine the genetic study with analysis of phenotypic traits of potential ecological and adaptive significance. We demonstrate that hybrid individuals have brown mantle edges unlike the white or purple in the parental species, suggesting allelic or non-allelic genomic interactions. We report differences in gonad development stage between the species consistent with a prezygotic barrier between the species. By incorporating results from publications dating back to 1980, we confirm the long-term stability of the hybrid zone despite higher viability of M. galloprovincialis. This stability coincides with a dramatic change in temperature of UK coastal waters and suggests that these hybrid populations might be resisting the effects of global warming. However, a single SNP locus associated with the Notch transmembrane signalling protein shows a markedly different pattern of variation to the others and might be associated with adaptation of M. galloprovincialis to colder northern temperatures.
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Affiliation(s)
- Angel P Diz
- Centro de Investigación Mariña, Universidade de Vigo (CIM-UVIGO), Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
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Cozzolino L, Nicastro KR, Hubbard PC, Seuront L, McQuaid CD, Zardi GI. Intraspecific genetic lineages of a marine mussel show behavioural divergence when exposed to microplastic leachates. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 340:122779. [PMID: 37863252 DOI: 10.1016/j.envpol.2023.122779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/02/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023]
Abstract
Worldwide, microplastic pollution has numerous negative implications for marine biota, exacerbating the effects of other forms of global anthropogenic disturbance. Mounting evidence shows that microplastics (MPs) not only cause physical damage through their ingestion, but also act as vectors for hazardous compounds by leaching absorbed and adsorbed chemicals. Research on the effects of plastic pollution has, however, largely assumed that species respond uniformly, while ignoring intraspecific diversity (i.e., variation within a single species). We investigated the effects of plastic leachates derived from factory-fresh (virgin) and beached microplastics on the behavioural responses of two genetic lineages of the Mediterranean mussel Mytilus galloprovincialis. Through laboratory behavioural experiments, we found that during exposure to leachates from beached microplastics (beached MPLs), Atlantic specimens moved significantly less than Mediterranean individuals in terms of both (i) proportion of individuals responding through movement and (ii) net and gross distances crawled. In contrast, no significant intraspecific differences were observed in the behaviour of either adults or recruits when exposed to MPLs from virgin microplastics (virgin MPLs). Additionally, the reception of cues from three amino acids (L-cysteine, proline and L-leucine) at increasing concentrations (10-5 M to 10-3 M in charcoal-filtered seawater) was tested by electrophysiological analysis using mussels exposed to beached MPLs or control seawater. We found significant intraspecific differences in response to 10-3 M L-cysteine (regardless of treatment) and 10-4 M L-cysteine (in mussels exposed to beached MPLs) and to 10-3 M proline (in mussels exposed to beached MPLs) and 10-5 M L-leucine. Our study suggests that intraspecific variation in a marine mussel may prompt different responses to plastic pollution, potentially triggered by local adaptation and physiological variability between lineages. Our work highlights the importance of assessing the effects of intraspecific variation, especially in environmental sentinel species as this level of diversity could modulate responses to plastic pollution.
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Affiliation(s)
- Lorenzo Cozzolino
- CCMAR-Centro de Ciências do Mar, CIMAR Laboratório Associado, Universidade do Algarve, Campus de Gambelas, Faro, 8005-139, Portugal.
| | - Katy R Nicastro
- CCMAR-Centro de Ciências do Mar, CIMAR Laboratório Associado, Universidade do Algarve, Campus de Gambelas, Faro, 8005-139, Portugal; Univ. Lille, CNRS, Univ. Littoral Côte d'Opale, IRD, UMR 8187 - LOG - Laboratoire d'Océanologie et de Géosciences, F-59000, Lille, France; Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140, South Africa
| | - Peter C Hubbard
- CCMAR-Centro de Ciências do Mar, CIMAR Laboratório Associado, Universidade do Algarve, Campus de Gambelas, Faro, 8005-139, Portugal
| | - Laurent Seuront
- Univ. Lille, CNRS, Univ. Littoral Côte d'Opale, IRD, UMR 8187 - LOG - Laboratoire d'Océanologie et de Géosciences, F-59000, Lille, France; Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140, South Africa; Department of Marine Resources and Energy, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108- 8477, Japan
| | - Christopher D McQuaid
- Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140, South Africa
| | - Gerardo I Zardi
- CCMAR-Centro de Ciências do Mar, CIMAR Laboratório Associado, Universidade do Algarve, Campus de Gambelas, Faro, 8005-139, Portugal; Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140, South Africa; Normandie Université, UNICAEN, Laboratoire Biologie des Organismes et Ecosystèmes Aquatiques, UMR 8067 BOREA (CNRS, MNHN, UPMC, UCBN, IRD-207), CS 14032, 14000, Caen, France
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4
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Jilberto F, Zbawicka M, Wenne R, Larraín MA, Araneda C. SNP genotyping revealed a hybrid zone between Mytilus chilensis and M. platensis in southern South America (the Strait of Magellan, Isla Grande de Tierra del Fuego and the Falkland Islands). Mol Ecol 2024; 33:e17211. [PMID: 37996993 DOI: 10.1111/mec.17211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023]
Abstract
Hybrid zones among mussel species have been extensively studied in the northern hemisphere. In South America, it has only recently become possible to study the natural hybrid zones, due to the clarification of the taxonomy of native mussels of the Mytilus genus. Analysing 54 SNP markers, we show the genetic species composition and admixture in the hybrid zone between M. chilensis and M. platensis in the southern end of South America. Bayesian, non-Bayesian clustering and re-assignment algorithms showed that the natural hybrid zone between M. chilensis and M. platensis in the Strait of Magellan, Isla Grande de Tierra del Fuego and the Falkland Islands shows clinal architecture. The hybrid zone can be divided into three different areas: the first one is on the Atlantic coast where only pure M. platensis and hybrid were found. In the second one, inside the Strait of Magellan, pure individuals of both species and mussels with variable degrees of hybridisation coexist. In the last area at the Strait in front of Punta Arenas City, fjords on the Isla Grande de Tierra del Fuego, and at the Beagle Channel, only M. chilensis and a low number of hybrids were found. According to the proportion of hybrids, bays with protected conditions away from strong currents would give better conditions for hybridisation. We do not find evidence of any other mussel species such as M. edulis, M. galloprovincialis, M. planulatus or M. trossulus in the zone.
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Affiliation(s)
- Felipe Jilberto
- Food Quality Research Center, Universidad de Chile, Santiago, Chile
| | | | - Roman Wenne
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | - María Angélica Larraín
- Food Quality Research Center, Universidad de Chile, Santiago, Chile
- Departamento de Ciencia de los Alimentos y Tecnología Química, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Cristián Araneda
- Food Quality Research Center, Universidad de Chile, Santiago, Chile
- Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
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5
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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] [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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6
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Coupé S, Giantsis IA, Vázquez Luis M, Scarpa F, Foulquié M, Prévot J, Casu M, Lattos A, Michaelidis B, Sanna D, García‐March JR, Tena‐Medialdea J, Vicente N, Bunet R. The characterization of toll-like receptor repertoire in Pinna nobilis after mass mortality events suggests adaptive introgression. Ecol Evol 2023; 13:e10383. [PMID: 37546570 PMCID: PMC10401143 DOI: 10.1002/ece3.10383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 08/08/2023] Open
Abstract
The fan mussel Pinna nobilis is currently on the brink of extinction due to a multifactorial disease mainly caused to the highly pathogenic parasite Haplosporidium pinnae, meaning that the selection pressure outweighs the adaptive potential of the species. Hopefully, rare individuals have been observed somehow resistant to the parasite, stretching the need to identify the traits underlying this better fitness. Among the candidate to explore at first intention are fast-evolving immune genes, of which toll-like receptor (TLR). In this study, we examined the genetic diversity at 14 TLR loci across P. nobilis, Pinna rudis and P. nobilis × P. rudis hybrid genomes, collected at four physically distant regions, that were found to be either resistant or sensitive to the parasite H. pinnae. We report a high genetic diversity, mainly observed at cell surface TLRs compared with that of endosomal TLRs. However, the endosomal TLR-7 exhibited unexpected level of diversity and haplotype phylogeny. The lack of population structure, associated with a high genetic diversity and elevated dN/dS ratio, was interpreted as balancing selection, though both directional and purifying selection were detected. Interestingly, roughly 40% of the P. nobilis identified as resistant to H. pinnae were introgressed with P. rudis TLR. Specifically, they all carried a TLR-7 of P. rudis origin, whereas sensitive P. nobilis were not introgressed, at least at TLR loci. Small contributions of TLR-6 and TLR-4 single-nucleotide polymorphisms to the clustering of resistant and susceptible individuals could be detected, but their specific role in resistance remains highly speculative. This study provides new information on the diversity of TLR genes within the P. nobilis species after MME and additional insights into adaptation to H. pinnae that should contribute to the conservation of this Mediterranean endemic species.
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Affiliation(s)
- Stéphane Coupé
- Université de Toulon, Aix Marseille Univ, CNRS, IRD, MIOMarseilleFrance
| | | | - Maite Vázquez Luis
- Instituto Español de Oceanografía (IEO, CSIC), Centro Oceanográfico de BalearesPalma de MallorcaSpain
| | - Fabio Scarpa
- Department of Biomedical SciencesFabio Scarpa, Daria Sanna: University of SassariSassariItaly
| | - Mathieu Foulquié
- Université de Toulon, Aix Marseille Univ, CNRS, IRD, MIOMarseilleFrance
- Institut océanographique Paul RicardIle des Embiez, VarFrance
| | | | - Marco Casu
- Department of Veterinary MedicineUniversity of SassariSassariItaly
| | - Athanasios Lattos
- Faculty of Agricultural SciencesUniversity of Western MacedoniaKozaniGreece
| | - Basile Michaelidis
- Faculty of Agricultural SciencesUniversity of Western MacedoniaKozaniGreece
| | - Daria Sanna
- Department of Biomedical SciencesFabio Scarpa, Daria Sanna: University of SassariSassariItaly
| | - José Rafa García‐March
- IMEDMAR‐UCV, Institute of Environment and Marine Science ResearchUniversidad Católica de Valencia SVMCalpe, AlicanteSpain
| | - José Tena‐Medialdea
- IMEDMAR‐UCV, Institute of Environment and Marine Science ResearchUniversidad Católica de Valencia SVMCalpe, AlicanteSpain
| | - Nardo Vicente
- Institut Méditerranéen de Biodiversité et Ecologie marine et continentale (IMBE), Aix‐Marseille Université, CNRS, IRD, Avignon UniversitéAvignonFrance
| | - Robert Bunet
- Institut océanographique Paul RicardIle des Embiez, VarFrance
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Glasenapp MR, Pogson GH. Extensive introgression among strongylocentrotid sea urchins revealed by phylogenomics. Ecol Evol 2023; 13:e10446. [PMID: 37636863 PMCID: PMC10451471 DOI: 10.1002/ece3.10446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/29/2023] Open
Abstract
Gametic isolation is thought to play an important role in the evolution of reproductive isolation in broadcast-spawning marine invertebrates. However, it is unclear whether gametic isolation commonly evolves early in the speciation process or only accumulates after other reproductive barriers are already in place. It is also unknown whether gametic isolation is an effective barrier to introgression following speciation. Here, we used whole-genome sequencing data and multiple complementary phylogenomic approaches to test whether the well-documented gametic incompatibilities among the strongylocentrotid sea urchins have limited introgression. We quantified phylogenetic discordance, inferred reticulate phylogenetic networks, and applied the Δ statistic using gene tree topologies reconstructed from multiple sequence alignments of protein-coding single-copy orthologs. In addition, we conducted ABBA-BABA tests on genome-wide single nucleotide variants and reconstructed a phylogeny of mitochondrial genomes. Our results revealed strong mito-nuclear discordance and considerable nonrandom gene tree discordance that cannot be explained by incomplete lineage sorting alone. Eight of the nine species examined demonstrated a history of introgression with at least one other species or ancestral lineage, indicating that introgression was common during the diversification of the strongylocentrotid urchins. There was strong support for introgression between four extant species pairs (Strongylocentrotus pallidus ⇔ S. droebachiensis, S. intermedius ⇔ S. pallidus, S. purpuratus ⇔ S. fragilis, and Mesocentrotus franciscanus ⇔ Pseudocentrotus depressus) and additional evidence for introgression on internal branches of the phylogeny. Our results suggest that the existing gametic incompatibilities among the strongylocentrotid urchin species have not been a complete barrier to hybridization and introgression following speciation. Their continued divergence in the face of widespread introgression indicates that other reproductive isolating barriers likely exist and may have been more critical in establishing reproductive isolation early in speciation.
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Affiliation(s)
- Matthew R. Glasenapp
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCaliforniaUSA
| | - Grant H. Pogson
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCaliforniaUSA
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Nascimento‐Schulze JC, Bean TP, Peñaloza C, Paris JR, Whiting JR, Simon A, Fraser BA, Houston RD, Bierne N, Ellis RP. SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP-array. Evol Appl 2023; 16:1044-1060. [PMID: 37216031 PMCID: PMC10197230 DOI: 10.1111/eva.13552] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/15/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023] Open
Abstract
Blue mussels from the genus Mytilus are an abundant component of the benthic community, found in the high latitude habitats. These foundation species are relevant to the aquaculture industry, with over 2 million tonnes produced globally each year. Mussels withstand a wide range of environmental conditions and species from the Mytilus edulis complex readily hybridize in regions where their distributions overlap. Significant effort has been made to investigate the consequences of environmental stress on mussel physiology, reproductive isolation, and local adaptation. Yet our understanding on the genomic mechanisms underlying such processes remains limited. In this study, we developed a multi species medium-density 60 K SNP-array including four species of the Mytilus genus. SNPs included in the platform were called from 138 mussels from 23 globally distributed mussel populations, sequenced using a whole-genome low coverage approach. The array contains polymorphic SNPs which capture the genetic diversity present in mussel populations thriving across a gradient of environmental conditions (~59 K SNPs) and a set of published and validated SNPs informative for species identification and for diagnosis of transmissible cancer (610 SNPs). The array will allow the consistent genotyping of individuals, facilitating the investigation of ecological and evolutionary processes in these taxa. The applications of this array extend to shellfish aquaculture, contributing to the optimization of this industry via genomic selection of blue mussels, parentage assignment, inbreeding assessment and traceability. Further applications such as genome wide association studies (GWAS) for key production traits and those related to environmental resilience are especially relevant to safeguard aquaculture production under climate change.
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Affiliation(s)
- Jennifer C. Nascimento‐Schulze
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
- Centre for Environment, Fisheries and Aquaculture ScienceWeymouth LaboratoryWeymouthUK
| | - Tim P. Bean
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Josephine R. Paris
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | - James R. Whiting
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | - Alexis Simon
- ISEMUniversity of Montpellier, CNRS, IRDMontpellierFrance
| | - Bonnie A. Fraser
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | | | - Nicolas Bierne
- ISEMUniversity of Montpellier, CNRS, IRDMontpellierFrance
| | - Robert P. Ellis
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
- Centre for Sustainable Aquaculture FuturesUniversity of ExeterExeterUK
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9
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Gualandi N, Fracarossi D, Riommi D, Sollitto M, Greco S, Mardirossian M, Pacor S, Hori T, Pallavicini A, Gerdol M. Unveiling the Impact of Gene Presence/Absence Variation in Driving Inter-Individual Sequence Diversity within the CRP-I Gene Family in Mytilus spp. Genes (Basel) 2023; 14:genes14040787. [PMID: 37107545 PMCID: PMC10138031 DOI: 10.3390/genes14040787] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/14/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Mussels (Mytilus spp.) tolerate infections much better than other species living in the same marine coastal environment thanks to a highly efficient innate immune system, which exploits a remarkable diversification of effector molecules involved in mucosal and humoral responses. Among these, antimicrobial peptides (AMPs) are subjected to massive gene presence/absence variation (PAV), endowing each individual with a potentially unique repertoire of defense molecules. The unavailability of a chromosome-scale assembly has so far prevented a comprehensive evaluation of the genomic arrangement of AMP-encoding loci, preventing an accurate ascertainment of the orthology/paralogy relationships among sequence variants. Here, we characterized the CRP-I gene cluster in the blue mussel Mytilus edulis, which includes about 50 paralogous genes and pseudogenes, mostly packed in a small genomic region within chromosome 5. We further reported the occurrence of widespread PAV within this family in the Mytilus species complex and provided evidence that CRP-I peptides likely adopt a knottin fold. We functionally characterized the synthetic peptide sCRP-I H1, assessing the presence of biological activities consistent with other knottins, revealing that mussel CRP-I peptides are unlikely to act as antimicrobial agents or protease inhibitors, even though they may be used as defense molecules against infections from eukaryotic parasites.
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Affiliation(s)
- Nicolò Gualandi
- Area of Neuroscience, International School for Advanced Studies, 34136 Trieste, Italy;
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (D.F.); (D.R.); (M.S.); (S.G.); (M.M.); (S.P.); (A.P.)
| | - Davide Fracarossi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (D.F.); (D.R.); (M.S.); (S.G.); (M.M.); (S.P.); (A.P.)
| | - Damiano Riommi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (D.F.); (D.R.); (M.S.); (S.G.); (M.M.); (S.P.); (A.P.)
| | - Marco Sollitto
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (D.F.); (D.R.); (M.S.); (S.G.); (M.M.); (S.P.); (A.P.)
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, 6000 Koper, Slovenia
| | - Samuele Greco
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (D.F.); (D.R.); (M.S.); (S.G.); (M.M.); (S.P.); (A.P.)
| | - Mario Mardirossian
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (D.F.); (D.R.); (M.S.); (S.G.); (M.M.); (S.P.); (A.P.)
| | - Sabrina Pacor
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (D.F.); (D.R.); (M.S.); (S.G.); (M.M.); (S.P.); (A.P.)
| | - Tiago Hori
- Atlantic Aqua Farms Ltd., Vernon Bridge, PE C0A 2E0, Canada;
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (D.F.); (D.R.); (M.S.); (S.G.); (M.M.); (S.P.); (A.P.)
- Anton Dohrn Zoological Station, 80121 Naples, Italy
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (D.F.); (D.R.); (M.S.); (S.G.); (M.M.); (S.P.); (A.P.)
- Correspondence:
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10
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Wenne R. Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations. Animals (Basel) 2023; 13:1089. [PMID: 36978629 PMCID: PMC10044284 DOI: 10.3390/ani13061089] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023] Open
Abstract
An increasing number of aquatic species have been studied for genetic polymorphism, which extends the knowledge on their natural populations. One type of high-resolution molecular marker suitable for studying the genetic diversity of large numbers of individuals is single nucleotide polymorphism (SNP). This review is an attempt to show the range of applications of SNPs in studies of natural populations of aquatic animals. In recent years, SNPs have been used in the genetic analysis of wild and enhanced fish and invertebrate populations in natural habitats, exploited migratory species in the oceans, migratory anadromous and freshwater fish and demersal species. SNPs have been used for the identification of species and their hybrids in natural environments, to study the genetic consequences of restocking for conservation purposes and the negative effects on natural populations of fish accidentally escaping from culture. SNPs are very useful for identifying genomic regions correlated with phenotypic variants relevant for wildlife protection, management and aquaculture. Experimental size-selective catches of populations created in tanks have caused evolutionary changes in life cycles of fishes. The research results have been discussed to clarify whether the fish populations in natural conditions can undergo changes due to selective harvesting targeting the fastest-growing fishes.
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Affiliation(s)
- Roman Wenne
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
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11
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Wenne R, Zbawicka M, Prądzińska A, Kotta J, Herkül K, Gardner JPA, Apostolidis AP, Poćwierz-Kotus A, Rouane-Hacene O, Korrida A, Dondero F, Baptista M, Reizopoulou S, Hamer B, Sundsaasen KK, Árnyasi M, Kent MP. Molecular genetic differentiation of native populations of Mediterranean blue mussels, Mytilus galloprovincialis Lamarck, 1819, and the relationship with environmental variables. THE EUROPEAN ZOOLOGICAL JOURNAL 2022. [DOI: 10.1080/24750263.2022.2086306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- R. Wenne
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland
| | - M. Zbawicka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland
| | - A. Prądzińska
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland
| | - J. Kotta
- Department of Marine Systems, Estonian Marine Institute, University of Tartu, 12619 Tallinn, Estonia
| | - K. Herkül
- Department of Marine Systems, Estonian Marine Institute, University of Tartu, 12619 Tallinn, Estonia
| | - J. P. A. Gardner
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand
| | - A. P. Apostolidis
- Department of Animal Production, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - A. Poćwierz-Kotus
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland
| | - O. Rouane-Hacene
- Department of Biology, Faculty of Nature and Life Sciences, University of Oran 1 - Ahmed Ben Bella, Algeria
| | - A. Korrida
- High Institute of Nursing Professions and Health Techniques, ISPITS-Agadir, Moroccan Ministry of Health and Social Protection, Kingdom of Morocco
| | - F. Dondero
- Department of Science and Technological Innovation (DISIT), Ecotoxicology and Ecology, Università del Piemonte Orientale “Amedeo Avogadro”, Novara, 15121, Italy
| | - M. Baptista
- Marine and Environmental Sciences Centre, University of Lisbon, Portugal
| | - S. Reizopoulou
- Department of Biological Oceanography, Institute of Oceanography, Hellenic Centre for Marine Research, Athens Sounio, 19013 Anavyssos, Greece
| | - B. Hamer
- Ruđer Bošković Institute, Center for Marine Research Rovinj, Rovinj, Croatia
| | - K. K. Sundsaasen
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (Cigene), Faculty of Biosciences, Norwegian University of Life Sciences, No-1432 Ås, Norway
| | - M. Árnyasi
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (Cigene), Faculty of Biosciences, Norwegian University of Life Sciences, No-1432 Ås, Norway
| | - M. P. Kent
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (Cigene), Faculty of Biosciences, Norwegian University of Life Sciences, No-1432 Ås, Norway
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12
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Tran Lu Y A, Ruault S, Daguin-Thiébaut C, Castel J, Bierne N, Broquet T, Wincker P, Perdereau A, Arnaud-Haond S, Gagnaire PA, Jollivet D, Hourdez S, Bonhomme F. Subtle limits to connectivity revealed by outlier loci within two divergent metapopulations of the deep-sea hydrothermal gastropod Ifremeria nautilei. Mol Ecol 2022; 31:2796-2813. [PMID: 35305041 DOI: 10.1111/mec.16430] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 02/14/2022] [Accepted: 03/01/2022] [Indexed: 11/30/2022]
Abstract
Hydrothermal vents form archipelagos of ephemeral deep-sea habitats that raise interesting questions about the evolution and dynamics of the associated endemic fauna, constantly subject to extinction-recolonization processes. These metal-rich environments are coveted for the mineral resources they harbor, thus raising recent conservation concerns. The evolutionary fate and demographic resilience of hydrothermal species strongly depend on the degree of connectivity among and within their fragmented metapopulations. In the deep sea, however, assessing connectivity is difficult and usually requires indirect genetic approaches. Improved detection of fine-scale genetic connectivity is now possible based on genome-wide screening for genetic differentiation. Here, we explored population connectivity in the hydrothermal vent snail Ifremeria nautilei across its species range encompassing five distinct back-arc basins in the Southwest Pacific. The global analysis, based on 10 570 single nucleotide polymorphism (SNP) markers derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), depicted two semi-isolated and homogeneous genetic clusters. Demo-genetic modeling suggests that these two groups began to diverge about 70 000 generations ago, but continue to exhibit weak and slightly asymmetrical gene flow. Furthermore, a careful analysis of outlier loci showed subtle limitations to connectivity between neighboring basins within both groups. This finding indicates that migration is not strong enough to totally counterbalance drift or local selection, hence questioning the potential for demographic resilience at this latter geographical scale. These results illustrate the potential of large genomic datasets to understand fine-scale connectivity patterns in hydrothermal vents and the deep sea.
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Affiliation(s)
- Adrien Tran Lu Y
- ISEM, Institut des Sciences de l'Evolution, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Stéphanie Ruault
- Sorbonne Université, CNRS, UMR 7144, 'Dynamique de la Diversité Marine' (DyDiv) Lab, Station biologique de Roscoff, Place G. Teissier, 29680, Roscoff, France
| | - Claire Daguin-Thiébaut
- Sorbonne Université, CNRS, UMR 7144, 'Dynamique de la Diversité Marine' (DyDiv) Lab, Station biologique de Roscoff, Place G. Teissier, 29680, Roscoff, France
| | - Jade Castel
- Sorbonne Université, CNRS, UMR 7144, 'Dynamique de la Diversité Marine' (DyDiv) Lab, Station biologique de Roscoff, Place G. Teissier, 29680, Roscoff, France
| | - Nicolas Bierne
- ISEM, Institut des Sciences de l'Evolution, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Thomas Broquet
- Sorbonne Université, CNRS, UMR 7144, 'Dynamique de la Diversité Marine' (DyDiv) Lab, Station biologique de Roscoff, Place G. Teissier, 29680, Roscoff, France
| | - Patrick Wincker
- Génomique Métabolique, Génoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Aude Perdereau
- Génomique Métabolique, Génoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Sophie Arnaud-Haond
- MARBEC, Marine Biodiversity Exploitation and Conservation, Univ Montpellier, CNRS, IFREMER, IRD, Sète, France
| | | | - Didier Jollivet
- Sorbonne Université, CNRS, UMR 7144, 'Dynamique de la Diversité Marine' (DyDiv) Lab, Station biologique de Roscoff, Place G. Teissier, 29680, Roscoff, France
| | - Stéphane Hourdez
- Sorbonne Université, CNRS, UMR 8222, Laboratoire d'Ecogéochimie des Environnements Benthiques, Observatoire Océanologique de Banyuls, Avenue Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | - François Bonhomme
- ISEM, Institut des Sciences de l'Evolution, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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13
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Hammel M, Simon A, Arbiol C, Villalba A, Burioli EAV, Pépin JF, Lamy JB, Benabdelmouna A, Bernard I, Houssin M, Charrière G, Destoumieux-Garzon D, Welch J, Metzger MJ, Bierne N. Prevalence and polymorphism of a mussel transmissible cancer in Europe. Mol Ecol 2022; 31:736-751. [PMID: 34192383 PMCID: PMC8716645 DOI: 10.1111/mec.16052] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/03/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023]
Abstract
Transmissible cancers are parasitic malignant cell lineages that have acquired the ability to infect new hosts from the same species, or sometimes related species. First described in dogs and Tasmanian devils, transmissible cancers were later discovered in some marine bivalves affected by a leukaemia-like disease. In Mytilus mussels, two lineages of bivalve transmissible neoplasia (BTN) have been described to date (MtrBTN1 and MtrBTN2), both of which emerged in a Mytilus trossulus founder individual. Here, we performed extensive screening of genetic chimerism, a hallmark of transmissible cancer, by genotyping 106 single nucleotide polymorphisms of 5,907 European Mytilus mussels. Genetic analysis allowed us to simultaneously obtain the genotype of hosts - Mytilus edulis, M. galloprovincialis or hybrids - and the genotype of tumours of heavily infected individuals. In addition, a subset of 222 individuals were systematically genotyped and analysed by histology to screen for possible nontransmissible cancers. We detected MtrBTN2 at low prevalence in M. edulis, and also in M. galloprovincialis and hybrids although at a much lower prevalence. No MtrBTN1 or new BTN were found, but eight individuals with nontransmissible neoplasia were observed at a single polluted site on the same sampling date. We observed a diversity of MtrBTN2 genotypes that appeared more introgressed or more ancestral than MtrBTN1 and reference healthy M. trossulus individuals. The observed polymorphism is probably due to somatic null alleles caused by structural variations or point mutations in primer-binding sites leading to enhanced detection of the host alleles. Despite low prevalence, two sublineages divergent by 10% fixed somatic null alleles and one nonsynonymous mtCOI (mitochondrial cytochrome oxidase I) substitution are cospreading in the same geographical area, suggesting a complex diversification of MtrBTN2 since its emergence and host species shift.
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Affiliation(s)
- Maurine Hammel
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier,
France,IHPE, Univ Montpellier, CNRS, Ifremer, Univ Perpignan,
Via Domitia, France
| | - Alexis Simon
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier,
France
| | | | - Antonio Villalba
- Centro de Investigacións Mariñas,
Consellería do Mar, Xunta de Galicia, Vilanova de Arousa, Spain,Departamento de Ciencias de la Vida, Universidad de
Alcalá, Alcalá de Henares, Spain.,Research Centre for Experimental Marine Biology and
Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque
Country, Spain
| | - Erika AV Burioli
- IHPE, Univ Montpellier, CNRS, Ifremer, Univ Perpignan,
Via Domitia, France,LABÉO, Caen, France
| | - Jean-François Pépin
- Laboratoire Environnement ressources des Pertuis
Charentais, IFREMER, La Tremblade, France
| | - Jean-Baptiste Lamy
- Santé, Génétique, Microbiologie des
Mollusques, IFREMER, La Tremblade, France
| | | | | | | | | | | | - John Welch
- Department of Genetics, University of Cambridge,
Downing Street, Cambridge, UK
| | | | - Nicolas Bierne
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier,
France
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14
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Boutet I, Lacroix C, Devin S, Tanguy A, Moraga D, Auffret M. Does the environmental history of mussels have an effect on the physiological response to additional stress under experimental conditions? THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:149925. [PMID: 34555605 DOI: 10.1016/j.scitotenv.2021.149925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/11/2021] [Accepted: 08/22/2021] [Indexed: 06/13/2023]
Abstract
Expected effects on marine biota of the ongoing elevation of water temperature and high latitudes is of major concern when considering the reliability of coastal ecosystem production. To compare the capacity of coastal organisms to cope with a temperature increase depending on their environmental history, responses of adult blue mussels (Mytilus spp.) taken from two sites differentially exposed to chemical pollution were investigated during an experimental exposure to a thermal stress. Immune parameters were notably altered by extreme warming and transcriptional changes for a broad selection of genes were associated to the temperature increase following a two-step response pattern. Site-specific responses suggested an influence of environmental history and support the possibility of a genetic basis in the physiological response. However no meaningful difference was detected between the response of hybrids and M galloprovincialis. This study brings new information about the capacity of mussels to cope with the ongoing elevation of water temperature in these coastal ecosystems.
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Affiliation(s)
- Isabelle Boutet
- Station Biologique de Roscoff, Laboratoire Adaptation et Diversité en Milieu Marin (UMR 7144 AD2M CNRS-Sorbonne Université), Place Georges Tessier, 29680 Roscoff, France
| | - Camille Lacroix
- Institut Universitaire Européen de la Mer, Laboratoire de Sciences de l'Environnement Marin (UMR 6539 LEMAR CNRS-UBO-IFREMER-IRD), Technopôle Brest-Iroise, 29280 Plouzané, France; CEDRE Conseil et Expertise en Pollutions Accidentelles des Eaux, 715 Rue Alain Colas, CS 41836, 29218 Brest Cedex 2, France
| | - Simon Devin
- Laboratoire Interdisciplinaire des Environnements Continentaux (UMR 7360 LIEC CNRS-Université de Lorraine), 8 rue du Général Delestraint, 57070 Metz. France
| | - Arnaud Tanguy
- Station Biologique de Roscoff, Laboratoire Adaptation et Diversité en Milieu Marin (UMR 7144 AD2M CNRS-Sorbonne Université), Place Georges Tessier, 29680 Roscoff, France
| | - Dario Moraga
- Institut Universitaire Européen de la Mer, Laboratoire de Sciences de l'Environnement Marin (UMR 6539 LEMAR CNRS-UBO-IFREMER-IRD), Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Michel Auffret
- Institut Universitaire Européen de la Mer, Laboratoire de Sciences de l'Environnement Marin (UMR 6539 LEMAR CNRS-UBO-IFREMER-IRD), Technopôle Brest-Iroise, 29280 Plouzané, France.
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15
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Teixeira MAL, Vieira PE, Ravara A, Costa FO, Nygren A. From 13 to 22 in a second stroke: revisiting the European Eumida sanguinea (Phyllodocidae: Annelida) species complex. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlab100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Eumida sanguinea is a recognized polychaete species complex which, in previous studies, has been reported to have additional undescribed diversity. We detected nine additional lineages by analysing DNA sequence data (mitochondrial: COI, 16S rRNA and nuclear loci: ITS region and 28S rRNA) of E. sanguinea morphotype populations from a broader sampling effort in European marine waters. Traditional morphological features failed to provide consistent differences or unique characters that could be used to distinguish these Eumida species. However, by complementing DNA data with morphometrics, geographic range, colour and pigmentation patterns, we revealed five new species. Two of these undescribed species derived from the previously signalled Eumida lineages S21 and GB22, which are here named as E. schanderi sp. nov. and E. fenwicki sp. nov., respectively. Three other species are based on newly discovered lineages, namely E. fauchaldi sp. nov., E. langenecki sp. nov. and E. pleijeli sp. nov. From the six new lineages remaining, three are represented by fewer than two well-preserved specimens, which prevented further comprehensive analysis. The last three lineages were only distinct when using mitochondrial markers. Integrative taxonomy is essential to elucidate evolutionary phenomena and eventually allow informed use of species complexes exhibiting stasis in biomonitoring or other ecological studies.
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Affiliation(s)
- Marcos A L Teixeira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Pedro E Vieira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Ascensão Ravara
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Arne Nygren
- Institutionen for marina vetenskaper, Göteborgs Universitet, Tjärnö, Strömstad, Sweden
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16
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Khaitov V, Marchenko J, Katolikova M, Väinölä R, Kingston SE, Carlon DB, Gantsevich M, Strelkov P. Species identification based on a semi-diagnostic marker: Evaluation of a simple conchological test for distinguishing blue mussels Mytilus edulis L. and M. trossulus Gould. PLoS One 2021; 16:e0249587. [PMID: 34297723 PMCID: PMC8301678 DOI: 10.1371/journal.pone.0249587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 03/22/2021] [Indexed: 11/19/2022] Open
Abstract
Cryptic and hybridizing species may lack diagnostic taxonomic characters leaving researchers with semi-diagnostic ones. Identification based on such characters is probabilistic, the probability of correct identification depending on the species composition in a mixed population. Here we test the possibilities of applying a semi-diagnostic conchological character for distinguishing two cryptic species of blue mussels, Mytilus edulis and M. trossulus. These ecologically, stratigraphically and economically important molluscs co-occur and hybridize in many areas of the North Atlantic and the neighboring Arctic. Any cues for distinguishing them in sympatry without genotyping would save much research effort. Recently these species have been shown to statistically differ in the White Sea, where a simple character of the shell was used to distinguish two mussel morphotypes. In this paper, we analyzed the associations between morphotypes and species-specific genotypes based on an abundant material from the waters of the Kola Peninsula (White Sea, Barents Sea) and a more limited material from Norway, the Baltic Sea, Scotland and the Gulf of Maine. The performance of the "morphotype test" for species identification was formally evaluated using approaches from evidence-based medicine. Interspecific differences in the morphotype frequencies were ubiquitous and unidirectional, but their scale varied geographically (from 75% in the White Sea to 15% in the Baltic Sea). In addition, salinity-related variation of this character within M. edulis was revealed in the Arctic Barents Sea. For every studied region, we established relationships between the proportions of the morphotypes in the populations as well as between the proportions of the morphotypes in samples and the probabilities of mussels of different morphotypes being M. trossulus and M. edulis. We provide recommendations for the application of the morphotype test to mussels from unstudied contact zones and note that they may apply equally well to other taxa identified by semi-diagnostic traits.
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Affiliation(s)
- Vadim Khaitov
- St. Petersburg State University, St. Petersburg, Russia
- Kandalaksha State Nature Reserve, Kandalaksha, Murmansk Region, Russia
| | | | - Marina Katolikova
- St. Petersburg State University, St. Petersburg, Russia
- Murmansk Marine Biological Institute, Murmansk, Russia
| | - Risto Väinölä
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Sarah E. Kingston
- Department of Biology & Schiller Coastal Studies Center, Bowdoin College, Brunswick, Maine, United States of America
- School of Marine Sciences and Darling Marine Center, University of Maine, Walpole, Maine, United States of America
| | - David B. Carlon
- Department of Biology & Schiller Coastal Studies Center, Bowdoin College, Brunswick, Maine, United States of America
| | - Michael Gantsevich
- Department of Invertebrate Zoology, Lomonosov Moscow State University, Moscow, Russia
| | - Petr Strelkov
- St. Petersburg State University, St. Petersburg, Russia
- Laboratory of Monitoring and Conservation of Natural Arctic Ecosystems, Murmansk Arctic State University, Murmansk, Russia
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17
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Menon M, Bagley JC, Page GFM, Whipple AV, Schoettle AW, Still CJ, Wehenkel C, Waring KM, Flores-Renteria L, Cushman SA, Eckert AJ. Adaptive evolution in a conifer hybrid zone is driven by a mosaic of recently introgressed and background genetic variants. Commun Biol 2021; 4:160. [PMID: 33547394 PMCID: PMC7864969 DOI: 10.1038/s42003-020-01632-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 11/18/2020] [Indexed: 01/30/2023] Open
Abstract
Extant conifer species may be susceptible to rapid environmental change owing to their long generation times, but could also be resilient due to high levels of standing genetic diversity. Hybridisation between closely related species can increase genetic diversity and generate novel allelic combinations capable of fuelling adaptive evolution. Our study unravelled the genetic architecture of adaptive evolution in a conifer hybrid zone formed between Pinus strobiformis and P. flexilis. Using a multifaceted approach emphasising the spatial and environmental patterns of linkage disequilibrium and ancestry enrichment, we identified recently introgressed and background genetic variants to be driving adaptive evolution along different environmental gradients. Specifically, recently introgressed variants from P. flexilis were favoured along freeze-related environmental gradients, while background variants were favoured along water availability-related gradients. We posit that such mosaics of allelic variants within conifer hybrid zones will confer upon them greater resilience to ongoing and future environmental change and can be a key resource for conservation efforts.
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Affiliation(s)
- Mitra Menon
- grid.27860.3b0000 0004 1936 9684Department of Evolution and Ecology, University of California, Davis, CA USA
| | - Justin C. Bagley
- grid.257992.20000 0001 0019 1845Department of Biology, Jacksonville State University, Jacksonville, AL USA
| | - Gerald F. M. Page
- grid.4391.f0000 0001 2112 1969Forest Ecosystems and Society, Oregon State University, Corvallis, OR USA
| | - Amy V. Whipple
- grid.261120.60000 0004 1936 8040Department of Biological Sciences and Merriam Powel Center for Environmental Research, Northern Arizona University, Flagstaff, AZ USA
| | - Anna W. Schoettle
- grid.497401.f0000 0001 2286 5230Rocky Mountain Research Station, USDA Forest Service, Fort Collins, CO USA
| | - Christopher J. Still
- grid.4391.f0000 0001 2112 1969Forest Ecosystems and Society, Oregon State University, Corvallis, OR USA
| | - Christian Wehenkel
- grid.412198.70000 0000 8724 8383Instituto de Silvicultura e Industria de la Madera, Universidad Juarez del Estado de Durango, Durango, Mexico
| | - Kristen M. Waring
- grid.261120.60000 0004 1936 8040School of Forestry, Northern Arizona University, Flagstaff, AZ USA
| | - Lluvia Flores-Renteria
- grid.263081.e0000 0001 0790 1491Department of Biology, San Diego State University, San Diego, CA USA
| | - Samuel A. Cushman
- grid.472551.00000 0004 0404 3120Rocky Mountain Research Station, USDA Forest Service, Flagstaff, AZ USA
| | - Andrew J. Eckert
- grid.224260.00000 0004 0458 8737Department of Biology, Virginia Commonwealth University, Richmond, VA USA
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18
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Popovic I, Bierne N, Gaiti F, Tanurdžić M, Riginos C. Pre-introduction introgression contributes to parallel differentiation and contrasting hybridization outcomes between invasive and native marine mussels. J Evol Biol 2020; 34:175-192. [PMID: 33251632 DOI: 10.1111/jeb.13746] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 11/01/2020] [Accepted: 11/11/2020] [Indexed: 12/28/2022]
Abstract
Non-native species experience novel selection pressures in introduced environments and may interbreed with native lineages. Species introductions therefore provide opportunities to investigate repeated patterns of adaptation and introgression across replicated contact zones. Here, we investigate genetic parallelism between multiple introduced populations of the invasive marine mussel, Mytilus galloprovincialis, in the absence (South Africa and California) and presence of hybridization with a native congener (Mytilus planulatus in Batemans Bay and Sydney Harbour, Australia). Repeatability in post-introduction differentiation from native-range populations varied between genetically distinct Atlantic and Mediterranean lineages, with Atlantic-derived introductions displaying high differentiation (maxFST > 0.4) and parallelism at outlier loci. Identification of long noncoding RNA transcripts (lncRNA) additionally allowed us to clarify that parallel responses are largely limited to protein-coding loci, with lncRNAs likely evolving under evolutionary constraints. Comparisons of independent hybrid zones revealed differential introgression most strongly in Batemans Bay, with an excess of M. galloprovincialis ancestry and resistance to introgression at loci differentiating parental lineages (M. planulatus and Atlantic M. galloprovincialis). Additionally, contigs putatively introgressed with divergent alleles from a closely related species, Mytilus edulis, showed stronger introgression asymmetries compared with genome-wide trends and also diverged in parallel in both Atlantic-derived introductions. These results suggest that divergent demographic histories experienced by introduced lineages, including pre-introduction introgression, influence contemporary admixture dynamics. Our findings build on previous investigations reporting contributions of historical introgression to intrinsic reproductive architectures shared between marine lineages and illustrate that interspecific introgression history can shape differentiation between colonizing populations and their hybridization with native congeners.
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Affiliation(s)
- Iva Popovic
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
| | - Nicolas Bierne
- Institut des Sciences de l'Evolution UMR 5554, Université de Montpellier, CNRS-IRD-EPHE-UM, Montpellier, France
| | - Federico Gaiti
- Weill Cornell Medicine, New York, NY, USA.,New York Genome Center, New York, NY, USA
| | - Miloš Tanurdžić
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
| | - Cynthia Riginos
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
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19
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Gerdol M, Moreira R, Cruz F, Gómez-Garrido J, Vlasova A, Rosani U, Venier P, Naranjo-Ortiz MA, Murgarella M, Greco S, Balseiro P, Corvelo A, Frias L, Gut M, Gabaldón T, Pallavicini A, Canchaya C, Novoa B, Alioto TS, Posada D, Figueras A. Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel. Genome Biol 2020; 21:275. [PMID: 33168033 PMCID: PMC7653742 DOI: 10.1186/s13059-020-02180-3] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 10/15/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The Mediterranean mussel Mytilus galloprovincialis is an ecologically and economically relevant edible marine bivalve, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive mortalities in other bivalves. Although these traits have been recently linked with the maintenance of a high genetic variation within natural populations, the factors underlying the evolutionary success of this species remain unclear. RESULTS Here, after the assembly of a 1.28-Gb reference genome and the resequencing of 14 individuals from two independent populations, we reveal a complex pan-genomic architecture in M. galloprovincialis, with a core set of 45,000 genes plus a strikingly high number of dispensable genes (20,000) subject to presence-absence variation, which may be entirely missing in several individuals. We show that dispensable genes are associated with hemizygous genomic regions affected by structural variants, which overall account for nearly 580 Mb of DNA sequence not included in the reference genome assembly. As such, this is the first study to report the widespread occurrence of gene presence-absence variation at a whole-genome scale in the animal kingdom. CONCLUSIONS Dispensable genes usually belong to young and recently expanded gene families enriched in survival functions, which might be the key to explain the resilience and invasiveness of this species. This unique pan-genome architecture is characterized by dispensable genes in accessory genomic regions that exceed by orders of magnitude those observed in other metazoans, including humans, and closely mirror the open pan-genomes found in prokaryotes and in a few non-metazoan eukaryotes.
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Affiliation(s)
- Marco Gerdol
- Department of Life Sciences, Università degli Studi di Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Rebeca Moreira
- Instituto de Investigaciones Marinas (IIM - CSIC), Eduardo Cabello, 6, 36208 Vigo, Spain
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Jessica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Anna Vlasova
- CRG - Centre for Genomic Regulation, Doctor Aiguader, 88, 08003 Barcelona, Spain
| | - Umberto Rosani
- Department of Biology, Università degli Studi di Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Paola Venier
- Department of Biology, Università degli Studi di Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Miguel A. Naranjo-Ortiz
- CRG - Centre for Genomic Regulation, Doctor Aiguader, 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Maria Murgarella
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Samuele Greco
- Department of Life Sciences, Università degli Studi di Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Pablo Balseiro
- Instituto de Investigaciones Marinas (IIM - CSIC), Eduardo Cabello, 6, 36208 Vigo, Spain
- Norce Norwegian Research Centre AS, Bergen, Norway
| | - André Corvelo
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- New York Genome Center, New York, NY 10013 USA
| | - Leonor Frias
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Toni Gabaldón
- CRG - Centre for Genomic Regulation, Doctor Aiguader, 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
- Current address: Barelona Supercomputing Centre (BSC-CNS) and Institute for Research in Biomedicine (IRB), 08034 Barcelona, Spain
| | - Alberto Pallavicini
- Department of Life Sciences, Università degli Studi di Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
- Anton Dohrn Zoological Station, 80121 Villa Comunale, Naples, Italy
| | - Carlos Canchaya
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute, 36310 Vigo, Spain
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas (IIM - CSIC), Eduardo Cabello, 6, 36208 Vigo, Spain
| | - Tyler S. Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - David Posada
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute, 36310 Vigo, Spain
| | - Antonio Figueras
- Instituto de Investigaciones Marinas (IIM - CSIC), Eduardo Cabello, 6, 36208 Vigo, Spain
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20
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Simon A, Fraïsse C, El Ayari T, Liautard-Haag C, Strelkov P, Welch JJ, Bierne N. How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. J Evol Biol 2020; 34:208-223. [PMID: 33045123 DOI: 10.1111/jeb.13709] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 08/20/2020] [Accepted: 09/16/2020] [Indexed: 12/19/2022]
Abstract
The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study 'replicated' instances of secondary contact between closely related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.
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Affiliation(s)
- Alexis Simon
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Christelle Fraïsse
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France.,Institute of Science and Technology Austria, Klosterneuburg, Austria, Austria
| | - Tahani El Ayari
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | - Petr Strelkov
- St. Petersburg State University, St. Petersburg, Russia.,Laboratory of Monitoring and Conservation of Natural Arctic Ecosystems, Murmansk Arctic State University, Murmansk, Russia
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Nicolas Bierne
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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21
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Wenne R, Zbawicka M, Bach L, Strelkov P, Gantsevich M, Kukliński P, Kijewski T, McDonald JH, Sundsaasen KK, Árnyasi M, Lien S, Kaasik A, Herkül K, Kotta J. Trans-Atlantic Distribution and Introgression as Inferred from Single Nucleotide Polymorphism: Mussels Mytilus and Environmental Factors. Genes (Basel) 2020; 11:genes11050530. [PMID: 32397617 PMCID: PMC7288462 DOI: 10.3390/genes11050530] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/30/2020] [Accepted: 05/02/2020] [Indexed: 12/11/2022] Open
Abstract
Large-scale climate changes influence the geographic distribution of biodiversity. Many taxa have been reported to extend or reduce their geographic range, move poleward or displace other species. However, for closely related species that can hybridize in the natural environment, displacement is not the only effect of changes of environmental variables. Another option is subtler, hidden expansion, which can be found using genetic methods only. The marine blue mussels Mytilus are known to change their geographic distribution despite being sessile animals. In addition to natural dissemination at larval phase—enhanced by intentional or accidental introductions and rafting—they can spread through hybridization and introgression with local congeners, which can create mixed populations sustaining in environmental conditions that are marginal for pure taxa. The Mytilus species have a wide distribution in coastal regions of the Northern and Southern Hemisphere. In this study, we investigated the inter-regional genetic differentiation of the Mytilus species complex at 53 locations in the North Atlantic and adjacent Arctic waters and linked this genetic variability to key local environmental drivers. Of seventy-nine candidate single nucleotide polymorphisms (SNPs), all samples were successfully genotyped with a subset of 54 SNPs. There was a clear interregional separation of Mytilus species. However, all three Mytilus species hybridized in the contact area and created hybrid zones with mixed populations. Boosted regression trees (BRT) models showed that inter-regional variability was important in many allele models but did not prevail over variability in local environmental factors. Local environmental variables described over 40% of variability in about 30% of the allele frequencies of Mytilus spp. For the 30% of alleles, variability in their frequencies was only weakly coupled with local environmental conditions. For most studied alleles the linkages between environmental drivers and the genetic variability of Mytilus spp. were random in respect to “coding” and “non-coding” regions. An analysis of the subset of data involving functional genes only showed that two SNPs at Hsp70 and ATPase genes correlated with environmental variables. Total predictive ability of the highest performing models (r2 between 0.550 and 0.801) were for alleles that discriminated most effectively M. trossulus from M. edulis and M. galloprovincialis, whereas the best performing allele model (BM101A) did the best at discriminating M. galloprovincialis from M. edulis and M. trossulus. Among the local environmental variables, salinity, water temperature, ice cover and chlorophyll a concentration were by far the greatest predictors, but their predictive performance varied among different allele models. In most cases changes in the allele frequencies along these environmental gradients were abrupt and occurred at a very narrow range of environmental variables. In general, regions of change in allele frequencies for M. trossulus occurred at 8–11 psu, 0–10 °C, 60%–70% of ice cover and 0–2 mg m−3 of chlorophyll a, M. edulis at 8–11 and 30–35 psu, 10–14 °C and 60%–70% of ice cover and for M. galloprovincialis at 30–35 psu, 14–20 °C.
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Affiliation(s)
- Roman Wenne
- Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland; (M.Z.); (P.K.); (T.K.)
- Correspondence: ; Tel.: +48-58-7311763
| | - Małgorzata Zbawicka
- Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland; (M.Z.); (P.K.); (T.K.)
| | - Lis Bach
- Arctic Research Centre, Department of Bioscience, Aarhus University, 4000 Roskilde, Denmark;
| | - Petr Strelkov
- Department of Ichthyology and Hydrobiology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Mikhail Gantsevich
- Department of Invertebrate Zoology, Faculty of Biology, Moscow MV Lomonosov State University, 119234 Moscow, Russia;
| | - Piotr Kukliński
- Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland; (M.Z.); (P.K.); (T.K.)
| | - Tomasz Kijewski
- Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland; (M.Z.); (P.K.); (T.K.)
| | - John H. McDonald
- Biology Department, Western Washington University, Bellingham, WA 98225, USA;
| | - Kristil Kindem Sundsaasen
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1432 Ås, Norway; (K.K.S.); (M.Á.); (S.L.)
| | - Mariann Árnyasi
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1432 Ås, Norway; (K.K.S.); (M.Á.); (S.L.)
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1432 Ås, Norway; (K.K.S.); (M.Á.); (S.L.)
| | - Ants Kaasik
- Estonian Marine Institute, University of Tartu, 12619 Tallinn, Estonia; (A.K.); (K.H.); (J.K.)
| | - Kristjan Herkül
- Estonian Marine Institute, University of Tartu, 12619 Tallinn, Estonia; (A.K.); (K.H.); (J.K.)
| | - Jonne Kotta
- Estonian Marine Institute, University of Tartu, 12619 Tallinn, Estonia; (A.K.); (K.H.); (J.K.)
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22
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Lapègue S, Heurtebise S, Cornette F, Guichoux E, Gagnaire PA. Genetic Characterization of Cupped Oyster Resources in Europe Using Informative Single Nucleotide Polymorphism (SNP) Panels. Genes (Basel) 2020; 11:E451. [PMID: 32326303 PMCID: PMC7230726 DOI: 10.3390/genes11040451] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/07/2020] [Accepted: 04/15/2020] [Indexed: 11/16/2022] Open
Abstract
The Pacific oyster, Crassostrea gigas, was voluntarily introduced from Japan and British Columbia into Europe in the early 1970s, mainly to replace the Portuguese oyster, Crassostrea angulata, in the French shellfish industry, following a severe disease outbreak. Since then, the two species have been in contact in southern Europe and, therefore, have the potential to exchange genes. Recent evolutionary genomic works have provided empirical evidence that C. gigas and C. angulata exhibit partial reproductive isolation. Although hybridization occurs in nature, the rate of interspecific gene flow varies across the genome, resulting in highly heterogeneous genome divergence. Taking this biological property into account is important to characterize genetic ancestry and population structure in oysters. Here, we identified a subset of ancestry-informative makers from the most differentiated regions of the genome using existing genomic resources. We developed two different panels in order to (i) easily differentiate C. gigas and C. angulata, and (ii) describe the genetic diversity and structure of the cupped oyster with a particular focus on French Atlantic populations. Our results confirm high genetic homogeneity among Pacific cupped oyster populations in France and reveal several cases of introgressions between Portuguese and Japanese oysters in France and Portugal.
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Affiliation(s)
- Sylvie Lapègue
- Ifremer, SG2M-LGPMM, 17390 La Tremblade, France; (S.H.); (F.C.)
| | | | | | - Erwan Guichoux
- BIOGECO, INRAE, University Bordeaux, F-33610 Cestas, France;
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23
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Der Sarkissian C, Möller P, Hofman CA, Ilsøe P, Rick TC, Schiøtte T, Sørensen MV, Dalén L, Orlando L. Unveiling the Ecological Applications of Ancient DNA From Mollusk Shells. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00037] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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24
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Simon A, Arbiol C, Nielsen EE, Couteau J, Sussarellu R, Burgeot T, Bernard I, Coolen JWP, Lamy J, Robert S, Skazina M, Strelkov P, Queiroga H, Cancio I, Welch JJ, Viard F, Bierne N. Replicated anthropogenic hybridisations reveal parallel patterns of admixture in marine mussels. Evol Appl 2020; 13:575-599. [PMID: 32431737 PMCID: PMC7045717 DOI: 10.1111/eva.12879] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 09/27/2019] [Accepted: 10/02/2019] [Indexed: 12/29/2022] Open
Abstract
Human-mediated transport creates secondary contacts between genetically differentiated lineages, bringing new opportunities for gene exchange. When similar introductions occur in different places, they provide informally replicated experiments for studying hybridisation. We here examined 4,279 Mytilus mussels, sampled in Europe and genotyped with 77 ancestry-informative markers. We identified a type of introduced mussels, called "dock mussels," associated with port habitats and displaying a particular genetic signal of admixture between M. edulis and the Mediterranean lineage of M. galloprovincialis. These mussels exhibit similarities in their ancestry compositions, regardless of the local native genetic backgrounds and the distance separating colonised ports. We observed fine-scale genetic shifts at the port entrance, at scales below natural dispersal distance. Such sharp clines do not fit with migration-selection tension zone models, and instead suggest habitat choice and early-stage adaptation to the port environment, possibly coupled with connectivity barriers. Variations in the spread and admixture patterns of dock mussels seem to be influenced by the local native genetic backgrounds encountered. We next examined departures from the average admixture rate at different loci, and compared human-mediated admixture events, to naturally admixed populations and experimental crosses. When the same M. galloprovincialis background was involved, positive correlations in the departures of loci across locations were found; but when different backgrounds were involved, no or negative correlations were observed. While some observed positive correlations might be best explained by a shared history and saltatory colonisation, others are likely produced by parallel selective events. Altogether, genome-wide effect of admixture seems repeatable and more dependent on genetic background than environmental context. Our results pave the way towards further genomic analyses of admixture, and monitoring of the spread of dock mussels both at large and at fine spacial scales.
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Affiliation(s)
- Alexis Simon
- ISEMUniv MontpellierCNRSEPHEIRDMontpellierFrance
| | | | - Einar Eg Nielsen
- Section for Marine Living ResourcesNational Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | | | - Rossana Sussarellu
- Ifremer Unité Biogéochimie et ÉcotoxicologieCentre AtlantiqueNantesFrance
| | - Thierry Burgeot
- Ifremer Unité Biogéochimie et ÉcotoxicologieCentre AtlantiqueNantesFrance
| | | | - Joop W. P. Coolen
- Wageningen Marine ResearchDen HelderThe Netherlands
- Aquatic Ecology and Water Quality Management GroupWageningen UniversityWageningenThe Netherlands
| | - Jean‐Baptiste Lamy
- SG2M‐LGPMMLaboratoire de Génétique et Pathologie des Mollusques MarinsIfremerLa TrembladeFrance
| | - Stéphane Robert
- SG2M‐LGPMMLaboratoire de Génétique et Pathologie des Mollusques MarinsIfremerLa TrembladeFrance
| | - Maria Skazina
- St. Petersburg State UniversitySt. PetersburgRussia
- Laboratory of Monitoring and Conservation of Natural Arctic EcosystemsMurmansk Arctic State UniversityMurmanskRussia
| | - Petr Strelkov
- St. Petersburg State UniversitySt. PetersburgRussia
- Laboratory of Monitoring and Conservation of Natural Arctic EcosystemsMurmansk Arctic State UniversityMurmanskRussia
| | | | - Ibon Cancio
- CBET Research GroupDepartment of Zoology and Animal Cell BiologyFaculty Science and Technology and Research Centre for Experimental Marine Biology and Biotechnology (PiE‐UPV/EHU)University of the Basque Country (UPV/EHU)BilbaoSpain
| | - John J. Welch
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Frédérique Viard
- Department AD2MUPMC Univ Paris 06CNRSUMR 7144Station BiologiqueSorbonne UniversitésRoscoffFrance
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25
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Popovic I, Matias AMA, Bierne N, Riginos C. Twin introductions by independent invader mussel lineages are both associated with recent admixture with a native congener in Australia. Evol Appl 2020; 13:515-532. [PMID: 32431733 PMCID: PMC7045716 DOI: 10.1111/eva.12857] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 06/27/2019] [Accepted: 07/24/2019] [Indexed: 01/04/2023] Open
Abstract
Introduced species can impose profound impacts on the evolution of receiving communities with which they interact. If native and introduced taxa remain reproductively semi-isolated, human-mediated secondary contact may promote genetic exchange across newly created hybrid zones, potentially impacting native genetic diversity and invasive species spread. Here, we investigate the contributions of recent divergence histories and ongoing (post-introduction) gene flow between the invasive marine mussel, Mytilus galloprovincialis, and a morphologically indistinguishable and taxonomically contentious native Australian taxon, Mytilus planulatus. Using transcriptome-wide markers, we demonstrate that two contemporary M. galloprovincialis introductions into south-eastern Australia originate from genetically divergent lineages from its native range in the Mediterranean Sea and Atlantic Europe, where both introductions have led to repeated instances of admixture between introduced and endemic populations. Through increased genome-wide resolution of species relationships, combined with demographic modelling, we validate that mussels sampled in Tasmania are representative of the endemic Australian taxon (M. planulatus), but share strong genetic affinities to M. galloprovincialis. Demographic inferences indicate late-Pleistocene divergence times and historical gene flow between the Tasmanian endemic lineage and northern M. galloprovincialis, suggesting that native and introduced taxa have experienced a period of historical isolation of at least 100,000 years. Our results demonstrate that many genomic loci and sufficient sampling of closely related lineages in both sympatric (e.g. Australian populations) and allopatric (e.g. northern hemisphere Mytilus taxa) ranges are necessary to accurately (a) interpret patterns of intraspecific differentiation and to (b) distinguish contemporary invasive introgression from signatures left by recent divergence histories in high dispersal marine species. More broadly, our study fills a significant gap in systematic knowledge of native Australian biodiversity and sheds light on the intrinsic challenges for invasive species research when native and introduced species boundaries are not well defined.
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Affiliation(s)
- Iva Popovic
- School of Biological SciencesUniversity of QueenslandSt LuciaQldAustralia
| | | | - Nicolas Bierne
- Institut des Sciences de l’EvolutionUMR 5554CNRS‐IRD‐EPHE‐UMUniversité de MontpellierMontpellierFrance
| | - Cynthia Riginos
- School of Biological SciencesUniversity of QueenslandSt LuciaQldAustralia
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26
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Popovic I, Riginos C. Comparative genomics reveals divergent thermal selection in warm‐ and cold‐tolerant marine mussels. Mol Ecol 2020; 29:519-535. [DOI: 10.1111/mec.15339] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Iva Popovic
- School of Biological Sciences University of Queensland St Lucia Qld Australia
| | - Cynthia Riginos
- School of Biological Sciences University of Queensland St Lucia Qld Australia
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27
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Yonemitsu MA, Giersch RM, Polo-Prieto M, Hammel M, Simon A, Cremonte F, Avilés FT, Merino-Véliz N, Burioli EAV, Muttray AF, Sherry J, Reinisch C, Baldwin SA, Goff SP, Houssin M, Arriagada G, Vázquez N, Bierne N, Metzger MJ. A single clonal lineage of transmissible cancer identified in two marine mussel species in South America and Europe. eLife 2019; 8:e47788. [PMID: 31686650 PMCID: PMC6831032 DOI: 10.7554/elife.47788] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/23/2019] [Indexed: 12/13/2022] Open
Abstract
Transmissible cancers, in which cancer cells themselves act as an infectious agent, have been identified in Tasmanian devils, dogs, and four bivalves. We investigated a disseminated neoplasia affecting geographically distant populations of two species of mussels (Mytilus chilensis in South America and M. edulis in Europe). Sequencing alleles from four loci (two nuclear and two mitochondrial) provided evidence of transmissible cancer in both species. Phylogenetic analysis of cancer-associated alleles and analysis of diagnostic SNPs showed that cancers in both species likely arose in a third species of mussel (M. trossulus), but these cancer cells are independent from the previously identified transmissible cancer in M. trossulus from Canada. Unexpectedly, cancers from M. chilensis and M. edulis are nearly identical, showing that the same cancer lineage affects both. Thus, a single transmissible cancer lineage has crossed into two new host species and has been transferred across the Atlantic and Pacific Oceans and between the Northern and Southern hemispheres.
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Affiliation(s)
| | | | | | - Maurine Hammel
- ISEM, Université de Montpellier, CNRS- EPHE-IRDMontpellierFrance
- IHPE, Université de Montpellier, CNRS-Ifremer-UPVDMontpellierFrance
| | - Alexis Simon
- ISEM, Université de Montpellier, CNRS- EPHE-IRDMontpellierFrance
| | - Florencia Cremonte
- Laboratorio de Parasitología (LAPA)Instituto de Biología de Organismos Marinos (IBIOMAR) (CCT CONICET - CENPAT)Puerto MadrynArgentina
| | - Fernando T Avilés
- Instituto de Ciencias Biomedicas, Facultad de Medicina y Facultad de Ciencias de la VidaUniversidad Andres BelloSantiagoChile
| | - Nicolás Merino-Véliz
- Instituto de Ciencias Biomedicas, Facultad de Medicina y Facultad de Ciencias de la VidaUniversidad Andres BelloSantiagoChile
| | | | | | - James Sherry
- Water Science & Technology DirectorateEnvironment and Climate Change CanadaBurlingtonCanada
| | - Carol Reinisch
- Water Science & Technology DirectorateEnvironment and Climate Change CanadaBurlingtonCanada
| | - Susan A Baldwin
- Chemical and Biological EngineeringUniversity of British ColumbiaVancouverCanada
| | - Stephen P Goff
- Howard Hughes Medical InstituteChevy ChaseUnited States
- Department of Microbiology and ImmunologyColumbia University Medical CenterNew YorkUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia University Medical CenterNew YorkUnited States
| | - Maryline Houssin
- Research and DevelopmentLABÉO Frank DuncombeSaint-ContestFrance
- FRE BOREA, MNHN, UPMC, UCN, CNRS-7208, IRD-207, Université de Caen NormandieCaenFrance
| | - Gloria Arriagada
- Instituto de Ciencias Biomedicas, Facultad de Medicina y Facultad de Ciencias de la VidaUniversidad Andres BelloSantiagoChile
| | - Nuria Vázquez
- Laboratorio de Parasitología (LAPA)Instituto de Biología de Organismos Marinos (IBIOMAR) (CCT CONICET - CENPAT)Puerto MadrynArgentina
| | - Nicolas Bierne
- ISEM, Université de Montpellier, CNRS- EPHE-IRDMontpellierFrance
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28
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Dudek K, Gaczorek TS, Zieliński P, Babik W. Massive introgression of major histocompatibility complex (MHC) genes in newt hybrid zones. Mol Ecol 2019; 28:4798-4810. [PMID: 31574568 DOI: 10.1111/mec.15254] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 12/22/2022]
Abstract
Variation in the vertebrate major histocompatibility complex (MHC) genes is crucial for fighting pathogen assault. Because new alleles confer a selective advantage, MHC should readily introgress between species, even under limited hybridization. Using replicated transects through two hybrid zones between strongly reproductively isolated European newts, Lissotriton montandoni and L. vulgaris, we demonstrated recent and ongoing MHC class I and II introgression in the Carpathian region. The extent of introgression correlated with the age of contact. In the older zone, MHC similarity between species within transects exceeded similarity between transects within species, implying pervasive introgression - a massive exchange of MHC genes, not limited to specific variants. In simulations, the observed pattern emerged under the combined action of balancing selection and hybridization, but not when these processes acted separately. Thus, massive introgression at advanced stages of divergence can introduce novel and restore previously lost MHC variation, boosting the adaptive potential of hybridizing taxa. In consequence, MHC genes may be the last to stop introgressing between incipient species.
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Affiliation(s)
- Katarzyna Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Tomasz S Gaczorek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Piotr Zieliński
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
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29
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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] [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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30
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Zbawicka M, Gardner JPA, Wenne R. Cryptic diversity in smooth-shelled mussels on Southern Ocean islands: connectivity, hybridisation and a marine invasion. Front Zool 2019; 16:32. [PMID: 31406494 PMCID: PMC6685288 DOI: 10.1186/s12983-019-0332-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/24/2019] [Indexed: 01/08/2023] Open
Abstract
Background Large numbers of endemic species inhabit subantarctic continental coasts and islands that are characterised by highly variable environmental conditions. Southern hemisphere populations of taxa that are morphologically similar to northern counterparts have traditionally been considered to be extensions of such Northern hemisphere taxa, and may not exhibit differentiation amongst geographically isolated populations in the Southern Ocean. Smooth-shelled blue mussels of the genus Mytilus that exhibit an anti-tropical distribution are a model group to study phylogeography, speciation and hybridisation in the sea, and contribute to the theory and practice of marine biosecurity. Methods We used a single nucleotide polymorphism (SNPs) panel that has the ability to accurately identify reference Northern and Southern hemisphere Mytilus taxa to test for evolutionary differentiation amongst native Southern Ocean island populations. Results Native mussels from the Falkland Islands and the Kerguelen Islands exhibited greatest affinity to native M. platensis d’Orbigny 1846 from the Atlantic coast of South America. The major Southern Ocean current flow from west to east is likely to explain the spreading of M. platensis to remote offshore islands, as adults via the process of rafting or perhaps directly as larvae. SNPs variation revealed that mussels from Tasmania were native and clearly differentiated from all other blue mussel groups in the Southern and Northern hemispheres. The native mussels M. planulatus from Tasmania and from mainland New Zealand (NZ), and tentatively M. aoteanus from the two NZ Southern Ocean offshore island groups (the Auckland Islands and Campbell Island), formed a distinct M. galloprovincialis–like Southern hemisphere group with closest affinity to Northern hemisphere M. galloprovincialis from the Mediterranean Sea. In all cases, the SNPs revealed evidence of hybridisation between two or more distinct taxa. The invasive Northern hemisphere M. galloprovincialis was identified only in Tasmania, amongst native mussels of a distinct Australian M. planulatus lineage. Conclusion Overall, our results reveal that Southern hemisphere island mussels have mixed genome ancestry and are native, not introduced by human activities. The preservation of distinct evolutionary lineages of Southern hemisphere species needs to be an ongoing focus of conservation efforts, given that population sizes on some of the remote offshore oceanic islands will be small and may be more easily adversely affected by invasion and subsequent hybridisation and introgression than larger populations elsewhere. Electronic supplementary material The online version of this article (10.1186/s12983-019-0332-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Małgorzata Zbawicka
- 1Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Jonathan P A Gardner
- 2School of Biological Sciences, Victoria University of Wellington, P O Box 600, Wellington, 6140 New Zealand
| | - Roman Wenne
- 1Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
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31
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Foote AD, Martin MD, Louis M, Pacheco G, Robertson KM, Sinding MHS, Amaral AR, Baird RW, Baker CS, Ballance L, Barlow J, Brownlow A, Collins T, Constantine R, Dabin W, Dalla Rosa L, Davison NJ, Durban JW, Esteban R, Ferguson SH, Gerrodette T, Guinet C, Hanson MB, Hoggard W, Matthews CJD, Samarra FIP, de Stephanis R, Tavares SB, Tixier P, Totterdell JA, Wade P, Excoffier L, Gilbert MTP, Wolf JBW, Morin PA. Killer whale genomes reveal a complex history of recurrent admixture and vicariance. Mol Ecol 2019; 28:3427-3444. [PMID: 31131963 DOI: 10.1111/mec.15099] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/06/2019] [Accepted: 04/08/2019] [Indexed: 02/06/2023]
Abstract
Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during postglacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.
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Affiliation(s)
- Andrew D Foote
- CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | | | - Marie Louis
- Department of Biology, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Denmark.,Scottish Oceans Institute, East Sands, University of St. Andrews, St. Andrews, UK
| | - George Pacheco
- Department of Biology, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Denmark
| | - Kelly M Robertson
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Mikkel-Holger S Sinding
- Department of Biology, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Ana R Amaral
- American Museum of Natural History, New York City, New York.,Faculdade de Ciências Universidade de Lisboa, Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal
| | | | - Charles Scott Baker
- Department of Fisheries and Wildlife, Marine Mammal Institute, Oregon State University, Newport, Oregon.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Lisa Ballance
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Jay Barlow
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, SRUC Veterinary Services Drummondhill, Inverness, UK
| | - Tim Collins
- Ocean Giants Program, Wildlife Conservation Society, New York City, New York
| | | | - Willy Dabin
- Observatoire Pelagis, Université de La Rochelle-CNRS, La Rochelle, France
| | - Luciano Dalla Rosa
- Laboratório de Ecologia e Conservação da Megafauna Marinha, Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Nicholas J Davison
- Scottish Marine Animal Stranding Scheme, SRUC Veterinary Services Drummondhill, Inverness, UK
| | - John W Durban
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Ruth Esteban
- CIRCE, Conservation, Information and Research on Cetaceans, Algeciras, Spain
| | | | - Tim Gerrodette
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Christophe Guinet
- Centre d'Etudes Biologiques de Chizé (CEBC), CNRS-ULR, UMR, Chizé, France
| | - M Bradley Hanson
- National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Northwest Fisheries Science Center, Seattle, Washington
| | - Wayne Hoggard
- National Marine Fisheries Service, NOAA, Southeast Fisheries Science Center, Pascagoula, Mississippi
| | | | | | - Renaud de Stephanis
- CIRCE, Conservation, Information and Research on Cetaceans, Algeciras, Spain
| | - Sara B Tavares
- Scottish Oceans Institute, East Sands, University of St. Andrews, St. Andrews, UK
| | - Paul Tixier
- Centre d'Etudes Biologiques de Chizé (CEBC), CNRS-ULR, UMR, Chizé, France.,School of Life and Environmental Sciences (Burwood Campus), Deakin University, Geelong, Victoria, Australia
| | - John A Totterdell
- Marine Information and Research Group-Australia (MIRG), Quinns Rocks, Western Australia, Australia
| | - Paul Wade
- National Marine Mammal Laboratory, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Alaska Fisheries Science Center, Seattle, Washington
| | - Laurent Excoffier
- CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - M Thomas P Gilbert
- NTNU University Museum, Trondheim, Norway.,Department of Biology, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Denmark
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany.,Department of Evolutionary Biology, Science of Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Phillip A Morin
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
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32
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Multilevel fine-scale diversity challenges the 'cryptic species' concept. Sci Rep 2019; 9:6732. [PMID: 31043629 PMCID: PMC6494890 DOI: 10.1038/s41598-019-42297-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 03/29/2019] [Indexed: 01/08/2023] Open
Abstract
‘Cryptic’ species are an emerging biological problem that is broadly discussed in the present study. Recently, a cryptic species definition was suggested for those species which manifest low morphological, but considerable genetic, disparity. As a case study we present unique material from a charismatic group of nudibranch molluscs of the genus Trinchesia from European waters to reveal three new species and demonstrate that they show a dual nature: on one hand, they can be considered a ‘cryptic’ species complex due to their overall similarity, but on the other hand, stable morphological differences as well as molecular differences are demonstrated for every species in that complex. Thus, this species complex can equally be named ‘cryptic’, ‘pseudocryptic’ or ‘non-cryptic’. We also present evidence for an extremely rapid speciation rate in this species complex and link the species problem with epigenetics. Available metazoan-wide data, which are broadly discussed in the present study, show the unsuitability of a ‘cryptic’ species concept because the degree of crypticity represents a continuum when a finer multilevel morphological and molecular scale is applied to uncover more narrowly defined species making the ‘cryptic’ addition to ‘species’ redundant. Morphological and molecular methods should be applied in concordance to form a fine-scale multilevel taxonomic framework, and not necessarily implying only an a posteriori transformation of exclusively molecular-based ‘cryptic’ species into morphologically-defined ‘pseudocryptic’ ones. Implications of the present study have importance for many fields, including conservation biology and fine-scale biodiversity assessments.
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Sromek L, Forcioli D, Lasota R, Furla P, Wolowicz M. Next-generation phylogeography of the cockle Cerastoderma glaucum: Highly heterogeneous genetic differentiation in a lagoon species. Ecol Evol 2019; 9:4667-4682. [PMID: 31031934 PMCID: PMC6476780 DOI: 10.1002/ece3.5070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 01/30/2019] [Accepted: 02/25/2019] [Indexed: 11/10/2022] Open
Abstract
AIM Coastal lagoons form an intriguing example of fragmented marine habitats. Restricted gene flow among isolated populations of lagoon species may promote their genetic divergence and may thus provide a first step toward speciation. In the present study, the population genetic structure of the lagoon cockle Cerastoderma glaucum has been investigated to clarify the complex phylogeographic pattern found in previous studies, to localize major genetic breaks, and to discuss their origin and maintenance. LOCATION The Atlantic and Mediterranean coasts, including the Baltic, North Sea, and Black Sea. METHODS A total of 204 C. glaucum individuals from 14 populations were genotyped using restriction site-associated DNA sequencing (RADseq). The genetic diversity, divergence, and structure were analyzed using genome-wide single nucleotide polymorphisms (SNPs). Phylogenetic relationships were inferred under a coalescent model using svdquartets. RESULTS The RADseq approach allowed inferring phylogeographic relationships with an unprecedented resolution. Three deeply divergent lineages were identified within C. glaucum that are separated by many genetic barriers: one lineage in the Aegean-Black Sea region, one in the Ionian Sea, and the last one widely distributed from the Western Mediterranean to the Baltic Sea. The nested branching pattern displayed on the species tree largely agrees with the likely scenario of C. glaucum postglacial expansion from the Mediterranean to the Baltic Sea. MAIN CONCLUSION The genetic differentiations between geographically separated lagoons proved to be strong, highlighting the evolutionary influence of these naturally fragmented habitats. The postglacial expansion created complex patterns of spatial segregation of genetic diversity with allele frequency gradients in many outlier loci, but also discrepancies between the nuclear and mitochondrial genetic markers that probably arose from genetic surfing of mitochondrial variation.
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Affiliation(s)
- Ludmila Sromek
- Department of Marine Ecosystems Functioning, Institute of Oceanography, Faculty of Oceanography and Geography University of Gdansk Gdynia Poland
- UPMC Université Paris 06, Université Antilles, Université Nice Sophia Antipolis, CNRS, Laboratoire Evolution Paris Seine, Institut de Biologie Paris Seine (EPS-IBPS) Sorbonne Universités Paris France
| | - Didier Forcioli
- UPMC Université Paris 06, Université Antilles, Université Nice Sophia Antipolis, CNRS, Laboratoire Evolution Paris Seine, Institut de Biologie Paris Seine (EPS-IBPS) Sorbonne Universités Paris France
| | - Rafal Lasota
- Department of Marine Ecosystems Functioning, Institute of Oceanography, Faculty of Oceanography and Geography University of Gdansk Gdynia Poland
| | - Paola Furla
- UPMC Université Paris 06, Université Antilles, Université Nice Sophia Antipolis, CNRS, Laboratoire Evolution Paris Seine, Institut de Biologie Paris Seine (EPS-IBPS) Sorbonne Universités Paris France
| | - Maciej Wolowicz
- Department of Marine Ecosystems Functioning, Institute of Oceanography, Faculty of Oceanography and Geography University of Gdansk Gdynia Poland
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El Ayari T, Trigui El Menif N, Hamer B, Cahill AE, Bierne N. The hidden side of a major marine biogeographic boundary: a wide mosaic hybrid zone at the Atlantic-Mediterranean divide reveals the complex interaction between natural and genetic barriers in mussels. Heredity (Edinb) 2019; 122:770-784. [PMID: 30675016 DOI: 10.1038/s41437-018-0174-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 11/25/2018] [Accepted: 11/30/2018] [Indexed: 01/26/2023] Open
Abstract
The Almeria-Oran Front (AOF) is a recognised hotspot of genetic differentiation in the sea, with genetic discontinuities reported in more than 50 species. The AOF is a barrier to dispersal and an ecological boundary; both can determine the position of these genetic breaks. However, the maintenance of genetic differentiation is likely reinforced by genetic barriers. A general drawback of previous studies is an insufficient density of sampling sites at the transition zone, with a conspicuous lack of samples from the southern coastline. We analysed the fine-scale genetic structure in the mussel Mytilus galloprovincialis using a few ancestry-informative loci previously identified from genome scans. We discovered a 600-km-wide mosaic hybrid zone eastward of the AOF along the Algerian coasts. This mosaic zone provides a new twist to our understanding of the Atlantic-Mediterranean transition because it demonstrates that the two lineages can live in sympatry with ample opportunities to interbreed in a large area, but they hardly do so. This implies that some form of reproductive isolation must exist to maintain the two genetic backgrounds locally cohesive. The mosaic zone ends with an abrupt genetic shift at a barrier to dispersal in the Gulf of Bejaia, Eastern Algeria. Simulations of endogenous or exogenous selection in models that account for the geography and hydrodynamic features of the region support the hypothesis that sister hybrid zones could have been differentially trapped at two alternative barriers to dispersal and/or environmental boundaries, at Almeria in the north and Bejaia in the south. A preponderantly unidirectional north-south gene flow next to the AOF can also maintain a patch of intrinsically maintained genetic background in the south and the mosaic structure, even in the absence of local adaptation. Our results concur with the coupling hypothesis that suggests that natural barriers can explain the position of genetic breaks, while their maintenance depends on genetic barriers.
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Affiliation(s)
- Tahani El Ayari
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France.,Faculty of Sciences of Bizerta, Laboratory of Environment Bio-monitoring, University of Carthage, 7021, Zarzouna, Bizerta, Tunisia
| | - Najoua Trigui El Menif
- Faculty of Sciences of Bizerta, Laboratory of Environment Bio-monitoring, University of Carthage, 7021, Zarzouna, Bizerta, Tunisia
| | - Bojan Hamer
- Ruđer Bošković Institute, Center for Marine and Environmental Research, Grad Zagreb, Croatia
| | | | - Nicolas Bierne
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France.
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35
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Simon A, Bierne N, Welch JJ. Coadapted genomes and selection on hybrids: Fisher's geometric model explains a variety of empirical patterns. Evol Lett 2018; 2:472-498. [PMID: 30283696 PMCID: PMC6145440 DOI: 10.1002/evl3.66] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/02/2018] [Accepted: 06/06/2018] [Indexed: 12/27/2022] Open
Abstract
Natural selection plays a variety of roles in hybridization, speciation, and admixture. Most research has focused on two extreme cases: crosses between closely related inbred lines, where hybrids are fitter than their parents, or crosses between effectively isolated species, where hybrids suffer severe breakdown. But many natural populations must fall into intermediate regimes, with multiple types of gene interaction, and these are more difficult to study. Here, we develop a simple fitness landscape model, and show that it naturally interpolates between previous modeling approaches, which were designed for the extreme cases, and invoke either mildly deleterious recessives, or discrete hybrid incompatibilities. Our model yields several new predictions, which we test with genomic data from Mytilus mussels, and published data from plants (Zea, Populus, and Senecio) and animals (Mus, Teleogryllus, and Drosophila). The predictions are generally supported, and the model explains a number of surprising empirical patterns. Our approach enables novel and complementary uses of genome-wide datasets, which do not depend on identifying outlier loci, or "speciation genes" with anomalous effects. Given its simplicity and flexibility, and its predictive successes with a wide range of data, the approach should be readily extendable to other outstanding questions in the study of hybridization.
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Affiliation(s)
- Alexis Simon
- Institut des Sciences de l'Évolution UMR5554, Université de MontpellierCNRS‐IRD‐EPHE‐UMFrance
- Department of GeneticsUniversity of CambridgeDowning St. CambridgeCB23EHUnited Kingdom
| | - Nicolas Bierne
- Institut des Sciences de l'Évolution UMR5554, Université de MontpellierCNRS‐IRD‐EPHE‐UMFrance
- Department of GeneticsUniversity of CambridgeDowning St. CambridgeCB23EHUnited Kingdom
| | - John J. Welch
- Department of GeneticsUniversity of CambridgeDowning St. CambridgeCB23EHUnited Kingdom
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36
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Gagnaire PA, Lamy JB, Cornette F, Heurtebise S, Dégremont L, Flahauw E, Boudry P, Bierne N, Lapègue S. Analysis of Genome-Wide Differentiation between Native and Introduced Populations of the Cupped Oysters Crassostrea gigas and Crassostrea angulata. Genome Biol Evol 2018; 10:2518-2534. [PMID: 30184067 PMCID: PMC6161763 DOI: 10.1093/gbe/evy194] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2018] [Indexed: 01/01/2023] Open
Abstract
The Pacific cupped oyster is genetically subdivided into two sister taxa, Crassostrea gigas and Crassostrea angulata, which are in contact in the north-western Pacific. The nature and origin of their genetic and taxonomic differentiation remains controversial due the lack of known reproductive barriers and the high degree of morphologic similarity. In particular, whether the presence of ecological and/or intrinsic isolating mechanisms contributes to species divergence is unknown. The recent co-introduction of both taxa into Europe offers a unique opportunity to test how genetic differentiation is maintained under new environmental and demographic conditions. We generated a pseudochromosome assembly of the Pacific oyster genome using a combination of BAC-end sequencing and scaffold anchoring to a new high-density linkage map. We characterized genome-wide differentiation between C. angulata and C. gigas in both their native and introduced ranges, and showed that gene flow between species has been facilitated by their recent co-introductions in Europe. Nevertheless, patterns of genomic divergence between species remain highly similar in Asia and Europe, suggesting that the environmental transition caused by the co-introduction of the two species did not affect the genomic architecture of their partial reproductive isolation. Increased genetic differentiation was preferentially found in regions of low recombination. Using historical demographic inference, we show that the heterogeneity of differentiation across the genome is well explained by a scenario whereby recent gene flow has eroded past differentiation at different rates across the genome after a period of geographical isolation. Our results thus support the view that low-recombining regions help in maintaining intrinsic genetic differences between the two species.
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Affiliation(s)
| | - Jean-Baptiste Lamy
- Ifremer, SG2M-LGPMM, Laboratoire de Génétique et Pathologie des Mollusques Marins, La Tremblade, France
| | - Florence Cornette
- Ifremer, SG2M-LGPMM, Laboratoire de Génétique et Pathologie des Mollusques Marins, La Tremblade, France
| | - Serge Heurtebise
- Ifremer, SG2M-LGPMM, Laboratoire de Génétique et Pathologie des Mollusques Marins, La Tremblade, France
| | - Lionel Dégremont
- Ifremer, SG2M-LGPMM, Laboratoire de Génétique et Pathologie des Mollusques Marins, La Tremblade, France
| | - Emilie Flahauw
- Ifremer, SG2M-LGPMM, Laboratoire de Génétique et Pathologie des Mollusques Marins, La Tremblade, France
| | - Pierre Boudry
- Ifremer, UMR LEMAR, Laboratoire des Sciences de l’Environnement Marin (UBO, CNRS, IRD, Ifremer), Plouzané, France
| | - Nicolas Bierne
- Institut des Sciences de l’Evolution, ISEM-CNRS, UMR5554, Montpellier, France
| | - Sylvie Lapègue
- Ifremer, SG2M-LGPMM, Laboratoire de Génétique et Pathologie des Mollusques Marins, La Tremblade, France
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Fraïsse C, Roux C, Gagnaire PA, Romiguier J, Faivre N, Welch JJ, Bierne N. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: the effects of sequencing techniques and sampling strategies. PeerJ 2018; 6:e5198. [PMID: 30083438 PMCID: PMC6071616 DOI: 10.7717/peerj.5198] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/19/2018] [Indexed: 01/25/2023] Open
Abstract
Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymous mutations computed either from exome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed.
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Affiliation(s)
- Christelle Fraïsse
- Institut des Sciences de l’Evolution UMR5554, University Montpellier, CNRS, IRD, EPHE, Montpellier, France
- Department of Genetics, University of Cambridge, Cambridge, UK
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Camille Roux
- Université de Lille, Unité Evo-Eco-Paléo (EEP), UMR 8198, Villeneuve d’Ascq, France
| | - Pierre-Alexandre Gagnaire
- Institut des Sciences de l’Evolution UMR5554, University Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Jonathan Romiguier
- Institut des Sciences de l’Evolution UMR5554, University Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Nicolas Faivre
- Institut des Sciences de l’Evolution UMR5554, University Montpellier, CNRS, IRD, EPHE, Montpellier, France
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - John J. Welch
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Nicolas Bierne
- Institut des Sciences de l’Evolution UMR5554, University Montpellier, CNRS, IRD, EPHE, Montpellier, France
- Department of Genetics, University of Cambridge, Cambridge, UK
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Storfer A, Patton A, Fraik AK. Navigating the Interface Between Landscape Genetics and Landscape Genomics. Front Genet 2018; 9:68. [PMID: 29593776 PMCID: PMC5859105 DOI: 10.3389/fgene.2018.00068] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/15/2018] [Indexed: 11/13/2022] Open
Abstract
As next-generation sequencing data become increasingly available for non-model organisms, a shift has occurred in the focus of studies of the geographic distribution of genetic variation. Whereas landscape genetics studies primarily focus on testing the effects of landscape variables on gene flow and genetic population structure, landscape genomics studies focus on detecting candidate genes under selection that indicate possible local adaptation. Navigating the transition between landscape genomics and landscape genetics can be challenging. The number of molecular markers analyzed has shifted from what used to be a few dozen loci to thousands of loci and even full genomes. Although genome scale data can be separated into sets of neutral loci for analyses of gene flow and population structure and putative loci under selection for inference of local adaptation, there are inherent differences in the questions that are addressed in the two study frameworks. We discuss these differences and their implications for study design, marker choice and downstream analysis methods. Similar to the rapid proliferation of analysis methods in the early development of landscape genetics, new analytical methods for detection of selection in landscape genomics studies are burgeoning. We focus on genome scan methods for detection of selection, and in particular, outlier differentiation methods and genetic-environment association tests because they are the most widely used. Use of genome scan methods requires an understanding of the potential mismatches between the biology of a species and assumptions inherent in analytical methods used, which can lead to high false positive rates of detected loci under selection. Key to choosing appropriate genome scan methods is an understanding of the underlying demographic structure of study populations, and such data can be obtained using neutral loci from the generated genome-wide data or prior knowledge of a species' phylogeographic history. To this end, we summarize recent simulation studies that test the power and accuracy of genome scan methods under a variety of demographic scenarios and sampling designs. We conclude with a discussion of additional considerations for future method development, and a summary of methods that show promise for landscape genomics studies but are not yet widely used.
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Affiliation(s)
- Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Austin Patton
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Alexandra K Fraik
- School of Biological Sciences, Washington State University, Pullman, WA, United States
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Schmickl R, Marburger S, Bray S, Yant L. Hybrids and horizontal transfer: introgression allows adaptive allele discovery. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5453-5470. [PMID: 29096001 DOI: 10.1093/jxb/erx297] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally. Especially striking are signals gained from contexts involving genetic transfers between populations, closely related species, or indeed between kingdoms. Here we discuss two major classes of these scenarios, adaptive introgression and horizontal gene flow, illustrating discoveries made across kingdoms.
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Affiliation(s)
- Roswitha Schmickl
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic
| | - Sarah Marburger
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sian Bray
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Levi Yant
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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40
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Blackburn GS, Brunet BMT, Muirhead K, Cusson M, Béliveau C, Levesque RC, Lumley LM, Sperling FAH. Distinct sources of gene flow produce contrasting population genetic dynamics at different range boundaries of aChoristoneurabudworm. Mol Ecol 2017; 26:6666-6684. [DOI: 10.1111/mec.14386] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 09/26/2017] [Accepted: 10/07/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Gwylim S. Blackburn
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
- Laurentian Forestry Centre; Natural Resources Canada; Canadian Forest Service; Quebec City QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Bryan M. T. Brunet
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
| | - Kevin Muirhead
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
| | - Michel Cusson
- Laurentian Forestry Centre; Natural Resources Canada; Canadian Forest Service; Quebec City QC Canada
| | - Catherine Béliveau
- Laurentian Forestry Centre; Natural Resources Canada; Canadian Forest Service; Quebec City QC Canada
| | - Roger C. Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Lisa M. Lumley
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
- Laurentian Forestry Centre; Natural Resources Canada; Canadian Forest Service; Quebec City QC Canada
| | - Felix A. H. Sperling
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
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Trucchi E, Frajman B, Haverkamp THA, Schönswetter P, Paun O. Genomic analyses suggest parallel ecological divergence in Heliosperma pusillum (Caryophyllaceae). THE NEW PHYTOLOGIST 2017; 216:267-278. [PMID: 28782803 PMCID: PMC5601199 DOI: 10.1111/nph.14722] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 06/20/2017] [Indexed: 05/24/2023]
Abstract
The mosaic distribution of interbreeding taxa with contrasting ecology and morphology offers an opportunity to study microevolutionary dynamics during ecological divergence. We investigate here the evolutionary history of an alpine and a montane ecotype of Heliosperma pusillum (Caryophyllaceae) in the south-eastern Alps. From six pairs of geographically close populations of the two ecotypes (120 individuals) we obtained a high-coverage restriction site associated DNA sequencing (RADseq) dataset that was used for demographic inference to test the hypothesis of parallel evolution of the two ecotypes. The data are consistent with repeated ecological divergence in H. pusillum, uncovering up to five polytopic origins of one ecotype from the other. A complex evolutionary history is evidenced, with local isolation-with-migration in two population pairs and intra-ecotype migration in two others. In all cases, the time of divergence or secondary contact was inferred as postglacial. A metagenomic analysis on exogenous contaminant RAD sequences suggests divergent microbial communities between the ecotypes. The lack of shared genomic regions of high divergence across population pairs illustrates the action of drift and/or local selection in shaping genetic divergence across repeated cases of ecological divergence.
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Affiliation(s)
- Emiliano Trucchi
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14Vienna1030Austria
- Department of Life Sciences and BiotechnologyUniversity of FerraraVia L. Borsari 46Ferrara44121Italy
| | - Božo Frajman
- Institute of BotanyUniversity of InnsbruckSternwartestraße 15Innsbruck6020Austria
| | - Thomas H. A. Haverkamp
- Department of BiosciencesCentre for Ecological and Evolutionary SynthesisUniversity of OsloPO Box, 1066 BlindernOslo0316Norway
| | - Peter Schönswetter
- Institute of BotanyUniversity of InnsbruckSternwartestraße 15Innsbruck6020Austria
| | - Ovidiu Paun
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14Vienna1030Austria
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Beyer J, Green NW, Brooks S, Allan IJ, Ruus A, Gomes T, Bråte ILN, Schøyen M. Blue mussels (Mytilus edulis spp.) as sentinel organisms in coastal pollution monitoring: A review. MARINE ENVIRONMENTAL RESEARCH 2017; 130:338-365. [PMID: 28802590 DOI: 10.1016/j.marenvres.2017.07.024] [Citation(s) in RCA: 285] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 07/28/2017] [Accepted: 07/31/2017] [Indexed: 05/16/2023]
Abstract
The blue mussel (Mytilus spp.) is widely used as a bioindicator for monitoring of coastal water pollution (mussel watch programs). Herein we provide a review of this study field with emphasis on: the suitability of Mytilus spp. as environmental sentinels; uptake and bioaccumulation patterns of key pollutant classes; the use of Mytilus spp. in mussel watch programs; recent trends in Norwegian mussel monitoring; environmental quality standards and background concentrations of key contaminants; pollutant effect biomarkers; confounding factors; particulate contaminants (microplastics, engineered nanomaterials); climate change; harmonization of monitoring procedures; and the use of deployed mussels (transplant caging) in pollution monitoring. Lastly, the overall state of the art of blue mussel pollution monitoring is discussed and some important issues for future research and development are highlighted.
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Affiliation(s)
- Jonny Beyer
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349, Oslo, Norway.
| | - Norman W Green
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349, Oslo, Norway
| | - Steven Brooks
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349, Oslo, Norway
| | - Ian J Allan
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349, Oslo, Norway
| | - Anders Ruus
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349, Oslo, Norway; University of Oslo, Department of Biosciences, NO-0316, Oslo, Norway
| | - Tânia Gomes
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349, Oslo, Norway
| | - Inger Lise N Bråte
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349, Oslo, Norway
| | - Merete Schøyen
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349, Oslo, Norway
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Turissini DA, Matute DR. Fine scale mapping of genomic introgressions within the Drosophila yakuba clade. PLoS Genet 2017; 13:e1006971. [PMID: 28873409 PMCID: PMC5600410 DOI: 10.1371/journal.pgen.1006971] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 09/15/2017] [Accepted: 08/09/2017] [Indexed: 12/15/2022] Open
Abstract
The process of speciation involves populations diverging over time until they are genetically and reproductively isolated. Hybridization between nascent species was long thought to directly oppose speciation. However, the amount of interspecific genetic exchange (introgression) mediated by hybridization remains largely unknown, although recent progress in genome sequencing has made measuring introgression more tractable. A natural place to look for individuals with admixed ancestry (indicative of introgression) is in regions where species co-occur. In west Africa, D. santomea and D. yakuba hybridize on the island of São Tomé, while D. yakuba and D. teissieri hybridize on the nearby island of Bioko. In this report, we quantify the genomic extent of introgression between the three species of the Drosophila yakuba clade (D. yakuba, D. santomea), D. teissieri). We sequenced the genomes of 86 individuals from all three species. We also developed and applied a new statistical framework, using a hidden Markov approach, to identify introgression. We found that introgression has occurred between both species pairs but most introgressed segments are small (on the order of a few kilobases). After ruling out the retention of ancestral polymorphism as an explanation for these similar regions, we find that the sizes of introgressed haplotypes indicate that genetic exchange is not recent (>1,000 generations ago). We additionally show that in both cases, introgression was rarer on X chromosomes than on autosomes which is consistent with sex chromosomes playing a large role in reproductive isolation. Even though the two species pairs have stable contemporary hybrid zones, providing the opportunity for ongoing gene flow, our results indicate that genetic exchange between these species is currently rare.
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Affiliation(s)
- David A. Turissini
- Biology Department, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Daniel R. Matute
- Biology Department, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
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44
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Myticalins: A Novel Multigenic Family of Linear, Cationic Antimicrobial Peptides from Marine Mussels (Mytilus spp.). Mar Drugs 2017. [DOI: 10.3390/md15080261 [doi link]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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45
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Myticalins: A Novel Multigenic Family of Linear, Cationic Antimicrobial Peptides from Marine Mussels (Mytilus spp.). Mar Drugs 2017; 15:md15080261. [PMID: 28829401 PMCID: PMC5577615 DOI: 10.3390/md15080261] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 08/11/2017] [Accepted: 08/18/2017] [Indexed: 12/18/2022] Open
Abstract
The application of high-throughput sequencing technologies to non-model organisms has brought new opportunities for the identification of bioactive peptides from genomes and transcriptomes. From this point of view, marine invertebrates represent a potentially rich, yet largely unexplored resource for de novo discovery due to their adaptation to diverse challenging habitats. Bioinformatics analyses of available genomic and transcriptomic data allowed us to identify myticalins, a novel family of antimicrobial peptides (AMPs) from the mussel Mytilus galloprovincialis, and a similar family of AMPs from Modiolus spp., named modiocalins. Their coding sequence encompasses two conserved N-terminal (signal peptide) and C-terminal (propeptide) regions and a hypervariable central cationic region corresponding to the mature peptide. Myticalins are taxonomically restricted to Mytiloida and they can be classified into four subfamilies. These AMPs are subject to considerable interindividual sequence variability and possibly to presence/absence variation. Functional assays performed on selected members of this family indicate a remarkable tissue-specific expression (in gills) and broad spectrum of activity against both Gram-positive and Gram-negative bacteria. Overall, we present the first linear AMPs ever described in marine mussels and confirm the great potential of bioinformatics tools for the de novo discovery of bioactive peptides in non-model organisms.
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46
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Myticalins: A Novel Multigenic Family of Linear, Cationic Antimicrobial Peptides from Marine Mussels (Mytilus spp.). Mar Drugs 2017. [PMID: 28829401 DOI: 10.3390/md15080261+[doi+link]] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The application of high-throughput sequencing technologies to non-model organisms has brought new opportunities for the identification of bioactive peptides from genomes and transcriptomes. From this point of view, marine invertebrates represent a potentially rich, yet largely unexplored resource for de novo discovery due to their adaptation to diverse challenging habitats. Bioinformatics analyses of available genomic and transcriptomic data allowed us to identify myticalins, a novel family of antimicrobial peptides (AMPs) from the mussel Mytilus galloprovincialis, and a similar family of AMPs from Modiolus spp., named modiocalins. Their coding sequence encompasses two conserved N-terminal (signal peptide) and C-terminal (propeptide) regions and a hypervariable central cationic region corresponding to the mature peptide. Myticalins are taxonomically restricted to Mytiloida and they can be classified into four subfamilies. These AMPs are subject to considerable interindividual sequence variability and possibly to presence/absence variation. Functional assays performed on selected members of this family indicate a remarkable tissue-specific expression (in gills) and broad spectrum of activity against both Gram-positive and Gram-negative bacteria. Overall, we present the first linear AMPs ever described in marine mussels and confirm the great potential of bioinformatics tools for the de novo discovery of bioactive peptides in non-model organisms.
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47
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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] [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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Gerdol M, Fujii Y, Hasan I, Koike T, Shimojo S, Spazzali F, Yamamoto K, Ozeki Y, Pallavicini A, Fujita H. The purplish bifurcate mussel Mytilisepta virgata gene expression atlas reveals a remarkable tissue functional specialization. BMC Genomics 2017; 18:590. [PMID: 28789640 PMCID: PMC5549309 DOI: 10.1186/s12864-017-4012-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/02/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Mytilisepta virgata is a marine mussel commonly found along the coasts of Japan. Although this species has been the subject of occasional studies concerning its ecological role, growth and reproduction, it has been so far almost completely neglected from a genetic and molecular point of view. In the present study we present a high quality de novo assembled transcriptome of the Japanese purplish mussel, which represents the first publicly available collection of expressed sequences for this species. RESULTS The assembled transcriptome comprises almost 50,000 contigs, with a N50 statistics of ~1 kilobase and a high estimated completeness based on the rate of BUSCOs identified, standing as one of the most exhaustive sequence resources available for mytiloid bivalves to date. Overall this data, accompanied by gene expression profiles from gills, digestive gland, mantle rim, foot and posterior adductor muscle, presents an accurate snapshot of the great functional specialization of these five tissues in adult mussels. CONCLUSIONS We highlight that one of the most striking features of the M. virgata transcriptome is the high abundance and diversification of lectin-like transcripts, which pertain to different gene families and appear to be expressed in particular in the digestive gland and in the gills. Therefore, these two tissues might be selected as preferential targets for the isolation of molecules with interesting carbohydrate-binding properties. In addition, by molecular phylogenomics, we provide solid evidence in support of the classification of M. virgata within the Brachidontinae subfamily. This result is in agreement with the previously proposed hypothesis that the morphological features traditionally used to group Mytilisepta spp. and Septifer spp. within the same clade are inappropriate due to homoplasy.
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Affiliation(s)
- Marco Gerdol
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34126 Trieste, Italy
| | - Yuki Fujii
- Department of Pharmacy, Faculty of Pharmaceutical Science, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo, Nagasaki, 859-3298 Japan
| | - Imtiaj Hasan
- Department of Life and Environmental System Science, Graduate School of NanoBio Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, 236-0027 Japan
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Rajshahi, Rajshahi, 6205 Bangladesh
| | - Toru Koike
- Department of Pharmacy, Faculty of Pharmaceutical Science, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo, Nagasaki, 859-3298 Japan
| | - Shunsuke Shimojo
- Department of Pharmacy, Faculty of Pharmaceutical Science, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo, Nagasaki, 859-3298 Japan
| | - Francesca Spazzali
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34126 Trieste, Italy
| | - Kaname Yamamoto
- Department of Pharmacy, Faculty of Pharmaceutical Science, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo, Nagasaki, 859-3298 Japan
| | - Yasuhiro Ozeki
- Department of Life and Environmental System Science, Graduate School of NanoBio Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, 236-0027 Japan
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34126 Trieste, Italy
| | - Hideaki Fujita
- Department of Pharmacy, Faculty of Pharmaceutical Science, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo, Nagasaki, 859-3298 Japan
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Vikhrev IV, Bolotov IN, Altun A, Gofarov MY, Dvoryankin GA, Kondakov AV, Ozcan T, Ozcan G. The revenant: rediscovery of Margaritifera homsensis from Orontes drainage with remarks on its taxonomic status and conservation (Bivalvia: Margaritiferidae). SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2017.1343876] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Ilya V. Vikhrev
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, Arkhangelsk 163000, Russian Federation
- Scientific Department, Northern (Arctic) Federal University, Severnaya Dvina Emb. 17, Arkhangelsk 163002, Russian Federation
| | - Ivan N. Bolotov
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, Arkhangelsk 163000, Russian Federation
- Scientific Department, Northern (Arctic) Federal University, Severnaya Dvina Emb. 17, Arkhangelsk 163002, Russian Federation
| | - Ayhan Altun
- Faculty of Marine Sciences and Technology, Iskenderun Technical University, Iskenderun 31200, Hatay, Turkey
| | - Mikhail Y. Gofarov
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, Arkhangelsk 163000, Russian Federation
- Scientific Department, Northern (Arctic) Federal University, Severnaya Dvina Emb. 17, Arkhangelsk 163002, Russian Federation
| | - Gennady A. Dvoryankin
- SevPINRO – Northern Branch of the Polar Scientific-Research Institute of Fish Husbandry and Oceanography, Uritskogo 17, Arkhangelsk 163000, Russian Federation
| | - Alexander V. Kondakov
- IBIGER – Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, Arkhangelsk 163000, Russian Federation
- Scientific Department, Northern (Arctic) Federal University, Severnaya Dvina Emb. 17, Arkhangelsk 163002, Russian Federation
| | - Tahir Ozcan
- Faculty of Marine Sciences and Technology, Iskenderun Technical University, Iskenderun 31200, Hatay, Turkey
| | - Gulnaz Ozcan
- Faculty of Marine Sciences and Technology, Iskenderun Technical University, Iskenderun 31200, Hatay, Turkey
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Almeida P, Barbosa R, Bensasson D, Gonçalves P, Sampaio JP. Adaptive divergence in wine yeasts and their wild relatives suggests a prominent role for introgressions and rapid evolution at noncoding sites. Mol Ecol 2017; 26:2167-2182. [PMID: 28231394 DOI: 10.1111/mec.14071] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 02/13/2017] [Accepted: 02/14/2017] [Indexed: 12/17/2022]
Abstract
In Saccharomyces cerevisiae, the main yeast in wine fermentation, the opportunity to examine divergence at the molecular level between a domesticated lineage and its wild counterpart arose recently due to the identification of the closest relatives of wine strains, a wild population associated with Mediterranean oaks. As genomic data are available for a considerable number of representatives belonging to both groups, we used population genomics to estimate the degree and distribution of nucleotide variation between wine yeasts and their closest wild relatives. We found widespread genomewide divergence, particularly at noncoding sites, which, together with above average divergence in trans-acting DNA binding proteins, may suggest an important role for divergence at the level of transcriptional regulation. Nine outlier regions putatively under strong divergent selection were highlighted by a genomewide scan under stringent conditions. Several cases of introgressions, originating in the sibling species Saccharomyces paradoxus, were also identified in the Mediterranean oak population. FZF1 and SSU1, mostly known for conferring sulphite resistance in wine yeasts, were among the introgressed genes, although not fixed. Because the introgressions detected in our study are not found in wine strains, we hypothesize that ongoing divergent ecological selection segregates the two forms between the different niches. Together, our results provide a first insight into the extent and kind of divergence between wine yeasts and their closest wild relatives.
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Affiliation(s)
- Pedro Almeida
- Departamento de Ciências da Vida, UCIBIO-REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Raquel Barbosa
- Departamento de Ciências da Vida, UCIBIO-REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Douda Bensasson
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Paula Gonçalves
- Departamento de Ciências da Vida, UCIBIO-REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - José Paulo Sampaio
- Departamento de Ciências da Vida, UCIBIO-REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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