The roles of speciation and divergence time in the loss of duplicate gene expression

Abstract

In 50 million years the tetraploid catostomid fishes have lost the expression of approximately half of their duplicate genes, with species rich taxa having lost more than species poor taxa. We have constructed a phylogenetic tree of the catostomids based primarily on morphological data, and have estimated the divergence times from the fossil record and genetic distances. The losses of duplicate gene expression were then analyzed conditionally given this tree. Three probabilistic models were generated to describe the process of loss of gene expression: gene dysfunction depends on (1) time alone, (2) the number of speciation events alone, or (3) a combination of speciation and time. A maximum likelihood analysis revealed that the two component model fits the data better than the other models. The loss of duplicate gene expression is mediated by null mutations at structural and/or regulatory genes, and the rate of fixation of these nulls might have been enhanced by any reductions in population size accompanying speciation events. This reduction may explain the lower number of duplicate genes expressed in the more speciose taxa.