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title: Social insect research lab - using innovative genomics and video technologies to improve understanding of ant evolution and pollinator health
description: Social insect research lab - using innovative genomics and video technologies to improve understanding of ant evolution and pollinator health
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    <h2>Genomic bases of sociality in insects</h2>
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      <p>Theory can explain benefits and costs of social evolution, but we are only beginning to understand
        its molecular bases.</p>
      <p>We examine the interplay between social evolution and genome evolution.
        As part of this, we identify genes and mechanisms involved in the evolution of insect societies. </p>
        <p>Our findings have general impacts on understanding how new phenotypes evolve.</p>
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      <img src="{{ site.url }}/img/frontpage/fireants-ongenome480w.jpg"  width="480" height="265" class="img-rounded img-fluid"
        alt="fire ants on the genomic sequence of their social chromosome">
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    <div id="section1-extra" class="col-sm-12" style="display:none;">
      <p>We use the 15,000 species of ants as a set of
        model systems to address questions about major transitions, the genetics of behavior, the genomic constraints modulating
        social evolution, and the molecular mechanisms responsible for differences between castes. We combine
        animal experiments and laboratory work with population genomics, molecular evolution, and comparative transcriptomics.
        </p>
      <p>For example:</p>
      <ul>
        <li>We discovered that alternate variants of a supergene carried by a pair of &#8220;social chromosomes&#8221; determine whether
          fire ant colonies include one or multiple queens (Nature 2013).</li>
        <li>We discovered the degenerative expansion of the Sb fire ant supergene variant: it carries almost 2x as much DNA as the SB variant (MBE 2019). This represents a rarely seen early stage of supergene evolution.</li>
        <li>We disentangled adaptive and neutral forces affecting gene expression in the supergene (eLife 2020). Some genes are socially antagonistic, while others have dosage compensation for the degeneration due to recombination suppression.</li>
        <li>We revealed the introgression of the fire ant social supergene across species boundaries (Nature Communications 2022).</li>
        <li>We found high divergence between supergene variants, and strikingly different patterns of genetic diversity (<a href="https://onlinelibrary.wiley.com/doi/10.1111/mec.14054/abstract">Molecular Ecology
              2017</a> and <a href="https://dx.doi.org/10.1002/evl3.22">Evolution Letters 2017</a>).</li>
        <li>We discovered that another social supergene convergently evolved in a second lineage of ants (Current Biology 2014).</li>
        <li>We reviewed recent research on ants (<a
            href="https://doi.org/10.1016/j.cois.2017.12.001">Current Opinion in Insect Science 2018</a>).</li>
        <li>We sequenced and analyzed the genome of the invasive red fire ant <em>Solenopsis invicta</em> (<a
            href="https://dx.doi.org/10.1073/pnas.1009690108">PNAS 2011</a>).</li>
        <li>We described the gene expression changes that occur in a virgin queen when she has the opportunity to
          replace her mother (<a href="https://dx.doi.org/10.1111/j.1365-294X.2010.04561.x">Molecular Ecology
            2010</a>).</li>
        <li>We examined selective regime (positive vs. neutral selection) and fate of duplicated genes (conserved vs.
          subfunctionalized vs. neofunctionalization) for gene families including <a
            href="https://rspb.royalsocietypublishing.org/content/280/1758/20122968">sex-determination loci
            (tranfsormer/feminiser)</a>, <a
            href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0045715">clock genes</a>, <a
            href="https://www.nature.com/hdy/journal/v110/n6/full/hdy2012122a.html">chemosensory proteins (CSPs)</a>, <a
            href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0016289">olfactory binding proteins
            (OBPs)</a>, <a href="https://dx.doi.org/10.1073/pnas.1009690108">olfactory receptors</a> and <a
            href="https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003730">vitellogenin genes</a>.
        </li>
      </ul>
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      <img src="{{ site.url }}/img/frontpage/fireants-ongenome480w.jpg"  width="480" height="265" class="img-rounded mx-auto d-block img-fluid"
        alt="fire ants on the genomic sequence of their social chromosome">
    </div>
  </article>
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    <h2>Empowering genomic data scientists</h2>
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      <p>The dramatic drop in the cost of DNA sequencing means that anyone can sequence anything - and lots
        of it. This creates exciting opportunities but also new challenges: how should we reliably and effectively handle, analyze and visualize large datasets?</p>
      <p>We develop innovative tools and approaches to facilitate modern biological work on species across the tree of life. We pay special attention to visualization and user experience.</p>
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      <img src="{{ site.url }}/img/frontpage/analyze-final.gif" width="440" height="240" class="img-rounded img-fluid"
        alt="how tools should be">
    </div>
    <div id="section2-extra" class="col-sm-12" style="display:none;">
      <ul>
        <li><strong>Genome Assembly.</strong> How do you know which genome assembly software or parameter works best for your species? Our <a href="https://doi.org/10.1101/2021.05.28.446135">CompareGenomeQualities</a> software can help. </li>
        <li><strong>Comparative Genomics.</strong> Our <a href="https://www.sequenceserver.com/">SequenceServer</a> BLAST interface is used by thousands daily and is cited weekly. It enables researchers to:
          <ul>
            <li>run BLAST on private unpublished datasets;</li>
            <li>access an intuitive graphical user interface that provides helpful visualization for interpreting genomic comparisons;</li>
            <li>run BLAST against Uniprot or NR without having to wait in NCBI's queue;</li>
            <li>help labs or communities share a BLAST server.</li>
          </ul>
        </li>
        <li><strong>Genome Evolution.</strong> We created a framework for simulating genome evolution of the ~15% of animal species with haplo-diploid sex determination systems (Pracana et al 2022).</li>
        <li><strong>Gene Prediction.</strong> Correctly identifying genes in a genome sequence remains challenging. This is a huge problem for multi-species multi-gene analyses on emerging model organisms (trash
          in trash out).
          <ul>
            <li><a href="/tools/genevalidator/">GeneValidator</a> identifies problems with gene predictions. Use it to prioritize curation or to choose the best geneset.</li>
            <li>How can you transfer high quality gene predictions from an old genome assembly to a newer one? Our <a href="https://github.com/wurmlab/flo">flo GFF transfer tool</a> helps with that.</li>
          </ul>
        </li>
        </ul>
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        alt="how tools should be">
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  </article>
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  <article id="section3" class="row">
    <h2>Protecting pollinators, biodiversity and crops</h2>
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      <p>Wild pollinators including bumblebees, solitary bees, butterflies, wasps, moths, and beetles are essential
        for ecosystem stability and food production. Their worldwide declines are thus worrying.</p>
        <p>
        A key challenge is our lack of tools for measuring pollinator health: we know whether an individual is dead, but when an insect is alive,
        one cannot tell whether it is unwell. We are <strong>developing high-resolution tools</strong> to improve our ability to measure pollinator health. We've also developed <a href="https://sensibee.io">Sensibee, an automated pollinator monitoring platform</a>.</p>

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      <img src="{{ site.url }}/img/frontpage/bumblebee-240.jpg" width="360" height="240" class="img-rounded img-fluid"
        alt="bumblebee on flower">
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    <div id="section3-extra" class="col-sm-12" style="display:none;">
      <p>We aim to improve pollinator health to protect biodiversity and agriculture. For this, we take inspiration from biomedical approaches for
        understanding cancer biology and personalized medicine. In particular, we use high-resolution molecular tools
        including population genomics and gene expression analyses to
        understand how pollinators are affected by changing environments (e.g., pesticide exposure, habitat loss,
        changing climates) and their ability to cope with such changes. We aim to give regulators the tools they need to better evaluate the potential impacts of insecticides, and to establish manners of monitoring pollinator health.</p>
      <ul>
        <li>We have outlined a vision of how molecular approaches can help to better evaluate the impacts of pesticides on beneficial pollinators (<a href="https://www.sciencedirect.com/science/article/pii/S016953471930357X">Trends in Ecology &amp; Evolution 2020</a>)</li>
        <li>We found that two insecticides targeting the same receptor disrupt organismal function in very different manners (<a href="http://dx.doi.org/10.1111/mec.15047">Molecular Ecology 2019</a>).</li>
        <li>We find that bumblebee queens and workers are affected differently by the same insecticide (<a href="http://dx.doi.org/10.1111/mec.15047">Molecular Ecology 2019</a>). </li>
        <li>We are quantifying the effects of pesticide exposure on gene expression in various bee species.</li>
        <li>By surveying populations of wild <em>Bombus terrestris</em> bumblebees, we have detected the genetic changes that have helped them respond to recent environmental pressures (<a href="http://dx.doi.org/10.1093/molbev/msab366">MBE 2022)</a>.</li>
        <li>We have contributed to several experiments examining the impact of pesticides on field colonies.</li>
      </ul>
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        alt="how tools should be">
    </div>
  </article>
</section>
<aside class="column col-sm-5 col-md-5">
  <h3><strong><a href="/postdoc_phd_positions">Open Postdoc &amp; PhD positions</a></strong></h3>
  <h3><strong><a href="/news">Latest news</a></strong></h3>
  <ul style="list-style-type: none; padding-left: 5px; border-bottom: 1px solid #eee">
    {% for post in site.categories.labnews offset: 0 limit: 3 %}
    <li style="line-height:120%; margin-bottom: 5pt">
      <strong><a href="{{ site.url }}{{ post.url }}">{{ post.title }}</a></strong> ({{ post.date | date: "%B %d" }})
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  <h3><strong><a href="/publications">Recent publications</a></strong></h3>
  <ul style="list-style-type: none; padding-left: 5px; border-bottom: 1px solid #eee;  line-height:120% ">
    <li style="margin-bottom: 5pt">
      <a href="https://doi.org/10.1098/rspb.2023.2274">
      <strong>Transcriptomic responses to location learning by honeybee dancers are partly mirrored in the brains of dance-followers</strong>
      </a> 
      Manfredini et al. Proceedings of the Royal Society B (2023)
    </li>
    <li style="margin-bottom: 5pt">
      <a href="https://doi.org/10.1016/j.tig.2023.01.005">
      <strong>How genomics can help biodiversity conservation</strong>
      </a> 
      Theissinger et al. Trend in Genetics (2023)
    </li>
    <li style="margin-bottom: 5pt">
      <a href="https://dx.doi.org/10.1111/mec.16811">
      <strong>Expression of subunits of an insecticide target receptor varies across tissues, life stages, castes, and species of social bees</strong>
      </a> 
      Witwicka et al. Molecular Ecology (2023)
    </li>
    <li style="margin-bottom: 5pt">
      <a href="https://dx.doi.org/10.1093/gbe/evac062">
      <strong>Individual-based modeling of genome evolution in haplodiploid organisms</strong>
      </a> 
      Pracana et al. Genome Biology and Evolution (2022)
    </li>
    <li style="margin-bottom:5pt">
      <a href="https://doi.org/10.1038/s41467-022-28806-7">
        <b>Recurring adaptive introgression of a supergene variant that determines social organization</b>
      </a>
      Stolle, Pracana et al. Nature Communications (2022)
    </li>
<li style="margin-bottom:5pt">
      <a href="https://doi.org/10.1111/mec.16284">
        <b>Larger, more connected societies of ants have a higher prevalence of viruses</b>
      </a>
      Brahma et al. Molecular Ecology (2022)
    </li>
<li style="margin-bottom:5pt">
      <a href="https://dx.doi.org/10.7554/eLife.55862">
        <b>Genomic architecture and evolutionary antagonism drive allelic expression bias in the social supergene of red
          fire ants</b>
      </a>
      Martinez-Ruiz et al. eLife (2020)
    </li>
    <li style="margin-bottom:5pt">
      <a href="https://dx.doi.org/10.1016/j.cub.2020.09.023">
        <b>The legacy of endosymbiosis in ants</b>
      </a>
      Jackson et al. Current Biology (2020)
    </li>
  </ul>
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    <p>We are grateful for support from our funders:</p>
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