Development and application of powerful methods for identifying selective sweeps

Abstract

Identifying regions of the genome under selection is an ongoing effort in population genetics and quantitative biology. Selection creates signals within the genome that can be detected using a variety of methods. One of the major obstacles is the effect of variable recombination rates that create regions of the genome containing highly correlated variants, confounding methods that rely on correlations as indicators of selection. This thesis is mainly focussed on developing the Zα method, which is a statistic that uses linkage disequilibrium patterns to identify sweeps while also integrating the recombination rate.
As recombination rates are an important confounder, and a key component of the Zα method, recombination rates in human populations were studied further. The aim was to see if populations with different ancestral backgrounds have different recombination rates, and if so, at what scale. This work shows that different human populations have similar recombination patterns at the wide scale, but at the fine scale they can be quite different. This result means that individual recombination maps are required for each population when using the Zα method.
To easily and efficiently generate the Zα statistics, an R package was developed, published, and made freely available. R is an open source programming language, which increases reproducibility, transparency and reliability of the method and any results generated using it. Finally, the statistic was applied to the genome of the domestic dog. Firstly, the recombination map was generated, and then the new R package was used to apply the Zα statistics including adjusting for the recombination rate. This study identified candidate regions for selection in the dog genome, both previously published and novel to this study.

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Identifiers

ORCID for Andrew Collins: orcid.org/0000-0001-7108-0771

ORCID for Reuben Pengelly: orcid.org/0000-0001-7022-645X

ORCID for Sarah Ennis: orcid.org/0000-0003-2648-0869

ORCID for Tim Sluckin: orcid.org/0000-0002-9163-0061

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