Drosophila melanogaster Bottleneck Simulations

Overview

This project involves the simulation of genetic differentiation in a neutrally evolving population of Drosophila after consecutive winter bottlenecks. The goal is to study the effects of these bottlenecks on the genetic diversity of a wild-caught population in Charlotteville, Virginia, USA. The scripts and data in this repository is part of the earlier work published in this article: (https://academic.oup.com/genetics/article/226/2/iyad207/7459204).

Author

Started by Connor S. Murray
Date: October 31, 2022

Workflow

1. Generate the Burn-in VCF

This step generates the VCF for a metapopulation to achieve a theta pi ~ 0.01, representing the genetic diversity of a wild Drosophila metapopulation.

Tools Used:

• msprime (Python)

2. Run the SLiM Scripts and Output Statistics

This step involves running SLiM scripts to independently replicate the simulated universe over 50 generations, including 2 overwintering bottleneck events.

Tools Used:

• SLiM

3. Merge Parsed Data

This step collects data from each simulation run and concatenates it for the analysis step.

Tools Used:

• bash
• python
• R

4. Analyze, Perform ABC, and Plot Data

This step involves performing Approximate Bayesian Computation (ABC) and plotting the results.

Tools Used:

• R