Long branch attraction

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Long branch attraction (LBA), a phenomenon in phylogenetic and clustering analyses, occurs if terminals or clades that are thought not to be one another's closest relatives cluster together due to misinterpretation of shared homoplasies, usually in DNA sequence data. It is a result of the way clustering algorithms work: terminals or taxa with many autapomorphies (character states unique to a single branch) may by chance (convergence) exhibit the same states as those on another branch. A phylogenetic analysis that does not down-weight these apparent similarities will group these taxa together as a clade if there are not other synapomorphies that outweigh these homoplastic features and group these taxa with their true sister taxa.

The result of LBA in evolutionary analyses is that rapidly evolving lineages may be inferred to be closely related, regardless of their true relationships. For example, in DNA sequence-based analyses, the problem arises when sequences from two (or more) lineages evolve rapidly. There are only four possible nucleotides and when DNA substitution rates are high, the probability that two lineages will evolve the same nucleotide at the same site increases. When this happens, parsimony may erroneously interpret this homoplasy as a synapomorphy (i.e., evolving once in the common ancestor of the two lineages).

This problem may be minimized by using methods that correct for multiple substitutions at the same site, by adding taxa related to those with the long branches that add additional true synapomorphies to the data, or by using alternative slower evolving traits (e. g., more conservative gene regions).

Of course, the recognition of an instance of long-branch attraction implies that there is some other evidence - often morphological - that suggests that the taxa so united are not, in fact, sister taxa. Otherwise, as per Hennig's Auxiliary Principle, putative synapomorphies should be viewed as de facto evidence of grouping (Hennig, 1966; Schuh and Brower, 2009).

References

Bergsten, J. (2005): A review of long-branch attraction. Cladistics 21(2): 163-193. PDF fulltext
Felsenstein, J. (2004): Inferring Phylogenies. Sinauer Associates, Sunderland, MA.
Hennig, W. (1966): Phylogenetic Systematics. University of Illinois Press, Urbana, IL.
Schuh, R. T. and Brower, A. V. Z. (2009): Biological Systematics: Principles and Applications, (2nd edn.) Cornell University Press, Ithaca, NY.

v t e Topics in phylogenetics

Relevant fields	Computational phylogenetics Molecular phylogenetics Cladistics Evolutionary taxonomy

Basic concepts	Phylogenetic tree Phylogenetic network Long branch attraction Clade vs Grade Ghost lineage

Inference methods	Maximum parsimony Maximum likelihood Neighbor-joining UPGMA Bayesian inference Least squares Three-taxon analysis

Current topics	PhyloCode DNA barcoding

-morphy	Symplesiomorphy Apomorphy Synapomorphy Autapomorphy

-phyly	Monophyly/Holophyly Paraphyly Polyphyly

List of evolutionary biology topics

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