Long-branch attraction

Long-branch attraction is a phylogenetic inference error in which rapidly evolving lineages are grouped together because independent substitutions make them appear similar.

Homoplasy: Similarity between traits that arose independently rather than from a shared ancestral trait. Independent substitutions create the misleading similarities that draw long branches together.
Phylogenetics: The study of evolutionary relationships among organisms, genes, or other biological entities. Long-branch attraction is an error within the inference of evolutionary trees.
Bayesian phylogenetics: A framework that estimates phylogenetic trees and parameters using Bayesian probability. Model-based inference can reduce attraction when its evolutionary assumptions adequately fit the data.
Felsenstein's four-taxon example: A four-taxon tree arrangement demonstrating conditions where maximum parsimony converges on the wrong topology. This canonical example isolates the mechanism behind long-branch attraction.
Multiple sequence alignment: A method for arranging biological sequences so that homologous positions can be compared. Errors in matching homologous sites can compound the signal that misleads tree inference.
Phylogenetic tree: A branching diagram representing hypothesized evolutionary relationships among sampled taxa. The error changes which taxa appear as neighboring branches on the inferred tree.
Maximum likelihood estimation: A statistical method that selects parameter values maximizing the probability of observed data under a model. Likelihood methods can outperform parsimony under rate heterogeneity when the model is suitable.
Attraction of long branches in phylogenetics: The phenomenon in which long branches are inferred as close relatives despite separate origins. It is the characteristic observed pattern summarized by the concept.
Maximum parsimony: A phylogenetic method that selects the tree requiring the fewest character-state changes. Under some conditions, parsimony favors an incorrect grouping of rapidly evolving lineages.
Molecular clock: The principle that molecular changes can provide information about the timing of evolutionary divergences. Rate variation violates simple clock assumptions and helps produce long branches.

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