One problem commonly experienced in phylogeny reconstruction arises when two or more of the groups being compared have accumulated far more genetic changes (mutations) than the others in the comparison
This situation often results in a phenomenon known as "long branch attraction," in which the highly mutated lineages end up grouping together in a phylogenetic analysis even if they are distantly related. What do you think causes long branch attraction? How might it be compensated for?
Since nucleotides can change only among four states (A,C,T, and G), in lineages with disproportionately many base substitutions the odds of becoming convergently similar (or at least obscuring the underlying pattern of homology with their true nearest relative) increases greatly. This problem may be compensated for by using data from several different genes or regions of the genome.
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