The principle of heterotachy states that the substitution rate of sites in a 
gene can change through time. In this article, we propose a powerful statistical 
test to detect sites that evolve according to the process of heterotachy. We 
apply this test to an alignment of 1289 eukaryotic rRNA molecules to 1) 
determine how widespread the phenomenon of heterotachy is in ribosomal RNA, 2) 
to test whether these heterotachous sites are nonrandomly distributed, that is, 
linked to secondary structure features of ribosomal RNA, and 3) to determine the 
impact of heterotachous sites on the bootstrap support of monophyletic 
groupings. Our study revealed that with 21 monophyletic taxa, approximately 
two-thirds of the sites in the considered set of sequences is heterotachous. 
Although the detected heterotachous sites do not appear bound to specific 
structural features of the small subunit rRNA, their presence is shown to have a 
large beneficial influence on the bootstrap support of monophyletic groups. 
Using extensive testing, we show that this may not be due to heterotachy itself 
but merely due to the increased substitution rate at the detected heterotachous 
sites.