DLIGHT - Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework

  title={DLIGHT - Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework},
  author={Christophe Dessimoz and Daniel Margadant and Gaston H. Gonnet},
This paper presents an algorithm to detect lateral gene transfer (LGT) on the basis of pairwise evolutionary distances. The prediction is made from a likelihood ratio derived from hypotheses of LGT versus no LGT, using multivariate normal theory. In contrast to approaches based on explicit phylogenetic LGT detection, it avoids the high computational cost and pitfalls associated with gene tree inference, while maintaining the high level of characterization obtainable from such methods (species… 
Clustering Genes of Common Evolutionary History
A large-scale simulation study of phylogenetic distances and clustering methods to infer loci of common evolutionary history finds that the best-performing combinations are distances accounting for branch lengths followed by spectral clustering or Ward’s method.
Detecting laterally transferred genes.
Methods for identifying alien genes in genomes fall into two general classes:ylogenetic and Parametric methods, which examine the compositional properties of genes within a genome to find those with atypical properties, likely indicating the directional mutational pressures of a donor genome.
Inferring Horizontal Gene Transfer
HGT is a major source of phenotypic innovation and a mechanism of niche adaptation, and as HGT can bring into genomes radically different genotypes from distant lineages, or even new genes bearing new functions, it can be difficult to ascertain all but simple and clear-cut HGT events.
Evaluating Sequence Alignments and Phylogenies New Methods and Large-Scale Comparisons
New phylogeny based tests of alignment accuracy are introduced, which use large and representative samples of real biological data and overcome the flaws of traditional evaluation approaches and reveal phylogenetic signal that is poorly exploited by most alignment and phylogeny estimators.
Indirect identification of horizontal gene transfer
It is shown that a simple greedy graph editing scheme can be used to efficiently detect HGT events that are implicitly contained in LDT graphs, and the complete xenology relation is described by an rs-Fitch graph, i.e., a complete multipartite graph satisfying constraints on the vertex coloring.
A Survey of Combinatorial Methods for Phylogenetic Networks
This article gives an introduction to the topic of phylogenetic networks, very briefly describing the fundamental concepts and summarizing some of the most important combinatorial methods that are available for their computation.
Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise
An estimator for the covariance of distances from sequences aligned pairwise is introduced and shows no sign of bias when sequence divergence is below 150 PAM units and is compared to the well-known variance estimator of ML distances.
Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain
This work exploits that HGT creates long identical DNA sequences in the genomes of distant species, which can be found efficiently using alignment-free methods and develops a model to explain their statistical properties as well as estimate the transfer rate between pairs of taxa.
Comparative genomics using pairwise evolutionary distances
This thesis explores and develops comparative genomics methods that rely on pairwise distances and develops the largest effort of orthology inference, OMA, which computes evolutionary distances from pairwise maximum likelihood alignments and computes a likelihood ratio between hypotheses of LGT and no LGT.
Long identical sequences found in multiple bacterial genomes reveal frequent and widespread exchange of genetic material between distant species
A unique view of horizontal transfer across the bacterial tree of life is provided, illuminating a fundamental process driving bacterial evolution.


Inference of horizontal genetic transfer from molecular data: an approach using the bootstrap.
The method was successfully applied to data sets that were not found to be significantly different with existing methods that use comparisons of phylogenetic trees, and the new statistical framework is also applicable to the inference of horizontal transfer from restriction fragment length polymorphism distributions and protein sequences.
On surrogate methods for detecting lateral gene transfer.
  • M. Ragan
  • Biology
    FEMS microbiology letters
  • 2001
Four surrogate methods are applied to identify open reading frames (ORFs) in the genome of Escherichia coli K12 that may have arisen by lateral gene transfer that may require rigorous inference of trees.
Using the nucleotide substitution rate matrix to detect horizontal gene transfer
A new class of methods based on the changes in nucleotide substitution rates that occur when a gene is transferred to a new organism, which will be widely useful in detecting HGT events linked to the evolution of important bacterial traits, such as antibiotic resistance and pathogenicity.
The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer
Assessing the extent of HGT among core orthologous genes using a novel statistical method based on statistical comparisons of tree topology proposes that HGT events, even when relatively common, still leave the treelike history of phylogenies intact, much like cobwebs hanging from tree branches.
Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution
The results indicate that among 57,670 gene families distributed across 190 sequenced genomes, at least two-thirds and probably all, have been affected by LGT at some time in their evolutionary past and a component of common ancestry nonetheless remains detectable in gene distribution patterns.
Horizontal gene transfer and phylogenetics.
Inferring Genome Trees by Using a Filter To Eliminate Phylogenetically Discordant Sequences and a Distance Matrix Based on Mean Normalized BLASTP Scores
This study developed and assessed a distance-based approach, based on mean pairwise sequence similarity, for generating genome trees, and defined a phylogenetically discordant sequence (PDS) as an open reading frame (ORF) that exhibits patterns of similarity relationships statistically distinguishable from most other ORFs in the same genome.
Evidence for horizontal gene transfer in Escherichia coli speciation.
Reconciling the many faces of lateral gene transfer.
Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events.
Cyanobacterial genomes reveal a complex evolutionary history, which cannot be represented by a single strictly bifurcating tree for all genes or even most genes, although a single completely resolved phylogeny was recovered from the quartets' plurality signals.