Difference between revisions of "Long branch attraction"

Latest revision as of 04:51, 13 September 2006

Long branch attraction (LBA) is a phenomenon in phylogenetic analyses (most commonly those employing maximum parsimony) when rapidly evolving lineages are inferred to be closely related, regardless of their true evolutionary relationships. The problem arises when the DNA of two (or more) lineages evolves rapidly. There are only four possible nucleotides and when DNA substitution rates are high, the probability that two lineages will independently evolve the same nucleotide at the same site increases. When this happens, parsimony erroneously interprets this similarity as a synapomorphy (i.e., evolving once in the common ancestor of the two lineages).

This problem can be minimized by using methods that incorporate differential rates of substitution among lineages (e.g., maximum likeihood).

The most problematic and pervasive problem in molecular phylogeny is the problem of 'long branch attraction' (Felsenstein, 1978; Gribaldo and Philippe, 2002).

"[Long branch attraction] is the tendency of highly divergent sequences (i.e. those with long terminal branches) to group together in a tree regardless of their true relationships.

"This is at least partly because rapidly evolving sequences, or sequences without any close relatives, will have numerous unique mutations (with respect to the rest of the tree). Because there are only a limited number of possible states (20 amino acids or 4 nucleotides) for rapidly evolving sites to change to, sequences with a lot of these changes will start to pick up spurious similarities to each other. If their branches are very long (i.e. if there are a lot of these changes), these spurious similarities can override the true phylogenetic signal, and the sequences will be 'attracted' to each other." — Sandra L. Baldauf (2003).

LBA can cause bootstrap values all over the phylogenetic tree to deteriorate.

See also

• Maximum likelihood
• Maximum parsimony
• Bootstrapping

References

• Felsenstein J (2004). Inferring Phylogenies. Sinauer Associates (Sunderland, MA).
• Baldauf SL (2003). Phylogeny for the faint of heart: a tutorial. TRENDS in Genetics 19(6):345-351.
• Gribaldo S and Philippe H (2002). Ancient phylogenetic relationships. Theor Popul Biol 61:391-408.
• Felsenstein J (1978). Cases in which parsimony or compatability methods will be positively misleading. Syst Zool 27:401-410.

External links

• Wikipedia article on Long branch attraction