Estimating the tempo and mode of gene family evolution from comparative genomic data

Abstract

Comparison of whole genomes has revealed that changes in the size of gene families among organisms is quite common. However, there are as yet no models of gene family evolution that make it possible to estimate ancestral states or to infer upon which lineages gene families have contracted or expanded. In addition, large differences in family size have generally been attributed to the effects of natural selection, without a strong statistical basis for these conclusions. Here we use a model of stochastic birth and death for gene family evolution and show that it can be efficiently applied to multispecies genome comparisons. This model takes into account the lengths of branches on phylogenetic trees, as well as duplication and deletion rates, and hence provides expectations for divergence in gene family size among lineages. The model offers both the opportunity to identify large-scale patterns in genome evolution and the ability to make stronger inferences regarding the role of natural selection in gene family expansion or contraction. We apply our method to data from the genomes of five yeast species to show its applicability.

Figure 1.

Here, we visually explain the “large family bias” problem. The solid line shows the likelihood of gene families with sizes (k(k(k(kk)))) as a function of k, for values of k from 1 to 50. The dashed line shows the average likelihood of gene families evolved from a common ancestor with family size equal to k. The average is computed over 100 random samples for each value of k. Clearly, the likelihoods for large gene families are consistently and significantly smaller.

Figure 2.

The phylogenetic tree. Branch lengths t are given in millions of years. The branch numbers used in this study are shown in circles.