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.
| Identifer | oai:union.ndltd.org:uottawa.ca/oai:ruor.uottawa.ca:10393/39684 |
| Date | 01 October 2019 |
| Creators | Zhang, Yue |
| Contributors | Sankoff, David |
| Publisher | Université d'Ottawa / University of Ottawa |
| Source Sets | Université d’Ottawa |
| Language | English |
| Detected Language | English |
| Type | Thesis |
| Format | application/pdf |
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