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2 changes: 1 addition & 1 deletion .nojekyll
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10 changes: 5 additions & 5 deletions exercises/datasets/monkeyflowers.html
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Expand Up @@ -386,7 +386,7 @@ <h1 class="title">Monkeyflowers dataset</h1>
</header><!-- markdownlint-disable MD041 --><!-- markdownlint-disable MD041 --><!-- markdownlint-enable MD041 --><!-- markdownlint-disable MD041 --><!-- markdownlint-enable MD041 --><!-- markdownlint-enable MD041 --><div>
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<div class="quarto-figure quarto-figure-center">
<figure class="figure"><p><a href="https://www.science.org/cms/10.1126/science.365.6456.854/asset/db271bee-8914-4712-9965-dcf1615b6a43/assets/graphic/365_854_f1.jpeg" class="lightbox" data-gallery="quarto-lightbox-gallery-1" title="The allure of monkeyflowers (DOI: 10.1126/science.365.6456.854)"><img src="https://www.science.org/cms/10.1126/science.365.6456.854/asset/db271bee-8914-4712-9965-dcf1615b6a43/assets/graphic/365_854_f1.jpeg" class="img-fluid figure-img" alt="The allure of monkeyflowers (DOI: 10.1126/science.365.6456.854)"></a></p>
<figure class="figure"><p><a href="https://www.science.org/cms/10.1126/science.365.6456.854/asset/db271bee-8914-4712-9965-dcf1615b6a43/assets/graphic/365_854_f1.jpeg" class="lightbox" title="The allure of monkeyflowers (DOI: 10.1126/science.365.6456.854)" data-gallery="quarto-lightbox-gallery-1"><img src="https://www.science.org/cms/10.1126/science.365.6456.854/asset/db271bee-8914-4712-9965-dcf1615b6a43/assets/graphic/365_854_f1.jpeg" class="img-fluid figure-img" alt="The allure of monkeyflowers (DOI: 10.1126/science.365.6456.854)"></a></p>
</figure>
</div>
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Expand All @@ -397,13 +397,13 @@ <h1 class="title">Monkeyflowers dataset</h1>
<p>Recently, <span class="citation" data-cites="stankowski_WidespreadSelectionGene_2019">Stankowski et al. (<a href="#ref-stankowski_WidespreadSelectionGene_2019" role="doc-biblioref">2019</a>)</span> used the monkeyflower system to investigate what forces affect the genomic landscape. <span class="citation" data-cites="burri_InterpretingDifferentiationLandscapes_2017">Burri (<a href="#ref-burri_InterpretingDifferentiationLandscapes_2017" role="doc-biblioref">2017</a>)</span> has suggested that background selection (BGS) is one of the main causes for correlations between genomic landscapes, and that one way to study this phenomenon is to look at closely related taxa. This is one of the objectives of the <span class="citation" data-cites="stankowski_WidespreadSelectionGene_2019">Stankowski et al. (<a href="#ref-stankowski_WidespreadSelectionGene_2019" role="doc-biblioref">2019</a>)</span> paper.</p>
<p>They performed whole-genome resequencing of 37 individuals from 7 subspecies and 2 ecotypes of <em>Mimulus aurantiacus</em> and its sister taxon <em>M. clevelandii</em> (<a href="#fig-evolutionary-relationship">Figure&nbsp;1</a>), all sampled in California (<a href="#fig-monkeyflower-sampling-location">Figure&nbsp;2</a>).</p>
<div id="fig-evolutionary-relationship" class="quarto-figure quarto-figure-center anchored">
<figure class="figure"><p><a href="assets/images/stankowski-2019-fig1A.png" class="lightbox" data-gallery="quarto-lightbox-gallery-2" title="Evolutionary relationships across the radiation"><img src="assets/images/stankowski-2019-fig1A.png" class="img-fluid figure-img"></a></p>
<figure class="figure"><p><a href="assets/images/stankowski-2019-fig1A.png" class="lightbox" title="Evolutionary relationships across the radiation" data-gallery="quarto-lightbox-gallery-2"><img src="assets/images/stankowski-2019-fig1A.png" class="img-fluid figure-img"></a></p>
<figcaption class="figure-caption">Figure&nbsp;1: Evolutionary relationships across the radiation</figcaption></figure>
</div>

<div class="no-row-height column-margin column-container"><div class="">
<div id="fig-monkeyflower-sampling-location" class="quarto-figure quarto-figure-center anchored">
<figure class="figure"><p><a href="../../slides/simulation/assets/images/stankowski-2019-figs2.jpg" class="lightbox" data-gallery="quarto-lightbox-gallery-3" title="Sampling locations"><img src="../../slides/simulation/assets/images/stankowski-2019-figs2.jpg" class="img-fluid figure-img"></a></p>
<figure class="figure"><p><a href="../../slides/simulation/assets/images/stankowski-2019-figs2.jpg" class="lightbox" title="Sampling locations" data-gallery="quarto-lightbox-gallery-3"><img src="../../slides/simulation/assets/images/stankowski-2019-figs2.jpg" class="img-fluid figure-img"></a></p>
<figcaption class="figure-caption">Figure&nbsp;2: Sampling locations</figcaption></figure>
</div>
</div></div><p>Genomewide statistics, such as diversity (<span class="math inline">\(\pi\)</span>), divergence (<span class="math inline">\(d_{XY}\)</span>) and differentiation <span class="math inline">\(F_{ST}\)</span>, were calculated within and between taxa to generate genomic diversity landscapes. The landscapes were highly similar across taxa, and local variation in genomic features, such as gene density and recombination rate, was predictive of variation in landscape patterns. These features suggest the influence of selection, in particular BGS.</p>
Expand All @@ -419,7 +419,7 @@ <h1 class="title">Monkeyflowers dataset</h1>
</ol>
<p><a href="#fig-slim-simulations">Figure&nbsp;3</a> shows typical results of the simulations.</p>
<div id="fig-slim-simulations" class="quarto-figure quarto-figure-center anchored">
<figure class="figure"><p><a href="../../slides/simulation/assets/images/stankowski-2019-fig7.png" class="lightbox" data-gallery="quarto-lightbox-gallery-4" title="Genomic landscapes simulated under different divergence histories."><img src="../../slides/simulation/assets/images/stankowski-2019-fig7.png" class="img-fluid figure-img"></a></p>
<figure class="figure"><p><a href="../../slides/simulation/assets/images/stankowski-2019-fig7.png" class="lightbox" title="Genomic landscapes simulated under different divergence histories." data-gallery="quarto-lightbox-gallery-4"><img src="../../slides/simulation/assets/images/stankowski-2019-fig7.png" class="img-fluid figure-img"></a></p>
<figcaption class="figure-caption">Figure&nbsp;3: Genomic landscapes simulated under different divergence histories.</figcaption></figure>
</div>
<p>In conclusion, the authors found that although BGS plays a role, it does not sufficiently explain all observations, and that other aspects of natural selection (such as rapid adaptation) are responsible for the similarities between genomic landscapes.</p>
Expand Down Expand Up @@ -766,7 +766,7 @@ <h1 class="title">Monkeyflowers dataset</h1>
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8 changes: 4 additions & 4 deletions exercises/genetic_diversity/index.html
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Expand Up @@ -707,11 +707,11 @@ <h1 class="title">Genetic diversity landscapes</h1>

<div class="no-row-height column-margin column-container"><div class="">
<div id="fig-evolutionary-relationship" class="quarto-figure quarto-figure-center anchored">
<figure class="figure"><p><a href="../datasets/assets/images/stankowski-2019-fig1A.png" class="lightbox" title="Evolutionary relationships across the radiation" data-gallery="quarto-lightbox-gallery-1"><img src="../datasets/assets/images/stankowski-2019-fig1A.png" class="img-fluid figure-img"></a></p>
<figure class="figure"><p><a href="../datasets/assets/images/stankowski-2019-fig1A.png" class="lightbox" data-gallery="quarto-lightbox-gallery-1" title="Evolutionary relationships across the radiation"><img src="../datasets/assets/images/stankowski-2019-fig1A.png" class="img-fluid figure-img"></a></p>
<figcaption class="figure-caption">Figure&nbsp;1: Evolutionary relationships across the radiation</figcaption></figure>
</div>
<div id="fig-monkeyflower-sampling-location" class="quarto-figure quarto-figure-center anchored">
<figure class="figure"><p><a href="../../slides/simulation/assets/images/stankowski-2019-figs2.jpg" class="lightbox" title="Monkeyflower sampling locations" data-gallery="quarto-lightbox-gallery-2"><img src="../../slides/simulation/assets/images/stankowski-2019-figs2.jpg" class="img-fluid figure-img"></a></p>
<figure class="figure"><p><a href="../../slides/simulation/assets/images/stankowski-2019-figs2.jpg" class="lightbox" data-gallery="quarto-lightbox-gallery-2" title="Monkeyflower sampling locations"><img src="../../slides/simulation/assets/images/stankowski-2019-figs2.jpg" class="img-fluid figure-img"></a></p>
<figcaption class="figure-caption">Figure&nbsp;2: Monkeyflower sampling locations</figcaption></figure>
</div>
</div></div><p>We convert the sample information with <code>csvtk</code>. We also add a populations file with all samples belonging to the same population:</p>
Expand Down Expand Up @@ -783,7 +783,7 @@ <h1 class="title">Genetic diversity landscapes</h1>
<div class="no-row-height column-margin column-container"><div class="callout-6-contents callout-collapse collapse callout-margin-content">
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<div id="fig-ld-decay-fuller" class="quarto-figure quarto-figure-center anchored">
<figure class="figure"><p><a href="https://www.science.org/cms/10.1126/science.aba4674/asset/661d50bb-a085-41af-abdb-06c487ed4e63/assets/graphic/369_aba4674_f2.jpeg" class="lightbox" title="Properties of genetic variation and inferred demographic history in sampled A. millepora. @fuller_PopulationGeneticsCoral_2020, Figure 2. Upper left plot illustrates LD as a function of physical distance. Here, choosing a window size 20-30kb would ensure that most windows are independent." data-gallery="quarto-lightbox-gallery-8"><img src="https://www.science.org/cms/10.1126/science.aba4674/asset/661d50bb-a085-41af-abdb-06c487ed4e63/assets/graphic/369_aba4674_f2.jpeg" class="img-fluid figure-img"></a></p>
<figure class="figure"><p><a href="https://www.science.org/cms/10.1126/science.aba4674/asset/661d50bb-a085-41af-abdb-06c487ed4e63/assets/graphic/369_aba4674_f2.jpeg" class="lightbox" data-gallery="quarto-lightbox-gallery-8" title="Properties of genetic variation and inferred demographic history in sampled A. millepora. @fuller_PopulationGeneticsCoral_2020, Figure 2. Upper left plot illustrates LD as a function of physical distance. Here, choosing a window size 20-30kb would ensure that most windows are independent."><img src="https://www.science.org/cms/10.1126/science.aba4674/asset/661d50bb-a085-41af-abdb-06c487ed4e63/assets/graphic/369_aba4674_f2.jpeg" class="img-fluid figure-img"></a></p>
<figcaption class="figure-caption">Figure&nbsp;3: Properties of genetic variation and inferred demographic history in sampled <em>A. millepora</em>. <span class="citation" data-cites="fuller_PopulationGeneticsCoral_2020">Fuller et al. (<a href="#ref-fuller_PopulationGeneticsCoral_2020" role="doc-biblioref">2020</a>)</span>, Figure 2. Upper left plot illustrates LD as a function of physical distance. Here, choosing a window size 20-30kb would ensure that most windows are independent.</figcaption></figure>
</div>
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Expand Down Expand Up @@ -1335,7 +1335,7 @@ <h1 class="title">Genetic diversity landscapes</h1>
</div>
<div class="nav-footer-right">Published with <a href="https://quarto.org/">Quarto</a> v<!--?quarto.version ?--></div>
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20 changes: 10 additions & 10 deletions exercises/index.html
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Expand Up @@ -283,7 +283,7 @@ <h2 class="anchored" data-anchor-id="exercises">Exercises</h2>

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4 changes: 2 additions & 2 deletions exercises/population_structure/index.html
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Expand Up @@ -513,8 +513,8 @@ <h1 class="title">Population structure</h1>
<h2 class="anchored" data-anchor-id="jupyter-notebooks">Jupyter notebooks</h2>
<!-- markdownlint-disable MD013 -->
<p>The rendered notebook instructions are located as html files, with embedded buttons to download the actual notebooks (keep an eye out for the <code>Download Notebook</code> button in the top right), here:</p>
<p><a class="quarto-notebook-link" id="nblink-1" href="pca_mds_toy_example.ipynb.html">Source: pca_mds_toy_example.ipynb</a></p>
<p><a class="quarto-notebook-link" id="nblink-1" href="pca_admixture_1000G.html">Source: pca_admixture_1000G.ipynb</a></p>
<p><a class="quarto-notebook-link" id="pca_mds_toy_example" href="pca_mds_toy_example.ipynb.html">Source: pca_mds_toy_example.ipynb</a></p>
<p><a class="quarto-notebook-link" id="pca_admixture_1000G" href="pca_admixture_1000G.ipynb.html">Source: pca_admixture_1000G.ipynb</a></p>
<!-- markdownlint-enable MD013 -->
<p>Notebooks are also available for download at <a href="https://uppsala.instructure.com/courses/86976/pages/population-structure-notebooks" class="uri">https://uppsala.instructure.com/courses/86976/pages/population-structure-notebooks</a></p>

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