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Genomes and Genes | Emmanuel J P DouzerySummaryCountry: France Publications
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[Molecular dating in the genomic era]Emmanuel J P Douzery
Laboratoire de Paléontologie, Phylogénie et Paléobiologie CC064, Institut des Sciences de l Evolution UMR 5554 CNRS, Universite Montpellier II, Place E Bataillon, 34095 Montpellier Cedex 05, France
Med Sci (Paris) 22:374-80. 2006..Among mammals, the initial diversification of major placental groups may have taken place around 100 Mya, well before the Cretaceous/Tertiary boundary marking the extinction of dinosaurs...
OrthoMaM: a database of orthologous genomic markers for placental mammal phylogeneticsVincent Ranwez
Universite Montpellier 2, CC064, Place Eugene Bataillon, 34 095 Montpellier Cedex 05, France
BMC Evol Biol 7:241. 2007..Genomic data now provide the opportunity to select new markers that are potentially relevant for further resolving branches of the mammalian phylogenetic tree at various taxonomic levels...- The mitochondrial control region of Cervidae: evolutionary patterns and phylogenetic contentE Douzery
Laboratoire de Paléontologie, Paléobiologie et Phylogénie, CNRS, Universite Montpellier II, France
Mol Biol Evol 14:1154-66. 1997..7 and 10.4 MYA. The conserved central domain of CR can be aligned across ungulates and indicates the Pecora monophyly, their close association with cetaceans, and the earlier emergence of suiformes... - The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils?Emmanuel J P Douzery
Department of Paleontology, Phylogeny, and Paleobiology, Institut des Sciences de l Evolution Unité Mixte de Recherche 5554, Centre National de la Recherche Scientifique, Universite Montpellier II, Montpellier Cedex 5, France
Proc Natl Acad Sci U S A 101:15386-91. 2004.... - Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrationsEmmanuel J P Douzery
Laboratoire de Paléontologie, Paléobiologie et Phylogénie CC064, Institut des Sciences de l Evolution UMR 5554 CNRS, Universite Montpellier II, Place E Bataillon, 34 095 Montpellier Cedex 05, France
J Mol Evol 57:S201-13. 2003..Global clocks, local clocks, and quartet dating analyses suggested a Late Cretaceous origin of the crown placental clades followed by a Tertiary radiation of some placental orders like rodents... - Arrival and diversification of caviomorph rodents and platyrrhine primates in South AmericaCeline Poux
Laboratoire de Paléontologie, Phylogénie et Paléobiologie, CC064, Institut des Sciences de l Evolution UMR 5554 CNRS, Universite Montpellier II, Place E, Bataillon, 34 095, Montpellier Cedex 05, France
Syst Biol 55:228-44. 2006..By contrast, few platyrrhine fossils are known in the Oligocene, and the present-day taxa are the result of a quite recent, Early Miocene diversification... - Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthransFrédéric Delsuc
Laboratoire de Paléontologie, Paléobiologie et Phylogénie, Institut des Sciences de l Evolution, Universite Montpellier II, Montpellier, France
BMC Evol Biol 4:11. 2004.... - Molecular systematics of armadillos (Xenarthra, Dasypodidae): contribution of maximum likelihood and Bayesian analyses of mitochondrial and nuclear genesFrédéric Delsuc
Laboratoire de Paléontologie, Paléobiologie et Phylogénie, Institut des Sciences de l Evolution, Universite Montpellier II, Montpellier, France
Mol Phylogenet Evol 28:261-75. 2003..However, low statistical support values associated with almost equal distributions of apomorphies among alternatives suggested that two parallel events of rapid speciation occurred within these two armadillo subfamilies... - Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rootingFrédéric Delsuc
Laboratoire de Paléontologie, Paléobiologie et Phylogénie, Institut des Sciences de l Evolution, Universite Montpellier II, Montpellier, France
Mol Biol Evol 19:1656-71. 2002..By resampling taxa within Xenarthra, the conservative Shimodaira-Hasegawa likelihood-based test of alternative topologies was shown to be sensitive to both character and taxon sampling... 
Molecular phylogenetics unveils the ancient evolutionary origins of the enigmatic fairy armadillosFrédéric Delsuc
Institut des Sciences de l Evolution, UMR 5554 CNRS IRD, Universite Montpellier II, Place Eugene Bataillon, Montpellier, France
Mol Phylogenet Evol 62:673-80. 2012..Their phylogenetic distinctiveness and rarity in the wild argue in favor of high conservation priority...- An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure modelsGeorgia Tsagkogeorga
Universite Montpellier 2, Institut des Sciences de l Evolution UMR 5554, CC064, Place Eugene Bataillon, 34095 Montpellier Cedex 05, France
BMC Evol Biol 9:187. 2009..Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups such as the Aplousobranchia, Appendicularia, and Thaliacea... - Ecomorphological diversification among South American spiny rats (Rodentia; Echimyidae): a phylogenetic and chronological approachThomas Galewski
Laboratoire de Paléontologie, Paléobiologie et Phylogénie CC064, Institut des Sciences de l Evolution UMR 5554 CNRS, Universite Montpellier II, Place E Bataillon, 34 095 Montpellier Cedex 05, France
Mol Phylogenet Evol 34:601-15. 2005..The ecomorphological diversification of echimyids is discussed in the light of these new results and past environmental modifications in South America... - Primate phylogeny, evolutionary rate variations, and divergence times: a contribution from the nuclear gene IRBPCeline Poux
Laboratoire de Paléontologie, Paléobiologie et Phylogénie CC064, Institut des Sciences de l Evolution UMR 5554 CNRS, Université Montpellier II 34095 Montpellier, France
Am J Phys Anthropol 124:1-16. 2004.... - The evolutionary radiation of Arvicolinae rodents (voles and lemmings): relative contribution of nuclear and mitochondrial DNA phylogeniesThomas Galewski
Laboratoire de Paléontologie, Phylogénie et Paléobiologie CC064, Institut des Sciences de l Evolution UMR 5554 CNRS, Universite Montpellier II, France
BMC Evol Biol 6:80. 2006.... - PhySIC_IST: cleaning source trees to infer more informative supertreesCeline Scornavacca
Institut des Sciences de l Evolution ISEM, UMR 5554 CNRS, Universite Montpellier II, Place E, Bataillon CC 064 34095 Montpellier Cedex 5, France
BMC Bioinformatics 9:413. 2008..e. discard all conflicting resolutions. When the source trees host a significant number of topological conflicts or have a small taxon overlap, supertree methods of both kinds can propose poorly resolved, hence uninformative, supertrees... - Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genesDorothee Huchon
Laboratoire de Paléontologie, Paléobiologie et Phylogénie CC064, Institut des Sciences de l Evolution UMR 5554 CNRS, Universite Montpellier II, Place E Bataillon, Montpellier Cedex 05, France
Mol Biol Evol 19:1053-65. 2002..The divergence between rodents and lagomorphs is placed just at the K-T boundary and the first splits among placentals in the Late Cretaceous. Our results thus tend to reconcile molecular and morphological-paleontological insights... - Acetylcholinesterase genes within the Diptera: takeover and loss in true fliesElise Huchard
Institut des Sciences de l Evolution UMR 5554 CNRS, C C 065, Universite de Montpellier II, 34095 Montpellier Cedex 5, France
Proc Biol Sci 273:2595-604. 2006..We discuss the evolutionary scenarios for the takeover of ace-2 and the loss of ace-1, taking into account our limited knowledge of non-synaptic functions of ace genes and some specific adaptations of true flies... - SuperTriplets: a triplet-based supertree approach to phylogenomicsVincent Ranwez
Universite Montpellier 2, CC064, Place Eugene Bataillon, 34 095 Montpellier Cedex 05, France
Bioinformatics 26:i115-23. 2010..The relative performances of these representations have been discussed but are difficult to assess since both are limited to relatively small datasets... - Rabbits, if anything, are likely GliresEmmanuel J P Douzery
Laboratoire de Paléontologie, Phylogénie et Paléobiologie, CC064, Institut des Sciences de l Evolution UMR 5554 CNRS, Université Montpellier II Place E Bataillon, 34 095 Montpellier Cedex 05, France
Mol Phylogenet Evol 33:922-35. 2004.... - Protected and threatened components of fish biodiversity in the Mediterranean seaDavid Mouillot
UMR CNRS UM2 IRD IFREMER 5119 ECOSYM, Université Montpellier 2 CC 093, 34095 Montpellier Cedex 5, France
Curr Biol 21:1044-50. 2011..Our results highlight that future conservation strategies and assessment efficiency of current reserve systems will need to be revisited after deconstructing the different components of biodiversity... - New DNA data from a transthyretin nuclear intron suggest an Oligocene to Miocene diversification of living South America opossums (Marsupialia: Didelphidae)Cynthia Steiner
, , Institut des Sciences de l'Evolution (UMR 5554 CNRS, , Montpellier, France
Mol Phylogenet Evol 35:363-79. 2005..A Bayesian relaxed molecular clock dating of didelphid evolution using nuclear markers estimated their origin in the Middle Eocene (39.8 million years ago), with subsequent diversification during the Oligocene (Deseadan) and Miocene... - Environment drives high phylogenetic turnover among oceanic bacterial communitiesThomas Pommier
Universite de Lyon, INRA, CNRS, Universite Lyon 1, Ecologie Microbienne UMR 5557, USC 1193, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne, France
Biol Lett 8:562-6. 2012..Strong phenotype-environment mismatches observed in the ocean may surpass high connectivity between marine microbial communities... - PhySIC: a veto supertree method with desirable propertiesVincent Ranwez
Institut des Sciences de l Evolution ISEM, UMR 5554 CNRS, Universite Montpellier II, Montpellier, Cedex 5, France
Syst Biol 56:798-817. 2007..Lastly, we illustrate the behaviour of PhySIC on primate data sets of various sizes, and propose a supertree covering 95% of all primate extant genera. The PhySIC algorithm is available at http://atgc.lirmm.fr/cgi-bin/PhySIC... - MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codonsVincent Ranwez
Institut des Sciences de l Evolution, UMR5554 CNRS, Universite Montpellier II, Montpellier, France
PLoS ONE 6:e22594. 2011..MACSE is distributed as an open-source java file executable with freely available source code and can be used via a web interface at: http://mbb.univ-montp2.fr/macse... - Molecular and morphological phylogenies of ruminantia and the alternative position of the moschidaeAlexandre Hassanin
Laboratoire de Paléontologie, Paléobiologie et Phylogénie, Institut des Sciences de l Evolution UMR 5554 CNRS, Universite Montpellier II, CC064, Place E Bataillon, 34 095 Montpellier Cedex 05, France
Syst Biol 52:206-28. 2003..We propose a biogeographic scenario to explain the extraordinary expansion of this group during the Cenozoic era... - Conserved features and evolutionary shifts of the EDA signaling pathway involved in vertebrate skin appendage developmentSophie Pantalacci
Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, Universite de Lyon, Institut Fédératif Biosciences 128 Gerland Lyon Sud, CNRS, INRA, Universite Claude Bernard Lyon 1, 69364 Lyon Cedex 07, France
Mol Biol Evol 25:912-28. 2008.... - SDM: a fast distance-based approach for (super) tree building in phylogenomicsAlexis Criscuolo
, ISEM, , Montpellier, France
Syst Biol 55:740-55. 2006..2002, Syst. Biol. 51: 652-664) that involves 48 genes of 75 placental mammals. The results indicate that these genes have strong rate heterogeneity and confirm the simulation conclusions... - Molecular estimation of eulipotyphlan divergence times and the evolution of "Insectivora"Christophe J Douady
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
Mol Phylogenet Evol 28:285-96. 2003..quot; Eulipotyphlans diversification might have been sculpted by variations in paleoclimates of the cenozoic era... - Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliabilityChristophe J Douady
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
Mol Biol Evol 20:248-54. 2003..Both posterior probabilities and bootstrap supports are of great interest to phylogeny as potential upper and lower bounds of node reliability, but they are surely not interchangeable and cannot be directly compared... - Retroposed elements and their flanking regions resolve the evolutionary history of xenarthran mammals (armadillos, anteaters, and sloths)Maren Möller-Krull
Institute of Experimental Pathology ZMBE, University of Munster, Munster, Germany
Mol Biol Evol 24:2573-82. 2007..The data provide a stable phylogenetic framework for further evolutionary investigations of xenarthrans and important information for defining conservation priorities to save the diversity of one of the most curious groups of mammals... - Evolution under domestication: contrasting functional morphology of seedlings in domesticated cassava and its closest wild relativesBenoit Pujol
Department of Population Biology, Centre for Functional and Evolutionary Ecology CEFE, UMR 5175 CNRS, 1919, route de Mende, 34293 Montpellier Cedex 05, France
New Phytol 166:305-18. 2005.... - Genetic variability in MCF-7 sublines: evidence of rapid genomic and RNA expression profile modificationsMélanie Nugoli
Equipe Genome et Cancer, UMR 5535, CNRS and EMI 0229, INSERM, Centre de Recherche CRLC Val d Aurelle, Montpellier, France
BMC Cancer 3:13. 2003..Both phenotypic and cytogenetic variability have been reported for clones of breast carcinoma cell lines but have not been comprehensively studied. Despite this, cell lines such as MCF-7 cells are extensively used as model systems... - Genetic clustering of Trypanosoma cruzi I lineage evidenced by intergenic miniexon gene sequencingMarie France Bosseno
Institut de recherche pour le developpement IRD, département Sociétés et Santé, UR 008 et 165, Montpellier, France
Infect Genet Evol 7:587-93. 2007..Thereby, the miniexon gene is an attractive marker to establish the phylogeny of lineage I and explore relationships between T. cruzi and mammal hosts... - Evidence for genetic exchange and hybridization in Trypanosoma cruzi based on nucleotide sequences and molecular karyotypeSylvain Brisse
Génétique des Maladies Infectieuses, UMR CNRS IRD No 9926, Institut de Recherches pour le Dévelopement, Montpellier, France
Infect Genet Evol 2:173-83. 2003..Based on a CYb substitution rate of 1% per million years (Myr), the major lineages are estimated to have diverged around 10 million years ago...