Duplication — be it of a single gene, a chromosomal region or a whole genome — is a powerful tool for evolution. Being able to tell when duplication events took place is important for analysing the relationships between species. But the numerous rounds of copying and subsequent loss of genes, especially in plants, make carrying out comparative genomics studies a daunting task. A recent study by Bowers et al. describes how these difficulties might be circumvented to understand how duplication events have shaped the evolution of plant genomes.

Most studies date duplication events using a 'molecular clock' method, in which the number of nucleotide differences between a pair of duplicated genes is counted. The larger the number of differences, the longer the period since the duplication took place. This measurement is then calibrated against the number of changes that occur in a known period of time, for example, by using the fossil record.

Because different molecular clocks can run at different speeds, Bowers et al. chose a different approach. Instead of trying to put a precise date on duplication events, they concentrated on mapping them in relation to the divergence of different species — an all-important factor in comparative genomics. They compared duplicated Arabidopsis genes to those from other plants, and determined the amount of difference between pairs of genes from the different species. This allowed them to work out whether the duplication happened before or after the divergence of the various species.

In this way, the authors identified several important duplication events in Arabidopsis evolution. The first of these is extremely ancient, dating back to before the evolution of the flowering plants. A second event took place after the monocotyledons and dicotyledons went their separate ways. Relatively recently, a third duplication occurred in a common ancestor of Arabidopsis and cabbage.

So, without calculating actual time periods, Bowers et al. have pinpointed three major events that have shaped the genomes of the flowering plant lineage. A similar method has recently been used to determine when an important duplication event in Saccharomyces cereviseae occurred, so this approach might become a useful tool for mapping out important evolutionary events in a wide variety of species.