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#EffectivePopulationSize

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Joanna Masel<p>Our new <a href="https://ecoevo.social/tags/preprint" class="mention hashtag" rel="tag">#<span>preprint</span></a> changes the way we look at an “extinction vortex” in which a small population loses fitness, causing it to become even smaller <a href="https://www.biorxiv.org/content/10.1101/2024.10.25.620329v1" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://www.</span><span class="ellipsis">biorxiv.org/content/10.1101/20</span><span class="invisible">24.10.25.620329v1</span></a>. <br /><a href="https://ecoevo.social/tags/MutationalMeltdown" class="mention hashtag" rel="tag">#<span>MutationalMeltdown</span></a> <a href="https://ecoevo.social/tags/EffectivePopulationSize" class="mention hashtag" rel="tag">#<span>EffectivePopulationSize</span></a> <a href="https://ecoevo.social/tags/EvolutionaryRescue" class="mention hashtag" rel="tag">#<span>EvolutionaryRescue</span></a> <a href="https://ecoevo.social/tags/PopulationGenetics" class="mention hashtag" rel="tag">#<span>PopulationGenetics</span></a> <a href="https://ecoevo.social/tags/EvolGenPaper" class="mention hashtag" rel="tag">#<span>EvolGenPaper</span></a> <span class="h-card" translate="no"><a href="https://ecoevo.social/@wmawass" class="u-url mention">@<span>wmawass</span></a></span> <span class="h-card" translate="no"><a href="https://fediscience.org/@jdmatheson" class="u-url mention">@<span>jdmatheson</span></a></span> <span class="h-card" translate="no"><a href="https://ecoevo.social/@uliseshmc" class="u-url mention">@<span>uliseshmc</span></a></span> 1/7</p>
Joanna Masel<p>Our latest paper <a href="https://elifesciences.org/articles/87335" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="ellipsis">elifesciences.org/articles/873</span><span class="invisible">35</span></a><br />directly measures the <a href="https://ecoevo.social/tags/EffectivePopulationSize" class="mention hashtag" rel="tag">#<span>EffectivePopulationSize</span></a> that matters to <a href="https://ecoevo.social/tags/NearlyNeutralTheory" class="mention hashtag" rel="tag">#<span>NearlyNeutralTheory</span></a> / <a href="https://ecoevo.social/tags/DriftBarrier" class="mention hashtag" rel="tag">#<span>DriftBarrier</span></a> theory, as the degree to which <a href="https://ecoevo.social/tags/CodonBias" class="mention hashtag" rel="tag">#<span>CodonBias</span></a> differs from expectations from GC content. Surprisingly, stronger <a href="https://ecoevo.social/tags/NaturalSelection" class="mention hashtag" rel="tag">#<span>NaturalSelection</span></a> -&gt; higher <a href="https://ecoevo.social/tags/IntrinsicStructuralDisorder" class="mention hashtag" rel="tag">#<span>IntrinsicStructuralDisorder</span></a> proteins<br /><a href="https://ecoevo.social/tags/MolecularEvolution" class="mention hashtag" rel="tag">#<span>MolecularEvolution</span></a> <a href="https://ecoevo.social/tags/PopulationGenetics" class="mention hashtag" rel="tag">#<span>PopulationGenetics</span></a> <a href="https://ecoevo.social/tags/EvolgenPaper" class="mention hashtag" rel="tag">#<span>EvolgenPaper</span></a> 1/</p>
Joanna Masel<p>⬆️⬆️⬆️⬆️⬆️<br />Paper now published in <span class="h-card" translate="no"><a href="https://ecoevo.social/@GenomeBiolEvol" class="u-url mention">@<span>GenomeBiolEvol</span></a></span> <a href="https://academic.oup.com/gbe/article/16/3/evae050/7628489" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="ellipsis">academic.oup.com/gbe/article/1</span><span class="invisible">6/3/evae050/7628489</span></a>, details in preprint thread above. <a href="https://ecoevo.social/tags/BackgroundSelection" class="mention hashtag" rel="tag">#<span>BackgroundSelection</span></a> <a href="https://ecoevo.social/tags/EffectivePopulationSize" class="mention hashtag" rel="tag">#<span>EffectivePopulationSize</span></a> <span class="h-card" translate="no"><a href="https://fediscience.org/@jdmatheson" class="u-url mention">@<span>jdmatheson</span></a></span></p>
Joanna Masel<p>The neutralist-selectionist debate needs moderating, and this paper makes some good contributions, but ultimately disappoints. It defends <a href="https://ecoevo.social/tags/NeutralTheory" class="mention hashtag" rel="tag">#<span>NeutralTheory</span></a> as acknowledging <a href="https://ecoevo.social/tags/BackgroundSelection" class="mention hashtag" rel="tag">#<span>BackgroundSelection</span></a>, but does not qualify that this is only a limited form of background selection - one with strong deleterious effects and Ud&lt;1, such that background selection can be captured by a 1-locus model of random <a href="https://ecoevo.social/tags/GeneticDrift" class="mention hashtag" rel="tag">#<span>GeneticDrift</span></a> with lower <a href="https://ecoevo.social/tags/EffectivePopulationSize" class="mention hashtag" rel="tag">#<span>EffectivePopulationSize</span></a>. <a href="https://onlinelibrary.wiley.com/doi/10.1111/brv.13010?af=R" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="ellipsis">onlinelibrary.wiley.com/doi/10</span><span class="invisible">.1111/brv.13010?af=R</span></a> 1/n</p>
Joanna Masel<p>Our preprint describes how <a href="https://ecoevo.social/tags/EffectivePopulationSize" class="mention hashtag" rel="tag">#<span>EffectivePopulationSize</span></a> affects <a href="https://ecoevo.social/tags/AminoAcid" class="mention hashtag" rel="tag">#<span>AminoAcid</span></a> usage. <a href="https://www.biorxiv.org/content/10.1101/2023.02.01.526552v2" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://www.</span><span class="ellipsis">biorxiv.org/content/10.1101/20</span><span class="invisible">23.02.01.526552v2</span></a>. Within highly exchangeable pairs of amino acids, high Ne species are able to prefer <a href="https://ecoevo.social/tags/arginine" class="mention hashtag" rel="tag">#<span>arginine</span></a> over <a href="https://ecoevo.social/tags/lysine" class="mention hashtag" rel="tag">#<span>lysine</span></a>, and <a href="https://ecoevo.social/tags/valine" class="mention hashtag" rel="tag">#<span>valine</span></a> over <a href="https://ecoevo.social/tags/isoleucine" class="mention hashtag" rel="tag">#<span>isoleucine</span></a>. This matches <a href="https://ecoevo.social/tags/thermophile" class="mention hashtag" rel="tag">#<span>thermophile</span></a> preferences, as expected from theories of marginal protein stability at mutation-selection-drift balance. 1/6<br /><span class="h-card" translate="no"><a href="https://ecoevo.social/@hanonmcshea" class="u-url mention">@<span>hanonmcshea</span></a></span> <a href="https://ecoevo.social/tags/NearlyNeutralTheory" class="mention hashtag" rel="tag">#<span>NearlyNeutralTheory</span></a> <a href="https://ecoevo.social/tags/MolecularEvolution" class="mention hashtag" rel="tag">#<span>MolecularEvolution</span></a> <a href="https://ecoevo.social/tags/EvolgenPaper" class="mention hashtag" rel="tag">#<span>EvolgenPaper</span></a></p>
Joanna Masel<p>Background selection at unlinked sites might not matter if it can be well captured by a lower <a href="https://ecoevo.social/tags/EffectivePopulationSize" class="mention hashtag" rel="tag">#<span>EffectivePopulationSize</span></a> describing <a href="https://ecoevo.social/tags/GeneticDrift" class="mention hashtag" rel="tag">#<span>GeneticDrift</span></a> in a 1-locus idealized model. So we added a figure to demonstrate that this isn&#39;t the case. 6/5</p>
Joanna Masel<p>Our latest <a href="https://ecoevo.social/tags/preprint" class="mention hashtag" rel="tag">#<span>preprint</span></a> develops a new metric of <a href="https://ecoevo.social/tags/CodonAdaptation" class="mention hashtag" rel="tag">#<span>CodonAdaptation</span></a> (not just <a href="https://ecoevo.social/tags/CodonBias" class="mention hashtag" rel="tag">#<span>CodonBias</span></a>) to measure the kind of <a href="https://ecoevo.social/tags/EffectivePopulationSize" class="mention hashtag" rel="tag">#<span>EffectivePopulationSize</span></a> that matters to <a href="https://ecoevo.social/tags/NearlyNeutralTheory" class="mention hashtag" rel="tag">#<span>NearlyNeutralTheory</span></a>, and uses it to discover that <a href="https://ecoevo.social/tags/NaturalSelection" class="mention hashtag" rel="tag">#<span>NaturalSelection</span></a> prefers high <a href="https://ecoevo.social/tags/IntrinsicStructuralDisorder" class="mention hashtag" rel="tag">#<span>IntrinsicStructuralDisorder</span></a> <a href="https://www.biorxiv.org/content/10.1101/2023.03.02.530449v1" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://www.</span><span class="ellipsis">biorxiv.org/content/10.1101/20</span><span class="invisible">23.03.02.530449v1</span></a> 1/6<br /><a href="https://ecoevo.social/tags/MolecularEvolution" class="mention hashtag" rel="tag">#<span>MolecularEvolution</span></a> <a href="https://ecoevo.social/tags/PopulationGenetics" class="mention hashtag" rel="tag">#<span>PopulationGenetics</span></a> <a href="https://ecoevo.social/tags/EvolgenPaper" class="mention hashtag" rel="tag">#<span>EvolgenPaper</span></a></p>
Joanna Masel<p>Our latest <a href="https://ecoevo.social/tags/preprint" class="mention hashtag" rel="tag">#<span>preprint</span></a> <a href="https://www.biorxiv.org/content/10.1101/2022.01.11.475913v2" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://www.</span><span class="ellipsis">biorxiv.org/content/10.1101/20</span><span class="invisible">22.01.11.475913v2</span></a> <span class="h-card" translate="no"><a href="https://fediscience.org/@jdmatheson" class="u-url mention">@<span>jdmatheson</span></a></span> calls for significant change to the theory of <a href="https://ecoevo.social/tags/BackgroundSelection" class="mention hashtag" rel="tag">#<span>BackgroundSelection</span></a>, a phenomenon by which some genomic segments of some individuals don’t count toward an <a href="https://ecoevo.social/tags/EffectivePopulationSize" class="mention hashtag" rel="tag">#<span>EffectivePopulationSize</span></a> because they contain too many deleterious mutations. 1/5</p><p><a href="https://ecoevo.social/tags/MolecularEvolution" class="mention hashtag" rel="tag">#<span>MolecularEvolution</span></a> <a href="https://ecoevo.social/tags/PopulationGenetics" class="mention hashtag" rel="tag">#<span>PopulationGenetics</span></a> <a href="https://ecoevo.social/tags/MutationLoad" class="mention hashtag" rel="tag">#<span>MutationLoad</span></a> <a href="https://ecoevo.social/tags/EvolgenPaper" class="mention hashtag" rel="tag">#<span>EvolgenPaper</span></a></p>
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