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4 results for “Modelling (Disease Ecology)”
Emergent Ecological Patterns and Modelling of Gut Microbiomes in Health and in Disease
<p><strong><em>Data associated with the paper "Emergent Ecological Patterns and Modelling of Gut Microbiomes in Health and in Disease".</em></strong></p> <p><strong>Content:</strong></p> <ul> <li><strong>Metagenomic curated data considering healthy and diseased state of the human individuals. Aligned against RefSeq with Kaiju.</strong></li> <li><strong>Curated metadata with anonymised physiological and medical information</strong></li> </ul> <p><strong>Paper authors</strong>: Jacopo Pasqualini, Sonia Facchin, Andrea Rinaldo, Amos Maritan, Edoardo Vincenzo Savarino, Samir Suweis</p> <p><strong>Paper preprint</strong>: https://www.biorxiv.org/content/10.1101/2023.10.19.563037v2</p> <p><strong>Data Curator</strong>: Jacopo Pasqualini.</p> <p><strong>Pipeline used to generate the data</strong>: https://github.com/jacopopasqualini/MetaGym</p> <p><strong>Complete description of data generation</strong>: https://www.biorxiv.org/content/10.1101/2023.10.19.563037v2</p>
Evolution of Castanea in North America: RADseq and ecological modeling reveal a history of radiation, range shifts, and disease
<p><b>Premise of the Study: </b>Chestnuts and chinquapins are some of the best known and most widely loved of any plants in North America. Despite the fame of this clade, relatively little genomic sequencing has been done, and much is still unknown about their evolution. </p> <p><b>Methods: </b>Here we use ddRAD data to infer the species-level phylogeny for <i>Castanea </i>and assess the phylogeography of the North American species using samples collected from populations that span the full extent of the species' ranges. We also construct species distribution models using digitized herbarium specimens and observational data from field surveys. </p> <p><b>Key Results: </b>We identified strong population structure within <i>Castanea dentata</i> (American Chestnut) that reflects a stepwise northern migration since the last glacial maximum. Our species distribution models further confirm this scenario and match closely with the <i>Castanea</i> fossil pollen record. We also found significant structure within the <i>Castanea pumila</i> lineage, most notably a genetic cluster that corresponds to the frequently recognized "<i>Castanea pumila var. ozarkensis</i>."</p> <p><b>Conclusions: </b>The two North American <i>Castanea</i> species have contrasting patterns of population structure, but each is typical of plant phylogeography in North America. Within the <i>C. pumila</i> complex we find novel genetic structure that provides new insights to <i>C. pumila</i> taxonomy. Our results also identify a series of distinctive populations that will be valuable in on going efforts to conserve and restore the Chestnuts and Chinquapins in North America.</p>
Evolution of Castanea in North America: RADseq and ecological modeling reveal a history of radiation, range shifts, and disease
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List of papers reviewed to uncover trends in the use of model systems in infectious disease ecology & evolutionary biology
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.