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<h1 class="title toc-ignore">Research topics & aims</h1>
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<p><img src="images/fishhut_pic.jpg" width="2376" /></p>
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<p><br></p>
<div id="global-change" class="section level2">
<h2>Global change</h2>
<p><strong>Adaptation and acclimation to global change</strong></p>
<p>My research is motivated by the goal of improving predictions of
biodiversity’s adaptation to global change. Like the field of global
change biology, this work is highly integrative and spans experimental
biology, physiology, and genome biology. I characterize organismal
responses to global change stressors, evaluate fitness benefits these
physiological responses, and interrogate their regulatory and genomic
basis. This information is critical for identifying traits that promote
resistance and resilience to global change, their mechanistic basis, and
how they may evolve.</p>
<p><u>Example:</u> <strong>Bogan SN</strong>, Johnson KM, and Hofmann
GE. 2020. <a
href="https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2019.00788/full">Changes
in Genome-wide Methylation and Gene Expression in Response to Future
<em>p</em>CO2 Extremes in the Antarctic Pteropod <em>Limacina helicina
antarctica</em></a>. <em>Frontiers in Marine Science</em> 6: 788.</p>
<p><br></p>
</div>
<div id="genome-biology" class="section level2">
<h2>Genome biology</h2>
<p><strong>Genomic constraints on environmental adaptation</strong></p>
<p>Environmental adaptation can be constrained or facilitated by the
structure and diversity of genomes. For example, chromosomal inversions
can yield phenotypic effects of great fitness cost or benefit in a given
environment. Repetitive genomic regions can facilitate copy number
variation and subsequent selection on copy number in environments where
more or fewer copies are beneficial. My research in evolutionary
genomics seeks to understand how environmental adaptation is constrained
or limited by these processes.</p>
<p><u>Example:</u> <strong>Bogan SN</strong>, Surendran N, Hotaling S,
<em>et al.</em> and Kelley JL. 2024. <a
href="https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaf219/8251091?searchresult=1">Temperature
and Pressure Shaped the Evolution of Antifreeze Proteins in Polar and
Deep Sea Zoarcoid Fishes</a>. <em>Molecular Biology and Evolution</em>
42(10): msaf219.</p>
<p><br></p>
</div>
<div id="epigenetics" class="section level2">
<h2>Epigenetics</h2>
<p><strong>Epigenetics of phenotypic plasticity and
acclimation</strong></p>
<p>Epigenetic modifications to DNA and chromatin and hypothesized to
underpin plastic responses to environmental change by affecting gene
expression and subsequent phenotypes. I have studied and reviewed
complex associations between DNA methylation, chromatin accessibility,
and gene expression associated with transgenerational and developmental
plasticity.</p>
<p><u>Examples:</u> <strong>Bogan SN</strong>, Strader ME, and Hofmann
GE. 2023. <a
href="https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-023-01645-8">Associations
between DNA Methylation and Gene Expression Depend on Chromatin
Accessibility during Transgenerational Plasticity</a>. <em>BMC
Biology</em> 21: 149.</p>
<p><strong>Bogan SN</strong> and Yi SV. 2024. <a
href="https://academic.oup.com/gbe/article/16/2/evae022/7602727">Potential
Role of DNA Methylation in Plastic Responses to the Environment across
Cells, Organisms, and Populations</a>. <em>Genome Biology and
Evolution</em> 16: evae022.</p>
<p><br></p>
</div>
<div id="phenotypic-plasticity" class="section level2">
<h2>Phenotypic plasticity</h2>
<p><strong>Evolutionary biology of phenotypic plasticity</strong></p>
<p>Phenotypic plasticity can both evolve by - and affect - natural
selection. However, evolutionary biology maintains a poor ability to
predict when plasticity or environmental acclimation is adaptive.
Furthermore, direct evidence of plasticity’s role in modifying selection
on phenotypes is largely indirect. I am investigating the ecological and
evolutionary processes that shape the fitness effects of plasticity and
acclimation in addition to developing directly testable theory and
evolutionary genetic models for plasticity’s role in evolution.</p>
<p><u>Example:</u> <strong>Bogan SN</strong>, Porat OI, Meneses M, and
Hofmann GE. 2024. <a
href="https://besjournals.onlinelibrary.wiley.com/doi/10.1111/1365-2435.14568">Thermal
Plasticity Has Greater Fitness Costs among Thermally Tolerant Genotypes
of <em>Tigriopus californicus</em></a>. <em>Functional Ecology</em> 38:
1562–1577.</p>
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