Supervisors: Dr Matthew Hartfield, Dr Jarrod Hadfield

Project Description:

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 pathogenic fungi, are instead capable of some degree of ‘uniparental reproduction’; that is, individuals can produce offspring without the need of 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. This highly interdisciplinary project will use mathematical modelling to understand genome-wide adaptation, and the development of novel methods to test those models using genetic data. There will be potential to investigate data from 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 pathogenic fungi (e.g. the Phytophthora genus that infects strawberries). The project will provide the student with cutting-edge mathematical and bioinformatics skills, which are essential for modern biological and genetics 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 the onset of uniparental reproduction mean that multiple adaptive mutations clump together in the genome? If so, how can these adaptive clusters be detected?

•    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 analyses 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?

References:

•    Field et al. 2016 “Detection of human adaptation during the past 2000 years”. Science 354(6313): 760–764.

•    Hartfield M. et al. 2017 “The Evolutionary Interplay between Adaptation and Self-Fertilization”. Trends Genet. 33(6): 420—431.

•    Kamran-Disfani, A. and Agrawal, A. F. 2014 “Selfing, adaptation and background selection in finite populations”. J. Evol. Biol. 27(7): 1360–1371.

If you wish to apply for this project, please go to this link.