The easiest way to create new genes is to duplicate the ones that are already there, and the quickest way of doing this for many of them is to duplicate the whole genome. This can then be shrunk back down to its previous size while sporting a new collection of genes. This simple theory, which Susumo Ohno proposed more than 30 years ago, has now been validated in yeast by two groups that have compared the genome of the most commonly studied member of this taxon, Saccharomyces cerevisiae, with that of its two close relatives.

Finding conclusive evidence of whole-genome duplication (WGD) in S. cerevisiae has been a fruitless task, as most duplicated regions have diverged beyond recognition. What is needed is a yeast species that diverged from S. cerevisiae before the duplication took place — because if WGD really occurred, any one region in this species would have two corresponding regions in S. cerevisiae. As one of almost any two duplicated genes in S. cerevisiae has been lost as the genome returned to its pre-duplication size, regions of homology for each ancestral segment would alternate between the two copies in S.cerevisiae. This pattern is exactly what was seen in the genomes of the yeasts Kluyveromyces waltii and Ashbya gossypii, which were sequenced and analysed by Manolis Kellis and co-workers and by Fred Dietrich and colleagues, respectively.

Kellis et al. identified 253 blocks in K. waltii that could each be matched to two regions in the S. cerevisiae genome. These blocks — which tiled 85% of the K. waltii genome and were spread across all chromosomes — were then used to match up the long sought-after sister regions in S. cerevisiae that evolution had caused to drift apart. A total of 145 such sister blocks were found, corresponding to 457 gene pairs. So here is the first conclusive evidence that WGD occurred in yeast — but what happened next? Of the 457 gene pairs, 17% evolved more quickly than their counterparts in K. waltii, and the fact that most cases of accelerated evolution involved only one of the gene duplicates supports the popular idea that duplication leaves one gene copy free to diverge.

The sequencing and genome annotation of A. gossypii by Dietrich et al. led to the same conclusion. Ninety-five percent of all open reading frames in A. gossypii have homologues in S. cerevisiae and most of these are arranged in a conserved linear order. These syntenic regions were used to build a detailed map of ancient S. cerevisiae gene order that also provided definitive proof for the occurrence of WGD in the S. cerevisiae lineage after it split from its common ancestor with A. gossypii.

This work has settled the longstanding controversy over how to interpret the presence of duplicated blocks in the S. cerevisiae genome: are they evidence of WGD or were they caused by local duplications? Although Ohno's idea was an appealing one, it didn't necessarily describe the most plausible means of evolutionary innovation — after all, WGD takes the genome for a rather rocky ride. Now that this case has finally been closed, researchers can turn their attention to resolving similar issues in vertebrates, where the debate is still alive.