Because of functional constraints, substitution rates vary among the positions 
of a protein but are usually assumed to be constant at a given site during 
evolution. The distribution of the rates across the sequence positions generally 
fits a Gamma distribution. Models of sequence evolution were accordingly 
designed and led to improved phylogenetic reconstruction. However, it has been 
convincingly demonstrated that the evolutionary rate of a given position is not 
always constant throughout time. We called such within-site rate variations 
heterotachy (for "different speed" in Greek). Yet, heterotachy was found among 
homologous sequences of distantly related organisms, often with different 
functions. In such cases, the functional constraints are likely different, which 
would explain the different distribution of variable sites. To evaluate the 
importance of heterotachy, we focused on amino acid sequences of mitochondrial 
cytochrome b, for which the function is likely the same in all vertebrates. 
Using 2,038 sequences, we demonstrate that 95% of the variable positions are 
heterotachous, i.e., underwent dramatic variations of substitution rate among 
vertebrate lineages. Heterotachy even occurs at small evolutionary scale, and in 
these cases it is very unlikely to be related to functional changes. Since a 
large number of sequences are required to efficiently detect heterotachy, the 
extent of this phenomenon could not be estimated for all proteins yet. It could 
be as large as for cytochrome b, since this protein is not a peculiar case. The 
observations made here open several new avenues of research, such as the 
understanding of the evolution of functional constraints or the improvement of 
phylogenetic reconstruction methods.