Principal Investigator Manolis Kellis (Kamvysselis)
Co-investigator Eric Lander
Gene duplication is a fundamental aspect of genome evolution that produces large and small gene families of (usually) related function. We perform a phylogenomic analysis of gene duplication in the chicken (Gallus gallus) to characterize the dynamics and evolution of gene duplication on the evolutionary line to birds. In Gallus, the distribution of the number of paralogs per gene family is heavily skewed towards small families. This finding is in accord with other studies that find gene family size typically follows a power-law distribution in animals, a pattern thought to be produced by differential rates of pseudogenization among families. We also test for within-family evolutionary rate variation in Gallus, finding that the vast majority of gene families exhibit substantial rate variation among lineages. This rate variation probably stems from two sources: natural deviations in the clock as commonly found, for example, in phylogenetic analyses of different species; and bursts of adaptive evolution among newly evolved gene family members. The age of gene duplications in Gallus are distributed exponentially, with most duplications occurring recently, a pattern consistent with analyses on other eukaryotes. Taken together, these results begin to reveal the dynamics of gene family evolution in birds, the most speciose group of living amniotes, though whole genome data are required from more bird and reptile species to fully understand patterns of gene gain and loss in this group.