Exploring tree-building methods and distinct molecular data to recover a known asymmetric phage phylogeny

Sousa, Ana; Zé-Zé, Líbia; Silva, Pedro J. N.; Tenreiro, Rogério

doi:10.1016/j.ympev.2008.04.030

Cited by 5 publications

(4 citation statements)

References 47 publications

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“…When comparing long genome sequences, the small feature length of FFP allows for relationships to be determined regardless of variety in genome length or gene content in the comparative samples. Recently, Sousa et al demonstrated the ability of alignment-free methods to uncover the known phylogeny of T7 phage variants, all of which were similar in that they were evolved from a parental T7 phage [22]. In contrast to the highly similar T7 phage variants, mycobacteriophages are highly diverse with low sequence identity and novel gene order and content.…”

Section: Resultsmentioning

confidence: 99%

Phage cluster relationships identified through single gene analysis

et al. 2013

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BackgroundPhylogenetic comparison of bacteriophages requires whole genome approaches such as dotplot analysis, genome pairwise maps, and gene content analysis. Currently mycobacteriophages, a highly studied phage group, are categorized into related clusters based on the comparative analysis of whole genome sequences. With the recent explosion of phage isolation, a simple method for phage cluster prediction would facilitate analysis of crude or complex samples without whole genome isolation and sequencing. The hypothesis of this study was that mycobacteriophage-cluster prediction is possible using comparison of a single, ubiquitous, semi-conserved gene. Tape Measure Protein (TMP) was selected to test the hypothesis because it is typically the longest gene in mycobacteriophage genomes and because regions within the TMP gene are conserved.ResultsA single gene, TMP, identified the known Mycobacteriophage clusters and subclusters using a Gepard dotplot comparison or a phylogenetic tree constructed from global alignment and maximum likelihood comparisons. Gepard analysis of 247 mycobacteriophage TMP sequences appropriately recovered 98.8% of the subcluster assignments that were made by whole-genome comparison. Subcluster-specific primers within TMP allow for PCR determination of the mycobacteriophage subcluster from DNA samples. Using the single-gene comparison approach for siphovirus coliphages, phage groupings by TMP comparison reflected relationships observed in a whole genome dotplot comparison and confirm the potential utility of this approach to another widely studied group of phages.ConclusionsTMP sequence comparison and PCR results support the hypothesis that a single gene can be used for distinguishing phage cluster and subcluster assignments. TMP single-gene analysis can quickly and accurately aid in mycobacteriophage classification.

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Section: Resultsmentioning

confidence: 99%

Phage cluster relationships identified through single gene analysis

et al. 2013

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“…Because true phylogenetic relationships are rarely known with certainty (cf. Hillis et al 1992; Sousa et al 2008), simulated data are used to investigate the accuracy and efficiency of phylogenetic reconstruction methods (e.g., Gaut and Lewis 1995; Huelsenbeck 1995), ancestral sequence reconstruction methods (e.g., Blanchette et al 2004), or methods of sequence alignment (e.g., Nuin et al 2006). They can also be used in parametric bootstrap analysis to calculate confidence intervals for parameter estimates or to estimate the null distribution for hypothesis testing (e.g., Goldman 1993).…”

Section: Introductionmentioning

confidence: 99%

INDELible: A Flexible Simulator of Biological Sequence Evolution

Fletcher

Yang

2009

Molecular Biology and Evolution

428

399

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Many methods exist for reconstructing phylogenies from molecular sequence data, but few phylogenies are known and can be used to check their efficacy. Simulation remains the most important approach to testing the accuracy and robustness of phylogenetic inference methods. However, current simulation programs are limited, especially concerning realistic models for simulating insertions and deletions. We implement a portable and flexible application, named INDELible, for generating nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. Indels are simulated under several models of indel-length distribution. The program implements a rich repertoire of substitution models, including the general unrestricted model and nonstationary nonhomogeneous models of nucleotide substitution, mixture, and partition models that account for heterogeneity among sites, and codon models that allow the nonsynonymous/synonymous substitution rate ratio to vary among sites and branches. With its many unique features, INDELible should be useful for evaluating the performance of many inference methods, including those for multiple sequence alignment, phylogenetic tree inference, and ancestral sequence, or genome reconstruction.

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“…All tree-building methods will force a binary tree on the data, but it has seldom been tested at what point of the analysis the conclusions might stretch beyond the assumptions, and thus at what level of detail it would be warranted to stop [21]. One such limitation involves short interior branches (i.e., fast evolutionary radiations), which may be even more prone to error in reality than predicted by theoretical studies [36]. Actually, it may not be really necessary to resolve a multifurcation “bush” (i.e., non-binary splits, or polytomies) in rapidly branching parts of a tree, because the temporal information encoded in that unresolved topology may be more relevant than the detailed sequence of bifurcations [31].…”

Section: Discussionmentioning

confidence: 99%

“…Most of these methods extract a single summary index from the distribution of nodes, so it's not too surprising that the majority of such measures of tree shape are sensitive to the level, or depth in the phylogeny at which imbalance is concentrated [3], [71] and to the presence of polytomies [36]. As summarized in Fig.…”

Section: Discussionmentioning

confidence: 99%

Universal Artifacts Affect the Branching of Phylogenetic Trees, Not Universal Scaling Laws

Altaba

2009

PLoS ONE

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BackgroundThe superficial resemblance of phylogenetic trees to other branching structures allows searching for macroevolutionary patterns. However, such trees are just statistical inferences of particular historical events. Recent meta-analyses report finding regularities in the branching pattern of phylogenetic trees. But is this supported by evidence, or are such regularities just methodological artifacts? If so, is there any signal in a phylogeny?MethodologyIn order to evaluate the impact of polytomies and imbalance on tree shape, the distribution of all binary and polytomic trees of up to 7 taxa was assessed in tree-shape space. The relationship between the proportion of outgroups and the amount of imbalance introduced with them was assessed applying four different tree-building methods to 100 combinations from a set of 10 ingroup and 9 outgroup species, and performing covariance analyses. The relevance of this analysis was explored taking 61 published phylogenies, based on nucleic acid sequences and involving various taxa, taxonomic levels, and tree-building methods.Principal FindingsAll methods of phylogenetic inference are quite sensitive to the artifacts introduced by outgroups. However, published phylogenies appear to be subject to a rather effective, albeit rather intuitive control against such artifacts. The data and methods used to build phylogenetic trees are varied, so any meta-analysis is subject to pitfalls due to their uneven intrinsic merits, which translate into artifacts in tree shape. The binary branching pattern is an imposition of methods, and seldom reflects true relationships in intraspecific analyses, yielding artifactual polytomies in short trees. Above the species level, the departure of real trees from simplistic random models is caused at least by two natural factors –uneven speciation and extinction rates; and artifacts such as choice of taxa included in the analysis, and imbalance introduced by outgroups and basal paraphyletic taxa. This artifactual imbalance accounts for tree shape convergence of large trees.SignificanceThere is no evidence for any universal scaling in the tree of life. Instead, there is a need for improved methods of tree analysis that can be used to discriminate the noise due to outgroups from the phylogenetic signal within the taxon of interest, and to evaluate realistic models of evolution, correcting the retrospective perspective and explicitly recognizing extinction as a driving force. Artifacts are pervasive, and can only be overcome through understanding the structure and biological meaning of phylogenetic trees.Catalan Abstract in Translation S1.

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Exploring tree-building methods and distinct molecular data to recover a known asymmetric phage phylogeny

Cited by 5 publications

References 47 publications

Phage cluster relationships identified through single gene analysis

Phage cluster relationships identified through single gene analysis

INDELible: A Flexible Simulator of Biological Sequence Evolution

Universal Artifacts Affect the Branching of Phylogenetic Trees, Not Universal Scaling Laws

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