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64 results for “molecular rates”
The Data Related to Interfacial Shift Keying Allows a High Information Rate in Molecular Communication
<p>This dataset is related to a method for molecular communication in fluids described on "Fluorescent nanoparticles for reliable communication among implantable medical devices," Carbon, vol. 190, pp. 262-275, Apr. 2022, by Federico Calì, Luca Fichera, Giuseppe Trusso Sfrazzetto, Giuseppe Nicotra, Gianfranco Sfuncia, Elena Bruno, Luca Lanzanò, Ignazio Barbagallo, Giovanni Li-Destri, Nunzio Tuccitto; doi: 10.1016/J.CARBON.2022.01.016. <br> The dataset is linked to the manuscript entitled "Interfacial Shift Keying Allows a High Information Rate in Molecular Communication: Methods and Data" by F. Calì, G. Li-Destri, and N. Tuccitto submitted to IEEE Transactions on Molecular, Biological, and Multi-Scale Communications (T-MBMC).<br> The data, including elapsed time (s), starting from the injection and fluorescence intensity (a.u.), is given in tab-separated values format as .txt files. When present, a column includes the intensity subtracted for the baseline and the subtracted and normalized intensity. In all cases, the baseline was obtained by performing a linear fit between 10 and 110 s and subtracting the line obtained from the entire dataset.<br> </p>
Data for: Faster rates of molecular sequence evolution in reproduction-related genes and in species with hypodermic sperm morphologies
<p>This repository contains a record of analysis scripts and sequence alignments used for the analyses presented in the manuscript.</p> <p>Some of the R scripts depend on supplementary tables associated with the manuscript.</p>
Ultraconserved elements resolve the phylogeny and corroborate patterns of molecular rate variation in herons (Aves: Ardeidae)
<p>Thoroughly sampled and well-supported phylogenetic trees are essential to taxonomy and to guide studies of evolution and ecology. Despite extensive prior inquiry, a comprehensive tree of heron relationships (Aves: Ardeidae) has not yet been published. As a result, the classification of this family remains unstable, and their evolutionary history remains poorly studied. Here, we sample genome-wide ultraconserved elements (UCEs) and mitochondrial DNA sequences (mtDNA) of >90% of extant species to estimate heron phylogeny using a combination of maximum likelihood (ML), coalescent, and Bayesian inference (BI) methods. The UCE and mtDNA trees are mostly concordant with one another, providing a topology that resolves relationships among the five heron subfamilies and indicates that the genera <em>Gorsachius</em>, <em>Botaurus</em>, <em>Ardea</em>, and <em>Ixobrychus</em> are not monophyletic. We also present the first genetic data from the Forest Bittern <em>Zonerodius</em> <em>heliosylus</em>, an enigmatic species of New Guinea; our results suggest that it is a member of the genus <em>Ardeola</em> and not the Tigrisomatinae (tiger herons), as previously thought. Lastly, we compare molecular rates between heron clades in the UCE tree with those in previously constructed mtDNA and DNA-DNA hybridization trees. We show that rate variation in the UCE tree corroborates rate patterns in the previously constructed trees, i.e., that bitterns (<em>Ixobrychus</em> and <em>Botaurus</em>) evolved comparatively faster, and some tiger herons (<em>Tigrisoma</em>) and the Boat-billed Heron (<em>Cochlearius</em>) more slowly, than other heron taxa. </p>
Ultraconserved elements resolve the phylogeny and corroborate patterns of molecular rate variation in herons (Aves: Ardeidae)
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Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates
<p>As species richness varies along the tree of life, there is a great interest in identifying factors that affect the rates by which lineages speciate or go extinct. To this end, theoretical biologists have developed a suit of phylogenetic comparative methods that aim to identify where shifts in diversification rates had occurred along a phylogeny and whether they are associated with some traits. Using these methods, numerous studies have predicted that speciation and extinction rates vary across the tree of life. In this study we show that asymmetric rates of sequence evolution rates lead to systematic biases in the inferred phylogeny, which in turn lead to erroneous inferences regarding lineage diversification patterns. The results demonstrate that as the asymmetry in sequence evolution rates increases, so does the tendency to select more complicated models that include the possibility of diversification rate shifts. These results thus suggest that any inference regarding shifts in diversification pattern should be treated with great caution, at least until any biases regarding the molecular substitution rate have been ruled out.</p>
Rate-enhancing PETase mutations determined through DFT/MM molecular dynamics simulations†
<p>Raw data for classical MD simulations ran with Gromacs 2018.3 for the two mutants Asp83Asn and Asp89Asn.</p><p>Raw data for quantum mechanics/molecular mechanics simulations ran with CP2K 6.1 for the two mutants Asp83Asn and Asp89Asn.</p><p>Distance and free energy analysis from the QM/MM MD simulations for the wild-type and the two mutants Asp83Asn and Asp89Asn.</p>
Approaches for handling missing values and their impacts on biological inferences: a molecular rate case study
<p>GenBank accession numbers for nuclear sequence records used to build phylogenetic tree in manuscript entitled "Approaches for handling missing values and their impacts on biological inferences: a molecular rate case study". Nuclear sequences and GenBank accession numbers originally from multigene alignment and supplementary material published in Rabosky et al. (2018; 2019).</p> <p>Rabosky, D.L., Chang, J., Title, P.O. <em>et al.</em> An inverse latitudinal gradient in speciation rate for marine fishes. <em>Nature</em> <strong>559</strong>, 392–395 (2018). https://doi.org/10.1038/s41586-018-0273-1</p> <p>Rabosky, Daniel L. et al. (2019), Data from: An inverse latitudinal gradient in speciation rate for marine fishes, Dryad, Dataset, <a href="https://doi.org/10.5061/dryad.fc71cp4">https://doi.org/10.5061/dryad.fc71cp4</a> </p>
Data for: Approaches for handling missing values and their impacts on biological inferences: a molecular rate case study
<p>These data files are associated with the manuscript entitled: "Approaches for handling missing values and their impacts on biological inferences: a molecular rate case study" by Jacqueline A. May, Zeny Feng, and Sarah J. Adamowicz. This project entailed an evaluation of missing data handling approach on inferences using a molecular evolution case study. A target mixed-type dataset was first imputed using a real data-driven strategy for imputation method selection. Both trait-only (non-phylogenetic) and phylogenetic imputation methods were used to impute the dataset. Phylogenetic generalized least squares (PGLS) analyses were then applied to the complete-case and imputed datasets, specifying the traits as predictors and molecular evolutionary rates as the response variable. Those traits that associate significantly with molecular rates were identified and PGLS models compared to determine how the approach for handling missing data impacts biological inferences and conclusions.</p> <p>The files stored here are the trees built for phylogenetic imputation (RAxML tree and ultrametric tree versions) and the corresponding GenBank accession numbers.</p>
Data for dating in the dark: Elevated substitution rates in cave cockroaches (Blattodea: Nocticolidae) have negative impacts on molecular date estimates
<p>Rates of nucleotide substitution vary substantially across the Tree of Life, with potentially confounding effects on phylogenetic and evolutionary analyses. A large acceleration in mitochondrial substitution rate occurs in the cockroach family Nocticolidae, which predominantly inhabit subterranean environments. To evaluate the impacts of this among-lineage rate heterogeneity on estimates of phylogenetic relationships and evolutionary timescales, we analysed nuclear ultraconserved elements (UCEs) and mitochondrial genomes from nocticolids and other cockroaches. Substitution rates were substantially elevated in nocticolid lineages compared with other cockroaches, especially in mitochondrial protein-coding genes. This disparity in evolutionary rates is likely to have led to different evolutionary relationships being supported by mitochondrial genomes and UCE loci. Furthermore, analyses using relaxed-clock models inferred much deeper divergence times compared with a flexible local clock. Our phylogenetic analysis of UCEs, which is the first genome-scale study to include all nine major cockroach families, unites Corydiidae and Nocticolidae and places Anaplectidae as the sister lineage to the rest of Blattoidea. We uncover an extraordinary level of genetic divergence in Nocticolidae, including two highly distinct clades that separated ~115 million years ago despite both containing representatives of the genus <em>Nocticola</em>. The results of our study highlight the potential impacts of high among-lineage rate variation on estimates of phylogenetic relationships and evolutionary timescales.</p>
Data from: Evaluating the accuracy of methods for detecting correlated rates of molecular and morphological evolution
<p class="MsoNormal"><span>Determining the link between genomic and phenotypic change is a </span><span>fundamental goal in evolutionary biology. Insights into this link can be gained by using a phylogenetic approach to test for correlations between rates of molecular and morphological evolution. However, there has been persistent uncertainty about the relationship between these rates, partly because conflicting results have been obtained using various methods that have not been examined in detail. We carried out a simulation study to evaluate the performance of five statistical methods for detecting correlated rates of evolution. Our simulations explored the evolution of molecular sequences and morphological characters under a range of conditions. Of the methods tested, Bayesian relaxed-clock estimation of branch rates was able to detect correlated rates of evolution correctly in the largest number of cases. This was followed by correlations of root-to-tip distances, Bayesian model selection, independent sister-pairs contrasts, and likelihood-based model selection. As expected, the power to detect correlated rates increased with the amount of data, both in terms of tree size and number of morphological characters. Likewise, greater among-lineage rate variation in the data led to improved performance of all five methods, particularly for Bayesian relaxed-clock analysis when the rate model was mismatched. We then applied these methods to a data set from flowering plants and did not find evidence of a correlation in evolutionary rates between genomic data and morphological characters. The results of our study have practical implications for phylogenetic analyses of combined molecular and morphological data sets, and highlight the conditions under which the links between genomic and phenotypic rates of evolution can be evaluated quantitatively.</span></p>
Data from: All-atom molecular dynamics simulation and rate calculation for norepinephrine binding beta adrenergic receptor
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Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates
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Data from: Evaluating the accuracy of methods for detecting correlated rates of molecular and morphological evolution
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Data for dating in the dark: Elevated substitution rates in cave cockroaches (Blattodea: Nocticolidae) have negative impacts on molecular date estimates
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Data from: Estimating the molecular evolutionary rates of mitochondrial genes referring to Quaternary Ice Age events with inferred population expansions and dispersals in Japanese Apodemus
Background: Determining reliable evolutionary rates of molecular markers is essential in illustrating historical episodes with phylogenetic inferences. Although emerging evidence has suggested a high evolutionary rate for intraspecific genetic variation, it is unclear how long such high evolutionary rates persist because a recent calibration point is rarely available. Other than using fossil evidence, it is possible to estimate evolutionary rates by relying on the well-established temporal framework of the Quaternary glacial cycles that would likely have promoted both rapid expansion events and interisland dispersal events. Results: We examined mitochondrial cytochrome b (Cytb) and control region (CR) gene sequences in two Japanese wood mouse species, Apodemus argenteus and A. speciosus, of temperate origin and found signs of rapid expansion in the population from Hokkaido, the northern island of Japan. Assuming that global warming after the last glacial period 7–10 thousand years before present (kyr BP) was associated with the expansion, the evolutionary rates (sites per million years, myr) of Cytb and CR were estimated as 11–16% and 22–32%, respectively, for A. argenteus, and 12–17% and 17–24%, respectively, for A. speciosus. Additionally, the significant signature of rapid expansion detected in the mtDNA sequences of A. speciosus from the remaining southern main islands, Honshu, Shikoku, and Kyushu, provided an estimated Cytb evolutionary rate of 3.1%/site/myr under the assumption of a postglacial population expansion event long ago, most probably at 130 kyr BP. Bayesian analyses using the higher evolutionary rate of 11–17%/site/myr for Cytb supported the recent demographic or divergence events associated with the Last Glacial Maximum. However, the slower evolutionary rate of 3.1%/site/myr would be reasonable for several divergence events that were associated with glacial periods older than 130 kyr BP. Conclusions: The faster and slower evolutionary rates of Cytb can account for divergences associated with the last and earlier glacial maxima, respectively, in the phylogenetic inference of murine rodents. The elevated evolutionary rate seemed to decline within 100,000 years.
Data from: Inflation of molecular clock rates and dates: molecular phylogenetics, biogeography, and diversification of a global cicada radiation from Australasia (Hemiptera: Cicadidae: Cicadettini)
Dated phylogenetic trees are important for studying mechanisms of diversification, and molecular clocks are important tools for studies of organisms lacking good fossil records. However, studies have begun to identify problems in molecular clock dates caused by uncertainty of the modeled molecular substitution process. Here we explore Bayesian relaxed-clock molecular dating while studying the biogeography of ca. 200 species from the global cicada tribe Cicadettini. Because the available fossils are few and uninformative, we calibrate our trees in part with a cytochrome oxidase I (COI) clock prior encompassing a range of literature estimates for arthropods. We show that tribe-level analyses calibrated solely with the COI clock recover extremely old dates that conflict with published estimates for two well-studied New Zealand subclades within Cicadettini. Additional subclade analyses suggest that COI relaxed-clock rates and maximum-likelihood branch lengths become inflated relative to EF-1α intron and exon rates and branch lengths as clade age increases. We present corrected estimates derived from (1) an extrapolated EF-1α exon clock derived from COI-calibrated analysis within the largest New Zealand subclade, (2) post-hoc scaling of the tribe-level chronogram using results from subclade analyses, and (3) exploitation of a geological calibration point associated with New Caledonia. We caution that considerable uncertainty is generated due to dependence of substitution estimates on both the taxon sample and the choice of model, including gamma category number and the choice of empirical versus estimated base frequencies. Our results suggest that diversification of the tribe Cicadettini commenced in the early- to mid-Cenozoic and continued with the development of open, arid habitats in Australia and worldwide. We find that Cicadettini is a rare example of a global terrestrial animal group with an Australasian origin, with all non-Australasian genera belonging to two distal clades. Within Australia, we show that Cicadettini is more widely distributed than any other cicada tribe, diverse in temperate, arid and monsoonal habitats, and nearly absent from rainforests. We comment on the taxonomic implications of our findings for thirteen cicada genera.
Data from: A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves)
The phylogeny of Galliformes (landfowl) has been studied extensively; however, the associated chronologies have been criticized recently due to misplaced or misidentified fossil calibrations. As a consequence, it is unclear whether any crown-group lineages arose in the Cretaceous and survived the Cretaceous–Paleogene (K–Pg; 65.5 Ma) mass extinction. Using Bayesian phylogenetic inference on an alignment spanning 14,539 bp of mitochondrial and nuclear DNA sequence data, four fossil calibrations, and a combination of uncorrelated lognormally distributed relaxed-clock and strict-clock models, we inferred a time-calibrated molecular phylogeny for 225 of the 291 extant Galliform taxa. These analyses suggest that crown Galliformes diversified in the Cretaceous and that three-stem lineages survived the K–Pg mass extinction. Ideally, characterizing the tempo and mode of diversification involves a taxonomically complete phylogenetic hypothesis. We used simple constraint structures to incorporate 66 data-deficient taxa and inferred the first taxon-complete phylogenetic hypothesis for the Galliformes. Diversification analyses conducted on 10,000 timetrees sampled from the posterior distribution of candidate trees show that the evolutionary history of the Galliformes is best explained by a rate-shift model including 1–3 clade-specific increases in diversification rate. We further show that the tempo and mode of diversification in the Galliformes conforms to a three-pulse model, with three-stem lineages arising in the Cretaceous and inter and intrafamilial diversification occurring after the K–Pg mass extinction, in the Paleocene–Eocene (65.5–33.9 Ma) or in association with the Eocene–Oligocene transition (33.9 Ma).
Data from: Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles
Comparative analysis is a potentially powerful approach to study the effects of ecological traits on genetic variation and rate of evolution across species. However, the lack of suitable datasets means that comparative studies of correlates of genetic traits across an entire clade have been rare. Here, we use a large DNA-barcode dataset (5062 sequences) of water beetles to test the effects of species ecology and geographical distribution on genetic variation within species and rates of molecular evolution across species. We investigated species traits predicted to influence their genetic characteristics, such as surrogate measures of species population size, latitudinal distribution and habitat types, taking phylogeny into account. Genetic variation of cytochrome oxidase I in water beetles was positively correlated with occupancy (numbers of sites of species presence) and negatively with latitude, whereas substitution rates across species depended mainly on habitat types, and running water specialists had the highest rate. These results are consistent with theoretical predictions from nearly-neutral theories of evolution, and suggest that the comparative analysis using large databases can give insights into correlates of genetic variation and molecular evolution.
Temperature predicts the rate of molecular evolution in Australian Eugongylinae skinks
<p>Temperature differences over time and space has been hypothesized to cause variation in the rate of molecular evolution of species, but empirical evidence is mixed. To further test this hypothesis, we utilized a large exon-capture sequence data of Australian Eugongylinae skinks, exemplifying a radiation of temperature-sensitive ectotherms spanning a large latitudinal gradient. The association between temperature (and other species traits) and long-term substitution rate was assessed based on 1268 sequenced exons of 44 species pairs from the Eugongylinae subfamily using regression analyses. Temperature is the strongest, positively-correlated predictor of variation in substitution rate across the Australian Eugongylinae. It explains 45% of variation in synonymous substitution rate, and 11% after controlling for all the other factors. Synonymous substitution rate is also negatively associated with body size, with 6% variation explained by body size after controlling for the effects of temperature. Other factors are not associated with synonymous substitution rate after controlling for temperature. Overall, this study points to temperature as a strong predictor of the molecular evolution rate in the Eugongylinae subfamily, and demonstrates the power of large-scale exonic data to identify correlates of the rate of molecular evolution.</p>
Low-dose Molecular Breast Imaging: Comparison of Breast Cancer Detection Rate at Initial Screening and Two-year Follow-up
ClinicalTrials.gov study NCT01723124. IPD Sharing: NO. Countries: 1. Publications: 1.
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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.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.