Motivation: In genome-wide analyses, the relative age of gene duplications is often estimated by measuring the rate of synonymous substitutions (dS) between paralogous sequences. On the other hand, recent studies have shown the feasibility of inferring, at genomic scales, the relative age of duplication events from the topology of gene family trees. This represents a promising alternative for large surveys requiring an automatic methodology to establish a timeline of duplication events and that are usually limited to the use of dS, which presents known limitations such as a fast saturation of the signal. However, both measures have never been compared in a common framework.
Results: Topology-based placement of duplications on a relative time scale corresponding to periods between speciation events were found to be highly consistent, providing the same placement for 67-84% of a reliable set of gene pairs duplicated in a single event. For recent evolutionary periods, dS and topological measures showed a strong correlation. We conclude that the topology-based approach is more appropriate for assigning duplications to temporal scales when analyses need to include ancient events, and that the study of recent duplications may benefit from a combination of dS and topology information.