Sliding MinPD: building evolutionary networks of serial samples via an automated recombination detection approach

Buendia, Patricia; Narasimhan, Giri

doi:10.1093/bioinformatics/btm413

Cited by 9 publications

(18 citation statements)

References 24 publications

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“…Methods designed specifically for longitudinal datasets (e.g. Buendia and Narasimhan, 2007) could be used to confirm these recombinants. However, our analysis recovered far more recombinants within a single timepoint than the previous studies, which supports our overall conclusion.…”

Section: Discussionmentioning

confidence: 99%

“…It has been shown that this method is not very powerful, especially when sequences are closely related (Posada and Crandall, 2001; Salminen, 2003). Improved bootscanning methods have been introduced that either do not require prior identification of parental sequences and incorporate distance measures as well (Martin et al, 2005) or that can incorporate serially sampled sequences into the analysis (Buendia and Narasimhan, 2007), both of which are more powerful methods than the original bootscanning implementation. An alternative approach is to use phylogenetic networks to investigate data sets that are suspected to contain recombinants (Huson and Bryant, 2006).…”

Section: Introductionmentioning

confidence: 99%

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An exploratory algorithm to identify intra-host recombinant viral sequences

Salemi

Gray

Goodenow

2008

Molecular Phylogenetics and Evolution

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Since recombination leads to the generation of mosaic genomes that violate the assumption of traditional phylogenetic methods that sequence evolution can be accurately described by a single tree, results and conclusions based on phylogenetic analysis of data sets including recombinant sequences can be severely misleading. Many methods are able to adequately detect recombination between diverse sequences, for example between different HIV-1 subtypes. More problematic is the identification of recombinants among closely related sequences such as a viral population within a host. We describe a simple algorithmic procedure that enables detection of intra-host recombinants based on split-decomposition networks and a robust statistical test for recombination. By applying this algorithm to several published HIV-1 datasets we conclude that intra-host recombination was significantly underestimated in previous studies and that up to one-third of the env sequences longitudinally sampled from a given subject can be of recombinant origin. The results show that our procedure can be a valuable exploratory tool for detection of recombinant sequences before phylogenetic analysis, and also suggest that HIV-1 recombination in vivo is far more frequent and significant than previously thought.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

An exploratory algorithm to identify intra-host recombinant viral sequences

Salemi

Gray

Goodenow

2008

Molecular Phylogenetics and Evolution

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“…Despite much ongoing work in this area, there are currently no broadly applicable methods that can take as input multiple sequence alignments and give as output phylogenetic network graphs that explicitly depict recombination (called reticulate ⁄ recombination networks in Huson & Bryant 2006). However, some specialized applications exist, like SlidingMinPD (Buendia & Narasimhan 2007), which attempts to infer recombination networks for recombining viral sequences that have been serially sampled within an individual host.…”

Section: Dealing With Recombination In Molecular Evolution Studiesmentioning

confidence: 99%

Analysing recombination in nucleotide sequences

Martin

Lemey

Posada

2011

Molecular Ecology Resources

116

112

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Throughout the living world, genetic recombination and nucleotide substitution are the primary processes that create the genetic variation upon which natural selection acts. Just as analyses of substitution patterns can reveal a great deal about evolution, so too can analyses of recombination. Evidence of genetic recombination within the genomes of apparently asexual species can equate with evidence of cryptic sexuality. In sexually reproducing species, nonrandom patterns of sequence exchange can provide direct evidence of population subdivisions that prevent certain individuals from mating. Although an interesting topic in its own right, an important reason for analysing recombination is to account for its potentially disruptive influences on various phylogenetic-based molecular evolution analyses. Specifically, the evolutionary histories of recombinant sequences cannot be accurately described by standard bifurcating phylogenetic trees. Taking recombination into account can therefore be pivotal to the success of selection, molecular clock and various other analyses that require adequate modelling of shared ancestry and draw increased power from accurately inferred phylogenetic trees. Here, we review various computational approaches to studying recombination and provide guidelines both on how to gain insights into this important evolutionary process and on how it can be properly accounted for during molecular evolution studies.

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“…Furthermore, these traditional phylogenetic methods assume that all the sequence data are from contemporaneous taxa, which is not valid for serially-sampled data from longitudinal studies. Several methods that estimate the phylogenetic relationship of serially-sampled data have been published since 2000 [ 1 , 9 - 14 ]. However, only one of these methods takes recombination into account: Sliding MinPD [ 1 ].…”

Section: Introductionmentioning

confidence: 99%

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confidence: 99%

Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains

Buendia

Narasimhan

2009

BMC Syst Biol

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BackgroundThe HIV virus is known for its ability to exploit numerous genetic and evolutionary mechanisms to ensure its proliferation, among them, high replication, mutation and recombination rates. Sliding MinPD, a recently introduced computational method [1], was used to investigate the patterns of evolution of serially-sampled HIV-1 sequence data from eight patients with a special focus on the emergence of X4 strains. Unlike other phylogenetic methods, Sliding MinPD combines distance-based inference with a nonparametric bootstrap procedure and automated recombination detection to reconstruct the evolutionary history of longitudinal sequence data. We present serial evolutionary networks as a longitudinal representation of the mutational pathways of a viral population in a within-host environment. The longitudinal representation of the evolutionary networks was complemented with charts of clinical markers to facilitate correlation analysis between pertinent clinical information and the evolutionary relationships.ResultsAnalysis based on the predicted networks suggests the following:: significantly stronger recombination signals (p = 0.003) for the inferred ancestors of the X4 strains, recombination events between different lineages and recombination events between putative reservoir virus and those from a later population, an early star-like topology observed for four of the patients who died of AIDS. A significantly higher number of recombinants were predicted at sampling points that corresponded to peaks in the viral load levels (p = 0.0042).ConclusionOur results indicate that serial evolutionary networks of HIV sequences enable systematic statistical analysis of the implicit relations embedded in the topology of the structure and can greatly facilitate identification of patterns of evolution that can lead to specific hypotheses and new insights. The conclusions of applying our method to empirical HIV data support the conventional wisdom of the new generation HIV treatments, that in order to keep the virus in check, viral loads need to be suppressed to almost undetectable levels.

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Sliding MinPD: building evolutionary networks of serial samples via an automated recombination detection approach

Cited by 9 publications

References 24 publications

An exploratory algorithm to identify intra-host recombinant viral sequences

An exploratory algorithm to identify intra-host recombinant viral sequences

Analysing recombination in nucleotide sequences

Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains

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