Laboratory Notes

Evolutionary Innovation

Manolis Kellis

Computer Science and Artificial Intelligence Laboratory

Evolutionary Innovation, as revealed by the research of Manolis Kellis and the CSAIL Computational Biology Group.

Evolutionary Innovation, as revealed by the research of Manolis Kellis and the CSAIL Computational Biology Group.

When aligning the genomes of two distantly related yeast species, Manolis Kellis noticed a unique pattern of gene correspondence. Each region of the newly sequenced species (middle line) corresponded to exactly two regions of baker’s yeast (top and bottom line), whose genes perfectly interleaved to create a common ancestral gene order. Manolis recognized this as the signature of an ancient whole-genome duplication event (hence the duplicate mapping), followed by a period of massive gene loss, resulting in the pattern of gene interleaving. As many as 10% of the ancestrally duplicated genes are still kept today, many of which have taken on new functions to adapt and thrive in new environments.

A few months later, Manolis recognized the same signature in the comparison between the human genome and the puffer-fish genome, showing that the vertebrate bony fish have also arisen from a similar holegenome duplication (WGD) event. Recent evidence suggests that early vertebrates underwent an additional two rounds of WGD, giving rise to the incredible versatility of marine, terrestrial, and avian animals we see today, including of course, mammals, primates, and the human species.

Manolis and his computational biology group are now studying the mechanisms of post-duplication evolution in these species, at several levels of complexity: (a) the emergence of new functions by gene duplication, protein family expansion, and accelerated protein divergence; (b) the rewiring of the cellular circuitry by the appearance and disappearance of regulatory motifs in duplicated genes; and, (c) the formation of new patterns of network connectivity emerging from whole-genome duplication. They are thus aiming to shed new light on this powerful mechanism of evolutionary innovation that has shaped countless evolutionary bursts in the evolution of life.

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