What is the long branch attraction in phylogenetic analysis?

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.

How do you test long branch attraction?

A simple and effective method for determining whether or not long branch attraction is affecting tree topology is the SAW method, named for Siddal and Whiting. If long branch attraction is suspected between a pair of taxa (A and B), simply remove taxon A (“saw” off the branch) and re-run the analysis.

What causes long branch attraction?

Long branch attraction occurs because when relatively numerous state changes occur along lineages, random changes can begin to outweigh nonrandom, phylogenetically informative ones. The phylogenetic placement of a taxon with a long branch can be uncertain and can unduly influence the placement of other taxa.

What does a long branch mean in phylogeny?

A long, unbroken branch on a phylogeny indicates that little evolutionary change has occurred in that lineage and that this lineage is likely to retain ancestral characteristics — or may even be the ancestor of other organisms on the phylogeny.

What is maximum likelihood phylogenetic tree?

Maximum Likelihood is a method for the inference of phylogeny. It evaluates a hypothesis about evolutionary history in terms of the probability that the proposed model and the hypothesized history would give rise to the observed data set. The method searches for the tree with the highest probability or likelihood.

What is the Felsenstein zone?

The “Felsenstein Zone” – If one thinks of an abstract “tree space” as the set of all possible tree topologies (including branch lengths) for a given phylogeny, the Felsenstein Zone is the region where a phylogenetic method becomes inconsistent.

What is the meaning of branch lengths?

Branch lengths indicate genetic change i.e. the longer the branch, the more genetic change (or divergence) has occurred. Typically we measure the extent of genetic change by estimating the average number of nucleotide or protein substitutions per site.

What do branch lengths represent in Upgma?

branch length : often represents the number of changes that have occurred in that branch. root : is the common ancestor of all taxa. distance scale : scale which represents the number of differences between sequences (e.g. 0.1 means 10 % differences between two sequences)

What is maximum parsimony and maximum likelihood?

The method of maximum likelihood seeks to find the tree topology that confers the highest probability on the observed characteristics of tip species. The method of maximum parsimony seeks to find the tree topology that requires the fewest changes in character states to produce the characteristics of those tip species.

When is long branch attraction not a problem?

If either of the taxa appears at a different branch point in the absence of the other, there is evidence of long branch attraction. Since long branches can’t possibly attract one another when only one is in the analysis, consistent taxon placement between treatments would indicate long branch attraction is not a problem.

How to determine if long branch attraction is affecting tree topology?

Is the attraction of a long branch a phylogeny?

As such, “long branch attraction” can in some ways be better expressed as “branch length attraction”. However, it is typically long branches that exhibit attraction. The recognition of long-branch attraction implies that there is some other evidence that suggests that the phylogeny is incorrect.

How does LBA work in a phylogenetic analysis?

In phylogenetic and clustering analyses, LBA 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 exhibit the same states as those on another branch ( homoplasy ).