20 results on '"Puillandre, Nicolas"'
Search Results
2. Hidden diversity in the Asprella clade: description of Conus (Asprella) neocostatus sp. nov. (Gastropoda, Conidae)
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Olivera, Baldomero, Watkins, Maren, Puillandre, Nicolas, Tenorio, Manuel, and Ratti, Claudia
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[SDV] Life Sciences [q-bio] - Published
- 2021
3. Description of new genera and new species of Ergalataxinae (Gastropoda: Muricidae)
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Houart, Roland, Zuccon, Dario, Puillandre, Nicolas, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), and Puillandre, Nicolas
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South Atlantic ,New taxa ,Muricidae ,[SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,Gastropoda ,Ergalataxinae ,Indo-Pacific ,[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy - Abstract
International audience; The recent genetic analysis of the muricid subfamily Ergalataxinae has led to a better understanding of this subfamily, but some species were left without appropriate generic assignments and the classification of others required revision. This knowledge gap is partially filled herein, with new combinations and the description of three new genera. The examination of new material, along with a careful re-examination of and comparison to existing material, resulted also in the identification of nine new species. These new genera and new species are described herein, lectotypes are designated and new combinations are given. The geographical range of all the new species is provided on maps. All new species are compared with related or similar species.
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- 2019
4. Lack of signal for the impact of venom gene diversity on speciation Mark A
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Phuong, Mark A, Alfaro, Michael E, Mahardika, Gusti N, Marwoto, Ristiyanti M, Prabowo, Romanus Edy, Rintelen, Thomas von, Vogt, Philipp W. H., Hendricks, Jonathan R, Puillandre, Nicolas, University of California, Udayana University [Bali], Jenderal Soedirman University, Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)
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[SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,complex mixtures - Abstract
International audience; Understanding why some groups of organisms are more diverse than others is a central goal in macroevolution. Evolvability, or lineages’ intrinsic capacity for evolutionary change, is thought to influence disparities in species diversity across taxa. Over macroevolutionary time scales, clades that exhibit high evolvability are expected to have higher speciation rates. Cone snails (family: Conidae, >900 spp.) provide a unique opportunity to test this prediction because their venom genes can be used to characterize differences in evolvability between clades. Cone snails are carnivorous, use prey-specific venom (conotoxins) to capture prey, and the genes that encode venom are known and diversify through gene duplication. Theory predicts that higher gene diversity confers a greater potential to generate novel phenotypes for specialization and adaptation. Therefore, if conotoxin gene diversity gives rise to varying levels of evolvability, conotoxin gene diversity should be coupled with macroevolutionary speciation rates. We applied exon capture techniques to recover phylogenetic markers and conotoxin loci across 314 species, the largest venom discovery effort in a single study. We paired a reconstructed timetree using 12 fossil calibrations with species-specific estimates of conotoxin gene diversity and used trait-dependent diversification methods to test the impact of evolvability on diversification patterns. Surprisingly, did not detect any signal for the relationship between conotoxin gene diversity and speciation rates, suggesting that venom evolution may not be the rate-limiting factor controlling diversification dynamics in Conidae. Comparative analyses showed some signal for the impact of diet and larval dispersal strategy on diversification patterns, though whether or not we detected a signal depended on the dataset and the method. If our results remain true with increased sampling in future studies, they suggest that the rapid evolution of Conidae venom may cause other factors to become more critical to diversification, such as ecological opportunity or traits that promote isolation among lineages.
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- 2019
5. Exploration et étude de la biodiversité benthique profonde de Mayotte et des îles éparses
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Castelin, Magalie, Delavenne, Juliette, Brisset, Julien, chambart, cyril, Corbari, L., Keszler, Louise, Lozouet, P, Olu, Karine, Poncet, Laurent, Puillandre, Nicolas, SAMADI, S, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Patrimoine naturel (PatriNat), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Office français de la biodiversité (OFB), Muséum national d'Histoire naturelle (MNHN), Musée National d'Histoire Naturelle de Luxembourg (MNHN), IFREMER- Département Etude des Ecosystèmes Profonds (DEEP/LEP), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), MNHN, and Samadi, Sarah
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[SDE] Environmental Sciences ,[SDE]Environmental Sciences - Abstract
Rapport final de la convention MNHN-TAAF dans le cadre du Xème FED régional «gestion durable du patrimoine naturel de Mayotte et des îles Eparses
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- 2019
6. Impact des hypothèses taxonomiques en biologie évolutive
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Puillandre, Nicolas and Puillandre, Nicolas
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[SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,Taxonomie ,Taxonomy - Published
- 2017
7. The cones (Gastropoda) from Madagascar 'Deep South': composition, endemism and new taxa
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Monnier, Eric, Tenerio, Manuel, Bouchet, Philippe, Puillandre, Nicolas, and Ratti, Claudia
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[SDV] Life Sciences [q-bio] - Published
- 2018
8. From Integrative Taxonomy to Species Description: one Step Beyond
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Pante, Eric, Schoelinck, Charlotte, Puillandre, Nicolas, LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), and ANR-13-JSV7-0013,CONOTAX,Taxonomie, venins et évolution des Conoidea(2013)
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species delimitation ,literature review ,species hypotheses ,MESH: Cryptic species, grey zone, impact factor, literature review, species complex, species delimitation, species hypotheses, taxonomic impediment ,Cryptic species ,grey zone ,taxonomic impediment ,[SDV.BID]Life Sciences [q-bio]/Biodiversity ,impact factor ,species complex ,[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy - Abstract
International audience; Integrative taxonomy was formally introduced in 2005 as a comprehensive framework to delimit and describe taxa by integrating information from different types of data and methodologies (Dayrat 2005; Will et al. 2005). Even if debate remains about the hierarchy of the types of characters and criteria to use for species delimitation (Schlick-Steiner et al., 2009; Padial et al., 2010; Yeates et al., 2011), most, if not all taxonomists agree that objectively evaluating several lines of evidence within a formalized framework is the most efficient and theoretically-grounded approach to defining robust species hypotheses (Samadi and Barberousse 2006; de Queiroz 2007).The last ten years have seen a renewal of taxonomy, illustrated by the increasing number of published articles related to species concepts, species delimitation methodology and its application.In the early 90s, many systematists began to suspect that the majority of species would remain undescribed (Costello et al. 2013a; Erwin 1982; Mora et al. 2011 – but see Costello et al. 2013b) and that some of them will probably go extinct before we have a chance to describe them (Barnosky et al., 2011; Leakey and Lewin, 1995; Pimm et al., 2006). The use of molecular data, and in particular molecular barcoding (Hebert et al., 2003), was presented as one answer to this “taxonomic impediment” (as defined in Rodman and Cody, 2003), and welcomed as such by taxonomists. It thus adds to the toolkit of taxonomy, which continues its development as a synergic discipline involving morphological taxonomists, field ecologists, naturalists, and statisticians (Knapp 2008). Integrative taxonomy, used for many decades by taxonomists but only recently formalized concomitantly with the molecular revolution, is organised following a three-step workflow (see also Evenhuis 2007): first, we need to accumulate data on numerous specimens (from various types of data: DNA, morphology, ecology…); second, we need to circumscribe groups of organisms using concepts that ensure that these groups correspond to species (this second step may be coupled with the first, as biological data are continuously accumulated and species hypotheses re-discussed); and third, we need to provide a species description, i.e. a diagnosis and a name for the species recognized as new.Naming new species is a fundamental step when describing biodiversity and is the only way to ensure that scientists are talking about the same entity, and that all the data linked to conspecific specimens but produced by different researchers (or amateurs) can be associated in a comparative analysis (Patterson et al., 2010; Satler et al., 2013; Schlick-Steiner et al., 2007). Not linking biological data (should they be molecular, morphological, or ecological) to a formal species name will result in these data losing tremendous value (Goldstein and DeSalle 2011). Indeed, when authors publish data on entities that are not defined within the framework of a referencing system (e.g. solely identified by an alphanumeric label), they make it very difficult for other authors to build on these data. The best example is the need for taxa to be named to have a chance to be listed in an endangered species list and to benefit from a conservation program: no name, no surviving (Mace 2004). Beyond the need for communication among scientists, names are also key to communicating with non-scientist audiences. While it is now widely recognized that integrating several lines of evidence is the most efficient and theoretically grounded way to delimit new species (e.g. de Queiroz, 2007; Schlick-Steiner et al., 2009; Yeates et al., 2011), the formal naming of new entities may have become decoupled from species delimitation. Indeed, we noted that in several cases new delimited species were not accompanied by formal species description (see also Goldstein and DeSalle 2011). The aim of this article is therefore to test the hypothesis that integrative taxonomy, as defined in 2005 (Dayrat 2005; Will et al. 2005), and in particular the use of molecular data, helped to alleviate the taxonomic impediment by delimiting and describing new species. We reviewed part of the “integrative taxonomy” literature of the last eight years (2006-2013) and tested if authors that delimit new species also name them. We also looked at how the number and type of characters used, across different taxa, varies across articles.
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- 2015
9. Toxines et Signalisation -Toxins and Signalling Renewed taxonomy : phylogeny and species delimitation in an integrative framework
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Puillandre, Nicolas, Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), and Puillandre, Nicolas
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[SDV] Life Sciences [q-bio] ,Conoideans ,[SDV]Life Sciences [q-bio] ,conotoxin ,DNA barcoding ,integrative taxonomy ,molecular phylogeny - Abstract
International audience; The vast diversity of species included in the genus Conus and in the superfamily Conoidea make them one of the most promising taxa for the discovery of new toxin-derived drugs. To rationalize the search for new peptides, integrative taxonomy can be used to quickly identify new lineages that potentially evolved new toxins. In this context, molecular characters are now a major tool, whether for specimen identification ("barcoding"), species delimitation (alpha-taxonomy) or phylogeny. At the species level, different criteria have been successfully applied to analyze DNA sequences and propose hypotheses of species delimitation in the genus Benthomangelia that are supported by other characters such as morphology. At the phylogenetic level, molecular characters were also used to define highly divergent lineages within Conoidea and to infer their relationships. The methodology used, based on clearly stated concepts and integrating different criteria and characters allow the definition of robust, reproducible and testable hypotheses. Furthermore, discriminating these lineages (families, subfamilies, genera or species) is of great value in toxin research, as illustrated with the family Terebridae where three different lineages have been identified each of them susceptible to have evolved their own set of toxins. Le renouveau de la taxonomie : phylogénie et délimitation d'espèces dans un contexte intégratif La grande diversité spécifique inclue dans le genre Conus et dans la superfamille des Conoidea font de ces groupes certains des plus prometteurs pour la découverte de nouvelles thérapies dérivées de toxines. Pour rationaliser la recherche de nouveaux peptides, une approche de taxonomie intégrative peut permettre d'identifier rapidement des lignées évolutives qui auraient potentiellement développé de nouvelles toxines. Dans ce contexte, les caractères moléculaires sont devenus un outil majeur, que ce soit pour l'identification de spécimens (« barcoding »), la délimitation d'espèces (alpha-taxonomie) et la phylogénie. Au niveau spécifique, différents critères ont été appliqués avec succès pour analyser des séquences ADN et proposer des hypothèses de délimitation d'espèces au sein du genre Benthomangelia, hypothèses soutenues par d'autres caractères (morphologiques). Au niveau phylogénétique, les caractères moléculaires ont été également utilisés pour définir différentes lignées au sein des Conoidea. La méthodologie utilisée, basée sur des concepts clairement établis et intégrant différents critères et caractères, permet de proposer des hypothèses robustes, reproductibles et testables. De plus, discriminer ces lignées (familles, sous-familles, genres et espèces) est important pour la recherche de toxines, comme le montre l'analyse de la famille des Terebridae, où trois différentes lignées ont été identifiées, chacune susceptible d'avoir développé des toxines uniques.
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- 2009
10. Taxonomie intégrative des Turridae : phylogénie, délimitation d’espèces et barcoding
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Puillandre, Nicolas and Puillandre, Nicolas
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Turridae ,[SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,[SDV.BA.ZI] Life Sciences [q-bio]/Animal biology/Invertebrate Zoology ,Taxonomie ,Taxonomy - Abstract
The Turridae constitute a hyperdiverse group of marine gastropods within which most species are still undescribed. Traditional taxonomic approaches are challenged by the difficult interpretability of shell variability at both specific (α-taxonomy) and superior levels (phylogeny). In order to speed up the rate of species description, our goal was to replenish taxonomical practices within Turrinae by applying new tools and methods. Taxonomy becomes integrative, combining molecular, morphological and ecological characters, but also methods form phylogenetic and population genetics methods. The barcoding project is included in this new dynamics, providing a standardized method of genetic diversity analysis.In a first part, several mitochondrial and nuclear genes were sequenced to reconstruct the phylogeny of Conoidea, a group including the Turridae but also the genus Conus and the Terebridae. Our results evidenced new phylogenetic relationships and allowed us to propose a new classification of the group.In a second part, the integrative α-taxonomy approach was detailed. The latter lies on the following conceptual framework: species are segments of evolutionary lineages. Furthermore, species acquire several properties during their evolution that can be used to propose hypotheses of species delimitation, in particular using molecular characters. As a first step, the barcode fragment of the COI gene was sequenced. It was used to identify egg-capsules of marine gastropods and to test already available hypotheses of species delimitation in the genus Eumunida (Crustacea).The COI barcode can also be used to propose new hypotheses of species delimitation. Mainly two exploratory methods, of which one was developed during this Ph.D., were used to delimit groups of specimens. These groups were then tested in a second step through analysis of a nuclear gene (28S or ITS2), but also morphological variability. This integrative taxonomy approach was applied to four groups of Turridae for which a great number of samples from the Pacific was available: the genera Bathytoma, Benthomangelia and Xenuroturris, and the subfamily Turrinae. Finally, 111 species were delimited, of which 70 are potentially new for science.Molecular characters were thus useful to clarify phylogenetic relationships within the family Turridae. Combined with other characters, they also allowed the analysis of species diversity within the group. The methodology developed during this Ph.D. was thus adapted to a hyper-diversified group such as the Turridae, and accelerated the rate of species discovery and description., Les Turridae constituent un groupe de gastéropodes marins très diversifié, et dont une grande partie des espèces sont encore non décrites. Les approches taxonomiques traditionnelles se heurtent à des problèmes liés à la variabilité de la coquille, difficile à interpréter, aussi bien au niveau spécifique (α-taxonomie) qu’aux niveaux supérieurs (phylogénie). Afin d’accélérer le rythme de description des espèces, l’objectif de la thèse est de renouveler les pratiques taxonomiques au sein des Turridae en adaptant de nouvelles méthodes et de nouveaux outils. La taxonomie devient intégrative, et associe caractères moléculaires, morphologiques et écologiques mais également les méthodes issues de la phylogénie et de la génétique des populations. Le projet barcoding participe à cette nouvelle dynamique, en offrant une méthode d’analyse standardisée de ladiversité génétique.Dans une première partie, plusieurs gènes mitochondriaux et nucléaires ont été séquencés pour reconstruire la phylogénie des Conoidea, groupe incluant les Turridae mais également le genre Conus et les Terebridae. Les résultats obtenus mettent en évidence des relations phylogénétiques inédites, et permettent de proposer une nouvelle classification pour le groupe.Dans une seconde partie, l’approche d’α-taxonomie intégrative est détaillée. Elle repose sur le cadre conceptuel suivant : les espèces sont des segments de lignées évolutives. De plus, les espèces acquièrent au cours de leur évolution différentes propriétés qui peuvent être utilisées pour proposer des hypothèses de délimitation d’espèces, notamment en utilisant des caractères moléculaires. Dans une première étape, le fragment barcode du gène COI a été séquencé. Il a été utilisé pour identifier des pontes de gastéropodes marins et pour tester les hypothèses de délimitation d’espèces déjà disponibles pour le genre Eumunida (Crustacea).Le barcode COI peut également permettre de proposer de nouvelles hypothèses de délimitation d’espèces. Principalement deux méthodes exploratoires, dont l’une a été développée au cours de cette thèse, ont été utilisées pour délimiter des groupes de spécimens. Ces groupes ont ensuite été testés dans une seconde étape en analysant systématiquement un gène nucléaire (28S ou ITS2), mais également la variabilité morphologique. Cette approche de taxonomie intégrative a été appliquée à quatre groupes de Turridae, pour lesquels un grand nombre d’échantillons collectés dans le Pacifique étaient disponibles : les genres Bathytoma, Benthomangelia et Xenuroturris, et la sous-famille des Turrinae. Au total, 111 espèces ont été délimitées au sein de ces groupes, dont environ 70 seraient nouvelles pour la science.Les caractères moléculaires ont donc été utiles pour éclaircir les relations phylogénétiques au sein de la famille des Turridae. Associés à l’analyse d’autres caractères, ils ont également permis d’analyser la diversité spécifique de ce groupe. La méthodologie mise au point au cours de la thèse est donc adaptée à un groupe hyperdiversifé comme les Turridae, et accélère le rythme de découverte et de description de nouvelles espèces.
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- 2008
11. Hidden species diversity of Australian burrowing snakes (Ramphotyphlops)
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Marin, Julie, Donnellan, Stephen C., Hedges, S. Blair, Puillandre, Nicolas, Aplin, Ken P., Doughty, Paul, Hutchinson, Mark, Couloux, Arnaud, Vidal, Nicolas, Evolution Paris-Seine, Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Sorbonne Paris Cité (USPC)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), University of Adelaide, Pennsylvania State University (Penn State), Penn State System, Western Australian Museum (WAM), South Australian Museum (SAM), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
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cryptic species ,speciation ,Scolecophidia ,evolution ,[SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology ,hidden species ,[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,Ramphotyphlops - Abstract
International audience; The worm-like snakes (Scolecophidia; approximately 400 nominal extant species) have a conservative morphology and are among the most poorly-known terrestrial vertebrates. Although molecular evidence has helped determine their higher-level relationships, such data have rarely been used to discriminate among species. We generated a molecular data set for the continental Australian blindsnakes (genus Ramphotyphlops) to determine the concordance of molecular and morphological information in the taxonomic recognition of species. Our dataset included 741 specimens morphologically attributed to 27 nominal Ramphotyphlops species. We proposed species hypotheses (SHs) after analysis of sequences from a variable mitochondrial gene (cytochrome b) and examined these SHs with additional evidence from a nuclear gene (prolactin receptor) and geographical data. Although the nuclear marker was not as fast-evolving and discriminating as the mitochondrial marker, there was congruence among the mitochondrial, nuclear, and geographical data, suggesting that the actual number of species is at least two times the current number of recognized, nominal species. Several biogeographical barriers and complex phytogeographical and geological patterns appeared to be involved in the division of some burrowing snake populations and, by consequence, in their diversification and speciation through isolation.
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- 2013
12. Genetic divergence and geographical variation in the deep-water Conus orbignyi complex (Mollusca: Conoidea)
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Puillandre, Nicolas, Meyer, Christopher P., Bouchet, Philippe, Olivera, Baldomero M., Systématique, adaptation, évolution (SAE), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
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[SDV]Life Sciences [q-bio] ,ComputingMilieux_MISCELLANEOUS - Abstract
Genetic divergence and geographical variation in the deep-water Conus orbignyi complex (Mollusca: Conoidea). - Zoologica Scripta, 40, 350-363. The cone snails (family Conidae) are a hyperdiverse lineage of venomous gastropods. Two standard markers, COI and ITS2, were used to define six genetically divergent groups within a subclade of Conidae that includes Conus orbignyi; each of these was then evaluated based on their shell morphology. We conclude that three forms, previously regarded as subspecies of C. orbignyi are distinct species, now recognized as C. orbignyi, C. elokismenos and C. coriolisi. In addition, three additional species (C. pseudorbignyi, C. joliveti and C. comatosa) belong to this clade. Some of the proposed species (e. g. C. elokismenos) are possibly in turn complexes comprising multiple species. Groups such as Conidae illustrate the challenges generally faced in species delimitation in biodiverse lineages. In the case of C. orbignyi complex, they are not only definable, genetically divergent lineages, but also considerable geographical variation within each group. Our study suggests that an intensive analysis of multiple specimens within a single locality helps to minimize the confounding effects of geographical variation and can be a useful starting point for circumscribing different species within such a confusing complex.
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- 2011
13. Barcoding type specimens helps to identify synonyms and an unnamed new species in Eumunida Smith, 1883 (Decapoda : Eumunididae)
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Puillandre, Nicolas, Macpherson, Enrique, Lambourdière, Josie, Smith, Eumunida, Cruaud, Corinne, Boisselier-Dubayle, Marie-Catherine, Samadi, Sarah, Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Outils et Méthodes de la Systématique Intégrative (OMSI), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)
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0106 biological sciences ,Systematics ,0303 health sciences ,Entomology ,Species complex ,biology ,Systematic Entomology ,[SDV]Life Sciences [q-bio] ,Zoology ,PhyloCode ,Arachnology ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Cladistics ,03 medical and health sciences ,Taxonomy (biology) ,Ecology, Evolution, Behavior and Systematics ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology - Abstract
13 páginas, 2 figuras, 3 tablas., The primary purpose of DNA-barcoding projects is to generate an efficient expertise and identification tool. This is an important challenge to the taxonomy of the 21st century, as the demand increases and the expert capacity does not. However, identifying specimens using DNA-barcodes requires a preliminary analysis to relate molecular clusters to available scientific names. Through a case study of the genus Eumunida (Decapoda : Eumunididae), we illustrate how naming molecule-based units, and thus providing an accurate DNA-based identification tool, is facilitated by sequencing type specimens. Using both morphological and unlinked molecular markers (COI and 28S genes), we analysed 230 specimens from 12 geographic areas, covering two-thirds of the known diversity of the genus, including type specimens of 13 species. Most hypotheses of species delimitation are validated, as they correspond to molecular units linked to only one taxonomic name (and vice versa). However, a putative cryptic species is also revealed and three entities previously named as distinct species may in fact belong to a single one, and thus need to be synonymised. Our analyses, which integrate the current naming rules, enhance the a-taxonomy of the genus and provide an effective identification tool based on DNA-barcodes. They illustrate the ability, This work was supported by the ‘Consortium National de Recherche en Génomique’, and the ‘Service de Systematique Moléculaire’ of the Muséum National d’Histoire Naturelle (UMS 2700 CNRS-MNHN). It is part of the agreement n 2005/67 between the Genoscope and the Muséum National d’Histoire Naturelle on the project ‘Macrophylogeny of Life’ directed by Guillaume Lecointre. These data fed the MarBol project supported by the Sloan Foundation.
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- 2011
14. Loss of planktotrophy and speciation: geographical fragmentation in the deep-water gastropod genus Bathytoma (Gastropoda, Conoidea) in the western Pacific
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Puillandre, Nicolas, Sysoev, A.V, Olivera, B.M., Couloux, A., Bouchet, Philippe, Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), and Leballeur, Philippe
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[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2010
15. An integrative approach to species delimitation in Benthomangelia (Mollusca: Conoidea)
- Author
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Puillandre, Nicolas, Baylac, Michel, Boisselier, Marie-Catherine, Cruaud, Corinne, Samadi, Sarah, Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
molluscs ,COI gene ,[SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology ,Benthomangelia ,elliptic fourier analysis ,Integrative taxonomy ,Molluscs ,28S rRNA ,[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,DNA taxonomy ,integrative taxonomy ,Elliptic Fourier Analysis - Abstract
International audience; DNA sequences are currently used to propose primary hypotheses of species delimitation, especially when morphological variability is difficult to assess. In an integrative taxonomy framework, these hypotheses are then compared with other characters, such as morphology or geography, to produce robust species delimitations. For this purpose, the cytochrome oxidase subunit I (COI) gene has been sequenced for almost 50 specimens of the genus Benthomangelia, a deep-sea marine gastropod genus, collected in the South-West Pacific. Five genetic groups, displaying low and high genetic distances respectively within and between groups, were defined. COI hypotheses were compared with both the results obtained with the independent nuclear 28S gene and with an elliptic Fourier analysis of the shape of the last whorl of the shell. 28S gene analysis confirmed the same well-supported groups as COI, and elliptic Fourier analysis identified several morphological characters that vary similarly to genetic variability.
- Published
- 2009
16. Snails in depth: Integrative taxonomy of Famelica, Glaciotomella and Rimosodaphnella (Conoidea: Raphitomidae) from the deep sea of temperate Australia
- Author
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Anders Hallan, Alexander E. Fedosov, Francesco Criscione, Nicolas Puillandre, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), European Project: 865101,HYPERDIVERSE, Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), and Puillandre, Nicolas
- Subjects
0106 biological sciences ,Systematics ,species delineation ,Gastropoda ,mitochondrial DNA ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Monophyly ,morphology ,Conoidea ,14. Life underwater ,Invertebrate Systematics Manuscript ID IS21008.R2 Australia ,Endemism ,Ecology, Evolution, Behavior and Systematics ,ComputingMilieux_MISCELLANEOUS ,molecular systematics ,030304 developmental biology ,0303 health sciences ,biology ,Ecology ,biology.organism_classification ,[SDE.BE] Environmental Sciences/Biodiversity and Ecology ,Taxon ,Molecular phylogenetics ,Taxonomy (biology) ,Famelica ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology - Abstract
The deep sea of temperate south-eastern Australia appears to be a ‘hotspot’ for diversity and endemism of conoidean neogastropods of the family Raphitomidae. Following a series of expeditions in the region, a considerable amount of relevant DNA-suitable material has become available. A molecular phylogeny based on this material has facilitated the identification of diagnostic morphological characters, allowing the circumscription of monophyletic genera and the introduction of several new genus-level taxa. Both named and new genera are presently being investigated through integrative taxonomy, with the discovery of a significant number of undescribed species. As part of this ongoing investigation, our study focuses on the genera Famelica Bouchet & Warén, 1980, Glaciotomella Criscione, Hallan, Fedosov & Puillandre, 2020 and Rimosodaphnella Cossmann, 1914. We subjected a comprehensive mitochondrial DNA dataset of representative deep-sea raphitomids to the species delimitation methods ABGD and ASAP that recognised 18 and 15 primary species hypotheses (PSHs) respectively. Following additional evaluation of shell and radular features, and examination of geographic and bathymetric ranges, nine of these PSHs were converted to secondary species hypotheses (SSHs). Four SSHs (two in Famelica and two in Rimosodaphnella) were recognised as new, and formal descriptions are provided herein.
- Published
- 2021
17. Phylogenetic relationships of the conoidean snails (Gastropoda: Caenogastropoda) based on mitochondrial genomes
- Author
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Nicolas Puillandre, Rafael Zardoya, Juan E. Uribe, Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Puillandre, Nicolas, Ministerio de Ciencia e Innovación (España), Agence Nationale de la Recherche (France), and European Commission
- Subjects
0301 basic medicine ,Snails ,[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,Open Reading Frames ,03 medical and health sciences ,Monophyly ,Phylogenetics ,Turridae ,Gene Order ,[SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,Genetics ,Animals ,Conoidea ,14. Life underwater ,Conidae ,Clade ,Molecular Biology ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,ComputingMilieux_MISCELLANEOUS ,Base Sequence ,biology ,Phylogenetic tree ,biology.organism_classification ,Mitochondria ,030104 developmental biology ,Evolutionary biology ,Genome, Mitochondrial ,Mangeliidae - Abstract
With more than 5,000 species, Conoidea is one of the most diversified superfamilies of Gastropoda. Recently, the family-level classification of these venomous predator snails has undergone substantial changes, on the basis of a phylogenetic tree reconstructed combining partial mitochondrial and nuclear gene sequences, and up to 16 families are now recognized. However, phylogenetic relationships among these families remain largely unresolved. Here, we sequenced 20 complete or nearly complete mitochondrial (mt) genomes, which were combined with mt genomes available in GenBank to construct a dataset that included representatives of 80% of the known families, although for some we had only one species or genus as representative. Most of the sequenced conoidean mt genomes shared a constant genome organization, and observed rearrangements were limited exclusively to tRNA genes in a few lineages. Phylogenetic trees were reconstructed using probabilistic methods. Two main monophyletic groups, termed “Clade A” and “Clade B”, were recovered with strong support within a monophyletic Conoidea. Clade A (including families Clavatulidae, Horaiclavidae, Turridae s.s., Terebridae, Drilliidae, Pseudomelatomidae, and Cochlespiridae) was composed of four main lineages, one of which was additionally supported by a rearrangement in the gene order. Clade B (including families Conidae, Borsoniidae, Clathurellidae, Mangeliidae, Raphitomidae, and Mitromorphidae) was composed of five main lineages. The reconstructed phylogeny rejected the monophyly of Clavatulidae, Horaiclavidae, Turridae, Pseudomelatomidae, and Conidae, indicating that several of the currently accepted families may be ill-defined. The reconstructed tree also revealed new phylogenetic positions for genera characterized as tentative (Gemmuloborsonia, Lucerapex, and Leucosyrinx), enigmatic (Marshallena) or challenging to place (Fusiturris), which will potentially impact the classification of the Conoidea., This work was supported by the Spanish Ministry of Science and Innovation (CGL2013-45211-C2-2-P and CGL2016-75255-C2-1-P to RZ; BES-2011-051469, EEBB-I-15-10150 and EEBB-I-14-08866 to JEU), by the “Service de Systématique Moléculaire” (UMS 2700 CNRS-MNHN), by the ATM (“Action transversal du Muséum”) Emergences of the MNHN and by the project CONOTAX (funded by the French Agence Nationale de la Recherche, France; ANR-13-JSV7-0013-01 to NP). The access of JEU to the MNHN invertebrate collections and facilities was funded by the EU Synthesis Project.
- Published
- 2018
18. New and unusual deep-water Conoidea revised with shell, radula and DNA characters
- Author
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Alexander E. Fedosov, Yu. I. Kantor, Nicolas Puillandre, and Puillandre, Nicolas
- Subjects
biology ,Shell (structure) ,Aquatic Science ,biology.organism_classification ,Deep water ,Paleontology ,chemistry.chemical_compound ,Geography ,chemistry ,[SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,[SDV.BA.ZI] Life Sciences [q-bio]/Animal biology/Invertebrate Zoology ,Conoidea ,Animal Science and Zoology ,Ecology, Evolution, Behavior and Systematics ,DNA - Abstract
In the course of preparation of a new molecular phylogeny of Conoidea based on exon-capture some new species and species with notable morphology were revealed. The taxonomy of these species is discussed and the radula of most of them illustrated for the first time. New genera are described: Comispira gen. nov. (Cochlespiridae), type species Leucosyrinx mai Li et Li, 2008; Pagodaturris gen. nov. (Clavatulidae), type species Pleurotoma molengraaffi Tesch, 1915. New species: Comispira compta gen. et sp. nov., Sibogasyrinx sangeri sp. nov. (both Cochlespiridae), Pagodaturris philippinensis gen. et sp. nov. (Clavatulidae), Horaiclavus micans sp. nov., Iwaoa invenusta sp. nov. (both Horaiclavidae), Lucerapex cracens sp. nov., Lucerapex laevicarinatus sp. nov. (Turridae), Heteroturris kanacospira sp. nov. (Borsoniidae). Epideira Hedley, 1918 reallocated from Pseudomelatomidae to Horaiclavidae The radulae of Kuroshioturris nipponica (Shuto, 1961) (Turridae), Leucosyrinx verrillii (Dall, 1881), Leucosyrinx luzonica (Powell, 1969), comb. nov. are illustrated for the first time.
- Published
- 2018
19. Deep-sea wood-eating limpets of the genus Pectinodonta Dall, 1882 (Mollusca: Gastropoda: Patellogastropoda: Pectinodontidae) from the tropical West Pacific
- Author
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Marshall, Bruce A., Nicolas Puillandre, Josie Lambourdière, Arnaud Couloux, Sarah Samadi, Puillandre, Nicolas, Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Outils et Méthodes de la Systématique Intégrative (OMSI), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
[SDV] Life Sciences [q-bio] ,[SDV]Life Sciences [q-bio] ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience; Seven species of Pectinodonta Dall, 1882 are recorded from the tropical West Pacific, of which the following six are described as new: P. alpha n. sp. and P. alis n. sp. from the Solomon Islands and Vanuatu; P. aurora n. sp. and P. beta n. sp. from Papua New Guinea and the Solomon Islands; P. gamma n. sp. from Vanuatu and New Caledonia; and P. philippinarum n. sp. from off Luzon, Philippine Islands. Pectinodonta orientalis Schepman, 1908, previously known from off Sulawesi and southern Japan, is newly recorded from off Taiwan, the Philippines, Papua New Guinea and the Solomon Islands. Specimens were sorted into morphospecies and tentatively attributed to available species names. Morphospecies were then evaluated using COI, 28S and/or ITS1 gene polymorphism. The description of the six new species includes a molecular diagnosis. The New Zealand species P. marinovichi Marshall, 1998 is recovered as close to P. orientalis, whereas P. alis n. sp. from the Solomon Islands and Vanuatu is recovered as close to the New Zealand species P. aupouria Marshall, 1985 and P. morioria Marshall, 1985. Two other named tropical species, P. alta Schepman, 1908, from off Timor, and P. obtusa (Thiele, 1925), from off Sumatra (holotype illustrated), have not been recollected; Patelliformes xylophages du genre Pectinodonta Dall, 1882 (Mollusca: Gastropoda: Patellogastropoda: Pectinodontidae) de la zone tropicale profonde du Pacifique-Ouest Sept espèces de Pectinodonta Dall, 1882 sont reportées de la zone tropicale du Pacifique-Ouest. Parmi elles, six nouvelles espèces sont décrites: P. alpha n. sp. et P. alis n. sp. des Iles Salomon et du Vanuatu, P. aurora n. sp. et P. beta n. sp. de Papouasie-Nouvelle-Guinée et des Iles Salomon, P. gamma n. sp. du Vanuatu et de Nouvelle-Calédonie et P. philippinarum n. sp. de la province de Luzon aux Philippines. Pectinodonta orientalis Schepman, 1908,précédemment connus du Sulawesi et du sud du Japon, est ici reportée pour la première fois de Taïwan, des Philippines, de Papouasie-Nouvelle-Guinée et des Iles Salomon. Les spécimens collectés ont tout d’abord été triés en morpho-espèces, auxquelles ont été attribués les noms d’espèces. Ces morphoespèces ont ensuite été comparées aux résultats obtenus parl’analyse du polymorphisme des gènes COI, 28S et/ou ITS1. La description des six nouvelles espèces inclut une diagnose moléculaire. P. marinovichi Marshall, 1998, de Nouvelle-Zélande, est phylogénétiquement proche de P. orientalis, alors que P. alis n. sp. des Iles Salomon et du Vanuatu est proche de P. aupouria Marshall, 1985 and P. morioria Marshall, 1985 de Nouvelle-Zélande. Deux autres espèces tropicales déjà décrites, P. alta Schepman, 1908, du Timor, et P. obtusa (Thiele, 1925), de Sumatra (holotype illustré), n’ont pas été retrouvées.
- Published
- 2016
20. Molecular phylogeny and evolution of the cone snails (Gastropoda, Conoidea)
- Author
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Thomas F. Duda, Philippe Bouchet, Alan J. Kohn, Maren Watkins, S. Kauferstein, Christopher G. Meyer, Baldomero M. Olivera, Nicolas Puillandre, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Muséum national d'Histoire naturelle (MNHN), and Puillandre, Nicolas
- Subjects
0106 biological sciences ,12SrRNA ,Conidae ,Lineage (evolution) ,Conus ,Zoology ,[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,010603 evolutionary biology ,01 natural sciences ,Article ,Cone snail ,Evolution, Molecular ,COI ,03 medical and health sciences ,Gastropoda ,[SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,Genetics ,Animals ,Conoidea ,14. Life underwater ,Molecular Biology ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,0303 health sciences ,biology ,Conus Snail ,Ancestral state reconstruction ,Bayes Theorem ,biology.organism_classification ,Phylogeography ,Genes, Mitochondrial ,Molecular phylogenetics ,16SrRNA - Abstract
We present a large-scale molecular phylogeny that includes 320 of the 761 recognized valid species of the cone snails (Conus), one of the most diverse groups of marine molluscs, based on three mitochondrial genes (COI, 16S rDNA and 12S rDNA). This is the first phylogeny of the taxon to employ concatenated sequences of several genes, and it includes more than twice as many species as the last published molecular phylogeny of the entire group nearly a decade ago. Most of the numerous molecular phylogenies published during the last 15 years are limited to rather small fractions of its species diversity. Bayesian and maximum likelihood analyses are mostly congruent and confirm the presence of three previously reported highly divergent lineages among cone snails, and one identified here using molecular data. About 85% of the species cluster in the single Large Major Cade; the others are divided between the Small Major Cade (similar to 12%), the Conus califomicus lineage (one species), and a newly defined clade (similar to 3%). We also define several subclades within the Large and Small major clades, but most of their relationships remain poorly supported. To illustrate the usefulness of molecular phylogenies in addressing specific evolutionary questions, we analyse the evolution of the diet, the biogeography and the toxins of cone snails. All cone snails whose feeding biology is known inject venom into large prey animals and swallow them whole. Predation on polychaete worms is inferred as the ancestral state, and diet shifts to molluscs and fishes occurred rarely. The ancestor of cone snails probably originated from the Indo-Pacific; rather few colonisations of other biogeographic provinces have probably occurred. A new classification of the Conidae, based on the molecular phylogeny, is published in an accompanying paper.
- Published
- 2014
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