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University of Montpellier

EducationMontpellier, Languedoc-Roussillon, France
About: University of Montpellier is a education organization based out in Montpellier, Languedoc-Roussillon, France. It is known for research contribution in the topics: Population & Membrane. The organization has 26816 authors who have published 53843 publications receiving 1646905 citations. The organization is also known as: Université de Montpellier.


Papers
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Journal ArticleDOI
TL;DR: A Brooks parsimony analysis produced an unrooted area phylogram, showing that: (i) the northern regions were colonized generally from the Iberic and Balkanic refugia; and (ii) the Italian lineages were often isolated due to the presence of the Alpine barrier.
Abstract: The Quaternary cold periods in Europe are thought to have heavily influenced the amount and distribution of intraspecific genetic variation in both animals and plants. The phylogeographies of 10 taxa, including mammals (Ursus arctos, Sorex spp., Crocidura suaveolens, Arvicola spp.), amphibians (Triturus spp.), arthropods (Chorthippus parallelus), and plants (Abies alba, Picea abies, Fagus sylvatica, Quercus spp.), were analysed to elucidate general trends across Europe. Only a small degree of congruence was found amongst the phylogeographies of the 10 taxa, but the likely postglacial colonization routes exhibit some similarities. A Brooks parsimony analysis produced an unrooted area phylogram, showing that: (i) the northern regions were colonized generally from the Iberic and Balkanic refugia; and (ii) the Italian lineages were often isolated due to the presence of the Alpine barrier. The comparison of colonization routes highlighted four main suture-zones where lineages from the different refugia meet. Some of the intraspecific genetic distances among lineages indicated a prequaternary divergence that cannot be connected to any particular cold period, but are probably related mainly to the date of arrival of each taxon in the European continent. As a consequence, molecular genetics so far appears to be of limited use in dating Quaternary events.

2,855 citations

Journal ArticleDOI
TL;DR: This method further refine this method by incorporating the variability of evolutionary rates across sites in the matrix estimation and using a much larger and diverse database than BRKALN, which was used to estimate WAG.
Abstract: Amino acid replacement matrices are an essential basis of protein phylogenetics. They are used to compute substitution probabilities along phylogeny branches and thus the likelihood of the data. They are also essential in protein alignment. A number of replacement matrices and methods to estimate these matrices from protein alignments have been proposed since the seminal work of Dayhoff et al. (1972). An important advance was achieved by Whelan and Goldman (2001) and their WAG matrix, thanks to an efficient maximum likelihood estimation approach that accounts for the phylogenies of sequences within each training alignment. We further refine this method by incorporating the variability of evolutionary rates across sites in the matrix estimation and using a much larger and diverse database than BRKALN, which was used to estimate WAG. To estimate our new matrix (called LG after the authors), we use an adaptation of the XRATE software and 3,912 alignments from Pfam, comprising approximately 50,000 sequences and approximately 6.5 million residues overall. To evaluate the LG performance, we use an independent sample consisting of 59 alignments from TreeBase and randomly divide Pfam alignments into 3,412 training and 500 test alignments. The comparison with WAG and JTT shows a clear likelihood improvement. With TreeBase, we find that 1) the average Akaike information criterion gain per site is 0.25 and 0.42, when compared with WAG and JTT, respectively; 2) LG is significantly better than WAG for 38 alignments (among 59), and significantly worse with 2 alignments only; and 3) tree topologies inferred with LG, WAG, and JTT frequently differ, indicating that using LG impacts not only the likelihood value but also the output tree. Results with the test alignments from Pfam are analogous. LG and a PHYML implementation can be downloaded from http://atgc.lirmm.fr/LG

2,615 citations

Journal ArticleDOI
21 Aug 1997-Nature
TL;DR: In this article, it was shown that the growth mechanism for SWNTs must be independent of the details of the technique used to make them, and that the ready availability of large amounts of SWNT can make them much more accessible for further study.
Abstract: Single-walled carbon nanotubes (SWNTs) offer the prospect of both new fundamental science and useful (nano)technological applications1. High yields (70–90%) of SWNTs close-packed in bundles can be produced by laser ablation of carbon targets2. The electric-arc technique used to generate fullerenes and multi-walled nanotubes is cheaper and easier to implement, but previously has led to only low yields of SWNTs3,4. Here we show that this technique can generate large quantities of SWNTs with similar characteristics to those obtained by laser ablation. This suggests that the (still unknown) growth mechanism for SWNTs must be independent of the details of the technique used to make them. The ready availability of large amounts of SWNTs, meanwhile, should make them much more accessible for further study.

2,568 citations

Journal ArticleDOI
TL;DR: A new, fast, approximate likelihood-ratio test (aLRT) for branches is presented here as a competitive alternative to nonparametric bootstrap and Bayesian estimation of branch support and is shown to be accurate, powerful, and robust to certain violations of model assumptions.
Abstract: We revisit statistical tests for branches of evolutionary trees reconstructed upon molecular data. A new, fast, approximate likelihood-ratio test (aLRT) for branches is presented here as a competitive alternative to nonparametric bootstrap and Bayesian estimation of branch support. The aLRT is based on the idea of the conventional LRT, with the null hypothesis corresponding to the assumption that the inferred branch has length 0. We show that the LRT statistic is asymptotically distributed as a maximum of three random variables drawn from the chi(0)2 + chi(1)2 distribution. The new aLRT of interior branch uses this distribution for significance testing, but the test statistic is approximated in a slightly conservative but practical way as 2(l1- l2), i.e., double the difference between the maximum log-likelihood values corresponding to the best tree and the second best topological arrangement around the branch of interest. Such a test is fast because the log-likelihood value l2 is computed by optimizing only over the branch of interest and the four adjacent branches, whereas other parameters are fixed at their optimal values corresponding to the best ML tree. The performance of the new test was studied on simulated 4-, 12-, and 100-taxon data sets with sequences of different lengths. The aLRT is shown to be accurate, powerful, and robust to certain violations of model assumptions. The aLRT is implemented within the algorithm used by the recent fast maximum likelihood tree estimation program PHYML (Guindon and Gascuel, 2003).

2,369 citations

Journal ArticleDOI
TL;DR: A set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes are presented.
Abstract: Research in autophagy continues to accelerate,(1) and as a result many new scientists are entering the field Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms Recent reviews have described the range of assays that have been used for this purpose(2,3) There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi) Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response

2,310 citations


Authors

Showing all 27007 results

NameH-indexPapersCitations
Jean Bousquet145128896769
Tomas Ganz14148073316
Jean-Marie Tarascon136853137673
Johann Cohen-Tanugi13243458881
Beatrice H. Hahn12945869206
Nicholas A. Kotov12357455210
F. Piron11827047676
Robert H. Crabtree11367848634
Christian Serre11041956800
Alan Cooper10874645772
Serge Hercberg10694256791
Louis Bernatchez10656835682
Joël Bockaert10548039464
E. Nuss10422038488
Jordi Rello10369435994
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Performance
Metrics
No. of papers from the Institution in previous years
YearPapers
202381
2022444
20214,243
20203,999
20193,773
20183,458