Investigating the Role of Spatial Structure in Genetic Hitchhiking and Sweep Detection Open Access

Abstract

A ``selective sweep'' occurs when a beneficial allele (a variant form of a gene) rapidly increases in frequency and becomes common in the population. 

This process causes ``genetic hitchhiking'', in which some nearby genetic variants also rise in frequency because they are statistically associated with the beneficial allele in the population. 

Traditionally, studies on selective sweeps have been in the context of well-mixed populations, in which every individual has an equal opportunity of interaction and reproduction. However, many real-world scenarios involve spatially structured populations where individuals only interact locally. This raises the pertinent question: How does spatial structure influence the detection and interpretation of selective sweeps?

Our first step is to implement selective sweeps with spatial structure in the \texttt{msprime} simulation software package. 

Then we can use the simulation data to assess the impact of spatial structure on standard methods used to detect selective sweeps. 

Table of Contents

1 Introduction 3

1.1 Genetic hitchhiking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

1.2 Properties of Selective Sweeps . . . . . . . . . . . . . . . . . . . . . . . 4

1.3 The need to incorporate spatial structure in models of hitchhiking . . 6

2 Implementing hitchhiking with spatial structure in msprime 9

2.1 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

2.2 Research Question . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

2.3 Current Progress . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

3 Assessing the Impact of Spatial Structure on Sweep Inference Methods 14

3.1 Parameter choice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

3.2 Research Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

3.3 SweepFinder2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

3.4 diploS/HIC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

3.5 Preliminary Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

About this Master's Thesis

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School	Laney Graduate School
Department	Physics
Degree	M.S.
Submission	Master's Thesis
Language	English
Research Field	Biophysics, General Biology, Genetics
Keyword	Hitch-hiking effect
Committee Chair / Thesis Advisor	Daniel Weissman, Emory University
Committee Members	Ilya Nemenman, Emory University Laura Finzi, Emory University Daniel Sussman, Emory University

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