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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Tests of selection</title>
<meta name="author" content="Trevor Bedford">
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<section data-background="#C4B945">
<h2 class="title">Tests of selection</h2>
</section>
<section>
<h2>1. Tests of diversity</h2>
<h2>2. Tests of tree shape</h2>
<h2>3. Tests of evolutionary rates</h2>
</section>
<section>
<h2>Test: is there less genetic diversity than expected?</h2>
</section>
<section>
<h3>Influenza phylogeny and effective number of infections</h3>
<img class="stretch" src="images/flu_coalescence.png">
</section>
<section>
<h3>Coalescent rates in flu and measles</h3>
<img class="stretch" src="images/flu_vs_measles_coalescence.png">
<div class="citation">
<a href="http://bedford.io/papers/bedford-tree-topology/">
Bedford et al. 2011
</a>
</div>
</section>
<section>
<h3>Selective sweeps purge diversity</h3>
<img class="stretch" src="images/ncov_tree.png">
<div class="citation">
<a href="https://nextstrain.org/ncov/gisaid/global/all-time">
nextstrain.org
</a>
</div>
</section>
<section>
<h2>Test: is the tree shape different from the neutral expectation?</h2>
</section>
<section>
<h3>Tajima's <i>D</i> statistic summarizes deviation from neutrality</h3>
<img class="stretch" src="images/tajima.png">
</section>
<section>
<h3>Influenza has negative Tajima's <i>D</i></h3>
<img class="stretch" src="images/flu_tajima.png">
</section>
<section>
<h2>Test: is there an overabundance of fixed non-synonymous mutations?</h2>
</section>
<section>
<h3>"Trunk" branches show an excess of non-synonymous change at epitope sites in influenza</h3>
<img class="stretch" src="images/flu_mutation_table.png">
<div class="citation">
<a href="https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-1-34">
Wolf et al. 2006
</a>
</div>
</section>
<section>
<h3>Abundance of green epitope mutations on phylogeny trunk, relative to blue synonymous and red non-epitope mutations</h3>
<img class="stretch" src="images/flu_mutation_tree.png">
<div class="citation">
<a href="http://www.genetics.org/content/192/2/671">
Strelkowa and Lässig 2012
</a>
</div>
</section>
<section>
<h3>Can be extended to look at relationship between mutations and clade growth</h3>
<img class="stretch" src="images/sarscov2_adaptive_evolution_mut_accumulation_s1.png">
<div class="citation">
<a href="https://bedford.io/papers/kistler-sarscov2-adaptive-evolution/">
Kistler and Bedford 2022
</a>
</div>
</section>
</div>
</div>
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