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155. Mitochondrial DNA and population size - Response

Author

Bazin, E., Glémin, Sylvain, Galtier, Nicolas, Génome, populations, interactions, adaptation (GPIA), and Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2)

Subjects
[SDE.BE.GP]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.gp
Abstract

Letter; International audience

Published
2006

156. Phylogeographic support for horizontal gene transfer involving sympatric bruchid species

Author

Alvarez, Nadir, Benrey, Betty, Hossaert-McKey, Martine, Grill, Andrea, McKey, Doyle, Galtier, Nicolas, Laboratoire d'Entomologie Evolutive, Université de Neuchâtel (UNINE), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
BOMBYX-MORI, [SDE.BE.GP]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.gp, lcsh:Biology (General), SEQUENCES, ORIGIN, Research, [SDV]Life Sciences [q-bio], COLEOPTERA, MITOCHONDRIAL GENES, EUKARYOTES, lcsh:QH301-705.5, EVOLUTION
Abstract

Background We report on the probable horizontal transfer of a mitochondrial gene, cytb, between species of Neotropical bruchid beetles, in a zone where these species are sympatric. The bruchid beetles Acanthoscelides obtectus, A. obvelatus, A. argillaceus and Zabrotes subfasciatus develop on various bean species in Mexico. Whereas A. obtectus and A. obvelatus develop on Phaseolus vulgaris in the Mexican Altiplano, A. argillaceus feeds on P. lunatus in the Pacific coast. The generalist Z. subfasciatus feeds on both bean species, and is sympatric with A. obtectus and A. obvelatus in the Mexican Altiplano, and with A. argillaceus in the Pacific coast. In order to assess the phylogenetic position of these four species, we amplified and sequenced one nuclear (28S rRNA) and two mitochondrial (cytb, COI) genes. Results Whereas species were well segregated in topologies obtained for COI and 28S rRNA, an unexpected pattern was obtained in the cytb phylogenetic tree. In this tree, individuals from A. obtectus and A. obvelatus, as well as Z. subfasciatus individuals from the Mexican Altiplano, clustered together in a unique little variable monophyletic unit. In contrast, A. argillaceus and Z. subfasciatus individuals from the Pacific coast clustered in two separated clades, identically to the pattern obtained for COI and 28S rRNA. An additional analysis showed that Z. subfasciatus individuals from the Mexican Altiplano also possessed the cytb gene present in individuals of this species from the Pacific coast. Zabrotes subfasciatus individuals from the Mexican Altiplano thus demonstrated two cytb genes, an "original" one and an "infectious" one, showing 25% of nucleotide divergence. The "infectious" cytb gene seems to be under purifying selection and to be expressed in mitochondria. Conclusion The high degree of incongruence of the cytb tree with patterns for other genes is discussed in the light of three hypotheses: experimental contamination, hybridization, and pseudogenisation. However, none of these seem able to explain the patterns observed. A fourth hypothesis, involving recent horizontal gene transfer (HGT) between A. obtectus and A. obvelatus, and from one of these species to Z. subfasciatus in the Mexican Altiplano, seems the only plausible explanation. The HGT between our study species seems to have occurred recently, and only in a zone where the three beetles are sympatric and share common host plants. This suggests that transfer could have been effected by some external vector such as a eukaryotic or viral parasite, which might still host the transferred fragment. Reviewers This article was reviewed by Eric Bapteste, Adam Eyre-Walker and Alexey Kondrashov.

Published
2006
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157. Patterns of Genome-Wide Nucleotide Diversity in the Gynodioecious Plant Thymus vulgaris Are Compatible with Recent Sweeps of Cytoplasmic Genes.

Author

Mollion, Maeva, Ehlers, Bodil K., Figuet, Emeric, Santoni, Sylvain, Lenormand, Thomas, Maurice, Sandrine, Galtier, Nicolas, and Bataillon, Thomas

Subjects
SEXUAL dimorphism, GENETIC polymorphisms, CYTOPLASMIC male sterility, ANGIOSPERMS, GENOMES
Abstract

Gynodioecy is a sexual dimorphism where females coexist with hermaphrodite individuals. In most cases, this dimorphism involves the interaction of cytoplasmicmale sterility (CMS) genes and nuclear restorer genes. Two scenarios can account for how these interactions maintain gynodioecy. Either CMS genes recurrently enter populations at low frequency via mutation or migration and go to fixation unimpeded (successive sweeps), or CMS genes maintain polymorphism over evolutionary time through interactions with a nuclear restorer allele (balanced polymorphism). To distinguish between these scenarios, we used transcriptome sequencing in gynodioecious Thymus vulgaris and surveyed genome-wide diversity in 18 naturally occurring individuals sampled from populations at a local geographic scale. We contrast the amount and patterns of nucleotide diversity in the nuclear and cytoplasmic genome, and find ample diversity at the nuclear level (π=0.019 at synonymous sites) but reduced genetic diversity and an excess of rare polymorphisms in the cytoplasmic genome relative to the nuclear genome. Our finding is incompatible with the maintenance of gynodioecy via scenarios invoking long-term balancing selection, and instead suggests the recent fixation of CMS lineages in the populations studied. [ABSTRACT FROM AUTHOR]

Published
2018
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158. Statistical Methods in Molecular Evolution

Author

Galtier, Nicolas, Gascuel, Olivier, Jean-Marie, Alain, Carvalho De Matos, Christine, Nielsen Rasmus, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Algorithmes et Performance des Réseaux (APR)

Subjects
[INFO]Computer Science [cs], [INFO] Computer Science [cs], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2005

171. Reference-free population genomics from next-generation transcriptome data and the vertebrate–invertebrate gap

Author

Gayral, Philippe, Melo-Ferreira, José, Glemin, Sylvain, Bierne, Nicolas, Carneiro, Miguel, Nabholz, Benoit, Lourenco, Joao M., Alves, Paulo, Ballenghien, Marion, Faivre, Nicolas, Belkhir, Khalid, Cahais, Vincent, Loire, Etienne, Bernard, Aurélien, Galtier, Nicolas, Gayral, Philippe, Melo-Ferreira, José, Glemin, Sylvain, Bierne, Nicolas, Carneiro, Miguel, Nabholz, Benoit, Lourenco, Joao M., Alves, Paulo, Ballenghien, Marion, Faivre, Nicolas, Belkhir, Khalid, Cahais, Vincent, Loire, Etienne, Bernard, Aurélien, and Galtier, Nicolas

Abstract

In animals, the population genomic literature is dominated by two taxa, namely mammals and drosophilids, in which fully sequenced, well-annotated genomes have been available for years. Data from other metazoan phyla are scarce, probably because the vast majority of living species still lack a closely related reference genome. Here we achieve de novo, reference-free population genomic analysis from wild samples in five non-model animal species, based on next-generation sequencing transcriptome data. We introduce a pipe-line for cDNA assembly, read mapping, SNP/genotype calling, and data cleaning, with specific focus on the issue of hidden paralogy detection. In two species for which a reference genome is available, similar results were obtained whether the reference was used or not, demonstrating the robustness of our de novo inferences. The population genomic profile of a hare, a turtle, an oyster, a tunicate, and a termite were found to be intermediate between those of human and Drosophila, indicating that the discordant genomic diversity patterns that have been reported between these two species do not reflect a generalized vertebrate versus invertebrate gap. The genomic average diversity was generally higher in invertebrates than in vertebrates (with the notable exception of termite), in agreement with the notion that population size tends to be larger in the former than in the latter. The non-synonymous to synonymous ratio, however, did not differ significantly between vertebrates and invertebrates, even though it was negatively correlated with genetic diversity within each of the two groups. This study opens promising perspective regarding genome-wide population analyses of non-model organisms and the influence of population size on non-synonymous versus synonymous diversity.

Published
2013

172. Population genomics of the endangered giant Galápagos tortoise

Author

Loire, Etienne, Chiari, Ylenia, Bernard, Aurélien, Cahais, Vincent, Romiguier, J., Nabholz, Benoit, Lourenco, Joao M., Galtier, Nicolas, Loire, Etienne, Chiari, Ylenia, Bernard, Aurélien, Cahais, Vincent, Romiguier, J., Nabholz, Benoit, Lourenco, Joao M., and Galtier, Nicolas

Abstract

Background The giant Galápagos tortoise, Chelonoidis nigra, is a large-sized terrestrial chelonian of high patrimonial interest. The species recently colonized a small continental archipelago, the Galápagos Islands, where it has been facing novel environmental conditions and limited resource availability. To explore the genomic consequences of this ecological shift, we analyze the transcriptomic variability of five individuals of C. nigra, and compare it to similar data obtained from several continental species of turtles. Results Having clarified the timing of divergence in the Chelonoidis genus, we report in C. nigra a very low level of genetic polymorphism, signatures of a weakened efficacy of purifying selection, and an elevated mutation load in coding and regulatory sequences. These results are consistent with the hypothesis of an extremely low long-term effective population size in this insular species. Functional evolutionary analyses reveal a reduced diversity of immunity genes in C. nigra, in line with the hypothesis of attenuated pathogen diversity in islands, and an increased selective pressure on genes involved in response to stress, potentially related to the climatic instability of its environment and its elongated lifespan. Finally, we detect no population structure or homozygosity excess in our five-individual sample. Conclusions These results enlighten the molecular evolution of an endangered taxon in a stressful environment and point to island endemic species as a promising model for the study of the deleterious effects on genome evolution of a reduced long-term population size.

Published
2013

174. Overexpression of sucrose-phosphate synthase in tomato plants grown with CO2 enrichment leads to decreased foliar carbohydrate accumulation relative to untransformed controls

Author

Murchie, E.H., Sarrobert, C., Contard, P., Betsche, T., Foyer, C.H., Galtier, Nicolas, Unité de recherche Nutrition Azotée des Plantes (URNAP), Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration

Subjects
[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology
Published
1999

175. Soluble acid invertase activity in leaves is independent of species differences in leaf carbohydrates, diurnal sugar profiles and paths of phloem loading

Author

Kingston-Smith, A.H., Galtier, Nicolas, Pollock, C.J., Foyer, C.H., ProdInra, Migration, Unité de recherche Nutrition Azotée des Plantes (URNAP), and Institut National de la Recherche Agronomique (INRA)

Subjects
TRANSPORT DE SUBSTANCES NUTRITIVES, [SDV.BV.PEP] Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Published
1998

180. Reference-Free Population Genomics from Next-Generation Transcriptome Data and the Vertebrate–Invertebrate Gap

Author

Gayral, Philippe, primary, Melo-Ferreira, José, additional, Glémin, Sylvain, additional, Bierne, Nicolas, additional, Carneiro, Miguel, additional, Nabholz, Benoit, additional, Lourenco, Joao M., additional, Alves, Paulo C., additional, Ballenghien, Marion, additional, Faivre, Nicolas, additional, Belkhir, Khalid, additional, Cahais, Vincent, additional, Loire, Etienne, additional, Bernard, Aurélien, additional, and Galtier, Nicolas, additional

Published
2013
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181. Phylogeographic support for horizontal gene transfer involving sympatric bruchid species

Author

Alvarez, Nadir, Benrey, Betty, Hossaert-McKey, Martine, Grill, Andrea, McKey, Doyle, Galtier, Nicolas, Alvarez, Nadir, Benrey, Betty, Hossaert-McKey, Martine, Grill, Andrea, McKey, Doyle, and Galtier, Nicolas

Abstract

Background We report on the probable horizontal transfer of a mitochondrial gene, cytb, between species of Neotropical bruchid beetles, in a zone where these species are sympatric. The bruchid beetles Acanthoscelides obtectus, A. obvelatus, A. argillaceus and Zabrotes subfasciatus develop on various bean species in Mexico. Whereas A. obtectus and A. obvelatus develop on Phaseolus vulgaris in the Mexican Altiplano, A. argillaceus feeds on P. lunatus in the Pacific coast. The generalist Z. subfasciatus feeds on both bean species, and is sympatric with A. obtectus and A. obvelatus in the Mexican Altiplano, and with A. argillaceus in the Pacific coast. In order to assess the phylogenetic position of these four species, we amplified and sequenced one nuclear (28S rRNA) and two mitochondrial (cytb, COI) genes. Results Whereas species were well segregated in topologies obtained for COI and 28S rRNA, an unexpected pattern was obtained in the cytb phylogenetic tree. In this tree, individuals from A. obtectus and A. obvelatus, as well as Z. subfasciatus individuals from the Mexican Altiplano, clustered together in a unique little variable monophyletic unit. In contrast, A. argillaceus and Z. subfasciatus individuals from the Pacific coast clustered in two separated clades, identically to the pattern obtained for COI and 28S rRNA. An additional analysis showed that Z. subfasciatus individuals from the Mexican Altiplano also possessed the cytb gene present in individuals of this species from the Pacific coast. Zabrotes subfasciatus individuals from the Mexican Altiplano thus demonstrated two cytb genes, an "original" one and an "infectious" one, showing 25% of nucleotide divergence. The "infectious" cytb gene seems to be under pur

Published
2007

182. Manipulation of the pathways of sucrose biosynthesis and nitrogen assimilation in transformed plants to improve photosynthesis and productivity

Author

Ferrario Méry, Sylvie, Murchie, E., Hirel, Bertrand, Galtier, Nicolas, Quick, W.P., Foyer, C.H., ProdInra, Migration, C.H. Foyer (Editeur), W.P. Quick (Editeur), Unité de recherche Nutrition Azotée des Plantes (URNAP), and Institut National de la Recherche Agronomique (INRA)

Subjects
ASSIMILATION DE L'AZOTE, [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Abstract

chap. 6

Published
1997

187. Source-sink interaction and communication in leaves

Author

Foyer, C.H., Galtier, Nicolas, Unité de recherche Nutrition Azotée des Plantes (URNAP), Institut National de la Recherche Agronomique (INRA), E. Zamski (Editeur), A.A. Schaffer (Editeur), and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], RELATION PUITS SOURCE, [SDV]Life Sciences [q-bio]
Abstract

chap. 13

Published
1996

198. The sucrose/starch ratio in leaves is determined by SPS activity

Author

Galtier, Nicolas, Murchie, E., Signora, L., Foyer, C.H., Unité de recherche Nutrition Azotée des Plantes (URNAP), Institut National de la Recherche Agronomique (INRA), P. Mathis, and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ADN C
Published
1995

199. Effects of light and atmospheric carbon dioxide enrichment on photosynthesis and carbon partitioning in the leaves of tomato (Lycopersicon esculentum L.) plants over-expressing sucrose phosphate synthase

Author

Galtier, Nicolas, Foyer, C.H., Murchie, E., Alred, R., Quick, P., Voelker, T.A., Thépenier, C., Lasceve, G., Betsche, T., Unité de recherche Nutrition Azotée des Plantes (URNAP), Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration

Subjects
[SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, ComputingMilieux_MISCELLANEOUS, [SDV.BV.BOT] Life Sciences [q-bio]/Vegetal Biology/Botanics
Abstract

International audience

Published
1995

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