---
title: "Supplemental Material for Directed Digital Evolution Project"
author: "Alexander Lalejini, Emily Dolson, Anya E. Vostinar, and Luis Zaman"
date: "`r Sys.Date()`"
output: bookdown::gitbook
documentclass: book
bibliography: ["bib/packages.bib", "bib/supplemental.bib"]
biblio-style: apalike
nocite: '@*'
link-citations: yes
github-repo: amlalejini/directed-digital-evolution
description: "Supplemental material"
---

# Introduction

This is the supplemental material for the preprint, "Artificial selection methods from evolutionary computing show promise for directed evolution of microbes".

## About this supplemental material

This supplemental material is hosted on [GitHub](https://github.com/amlalejini/directed-digital-evolution) using GitHub pages.
This source code and configuration files used to generate this supplemental material can be found in the following repository: <https://github.com/amlalejini/directed-digital-evolution>.

### Contents

Our supplemental material includes the following:

- Software availability (Section \@ref(software-availability))
- Data availability (Section \@ref(data-availability))
- Guide for compiling and running our experiments (Section \@ref(compiling-and-running-our-experiments))
- Supplemental information about the digital organisms used in this work (Section \@ref(digital-organisms))
- Experiment analyses:
  - Directed digital evolution experiment (Section \@ref(directed-digital-evolution-experiment))
  - Aligned individual-level and population-level task directed evolution experiment (Section \@ref(aligned-individual-level-and-population-level-task-directed-evolution-experiment))
  - Varying population maturation period experiment (Section \@ref(varying-population-maturation-period))
  - Varied genome lengths experiment (Section \@ref(varied-genome-lengths))
  - Varied sample size for propagating populations (Section \@ref(population-propagule-sample-size))

## Contributing authors

- [Alexander Lalejini](https://lalejini.com/)
- [Emily Dolson](https://cse.msu.edu/~dolsonem/)
- [Anya E. Vostinar](https://anyaevostinar.github.io/)
- [Luis Zaman](https://zeeelab.com/)

## Research overview

Abstract:

> Directed microbial evolution harnesses evolutionary processes in the laboratory to construct microorganisms with enhanced or novel functional traits.
  Attempting to direct evolutionary processes for applied goals is fundamental to evolutionary computation, which harnesses the principles of Darwinian evolution as a general purpose search engine for solutions to challenging computational problems.
  Despite their overlapping approaches, artificial selection methods from evolutionary computing are not commonly applied to living systems in the laboratory.
  In this work, we ask if parent selection algorithms---procedures for choosing promising progenitors---from evolutionary computation might be useful for directing the evolution of microbial populations when selecting for multiple functional traits.
  To do so, we introduce an agent-based model of directed microbial evolution, which we used to evaluate how well three selection algorithms from evolutionary computing (tournament selection, lexicase selection, and non-dominated elite selection) performed relative to methods commonly used in the laboratory (elite and top-10\% selection).
  We found that multi-objective selection techniques from evolutionary computing (lexicase and non-dominated elite) generally outperformed the commonly used directed evolution approaches when selecting for multiple traits of interest.
  Our results motivate ongoing work transferring these multi-objective selection procedures into the laboratory.
  Additionally, our findings suggest that more sophisticated artificial selection methods from evolutionary computation should also be evaluated for use in directed microbial evolution.