Conserved noncoding elements (CNEs) in vertebrate genomes often act as 
developmental enhancers, but a critical issue is how well orthologous CNE 
sequences retain the same activity in their respective species, a characteristic 
important for generalization of model organism studies. To quantify how well CNE 
enhancer activity has been preserved, we compared the anatomy-specific 
activities of 41 zebra fish CNEs in zebra fish embryos with the activities of 
orthologous human CNEs in mouse embryos. We found that 13/41 (∼30%) of the 
orthologous CNE pairs exhibit conserved positive activity in zebra fish and 
mouse. Conserved positive activity is only weakly associated with either 
sequence conservation or the absence of bases undergoing accelerated evolution. 
A stronger effect is that disparate activity is associated with transcription 
factor binding site divergence. To distinguish the contributions of cis- versus 
trans-regulatory changes, we analyzed 13 CNEs in a three-way experimental 
comparison: human CNE tested in zebra fish, human CNE tested in mouse, and 
orthologous zebra fish CNE tested in zebra fish. Both cis- and trans-changes 
affect a significant fraction of CNEs, although human and zebra fish sequences 
exhibit disparate activity in zebra fish (indicating cis regulatory changes) 
twice as often as human sequences show disparate activity when tested in mouse 
and zebra fish (indicating trans regulatory changes). In all four cases where 
the zebra fish and human CNE display a similar expression pattern in zebra fish, 
the human CNE also displays a similar expression pattern in mouse. This suggests 
that the endogenous enhancer activity of ∼30% of human CNEs can be determined 
from experiments in zebra fish alone, and to identify these CNEs, both the zebra 
fish and the human sequences should be tested.