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101 results for “rapid radiation”
Data from: Analysis of a rapid evolutionary radiation using ultraconserved elements (UCEs): Evidence for a bias in some multi-species coalescent methods
Rapid evolutionary radiations are expected to require large amounts of sequence data to resolve. To resolve these types of relationships many systematists believe that it will be necessary to collect data by next-generation sequencing (NGS) and use multispecies coalescent ("species tree") methods. Ultraconserved element (UCE) sequence capture is becoming a popular method to leverage the high throughput of NGS to address problems in vertebrate phylogenetics. Here we examine the performance of UCE data for gallopheasants (true pheasants and allies), a clade that underwent a rapid radiation 10–15 Ma. Relationships among gallopheasant genera have been difficult to establish. We used this rapid radiation to assess the performance of species tree methods, using ∼600 kilobases of DNA sequence data from ∼1500 UCEs. We also integrated information from traditional markers (nuclear intron data from 15 loci and three mitochondrial gene regions). Species tree methods exhibited troubling behavior. Two methods [Maximum Pseudolikelihood for Estimating Species Trees (MP-EST) and Accurate Species TRee ALgorithm (ASTRAL)] appeared to perform optimally when the set of input gene trees was limited to the most variable UCEs, though ASTRAL appeared to be more robust than MP-EST to input trees generated using less variable UCEs. In contrast, the rooted triplet consensus method implemented in Triplec performed better when the largest set of input gene trees was used. We also found that all three species tree methods exhibited a surprising degree of dependence on the program used to estimate input gene trees, suggesting that the details of likelihood calculations (e.g., numerical optimization) are important for loci with limited phylogenetic information. As an alternative to summary species tree methods we explored the performance of SuperMatrix Rooted Triple - Maximum Likelihood (SMRT-ML), a concatenation method that is consistent even when gene trees exhibit topological differences due to the multispecies coalescent. We found that SMRT-ML performed well for UCE data. Our results suggest that UCE data have excellent prospects for the resolution of difficult evolutionary radiations, though specific attention may need to be given to the details of the methods used to estimate species trees.
Rapid radiation of Southern Ocean shags in response to receding sea ice
<p>Aim:</p> <p>Understanding how wild populations respond to climatic shifts is a fundamental goal of biological research in a fast-changing world. The Southern Ocean represents a fascinating system for assessing large-scale climate-driven biological change, as it contains extremely isolated island groups within a predominantly westerly, circumpolar wind and current system. The blue-eyed shags (<i>Leucocarbo</i> spp.) represent a paradoxical Southern Ocean seabird radiation; a circumpolar distribution implies strong dispersal capacity yet their speciose nature suggests local adaptation and isolation. Here we use genetic tools in an attempt to resolve this paradox.</p> <p>Location:</p> <p>Southern Ocean.</p> <p>Taxa:</p> <p>17 species and subspecies of blue-eyed shags (<i>Leucocarbo</i> spp.) across the geographical distribution of the genus.</p> <p>Methods:</p> <p>Here we use mitochondrial and nuclear sequence data to conduct the first global genetic analysis of this group using a temporal phylogenetic framework to test for rapid speciation.</p> <p>Results:</p> <p>Our analysis reveals remarkably shallow evolutionary histories among island-endemic lineages, consistent with a recent high-latitude circumpolar radiation. This rapid sub-Antarctic expansion contrasts with significantly deeper lineages detected in more temperate regions such as South America and New Zealand that may have acted as glacial refugia. The dynamic history of high-latitude expansions is further supported by ancestral demographic and biogeographic reconstructions.</p> <p>Main conclusions:</p> <p>The circumpolar distribution of blue-eyed shags, and their highly dynamic evolutionary history, potentially make <i>Leucocarbo</i> a strong sentinel of past and ongoing Southern Ocean ecosystem change given their sensitivity to climatic impacts.</p>
Rapid radiation and rampant reticulation: Phylogenomics of South American Liolaemus lizards
<p>Understanding the factors that cause heterogeneity among gene trees can increase the accuracy of species trees. Discordant signals across the genome are commonly produced by incomplete lineage sorting (ILS) and introgression, which in turn can result in reticulate evolution. Species tree inference using the multispecies coalescent is designed to deal with ILS and is robust to low levels of introgression, but extensive introgression violates the fundamental assumption that relationships are strictly bifurcating. In this study, we explore the phylogenomics of the iconic Liolaemus subgenus of South American lizards, a group of over 100 species mostly distributed in and around the Andes mountains. Using mitochondrial DNA (mtDNA) and genome-wide restriction site-associated DNA sequencing (RADseq; nDNA hereafter), we inferred a time-calibrated mtDNA gene tree, nDNA species trees, and phylogenetic networks. We found high levels of discordance between mtDNA and nDNA, which we attribute in part to extensive ILS resulting from rapid diversification. These data also reveal extensive and deep introgression, which combined with rapid diversification, explain the high level of phylogenetic discordance. We discuss these findings in the context of Andean orogeny and glacial cycles that fragmented, expanded, and contracted species distributions. Finally, we use the new phylogeny to resolve long-standing taxonomic issues in one of the most studied lizard groups in the New World.</p>
Out of the Andes and up to the Arctic: multiple drivers promote rapid radiation in Colias butterflies
<p>The drivers of insect radiation in mountain ecosystems are poorly understood compared to birds and plants. The drivers of insect radiation in mountain ecosystems are poorly understood compared to birds and plants. We studied the rapid radiation of the butterfly genus Colias, which has diversified in mountain ecosystems in Eurasia, Africa, and the Americas. Based on a dataset of 150 nuclear protein-coding genetic loci and whole mitochondrial genomes, we constructed a time-calibrated tree of the genus Colias with broad taxon sampling. We then inferred historical characteristics of this genus, including ancestral range reconstruction, historical diversification rates, and the evolution of host plant use. We found that rapid diversification was driven by several factors including favorably warm climates in the mid-Pliocene that promoted the population expansion, and the formation of the Isthmus of Panama and the Bering Land Bridge, which led to intercontinental dispersals that opened new ecological opportunities. These two extrinsic factors may simultaneously be the main extrinsic drivers of the genus' rapid diversification. Introgression may have improved the ecological adaptability of the genus Colias, and we propose that this is the primary intrinsic driver of diversification. Expansion of host plant breadth enabling population expansion was a secondary driving factor. We suggest that mountain uplift had little effect on the diversity of Colias after the initial split from the common ancestor shared with its sister taxon Zerene and emphasize the importance of historical climatic and geological events for studies of rapid radiations of montane species.</p>
Rapid Radiation Therapy for Painful Osseous Metastatic Disease
ClinicalTrials.gov study NCT01391234. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Can RNA-Seq resolve the rapid radiation of advanced moths (Lepidoptera: Apoditrysia)? An exploratory study
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Data from: Phylogeny of Saxifragales (angiosperms, eudicots): analysis of a rapid, ancient radiation
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Data from: Evolutionary dynamism in bryophytes: phylogenomic inferences confirm rapid radiation in the moss family Funariaceae
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Rapid radiation of Southern Ocean shags in response to receding sea ice
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Out of the Andes and up to the Arctic: multiple drivers promote rapid radiation in Colias butterflies
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Accelerated brain shape evolution is associated with rapid diversification in an avian radiation
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Rapid radiation and rampant reticulation: Phylogenomics of South American Liolaemus lizards
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Data from: Enemy at the gates: rapid defensive trait diversification in an adaptive radiation of lizards
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Data from: Analysis of a rapid evolutionary radiation using ultraconserved elements (UCEs): Evidence for a bias in some multi-species coalescent methods
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Cancer treatment with radiation-chemotherapy rapidly induces molecular pathways for both resistance and new therapeutic targets
GEO Series GSE230151. Homo sapiens. 74 samples. Type: Expression profiling by array; Non-coding RNA profiling by array.
Radiation and Adebrelimab in Prostate Cancer With Imaging-measurable Disease (RAPID)
ClinicalTrials.gov study NCT06251492. IPD Sharing: NO. Countries: 1. Publications: 0.
Rapid Diagnosis of Viral Acute Respiratory Infection to Decrease Unnecessary Antibiotic Utilization in the Emergency Department (RADIATE)
ClinicalTrials.gov study NCT06271655. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Phylogenomics of a rapid radiation: the Australian rainbow skinks
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Fingerstick Blood-Test for Rapid Estimation of Absorbed Radiation Dose
GEO Series GSE116880. Homo sapiens. 27 samples. Type: Non-coding RNA profiling by array.
Rapid maize leaf and immature ear responses to UV-B radiation
GEO Series GSE30278. Zea mays. 40 samples. Type: Expression profiling by array.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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.