Final Report Summary - SEXSEL (Investigating the joint role of balancing and positive selection in mating systems evolution)
The evolution of sex (and outcrossing more generally) is one of the biggest and most controversial research areas in evolutionary genetics. Investigating facultative outcrossers, who alternate between sex and a kind of uniparental reproduction, allows researchers to study the causes and consequences of different reproductive modes. Many organisms exhibit mixed reproduction, including insects, snails, plants and fungi, along with many organisms of societal importance (including crops and their pests).
It is also easier and cheaper than ever to obtain genomic data from many individuals using next-generation sequencing, enabling researchers to understand the evolutionary consequences of mixed reproductive modes. Hence now is the time to unite genomic and theoretical modelling to investigate the evolution of reproductive systems. However, our ability to fully interpret data from facultative sexuals has been hampered by a lack of inference tools that account for labile reproduction.
This project focuses on creating new mathematical models to determine the effects of mixed reproductive modes on neutral genetic diversity, and different types of selection. My fellowship was based on two stages. For the outgoing phase I was working with Aneil Agrawal and Stephen Wright at the University of Toronto. My initial goal was to investigate how a particular type of selection, balancing selection (where heterozygote genotypes have higher fitness than homozygotes), affected the evolution of recombination rates. I was then going to apply models to genetic data obtained from Lemna minor (common duckweed), a facultative sexual aquatic plant used to treat contaminated water systems. However, upon starting the project it was clear that a greater development of the mathematical models was needed to make the necessary genomic inference. To this end, I started working on creating a new set of coalescent models that account for facultative sex. Coalescent models are specifically designed for estimating the genealogy of genetic samples, and hence to determine how various processes (such as reproductive system, selection, demography) influence observed genetic diversity.
I started by developing these models for genomic tracts that do not undergo recombination. A classic idea for identifying ancient asexuals organisms is that of ‘allelic sequence divergence’; with rare segregation of genomes via sex, the two haplotypes will diverge within individuals. However, this evidence has been seldom observed. We extended these classic models to include more realistic scenarios, and found that even low rates of gene conversion were sufficient to remove this signature of rare sex.
We then investigated how different types of selection, specifically background selection (caused by removal of deleterious mutations) and balancing selection affected neutral diversity with facultative sex. A main finding was that more diversity is removed by background selection in facultative sexual organisms compared to obligate sexuals, due to the weakened ability of both recombination and segregation to place selected alleles on different backgrounds. Both studies were published in January 2016.
I am currently working on extending neutral coalescent models to consider multiple sites, to investigate the effects of recombination and facultative sex affects estimates of linkage disequilibrium. These models can provide greater power to determine the baseline rate of sex by averaging genealogies over many sites. I will ultimately provide a new simulation package that other researchers can use to investigate the forces affecting genetic evolution in their own studies.
In July 2016, I moved back to Europe to commence the return phase of my fellowship, working with Thomas Bataillon at Aarhus University, Denmark. My goal here is to investigate how different types of adaptations impact upon the evolution of self-fertilization; a reproductive mode where individuals produce both male and female sex cells that can fertilise one another. Since the majority of food crops are highly self-fertilising, the outcomes of this project will have important impacts on improving crop yields through improving the genetic health of these species. We have published a review paper on this topic in May 2017.
For further information about the research, visit https://matthartfield.wordpress.com/ or contact matthew.hartfield@birc.au.dk.
It is also easier and cheaper than ever to obtain genomic data from many individuals using next-generation sequencing, enabling researchers to understand the evolutionary consequences of mixed reproductive modes. Hence now is the time to unite genomic and theoretical modelling to investigate the evolution of reproductive systems. However, our ability to fully interpret data from facultative sexuals has been hampered by a lack of inference tools that account for labile reproduction.
This project focuses on creating new mathematical models to determine the effects of mixed reproductive modes on neutral genetic diversity, and different types of selection. My fellowship was based on two stages. For the outgoing phase I was working with Aneil Agrawal and Stephen Wright at the University of Toronto. My initial goal was to investigate how a particular type of selection, balancing selection (where heterozygote genotypes have higher fitness than homozygotes), affected the evolution of recombination rates. I was then going to apply models to genetic data obtained from Lemna minor (common duckweed), a facultative sexual aquatic plant used to treat contaminated water systems. However, upon starting the project it was clear that a greater development of the mathematical models was needed to make the necessary genomic inference. To this end, I started working on creating a new set of coalescent models that account for facultative sex. Coalescent models are specifically designed for estimating the genealogy of genetic samples, and hence to determine how various processes (such as reproductive system, selection, demography) influence observed genetic diversity.
I started by developing these models for genomic tracts that do not undergo recombination. A classic idea for identifying ancient asexuals organisms is that of ‘allelic sequence divergence’; with rare segregation of genomes via sex, the two haplotypes will diverge within individuals. However, this evidence has been seldom observed. We extended these classic models to include more realistic scenarios, and found that even low rates of gene conversion were sufficient to remove this signature of rare sex.
We then investigated how different types of selection, specifically background selection (caused by removal of deleterious mutations) and balancing selection affected neutral diversity with facultative sex. A main finding was that more diversity is removed by background selection in facultative sexual organisms compared to obligate sexuals, due to the weakened ability of both recombination and segregation to place selected alleles on different backgrounds. Both studies were published in January 2016.
I am currently working on extending neutral coalescent models to consider multiple sites, to investigate the effects of recombination and facultative sex affects estimates of linkage disequilibrium. These models can provide greater power to determine the baseline rate of sex by averaging genealogies over many sites. I will ultimately provide a new simulation package that other researchers can use to investigate the forces affecting genetic evolution in their own studies.
In July 2016, I moved back to Europe to commence the return phase of my fellowship, working with Thomas Bataillon at Aarhus University, Denmark. My goal here is to investigate how different types of adaptations impact upon the evolution of self-fertilization; a reproductive mode where individuals produce both male and female sex cells that can fertilise one another. Since the majority of food crops are highly self-fertilising, the outcomes of this project will have important impacts on improving crop yields through improving the genetic health of these species. We have published a review paper on this topic in May 2017.
For further information about the research, visit https://matthartfield.wordpress.com/ or contact matthew.hartfield@birc.au.dk.