A review of long‐branch attraction

  title={A review of long‐branch attraction},
  author={Johannes Bergsten},
The history of long‐branch attraction, and in particular methods suggested to detect and avoid the artifact to date, is reviewed. Methods suggested to avoid LBA‐artifacts include excluding long‐branch taxa, excluding faster evolving third codon positions, using inference methods less sensitive to LBA such as likelihood, the Aguinaldo et al. approach, sampling more taxa to break up long branches and sampling more characters especially of another kind, and the pros and cons of these are discussed… 

Heterotachy and long-branch attraction in phylogenetics

More realistic simulations to evaluate the relative performance of MP and ML methods when two kinds of heterogeneities are considered, finding that ML is always more accurate than MP and heterotachy, which constitutes a serious violation of existing models, decreases the accuracy of ML whatever the level of rate variation across lineages.

Maximum Likelihood Inference of Small Trees in the Presence of Long Branches

The effect of one long branch on three-taxon tree reconstruction is looked at, showing that, counterintuitively, long branches are preferentially placed at the tips of the tree, which can be understood through the use of analytical solutions to the ML equation and distance matrix methods.

Coalescent methods are robust to the simultaneous effects of long branches and incomplete lineage sorting.

The results collectively suggest that coalescent methods are more likely to infer the correct species tree in cases of ancient rapid radiations where long external and short internal branches are in close phylogenetic proximity.

Analysis of long branch extraction and long branch shortening

The long branch extraction method seems to mask the majority of the search space rendering it ineffective as a detection method of LBA, and a proposed alternative, the long branch shortening method, is also ineffective in predicting long branch attraction for all tree topologies.

Can quartet analyses combining maximum likelihood estimation and Hennigian logic overcome long branch attraction in phylogenomic sequence data?

It is demonstrated through extensive simulation experiments that, whereas maximum likeilihood estimation performs well in many cases, it can be outperformed by PhyQuart in cases where it fails due to extreme branch length asymmetries producing long-branch attraction artefacts where there is only very minor model misspecification.

Sources of Error and Incongruence in Phylogenomic Analyses

Phylogenomic analyses can be performed by analysing gene trees separately and using coalescent or supertree analyses to retrieve a tree or using the supermatrix approach, which is able to deal with incomplete lineage sorting and discordance.

Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics

It is shown that BI, unlike ML, is biased in favor of topologies that group long branches together, even when the true model and prior distributions of evolutionary parameters over a group of phylogenies are known, and that ML may be a more reliable framework for modern phylogenetic analysis.

The gene tree delusion.

Accurate branch length estimation in partitioned Bayesian analyses requires accommodation of among-partition rate variation and attention to branch length priors.

The importance of among-partition rate variation (APRV) and potential pitfalls in implementation of mixed models that accommodate APRV in Bayesian analyses are discussed.



Long‐Branch Abstractions

It is asserted, long‐branch attraction cannot explain the presence of nematocysts in Myxozoa and halteres in Strepsiptera, and it is suggested that maximum likelihood methods are extremely sensitive to taxon and character sampling and that these data sets are demonstrative of the long-branch repulsion problem.

Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA.

Is the Felsenstein zone a fly trap?

Several criteria for identifying long-branch attraction are outlined and these criteria are applied to 18S ribosomal DNA (rDNA) sequence data for 13 insects.

Data exploration in phylogenetic inference: scientific, heuristic, or neither

  • Taran GrantA. Kluge
  • Biology
    Cladistics : the international journal of the Willi Hennig Society
  • 2003
It is concluded that undue emphasis has been placed on data exploration in phylogenetic inference, and phylogeneticists are urged to consider more carefully the relevance of the methods that they employ.

Escaping from the Felsenstein zone by detecting long branches in phylogenetic data.

It is shown that the accuracy of evolutionary trees can be improved by detecting and combating the potentially misleading influences of long-branch taxa.

Success of Parsimony in the Four‐Taxon Case: Long‐Branch Repulsion by Likelihood in the Farris Zone

The accuracy of phylogenetic methods is reinvestigated for the four‐taxon case with a two‐ edge rate and a three‐edge rate and maximum likelihood methods are shown to be particularly prone to failure when closely related taxa have long branches.

A Higher Order Parsimony Method to Reduce Long-Branch Attraction

Higher order parsimony (HOP), a method for reconstructing a phylogenetic tree for a quartet of four species from DNA strings for the species, works best when the alphabet corresponds to sequences of nucleotides; hence, a modification is presented that applies when thephabet corresponds to amino acid residues.

The Root of the Tree of Life in the Light of the Covarion Model

A simple method for extracting the phylogenetic signal, by considering the variability of sequence positions within predefined phylogenetic groups, and it was shown that noise quantitatively prevailed upon signal.

Taxon sampling revisited

It is found, using computer simulations, that adding characters can be the more favourable strategy, even for long-branched trees, and that adding slowly evolving taxa to subdivide long branches can reduce accuracy.