Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative

Equipe Méthodes et Algorithmes pour la Bioinformatique LIRMM-CNRS, Université Montpellier II, Montpellier 34392, France.
Systematic Biology (Impact Factor: 14.39). 09/2006; 55(4):539-52. DOI: 10.1080/10635150600755453
Source: PubMed


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).

Download full-text


Available from: Maria Anisimova, Oct 05, 2015
61 Reads
  • Source
    • "Multiple sequence alignment of proteins was performed with the MUSCLE software (Edgar, 2004), curation of the alignment was done with the GBLOCKS program (Castresana, 2000), Maximum Likelihood trees with approximate Likelihood Ratio Test for branches (PhyML+ aLRT) was performed with the PhyML3.0 program (Guindon and Gascuel, 2003; Anisimova and Gascuel, 2006), and trees were drawn with TREEDYN software (Chevenet et al., 2006). NJ phylogeny was conducted with the MEGA4 program (Tamura et al., 2007). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Histone methylation is a conserved epigenetic mechanism in eukaryotes. Most of the histone lysine methyltransferases (HKMTases) conferring such modifications are proteins with a conserved SET domain responsible for enzymatic activity. Genetic studies in Arabidopsis thaliana have revealed that proteins from the Trithorax group (TrxG) are critical in activating transcription by methylating lysine 4 and lysine 36 of histone H3. Two TrxG proteins, ATXR3 and ATX1 (also called SET DOMAIN GROUP 2 and 27, respectively) are necessary for global genome-wide H3K4me3 deposition in Arabidopsis, whilst ASHH2 (also called SDG8) is a multi-functional enzyme with H3K4 and H3K36 methylation activity. Using phylogenetic analysis, we have identified the common bean (Phaseolus vulgaris L.) gene orthologs to Arabidopsis ATXR3, ASHH2, and ATX1 genes, which we have designated PvATXR3h, PvASHH2h, and PvTRX1h, respectively. Analysis of these genes with qRT-PCR reveals that all three are broadly expressed during plant and nodule development. Through a reverse genetics approach, we created common bean composite plants to knock-down PvATXR3h, PvTRX1h, and PvASHH2h expression. From analysis of the transgenic root phenotype, we conclude that transgenic root growth and development in the common bean was hindered by PvASHH2h gene downregulation.
    • "used the workflow ( with an approximate likelihood-ratio test for branches (Anisimova and Gascuel, 2006; Dereeper et al., 2008). "
    [Show abstract] [Hide abstract]
    ABSTRACT: In angiosperm seeds the embryo is embedded within the endosperm, which is in turn enveloped by the seed coat, making inter-compartmental communication primordial for coordinated seed growth. In this context the bHLH domain transcription factor AtZHOUPI (AtZOU) fulfills a key role both in the lysis of the transient endosperm and in embryo cuticle formation in Arabidopsis thaliana. In maize (Zea mays), a cereal with a persistent endosperm, a single gene, ZmZOU, falls into the same phylogenetic clade as AtZOU. Its expression is limited to the endosperm where it peaks during the filling stage. In ZmZOU-RNAi knock down lines embryo size is slightly reduced and the embryonic suspensor and the adjacent embryo surrounding region show retarded breakdown. Ectopic expression of ZmZOU reduces stomatal number, possibly due to inappropriate protein interactions. ZmZOU forms functional hetero-dimers with AtICE/AtSCREAM and the closely related maize proteins ZmICEb and ZmICEc, but its interaction is more efficient with the ZmICEa protein, which shows sequence divergence and only has close homologues in other monocotyledonous species. Consistent with the observation that these complexes can trans-activate target gene promoters from Arabidopsis, ZmZOU partially complements the Atzou-4 mutant. However, structural, trans-activation and gene expression data support the hypothesis that ZmZOU and ZmICEa may have co-evolved to form a functional complex unique to monocot seeds. This divergence may explain the reduced functionality of ZmZOU in Arabidopsis, and reflect functional specificities which are unique to the monocotyledon lineage.This article is protected by copyright. All rights reserved.
    The Plant Journal 09/2015; DOI:10.1111/tpj.13024 · 5.97 Impact Factor
  • Source
    • "The phylogenetic trees were reconstructed using the maximum likelihood method implemented in PhyML v3.0 aLRT (Anisimova and Gascuel, 2006; Guindon and Gascuel, 2003). The reliability for the internal branches was assessed using the approximate likelihood ratio test (aLRT e SH- Like) (Anisimova and Gascuel, 2006). The trees were visualised and edited using EvolView (Zhang et al., 2012). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Antimicrobial peptides are ubiquitous components of eukaryotic innate immunity. Defensins are a well-known family of antimicrobial peptides, widely distributed in ticks, insects, plants and mammals, showing activity against bacteria, viruses, fungi, yeast and protozoan parasites. Ixodes ricinus is the most common tick species in Europe and is a vector of pathogens affecting human and animal health. Recently, six defensins (including two isoforms) were identified in I. ricinus. We investigated the evolution of the antimicrobial activity of I. ricinus defensins. Among the five unique defensins, only DefMT3, DefMT5 and DefMT6 showed in vitro antimicrobial activity. Each defensin was active against rather distantly-related bacteria (P < 0.05), significantly among Gram-negative species (P < 0.0001). These three defensins represent different clades within the family of tick defensins, suggesting that the last common ancestor of tick defensins may have had comparable antimicrobial activity. Differences in electrostatic potential, and amino acid substitutions in the b-hairpin and the loop bridging the a-helix and b-sheet may affect the antimicrobial activity in DefMT2 and DefMT7, which needs to be addressed. Additionally, the antimicrobial activity of the g-core motif of selected defensins (DefMT3, DefMT6, and DefMT7) was also tested. Interestingly, compared to full length peptides, the g-core motifs of these defensins were effective against less species of bacteria. However, the antifungal activity of the g-core was higher than full peptides. Our results broaden the scope of research in the field of antimicrobial peptides highlighting the overlooked ability of arthropod defensins to act against distantly-related microorganisms.
    Developmental and comparative immunology 08/2015; 53(2):358-365. DOI:10.1016/j.dci.2015.08.001 · 2.82 Impact Factor
Show more