Research in our lab focuses on three questions at the intersection of evolution and genomics:
1) What are the causes and genomic consequences of mating system evolution and the loss of sex and recombination?
2) What is the genome-wide extent and genomic basis of positive and negative selection?
3) What factors are driving the activity and abundance of transposable elements and shaping genome size evolution?
We aim to use genomic approaches to try to help address long-standing evolutionary questions, as well as use evolutionary theory to help understand genome structure and function.
- Causes and Genomic Consequences of the evolution of self-fertilization and asexual reproduction (Capsella, Duckweed, Oenothera, Collinsia): There is a strong body of population genetic theory predicting the factors that can favor the evolution of selfing and asexual reproduction, and on the long-term fitness consequences of this evolution. We are using population, quantitative and comparative genomics to investigate these predictions, and to understand the role of genetic drift and natural selection in the morphological and genomic transitions associated with the evolution of selfing and clonal reproduction. We are combining QTL mapping, next generation sequencing approaches to population genomics, and expression studies to investigate this.
- Evolution of plant sex chromosomes (Rumex): Loss of recombination on the Y chromosome can have important consequences for selection and genetic variation. Evolutionary models predict that when regions of suppressed recombination evolve on Y chromosomes, the associated reduction in the effectiveness of selection should lead to a pattern of Y chromosome degeneration, in which genes carried on Y chromosomes become impaired in function may eventually be lost. We are studying patterns of molecular evolution in sex chromosomes to understand why X and Y chromosomes can be so different, what forces drive these differences, and how these differences relate to sex determination and sexual dimorphism.
- Selective consequences of whole genome duplication (Capsella bursa-pastoris): Whole genome duplication due to polyploidy is accompanied by a large potential for relaxed selection due to gene redundancy and positive selection due to the relaxation of pleiotropic constraints. We are studying the population genomics of the early stages of the shift to polyploidization to better understand the importance of genetic drift, positive selection and relaxed selection on the restructuring of the genome following polyploidy.
- Population dynamics and evolution of transposable elements (TEs) (Arabidopsis, Capsella, Oenothere):TEs represent the most dominant component of plant genomes, yet we still have very little understanding of the forces controlling their evolution. We are interested in understanding the factors driving the evolution of TE abundance and activity, and the importance of natural selection and genetic drift in TE evolution. Particular interests include the effects of breeding system, ploidy and population history on the success and accumulation of transposable elements. A long-term goal is to test for ongoing coevolutionary dynamics between elements and hosts.
- Inferring the genome-wide rates of positive and negative selection, and understanding the causes of the maintenance of genetic variation (Capsella): We are characterizing patterns of genome-wide DNA sequence variation to understand the relative role of demography and selection on the genome. The ultimate goal is to quantify the rate, strength and genetic basis of positive and negative selection across the genome. We also seek to understand the role of demographic history, ploidy and mating system on the strength and direction of selection. As a component of these goals, we are currently part of a collaborative Genome Canada/Genome Quebec funded project between the University of Toronto and McGill University to use comparative and population genomics transcriptomics to quantify the extent of selection on noncoding DNA, the genetic basis of differences in gene expression, and the selective forces maintaining variation on gene expression.