Browsing by Subject "evolutionary biology"
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Item Open Access A phylogenetic transform enhances analysis of compositional microbiota data.(Elife, 2017-02-15) Silverman, Justin D; Washburne, Alex D; Mukherjee, Sayan; David, Lawrence ASurveys of microbial communities (microbiota), typically measured as relative abundance of species, have illustrated the importance of these communities in human health and disease. Yet, statistical artifacts commonly plague the analysis of relative abundance data. Here, we introduce the PhILR transform, which incorporates microbial evolutionary models with the isometric log-ratio transform to allow off-the-shelf statistical tools to be safely applied to microbiota surveys. We demonstrate that analyses of community-level structure can be applied to PhILR transformed data with performance on benchmarks rivaling or surpassing standard tools. Additionally, by decomposing distance in the PhILR transformed space, we identified neighboring clades that may have adapted to distinct human body sites. Decomposing variance revealed that covariation of bacterial clades within human body sites increases with phylogenetic relatedness. Together, these findings illustrate how the PhILR transform combines statistical and phylogenetic models to overcome compositional data challenges and enable evolutionary insights relevant to microbial communities.Item Open Access Morphological and genomic shifts in mole-rat 'queens' increase fecundity but reduce skeletal integrity.(eLife, 2021-04-12) Johnston, Rachel A; Vullioud, Philippe; Thorley, Jack; Kirveslahti, Henry; Shen, Leyao; Mukherjee, Sayan; Karner, Courtney M; Clutton-Brock, Tim; Tung, JennyIn some mammals and many social insects, highly cooperative societies are characterized by reproductive division of labor, in which breeders and nonbreeders become behaviorally and morphologically distinct. While differences in behavior and growth between breeders and nonbreeders have been extensively described, little is known of their molecular underpinnings. Here, we investigate the consequences of breeding for skeletal morphology and gene regulation in highly cooperative Damaraland mole-rats. By experimentally assigning breeding 'queen' status versus nonbreeder status to age-matched littermates, we confirm that queens experience vertebral growth that likely confers advantages to fecundity. However, they also upregulate bone resorption pathways and show reductions in femoral mass, which predicts increased vulnerability to fracture. Together, our results show that, as in eusocial insects, reproductive division of labor in mole-rats leads to gene regulatory rewiring and extensive morphological plasticity. However, in mole-rats, concentrated reproduction is also accompanied by costs to bone strength.Item Open Access Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi.(Elife, 2016-05-10) Medina, Edgar M; Turner, Jonathan J; Gordân, Raluca; Skotheim, Jan M; Buchler, Nicolas EAlthough cell cycle control is an ancient, conserved, and essential process, some core animal and fungal cell cycle regulators share no more sequence identity than non-homologous proteins. Here, we show that evolution along the fungal lineage was punctuated by the early acquisition and entrainment of the SBF transcription factor through horizontal gene transfer. Cell cycle evolution in the fungal ancestor then proceeded through a hybrid network containing both SBF and its ancestral animal counterpart E2F, which is still maintained in many basal fungi. We hypothesize that a virally-derived SBF may have initially hijacked cell cycle control by activating transcription via the cis-regulatory elements targeted by the ancestral cell cycle regulator E2F, much like extant viral oncogenes. Consistent with this hypothesis, we show that SBF can regulate promoters with E2F binding sites in budding yeast.Item Open Access Statistical analysis of fruit fly wing vein topology(2018-04) Beriwal, SurabhiThe fruit fly Drosophila melanogaster is a commonly used model organism for evolution given that the species showcases interesting behaviors and is easy to modify and rear. Among other things, the Drosophila wings are studied because their structure is tractable, consistent, and traceable developmentally. Along with Dr. Ezra Miller and Ashleigh Thomas, I studied evolutionary changes to Drosophila melanogaster wings using persistent homology. The biological hypothesis posits that selecting for continuous wing deformation leads to higher rates of topological novelty. We are interested in understanding whether selection on a continuous trait can itself cause higher rates of variation of a (separate) discrete trait. We work joint with Dr. David Houle at Florida State University.Item Open Access To plasticity and back again.(Elife, 2015-03-12) Nijhout, H FrederikBoth the gain and the loss of flexibility in the development of phenotypes have led to an increased diversity of physical forms in nematode worms.