Distribution of Gene Pair Similarity in Syntenic Regions Within and Between Genomes: A Branching Process Account of the Polyploidization, Speciation and Fractionation Cycle

Abstract

The evolution of plant genomes is notable for manifesting a cycle of whole genome doubling, fractionation (gradual loss of redundant genes) and speciation. The thesis is based on a branching process model of the doubling and fractionation process, integrated with a standard model of sequence divergence. The immediate application of this work is to account for the distribution of sequence similarity for duplicate gene pairs, both within plant genomes and between two related plant genomes in terms of a cycle of polyploidization, fractionation and speciation. We derive a mixture distribution for duplicate gene pair similarities generated by speciation and/or repeated episodes of polyploidization. We account not only for the timing of these events in terms of local modes or peaks of the component distributions, but also their volume, or amplitude, and variance. We outline how to infer the parameters of the model. We illustrate with analyses of the distribution of homolog similarities in a number of plant families: Brassicaceae, Solanaceae and Malvaceae. To our knowledge, this is the first method to account for the volume of the component normals of a distribution of similarities, preliminary to an evolutionarily meaningful inference procedure. In addition, we solve the problem of identifying the ploidy level of a series of two or three polyploidizations by invoking the observed and predicted gene triple profiles for each model, i.e., by calculating the probability of the four types of triple with origins in one or the other event, or both.