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<meta name="author" content="Alexander Lalejini, Emily Dolson, Anya E. Vostinar, and Luis Zaman" />
<meta name="date" content="2022-06-29" />
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<li><a href="./">Supplemental material</a></li>
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<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Introduction</a><ul>
<li class="chapter" data-level="1.1" data-path="index.html"><a href="index.html#about-this-supplemental-material"><i class="fa fa-check"></i><b>1.1</b> About this supplemental material</a><ul>
<li class="chapter" data-level="1.1.1" data-path="index.html"><a href="index.html#contents"><i class="fa fa-check"></i><b>1.1.1</b> Contents</a></li>
</ul></li>
<li class="chapter" data-level="1.2" data-path="index.html"><a href="index.html#contributing-authors"><i class="fa fa-check"></i><b>1.2</b> Contributing authors</a></li>
<li class="chapter" data-level="1.3" data-path="index.html"><a href="index.html#research-overview"><i class="fa fa-check"></i><b>1.3</b> Research overview</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="software-availability.html"><a href="software-availability.html"><i class="fa fa-check"></i><b>2</b> Software availability</a></li>
<li class="chapter" data-level="3" data-path="data-availability.html"><a href="data-availability.html"><i class="fa fa-check"></i><b>3</b> Data availability</a></li>
<li class="chapter" data-level="4" data-path="compiling-and-running-our-experiments.html"><a href="compiling-and-running-our-experiments.html"><i class="fa fa-check"></i><b>4</b> Compiling and running our experiments</a><ul>
<li class="chapter" data-level="4.1" data-path="compiling-and-running-our-experiments.html"><a href="compiling-and-running-our-experiments.html#manual"><i class="fa fa-check"></i><b>4.1</b> Manual</a></li>
<li class="chapter" data-level="4.2" data-path="compiling-and-running-our-experiments.html"><a href="compiling-and-running-our-experiments.html#docker"><i class="fa fa-check"></i><b>4.2</b> Docker</a></li>
</ul></li>
<li class="chapter" data-level="5" data-path="digital-organisms.html"><a href="digital-organisms.html"><i class="fa fa-check"></i><b>5</b> Digital Organisms</a><ul>
<li class="chapter" data-level="5.1" data-path="digital-organisms.html"><a href="digital-organisms.html#virtual-hardware-components"><i class="fa fa-check"></i><b>5.1</b> Virtual Hardware Components</a></li>
<li class="chapter" data-level="5.2" data-path="digital-organisms.html"><a href="digital-organisms.html#instruction-set"><i class="fa fa-check"></i><b>5.2</b> Instruction set</a></li>
<li class="chapter" data-level="5.3" data-path="digital-organisms.html"><a href="digital-organisms.html#ancestral-genomes"><i class="fa fa-check"></i><b>5.3</b> Ancestral genomes</a><ul>
<li class="chapter" data-level="5.3.1" data-path="digital-organisms.html"><a href="digital-organisms.html#ancestral-genome-for-genetic-programming-experiment"><i class="fa fa-check"></i><b>5.3.1</b> Ancestral genome for genetic programming experiment</a></li>
<li class="chapter" data-level="5.3.2" data-path="digital-organisms.html"><a href="digital-organisms.html#ancestral-genome-for-directed-evolution-experiments"><i class="fa fa-check"></i><b>5.3.2</b> Ancestral genome for directed evolution experiments</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="6" data-path="conventional-genetic-programming-experiment.html"><a href="conventional-genetic-programming-experiment.html"><i class="fa fa-check"></i><b>6</b> Conventional genetic programming experiment</a><ul>
<li class="chapter" data-level="6.1" data-path="conventional-genetic-programming-experiment.html"><a href="conventional-genetic-programming-experiment.html#overview"><i class="fa fa-check"></i><b>6.1</b> Overview</a></li>
<li class="chapter" data-level="6.2" data-path="conventional-genetic-programming-experiment.html"><a href="conventional-genetic-programming-experiment.html#analysis-dependencies"><i class="fa fa-check"></i><b>6.2</b> Analysis dependencies</a></li>
<li class="chapter" data-level="6.3" data-path="conventional-genetic-programming-experiment.html"><a href="conventional-genetic-programming-experiment.html#setup"><i class="fa fa-check"></i><b>6.3</b> Setup</a></li>
<li class="chapter" data-level="6.4" data-path="conventional-genetic-programming-experiment.html"><a href="conventional-genetic-programming-experiment.html#number-of-successful-replicates"><i class="fa fa-check"></i><b>6.4</b> Number of successful replicates</a></li>
<li class="chapter" data-level="6.5" data-path="conventional-genetic-programming-experiment.html"><a href="conventional-genetic-programming-experiment.html#final-task-coverage"><i class="fa fa-check"></i><b>6.5</b> Final task coverage</a></li>
<li class="chapter" data-level="6.6" data-path="conventional-genetic-programming-experiment.html"><a href="conventional-genetic-programming-experiment.html#generation-2000-task-coverage"><i class="fa fa-check"></i><b>6.6</b> Generation 2,000 task coverage</a></li>
<li class="chapter" data-level="6.7" data-path="conventional-genetic-programming-experiment.html"><a href="conventional-genetic-programming-experiment.html#population-level-task-coverage"><i class="fa fa-check"></i><b>6.7</b> Population-level task coverage</a></li>
<li class="chapter" data-level="6.8" data-path="conventional-genetic-programming-experiment.html"><a href="conventional-genetic-programming-experiment.html#generations-elapsed-before-a-solution-evolves"><i class="fa fa-check"></i><b>6.8</b> Generations elapsed before a solution evolves</a></li>
<li class="chapter" data-level="6.9" data-path="conventional-genetic-programming-experiment.html"><a href="conventional-genetic-programming-experiment.html#best-task-coverage-over-time"><i class="fa fa-check"></i><b>6.9</b> Best task coverage over time</a></li>
<li class="chapter" data-level="6.10" data-path="conventional-genetic-programming-experiment.html"><a href="conventional-genetic-programming-experiment.html#manuscript-figure"><i class="fa fa-check"></i><b>6.10</b> Manuscript Figure</a></li>
</ul></li>
<li class="chapter" data-level="7" data-path="directed-digital-evolution-experiment.html"><a href="directed-digital-evolution-experiment.html"><i class="fa fa-check"></i><b>7</b> Directed digital evolution experiment</a><ul>
<li class="chapter" data-level="7.1" data-path="directed-digital-evolution-experiment.html"><a href="directed-digital-evolution-experiment.html#overview-1"><i class="fa fa-check"></i><b>7.1</b> Overview</a></li>
<li class="chapter" data-level="7.2" data-path="directed-digital-evolution-experiment.html"><a href="directed-digital-evolution-experiment.html#analysis-dependencies-1"><i class="fa fa-check"></i><b>7.2</b> Analysis dependencies</a></li>
<li class="chapter" data-level="7.3" data-path="directed-digital-evolution-experiment.html"><a href="directed-digital-evolution-experiment.html#setup-1"><i class="fa fa-check"></i><b>7.3</b> Setup</a></li>
<li class="chapter" data-level="7.4" data-path="directed-digital-evolution-experiment.html"><a href="directed-digital-evolution-experiment.html#best-single-population-task-coverage"><i class="fa fa-check"></i><b>7.4</b> Best single-population task coverage</a><ul>
<li class="chapter" data-level="7.4.1" data-path="directed-digital-evolution-experiment.html"><a href="directed-digital-evolution-experiment.html#best-single-population-task-coverage-time-series"><i class="fa fa-check"></i><b>7.4.1</b> Best single-population task coverage time series</a></li>
</ul></li>
<li class="chapter" data-level="7.5" data-path="directed-digital-evolution-experiment.html"><a href="directed-digital-evolution-experiment.html#metapopulation-task-coverage"><i class="fa fa-check"></i><b>7.5</b> Metapopulation task coverage</a><ul>
<li class="chapter" data-level="7.5.1" data-path="directed-digital-evolution-experiment.html"><a href="directed-digital-evolution-experiment.html#metapopulation-task-coverage-time-series"><i class="fa fa-check"></i><b>7.5.1</b> Metapopulation task coverage time series</a></li>
</ul></li>
<li class="chapter" data-level="7.6" data-path="directed-digital-evolution-experiment.html"><a href="directed-digital-evolution-experiment.html#metapopulation-task-profile-diversity"><i class="fa fa-check"></i><b>7.6</b> Metapopulation task profile diversity</a><ul>
<li class="chapter" data-level="7.6.1" data-path="directed-digital-evolution-experiment.html"><a href="directed-digital-evolution-experiment.html#number-of-different-task-profiles"><i class="fa fa-check"></i><b>7.6.1</b> Number of different task profiles</a></li>
<li class="chapter" data-level="7.6.2" data-path="directed-digital-evolution-experiment.html"><a href="directed-digital-evolution-experiment.html#task-profile-spread"><i class="fa fa-check"></i><b>7.6.2</b> Task profile spread</a></li>
<li class="chapter" data-level="7.6.3" data-path="directed-digital-evolution-experiment.html"><a href="directed-digital-evolution-experiment.html#task-profile-entropy"><i class="fa fa-check"></i><b>7.6.3</b> Task profile entropy</a></li>
</ul></li>
<li class="chapter" data-level="7.7" data-path="directed-digital-evolution-experiment.html"><a href="directed-digital-evolution-experiment.html#task-coverage-per-n-populations"><i class="fa fa-check"></i><b>7.7</b> Task coverage per N populations</a></li>
<li class="chapter" data-level="7.8" data-path="directed-digital-evolution-experiment.html"><a href="directed-digital-evolution-experiment.html#average-number-of-different-populations-selected-per-generation"><i class="fa fa-check"></i><b>7.8</b> Average number of different populations selected per generation</a><ul>
<li class="chapter" data-level="7.8.1" data-path="directed-digital-evolution-experiment.html"><a href="directed-digital-evolution-experiment.html#entropy-of-selected-population-ids"><i class="fa fa-check"></i><b>7.8.1</b> Entropy of selected population IDs</a></li>
</ul></li>
<li class="chapter" data-level="7.9" data-path="directed-digital-evolution-experiment.html"><a href="directed-digital-evolution-experiment.html#average-number-of-organisms-in-populations-at-end-of-maturation-period"><i class="fa fa-check"></i><b>7.9</b> Average number of organisms in populations at end of maturation period</a></li>
<li class="chapter" data-level="7.10" data-path="directed-digital-evolution-experiment.html"><a href="directed-digital-evolution-experiment.html#average-generations-per-maturation-period"><i class="fa fa-check"></i><b>7.10</b> Average generations per maturation period</a></li>
<li class="chapter" data-level="7.11" data-path="directed-digital-evolution-experiment.html"><a href="directed-digital-evolution-experiment.html#representative-task-profiles"><i class="fa fa-check"></i><b>7.11</b> Representative task profiles</a></li>
<li class="chapter" data-level="7.12" data-path="directed-digital-evolution-experiment.html"><a href="directed-digital-evolution-experiment.html#manuscript-figures"><i class="fa fa-check"></i><b>7.12</b> Manuscript figures</a></li>
</ul></li>
<li class="chapter" data-level="8" data-path="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html"><a href="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html"><i class="fa fa-check"></i><b>8</b> Aligned individual-level and population-level task directed evolution experiment</a><ul>
<li class="chapter" data-level="8.1" data-path="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html"><a href="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html#overview-2"><i class="fa fa-check"></i><b>8.1</b> Overview</a></li>
<li class="chapter" data-level="8.2" data-path="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html"><a href="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html#analysis-dependencies-2"><i class="fa fa-check"></i><b>8.2</b> Analysis dependencies</a></li>
<li class="chapter" data-level="8.3" data-path="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html"><a href="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html#setup-2"><i class="fa fa-check"></i><b>8.3</b> Setup</a></li>
<li class="chapter" data-level="8.4" data-path="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html"><a href="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html#best-single-population-task-coverage-1"><i class="fa fa-check"></i><b>8.4</b> Best single-population task coverage</a><ul>
<li class="chapter" data-level="8.4.1" data-path="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html"><a href="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html#best-single-population-task-coverage-time-series-1"><i class="fa fa-check"></i><b>8.4.1</b> Best single-population task coverage time series</a></li>
</ul></li>
<li class="chapter" data-level="8.5" data-path="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html"><a href="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html#metapopulation-task-coverage-1"><i class="fa fa-check"></i><b>8.5</b> Metapopulation task coverage</a><ul>
<li class="chapter" data-level="8.5.1" data-path="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html"><a href="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html#metapopulation-task-coverage-time-series-1"><i class="fa fa-check"></i><b>8.5.1</b> Metapopulation task coverage time series</a></li>
</ul></li>
<li class="chapter" data-level="8.6" data-path="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html"><a href="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html#metapopulation-task-profile-diversity-1"><i class="fa fa-check"></i><b>8.6</b> Metapopulation task profile diversity</a><ul>
<li class="chapter" data-level="8.6.1" data-path="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html"><a href="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html#number-of-different-task-profiles-1"><i class="fa fa-check"></i><b>8.6.1</b> Number of different task profiles</a></li>
<li class="chapter" data-level="8.6.2" data-path="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html"><a href="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html#task-profile-spread-1"><i class="fa fa-check"></i><b>8.6.2</b> Task profile spread</a></li>
<li class="chapter" data-level="8.6.3" data-path="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html"><a href="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html#task-profile-entropy-1"><i class="fa fa-check"></i><b>8.6.3</b> Task profile entropy</a></li>
</ul></li>
<li class="chapter" data-level="8.7" data-path="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html"><a href="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html#task-coverage-per-n-populations-1"><i class="fa fa-check"></i><b>8.7</b> Task coverage per N populations</a></li>
<li class="chapter" data-level="8.8" data-path="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html"><a href="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html#average-number-of-different-populations-selected-per-generation-1"><i class="fa fa-check"></i><b>8.8</b> Average number of different populations selected per generation</a><ul>
<li class="chapter" data-level="8.8.1" data-path="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html"><a href="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html#entropy-of-selected-population-ids-1"><i class="fa fa-check"></i><b>8.8.1</b> Entropy of selected population IDs</a></li>
</ul></li>
<li class="chapter" data-level="8.9" data-path="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html"><a href="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html#average-number-of-organisms-in-populations-at-end-of-maturation-period-1"><i class="fa fa-check"></i><b>8.9</b> Average number of organisms in populations at end of maturation period</a></li>
<li class="chapter" data-level="8.10" data-path="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html"><a href="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html#average-generations-per-maturation-period-1"><i class="fa fa-check"></i><b>8.10</b> Average generations per maturation period</a></li>
<li class="chapter" data-level="8.11" data-path="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html"><a href="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html#manuscript-figures-1"><i class="fa fa-check"></i><b>8.11</b> Manuscript figures</a></li>
</ul></li>
<li class="chapter" data-level="9" data-path="varying-population-maturation-period.html"><a href="varying-population-maturation-period.html"><i class="fa fa-check"></i><b>9</b> Varying population maturation period</a><ul>
<li class="chapter" data-level="9.1" data-path="varying-population-maturation-period.html"><a href="varying-population-maturation-period.html#overview-3"><i class="fa fa-check"></i><b>9.1</b> Overview</a></li>
<li class="chapter" data-level="9.2" data-path="varying-population-maturation-period.html"><a href="varying-population-maturation-period.html#analysis-dependencies-3"><i class="fa fa-check"></i><b>9.2</b> Analysis dependencies</a></li>
<li class="chapter" data-level="9.3" data-path="varying-population-maturation-period.html"><a href="varying-population-maturation-period.html#setup-3"><i class="fa fa-check"></i><b>9.3</b> Setup</a></li>
<li class="chapter" data-level="9.4" data-path="varying-population-maturation-period.html"><a href="varying-population-maturation-period.html#average-number-of-organisms"><i class="fa fa-check"></i><b>9.4</b> Average number of organisms</a></li>
<li class="chapter" data-level="9.5" data-path="varying-population-maturation-period.html"><a href="varying-population-maturation-period.html#average-generations-elapsed-during-the-maturation-period"><i class="fa fa-check"></i><b>9.5</b> Average generations elapsed during the maturation period</a></li>
<li class="chapter" data-level="9.6" data-path="varying-population-maturation-period.html"><a href="varying-population-maturation-period.html#total-generations"><i class="fa fa-check"></i><b>9.6</b> Total generations</a></li>
<li class="chapter" data-level="9.7" data-path="varying-population-maturation-period.html"><a href="varying-population-maturation-period.html#performance"><i class="fa fa-check"></i><b>9.7</b> Performance</a><ul>
<li class="chapter" data-level="9.7.1" data-path="varying-population-maturation-period.html"><a href="varying-population-maturation-period.html#cpu-cycles-per-replication"><i class="fa fa-check"></i><b>9.7.1</b> CPU cycles per replication</a></li>
<li class="chapter" data-level="9.7.2" data-path="varying-population-maturation-period.html"><a href="varying-population-maturation-period.html#best-population-task-coverage"><i class="fa fa-check"></i><b>9.7.2</b> Best-population task coverage</a></li>
<li class="chapter" data-level="9.7.3" data-path="varying-population-maturation-period.html"><a href="varying-population-maturation-period.html#metapopulation-task-coverage-2"><i class="fa fa-check"></i><b>9.7.3</b> Metapopulation task coverage</a></li>
</ul></li>
<li class="chapter" data-level="9.8" data-path="varying-population-maturation-period.html"><a href="varying-population-maturation-period.html#population-level-task-profile-diversity"><i class="fa fa-check"></i><b>9.8</b> Population-level Task Profile Diversity</a><ul>
<li class="chapter" data-level="9.8.1" data-path="varying-population-maturation-period.html"><a href="varying-population-maturation-period.html#task-profile-richness"><i class="fa fa-check"></i><b>9.8.1</b> Task profile richness</a></li>
<li class="chapter" data-level="9.8.2" data-path="varying-population-maturation-period.html"><a href="varying-population-maturation-period.html#task-profile-entropy-2"><i class="fa fa-check"></i><b>9.8.2</b> Task profile entropy</a></li>
<li class="chapter" data-level="9.8.3" data-path="varying-population-maturation-period.html"><a href="varying-population-maturation-period.html#spread-average-cosine-distance"><i class="fa fa-check"></i><b>9.8.3</b> Spread (average cosine distance)</a></li>
</ul></li>
<li class="chapter" data-level="9.9" data-path="varying-population-maturation-period.html"><a href="varying-population-maturation-period.html#selection"><i class="fa fa-check"></i><b>9.9</b> Selection</a><ul>
<li class="chapter" data-level="9.9.1" data-path="varying-population-maturation-period.html"><a href="varying-population-maturation-period.html#average-number-of-unique-populations-selected"><i class="fa fa-check"></i><b>9.9.1</b> Average number of unique populations selected</a></li>
<li class="chapter" data-level="9.9.2" data-path="varying-population-maturation-period.html"><a href="varying-population-maturation-period.html#average-entropy-of-selection-ids"><i class="fa fa-check"></i><b>9.9.2</b> Average entropy of selection ids</a></li>
</ul></li>
<li class="chapter" data-level="9.10" data-path="varying-population-maturation-period.html"><a href="varying-population-maturation-period.html#manuscript-figures-2"><i class="fa fa-check"></i><b>9.10</b> Manuscript Figures</a></li>
<li class="chapter" data-level="9.11" data-path="varying-population-maturation-period.html"><a href="varying-population-maturation-period.html#discussion"><i class="fa fa-check"></i><b>9.11</b> Discussion</a></li>
</ul></li>
<li class="chapter" data-level="10" data-path="varied-genome-lengths.html"><a href="varied-genome-lengths.html"><i class="fa fa-check"></i><b>10</b> Varied genome lengths</a><ul>
<li class="chapter" data-level="10.1" data-path="varied-genome-lengths.html"><a href="varied-genome-lengths.html#overview-4"><i class="fa fa-check"></i><b>10.1</b> Overview</a></li>
<li class="chapter" data-level="10.2" data-path="varied-genome-lengths.html"><a href="varied-genome-lengths.html#analysis-dependencies-4"><i class="fa fa-check"></i><b>10.2</b> Analysis dependencies</a></li>
<li class="chapter" data-level="10.3" data-path="varied-genome-lengths.html"><a href="varied-genome-lengths.html#setup-4"><i class="fa fa-check"></i><b>10.3</b> Setup</a></li>
<li class="chapter" data-level="10.4" data-path="varied-genome-lengths.html"><a href="varied-genome-lengths.html#average-generations-per-maturation-period-2"><i class="fa fa-check"></i><b>10.4</b> Average generations per maturation period</a></li>
<li class="chapter" data-level="10.5" data-path="varied-genome-lengths.html"><a href="varied-genome-lengths.html#total-generations-over-experiment"><i class="fa fa-check"></i><b>10.5</b> Total generations over experiment</a></li>
<li class="chapter" data-level="10.6" data-path="varied-genome-lengths.html"><a href="varied-genome-lengths.html#performance-1"><i class="fa fa-check"></i><b>10.6</b> Performance</a><ul>
<li class="chapter" data-level="10.6.1" data-path="varied-genome-lengths.html"><a href="varied-genome-lengths.html#cpu-cycles-per-replication-1"><i class="fa fa-check"></i><b>10.6.1</b> CPU cycles per replication</a></li>
<li class="chapter" data-level="10.6.2" data-path="varied-genome-lengths.html"><a href="varied-genome-lengths.html#best-single-population-task-coverage-2"><i class="fa fa-check"></i><b>10.6.2</b> Best single-population task coverage</a></li>
<li class="chapter" data-level="10.6.3" data-path="varied-genome-lengths.html"><a href="varied-genome-lengths.html#metapopulation-task-coverage-3"><i class="fa fa-check"></i><b>10.6.3</b> Metapopulation task coverage</a></li>
</ul></li>
<li class="chapter" data-level="10.7" data-path="varied-genome-lengths.html"><a href="varied-genome-lengths.html#population-level-task-profile-diversity-1"><i class="fa fa-check"></i><b>10.7</b> Population-level task profile diversity</a><ul>
<li class="chapter" data-level="10.7.1" data-path="varied-genome-lengths.html"><a href="varied-genome-lengths.html#task-profile-richness-1"><i class="fa fa-check"></i><b>10.7.1</b> Task profile richness</a></li>
<li class="chapter" data-level="10.7.2" data-path="varied-genome-lengths.html"><a href="varied-genome-lengths.html#task-profile-entropy-3"><i class="fa fa-check"></i><b>10.7.2</b> Task profile entropy</a></li>
<li class="chapter" data-level="10.7.3" data-path="varied-genome-lengths.html"><a href="varied-genome-lengths.html#spread-avg-cosine-distance"><i class="fa fa-check"></i><b>10.7.3</b> Spread (avg cosine distance)</a></li>
</ul></li>
<li class="chapter" data-level="10.8" data-path="varied-genome-lengths.html"><a href="varied-genome-lengths.html#selection-1"><i class="fa fa-check"></i><b>10.8</b> Selection</a><ul>
<li class="chapter" data-level="10.8.1" data-path="varied-genome-lengths.html"><a href="varied-genome-lengths.html#average-number-of-unique-populations-selected-1"><i class="fa fa-check"></i><b>10.8.1</b> Average number of unique populations selected</a></li>
<li class="chapter" data-level="10.8.2" data-path="varied-genome-lengths.html"><a href="varied-genome-lengths.html#average-entropy-of-selection-ids-1"><i class="fa fa-check"></i><b>10.8.2</b> Average entropy of selection ids</a></li>
</ul></li>
<li class="chapter" data-level="10.9" data-path="varied-genome-lengths.html"><a href="varied-genome-lengths.html#discussion-1"><i class="fa fa-check"></i><b>10.9</b> Discussion</a></li>
</ul></li>
<li class="chapter" data-level="11" data-path="population-propagule-sample-size.html"><a href="population-propagule-sample-size.html"><i class="fa fa-check"></i><b>11</b> Population propagule sample size</a><ul>
<li class="chapter" data-level="11.1" data-path="population-propagule-sample-size.html"><a href="population-propagule-sample-size.html#overview-5"><i class="fa fa-check"></i><b>11.1</b> Overview</a></li>
<li class="chapter" data-level="11.2" data-path="population-propagule-sample-size.html"><a href="population-propagule-sample-size.html#analysis-dependencies-5"><i class="fa fa-check"></i><b>11.2</b> Analysis dependencies</a></li>
<li class="chapter" data-level="11.3" data-path="population-propagule-sample-size.html"><a href="population-propagule-sample-size.html#setup-5"><i class="fa fa-check"></i><b>11.3</b> Setup</a></li>
<li class="chapter" data-level="11.4" data-path="population-propagule-sample-size.html"><a href="population-propagule-sample-size.html#average-number-of-organisms-1"><i class="fa fa-check"></i><b>11.4</b> Average number of organisms</a></li>
<li class="chapter" data-level="11.5" data-path="population-propagule-sample-size.html"><a href="population-propagule-sample-size.html#average-generations-per-maturation-period-3"><i class="fa fa-check"></i><b>11.5</b> Average generations per maturation period</a></li>
<li class="chapter" data-level="11.6" data-path="population-propagule-sample-size.html"><a href="population-propagule-sample-size.html#performance-2"><i class="fa fa-check"></i><b>11.6</b> Performance</a><ul>
<li class="chapter" data-level="11.6.1" data-path="population-propagule-sample-size.html"><a href="population-propagule-sample-size.html#best-population-task-coverage-1"><i class="fa fa-check"></i><b>11.6.1</b> Best population task coverage</a></li>
<li class="chapter" data-level="11.6.2" data-path="population-propagule-sample-size.html"><a href="population-propagule-sample-size.html#metapopulation-task-coverage-4"><i class="fa fa-check"></i><b>11.6.2</b> Metapopulation task coverage</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i>References</a></li>
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<h1>
<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">Supplemental Material for Directed Digital Evolution Project</a>
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<h1 class="title">Supplemental Material for Directed Digital Evolution Project</h1>
<p class="author"><em>Alexander Lalejini, Emily Dolson, Anya E. Vostinar, and Luis Zaman</em></p>
<p class="date"><em>2022-06-29</em></p>
</div>
<div id="introduction" class="section level1 hasAnchor">
<h1><span class="header-section-number">Chapter 1</span> Introduction<a href="index.html#introduction" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<p>This is the supplemental material for the preprint, “Artificial selection methods from evolutionary computing show promise for directed evolution of microbes”.</p>
<div id="about-this-supplemental-material" class="section level2 hasAnchor">
<h2><span class="header-section-number">1.1</span> About this supplemental material<a href="index.html#about-this-supplemental-material" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>This supplemental material is hosted on <a href="https://github.com/amlalejini/directed-digital-evolution">GitHub</a> using GitHub pages.
This source code and configuration files used to generate this supplemental material can be found in the following repository: <a href="https://github.com/amlalejini/directed-digital-evolution" class="uri">https://github.com/amlalejini/directed-digital-evolution</a>.</p>
<div id="contents" class="section level3 hasAnchor">
<h3><span class="header-section-number">1.1.1</span> Contents<a href="index.html#contents" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<p>Our supplemental material includes the following:</p>
<ul>
<li>Software availability (Section <a href="software-availability.html#software-availability">2</a>)</li>
<li>Data availability (Section <a href="data-availability.html#data-availability">3</a>)</li>
<li>Guide for compiling and running our experiments (Section <a href="compiling-and-running-our-experiments.html#compiling-and-running-our-experiments">4</a>)</li>
<li>Supplemental information about the digital organisms used in this work (Section <a href="digital-organisms.html#digital-organisms">5</a>)</li>
<li>Experiment analyses:
<ul>
<li>Directed digital evolution experiment (Section <a href="directed-digital-evolution-experiment.html#directed-digital-evolution-experiment">7</a>)</li>
<li>Aligned individual-level and population-level task directed evolution experiment (Section <a href="aligned-individual-level-and-population-level-task-directed-evolution-experiment.html#aligned-individual-level-and-population-level-task-directed-evolution-experiment">8</a>)</li>
<li>Varying population maturation period experiment (Section <a href="varying-population-maturation-period.html#varying-population-maturation-period">9</a>)</li>
<li>Varied genome lengths experiment (Section <a href="varied-genome-lengths.html#varied-genome-lengths">10</a>)</li>
<li>Varied sample size for propagating populations (Section <a href="population-propagule-sample-size.html#population-propagule-sample-size">11</a>)</li>
</ul></li>
</ul>
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<div id="contributing-authors" class="section level2 hasAnchor">
<h2><span class="header-section-number">1.2</span> Contributing authors<a href="index.html#contributing-authors" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<ul>
<li><a href="https://lalejini.com/">Alexander Lalejini</a></li>
<li><a href="https://cse.msu.edu/~dolsonem/">Emily Dolson</a></li>
<li><a href="https://anyaevostinar.github.io/">Anya E. Vostinar</a></li>
<li><a href="https://zeeelab.com/">Luis Zaman</a></li>
</ul>
</div>
<div id="research-overview" class="section level2 hasAnchor">
<h2><span class="header-section-number">1.3</span> Research overview<a href="index.html#research-overview" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>Abstract:</p>
<blockquote>
<p>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.</p>
</blockquote>
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