Fig. 1.

Two methods for inferring turnover rates in syntenically defined primate 3′-UTRs. In (A), the ancestral states of 3′-UTRs (containing or not containing a binding site) are inferred using presence/absence calls in extant species at the level of motifs, and gains and losses are in turn inferred from the inferred ancestors. Losses appear to occur much less frequently than gains. In (B), a revised maximum likelihood approach using individual reconstructed ancestral nucleotides was applied to primate 3′-UTRs. The skew toward gains is completely ameliorated.