Quantifying sex and asexuality using an Ancestral Recombination Graph (ARG) approach

Thesis

Although many testable hypotheses have been proposed, biologists still do not know why sexual reproduction exists. Sex is often portrayed as one of the major unresolved problems in evolutionary science. Intuitively, asexuality, the vertical transfer of genetic material from parent to offspring, appears to be a much simpler and effective mode of propagation. In this thesis, I focus on an essential prerequisite for testing hypotheses of sex – the methodology for reconstructing histories of sexual and asexual reproduction from DNA sequence data. Specifically, I use the lens of ancestral recombination graphs (ARGs) to distinguish and quantify genealogical signatures of sex from those of recombination occurring asexually. In Chapter 1, I introduce my ARG-based analytical framework and use biologically-realistic models of asexuality that include recombination via gene conversion or crossing-over to demonstrate its advantages over standard approaches. Concurrently, I develop a framework for the signatures expected across a range of asexuality–sex scenarios. Building on this foundation, in Chapter 2, I develop a new ARG-inspired approach for genealogical analysis, explicitly tailored to the problem of reproductive history reconstruction. Finally, in Chapter 3, I apply my methodology to genomic datasets for two species of bdelloid rotifers – a group famous for their asexuality, yet recently the subject of debate over presumed signatures of cryptic sex. The results are consistent with an asexual mode of reproduction. Throughout this research, I highlight issues of technical artefacts and uncertainty, which are critical to consider in systems where sex may occur only rarely, while other forms of recombination can be common. Collectively, my DPhil work provides the foundation for improved and flexible methodology of reproductive mode reconstruction from DNA sequence data, addressing a critical gap in the field.

Authors: Pieszko, T

• DOI: 10.5287/ora-kzakj0pyj
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: asexual reproduction; sexual reproduction; simulations; ancestral recombination graphs; bdelloid rotifers
• Subjects: Population genetics; Evolution (Biology)