Sequence alignments of multiple genes are routinely used to infer phylogenetic 
relationships among species. The analysis of their concatenation is more likely 
to give correct results under an assumption of homotachy (i.e., the evolutionary 
rates within lineages in each of the concatenated genes are constant during 
evolution). Here, we examine how the violation of homotachy (i.e., presence of 
within-site rate variation, called heterotachy) distorts species phylogenies. A 
theoretical examination has been conducted using a four taxon case and the 
neighbor joining (NJ) method, concluding that NJ recovers the incorrect tree 
when concatenated genes exhibit heterotachy. The application of average and 
weighted-average distance approaches, where gene boundaries are kept intact, 
overcomes the detrimental effect of heterotachy in multigene analysis using the 
NJ method.