Speciation and rate variation in a birth-and-death account of WGD and fractionation; the case of solanaceae

Abstract

We derive the mixture of distributions of sequence similarity for duplicate gene pairs generated by repeated episodes of whole genome doubling. This involves integrating sequence divergence and gene pair loss through fractionation, using a birth-and-death process and a mutational model. We account not only for the timing of these events in terms of local modes, but also the amplitude and variance of the component distributions. This model is then extended to orthologous gene pairs, applied to the evolution of the Solanaceae, focusing on the genomes of economically important crops. We assess how consistent or variable fractionation is from species to species and over time.