ABSTRACT
Long branch attraction (LBA) is a phylogenetic phenomenon where certain approaches like maximum parsimony become absolutely misleading. Joe Felsenstein showed that if two taxa in the four-taxon example had extraordinarily high rate changes compared to the two remaining taxa, the two rapidly evolving taxa would falsely attract each other and be inferred as sister taxa when MP is used. Random rooting is the phenomena where the root of a tree has extremely long branches resulting in the random attachment of the outgroup to the taxa. Rate heterogeneity is the phenomena where not all sites in a DNA or protein sequence evolve at the same rate. Rate heterogeneity can be included in likelihood models by use of a descriptor for invariant sites (I) and a gamma distribution (Γ or G). There is a multitude of substitution models in phylogenomics for both DNA and amino acid sequences. Likelihood models can be compared using statistical methods. Programs exist that can rapidly compare models (ModelTest, ProTest, etc.).
