How are multiple adaptive genes affected by an organisms’ frequency of sex?

Reduced costs of genome sequencing have seen an expansion in the amount of genetic data available from various species, from which researchers are learning more about the crucial evolutionary process of adaptation. Yet the vast majority of existing methods for quantifying selection acting on the genome assume that organisms are completely sexual. Many organisms, including crops and plant pathogens, are instead capable of some degree of ‘uniparental reproduction’, where individuals can produce offspring without needing a second parent. These includes hermaphrodites that are capable of self-fertilisation (where individuals produce both male and female sex cells that can fertilise one another), or facultative sexuals (where individuals produce some offspring via clonal reproduction).

While we understand how reproductive modes affect a few genes that carry adaptive mutations, these results are unlikely to scale to the more realistic scenario where adaptation is caused by many genes scattered through a genome. In this highly interdisciplinary project, the student will create mathematical models to understand the nature of genome-wide adaptation, and develop novel methods to test those models through analysing genetic data. There will be potential to investigate a wide range of organisms, including highly self-fertilising plants (Arabidopsis thaliana; Capsella rubella; Medicago truncatula), those whose occurrence of self-fertilisation varies throughout its range (Arabis alpina), and plant pathogens (e.g. the Phytophthora genus that infects strawberries). The project will provide the student with cutting-edge mathematical and bioinformatics skills for theoretical prediction and genome sequence analysis, which are essential for modern biology research.

The main themes of the project are as follows:

• The student will investigate the dynamics of multiple adaptive mutations, scattered throughout an individual’s genome in species that exhibit different reproductive modes. The onset of self-fertilisation or clonality can have contrasting effects on the adaptive process. Both modes of reproduction reduce the effect of gene mixing (e.g. meiotic recombination) between individuals, which can limit the efficacy of natural selection. Yet uniparential reproduction can also maintain an optimal genome that carries many adaptive mutations within the same individual. How likely is each mechanism to occur? Does uniparental reproduction either hamper or enhance the adaptive process?

• The student will develop novel methods for analysing genome data, to determine how adaptation is affected by different reproductive modes. The theoretical findings developed in point one will be used to guide the creation of these new methods, by determining how the reproductive mode affects the signatures that multi-gene adaptation leave in genome data. Does uniparental reproduction cause multiple adaptive mutations to clump together in the genome? If so, how can these adaptive clusters be detected? Methods for detecting recent human adaptation can provide a useful starting point for this analysis.

• The student will have the opportunity to apply their findings to genomic data, taken from species that either partially or fully self-fertilise/reproduce clonally. This analysis will determine potential genetic sites under selection, and how they interact under different mating systems (i.e., whether sites act independently or accumulate on the same genetic background). How prevalent is each mechanism in nature?

Personal website: http://matthartfield.wordpress.com/