Renewing Felsenstein’s phylogenetic bootstrap in the era of big data

Lemoine, Frédéric; Entfellner, Jean-Baka Domelevo; Wilkinson, Eduan; Correia, Damien; Felipe, Miraine Dávila; Oliveira, Túlio de; Gascuel, Olivier

doi:10.1038/s41586-018-0043-0

Cited by 530 publications

(548 citation statements)

References 53 publications

(96 reference statements)

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“…A ML phylogenetic tree was reconstructed for the resulting alignment using PhyML (48) (Le Gascuel [LG] evolutionary model with gamma-distributed site rates and empirical amino acid frequencies; support values were calculated using aBayes method implemented in PhyML). Another form of branch support, i.e., bootstrap support provided by the transfer (BOOSTER) phylogenetic bootstrap method (130), was also used to assess the reliability of the major tree divisions. Alternatively, the same RdRp alignment was used as the input for ML phylogenetic analysis using RAxML (LG evolutionary model with gamma-distributed site rates and empirical amino acid frequencies).…”

Section: Methodsmentioning

confidence: 99%

Origins and Evolution of the Global RNA Virome

Wolf

Kazlauskas

Iranzo

et al. 2018

mBio

409

333

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Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in animals and plants. The recent advances of metaviromics prompted us to perform a detailed phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. The only universal gene among RNA viruses is the gene encoding the RNA-dependent RNA polymerase (RdRp). We developed an iterative computational procedure that alternates the RdRp phylogenetic tree construction with refinement of the underlying multiple-sequence alignments. The resulting tree encompasses 4,617 RNA virus RdRps and consists of 5 major branches; 2 of the branches include positive-sense RNA viruses, 1 is a mix of positive-sense (ϩ) RNA and double-stranded RNA (dsRNA) viruses, and 2 consist of dsRNA and negative-sense (Ϫ) RNA viruses, respectively. This tree topology implies that dsRNA viruses evolved from ϩRNA viruses on at least two independent occasions, whereas ϪRNA viruses evolved from dsRNA viruses. Reconstruction of RNA virus evolution using the RdRp tree as the scaffold suggests that the last common ancestors of the major branches of ϩRNA viruses encoded only the RdRp and a single jelly-roll capsid protein. Subsequent evolution involved independent capture of additional genes, in particular, those encoding distinct RNA helicases, enabling replication of larger RNA genomes and facilitating virus genome expression and virus-host interactions. Phylogenomic analysis reveals extensive gene module exchange among diverse viruses and horizontal virus transfer between distantly related hosts. Although the network of evolutionary relationships within the RNA virome is bound to further expand, the present results call for a thorough reevaluation of the RNA virus taxonomy. IMPORTANCE The majority of the diverse viruses infecting eukaryotes have RNA genomes, including numerous human, animal, and plant pathogens. Recent advances of metagenomics have led to the discovery of many new groups of RNA viruses in a wide range of hosts. These findings enable a far more complete reconstruction of the evolution of RNA viruses than was attainable previously. This reconstruction reveals the relationships between different Baltimore classes of viruses and indicates extensive transfer of viruses between distantly related hosts, such as plants and animals. These results call for a major revision of the existing taxonomy of RNA viruses.

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Section: Methodsmentioning

confidence: 99%

Origins and Evolution of the Global RNA Virome

Wolf

Kazlauskas

Iranzo

et al. 2018

mBio

409

333

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“…RAxML-NG can compute the novel branch support metric called transfer bootstrap expectation (TBE) recently proposed in (Lemoine et al , 2018). When compared with the classic Felsenstein bootstrap, TBE is less sensitive to individual misplaced taxa in replicate trees, and thus better suited to reveal well-supported deep splits in large trees with thousands of taxa.…”

Section: New Features and Optimizationsmentioning

confidence: 99%

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

et al. 2019

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MotivationPhylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree under the popular maximum likelihood (ML) criterion is known to be NP-hard. Thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets.ResultsWe present RAxML-NG, a from-scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML. RAxML-NG offers improved accuracy, flexibility, speed, scalability, and usability compared with RAxML/ExaML. On taxon-rich datasets, RAxML-NG typically finds higher-scoring trees than IQTree, an increasingly popular recent tool for ML-based phylogenetic inference (although IQ-Tree shows better stability). Finally, RAxML-NG introduces several new features, such as the detection of terraces in tree space and the recently introduced transfer bootstrap support metric.Availability and implementationThe code is available under GNU GPL at . RAxML-NG web service (maintained by Vital-IT) is available at .Supplementary information Supplementary data are available at Bioinformatics online.

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“…A maximum likelihood (ML) tree topology was inferred from the alignment in RaXML v 8.2 with the General Time Reversible model of nucleotide substitution (GTR + G) and 1000 bootstrap replicates. The reference tree and bootstrap trees were analyzed in Booster to infer transfer bootstrap support values for branches in the ML‐tree topology. The subsequent tree was visualized and annotated in FigTree for publication purposes.…”

Section: Methodsmentioning

confidence: 99%

High rate of occult hepatitis B virus infection in hemodialysis units of KwaZulu‐Natal, South Africa

Msomi

Ndlovu

Giandhari

et al. 2019

Journal of Medical Virology

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Occult hepatitis B virus (HBV) infection (OBI) is defined as the presence of HBV DNA in the liver with or without detectable HBV DNA in the serum of individuals testing HBV surface antigen (HBsAg) negative using currently available assays. The prevalence of OBI among patients receiving hemodialysis (HD) treatment remains poorly characterized in South Africa despite the high prevalence of HBV. We sought to determine the prevalence of OBI in HD units in tertiary hospitals of KwaZulu‐Natal and to characterize the HBV S gene mutations potentially responsible for OBI. A cross‐sectional descriptive study of residual diagnostic plasma samples from 85 HBsAg‐negative patients receiving HD treatment was included. The PreS/S gene was amplified with a nested HBV polymerase chain reaction for downstream next‐generation sequencing, to determine the viral genotype and identify S gene mutations associated with OBI. Nine of the 85 samples had OBI, based on detectable HBV DNA. The point prevalence of OBI was 10.6% (95% control interval: 5.5%‐19.1%). Phylogenetic analysis of the samples with OBI showed that all belonged to genotype A. Three (~33%) samples had mutations in the major hydrophilic region (MHR) within the S gene, three (~33%) had mutations within the S gene but outside the MHR, whilst the remaining three had no mutations observed. The prevalence of OBI in HBsAg‐negative patients undergoing HD was 10.6%, suggesting that OBI is a clinically significant problem in patients with HD in this region. The screening methods for HBV infection need to be revised to include nucleic acid testing.

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Renewing Felsenstein’s phylogenetic bootstrap in the era of big data

Cited by 530 publications

References 53 publications

Origins and Evolution of the Global RNA Virome

Origins and Evolution of the Global RNA Virome

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

High rate of occult hepatitis B virus infection in hemodialysis units of KwaZulu‐Natal, South Africa

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