Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
64
datasets available to search
ShareScore release 0.9.0
Dataset results
64 results for “molecular rates”
Effect of LOW-molecular-weight Heparin in Reducing Radial Artery Occlusion Rate After Transradial Coronary Catheterization
ClinicalTrials.gov study NCT04196309. IPD Sharing: NO. Countries: 1. Publications: 1.
Temperature predicts the rate of molecular evolution in Australian Eugongylinae skinks
Open the record for dataset details and reuse information.
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
Open the record for dataset details and reuse information.
Data from: Inflation of molecular clock rates and dates: molecular phylogenetics, biogeography, and diversification of a global cicada radiation from Australasia (Hemiptera: Cicadidae: Cicadettini)
Open the record for dataset details and reuse information.
Data from: Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles
Open the record for dataset details and reuse information.
Data from: A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves)
Open the record for dataset details and reuse information.
Data from: A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary
The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting the impact of mass-extinction events on molecular phylogenies, even in the presence of tree-wide diversification-rate variation and in the absence of additional information from the fossil record. Our approach is based on an episodic stochastic-branching process model in which rates of speciation and extinction are constant between events. We model three types of events: (i) instantaneous tree-wide shifts in speciation rate; (ii) instantaneous tree-wide shifts in extinction rate and (iii) instantaneous tree-wide mass-extinction events. Each type of event is modelled as an independent compound Poisson process (CPP), where the waiting times between events are exponentially distributed with event-specific rate parameters. The magnitude of each event is drawn from an event-specific prior distribution. Parameters of the model are then estimated in a Bayesian statistical framework using a reversible-jump Markov chain Monte Carlo algorithm. This Bayesian approach enables us to distinguish between tree-wide diversification-rate variation and mass-extinction events by specifying a biologically informed prior on the magnitude of mass-extinction events and empirical hyperpriors on the diversification-rate parameters. We demonstrate via simulation that this method has substantial power to detect the number of mass-extinction events and provides unbiased estimates of the timing of mass-extinction events, while exhibiting an appropriate (i.e. <5%) false-discovery rate, even when background diversification rates vary. Finally, we provide an empirical demonstration of this approach, which reveals that conifers experienced a major episode of mass extinction ≈23 Ma. This new approach – the CPP on Mass-Extinction Times (CoMET) model – provides an effective tool for detecting the impact of mass-extinction events on molecular phylogenies, even when the history of those groups includes temporal variation in diversification rates and when the fossil history of those groups is poorly known.
Data from: Accelerated rate of molecular evolution for vittarioid ferns is strong and not due to selection
Molecular evolutionary rate heterogeneity—the violation of a molecular clock—is a prominent feature of many phylogenetic datasets. It has particular importance to systematists not only because of its biological implications, but also for its practical effects on our ability to infer and date evolutionary events. Here we show, using both maximum likelihood and Bayesian approaches, that a remarkably strong increase in substitution rate in the vittarioid ferns is consistent across the nuclear and plastid genomes. Contrary to some expectations, this rate increase is not due to selective forces; the vittarioids bear no signature of the change in the relative strengths of selection and drift that one would expect if the rate increase was caused by altered fixation rates. Instead, the substitution rate increase appears to stem from an elevated supply of mutations, perhaps limited to the vittarioid ancestral branch. This generalized rate increase is accompanied by extensive fine-scale heterogeneity in rates across loci, genomes, and taxa. Our analyses demonstrate the power and flexibility of trait-free investigations of rate heterogeneity within a model selection framework, emphasize the importance of explicit tests for signatures of selection prior to invoking selection-related or demography-based explanations for patterns of rate variation, and illustrate some unexpected nuances in the behavior of relaxed clock methods for modeling rate heterogeneity, with implications for our ability to confidently date divergence events. In addition, our data provide strong support for the monophylly of Adiantum, and for the position of Calciphilopteris in the cheilanthoid ferns, two relationships for which convincing support was previously lacking.
Data from: Molecular dating, evolutionary rates, and the age of the grasses
Many questions in evolutionary biology require an estimate of divergence times but, for groups with a sparse fossil record, such estimates rely heavily on molecular dating methods. The accuracy of these methods depends on both an adequate underlying model and the appropriate implementation of fossil evidence as calibration points. We explore the effect of these in Poaceae (grasses), a diverse plant lineage with a very limited fossil record, focusing particularly on dating the early divergences in the group. We show that molecular dating based on a dataset of plastid markers is strongly dependent on the model assumptions. In particular, an acceleration of evolutionary rates at the base of Poaceae followed by a deceleration in the descendants strongly biases methods that assume an autocorrelation of rates. This problem can be circumvented by using markers that have lower rate variation, and we show that phylogenetic markers extracted from complete nuclear genomes can be a useful complement to the more commonly used plastid markers. However, estimates of divergence times remain strongly affected by different implementations of fossil calibration points. Analyses calibrated with only macrofossils lead to estimates for the age of core Poaceae around 51-55 Ma, but the inclusion of microfossil evidence pushes this age to 74-82 Ma and leads to lower estimated evolutionary rates in grasses. These results emphasize the importance of considering markers from multiple genomes and alternative fossil placements when addressing evolutionary issues that depend on ages estimated for important groups.
Data from: Do saline taxa evolve faster? comparing relative rates of molecular evolution between freshwater and marine eukaryotes
The major branches of life diversified in the marine realm, and numerous taxa have since transitioned between marine and freshwaters. Previous studies have demonstrated higher rates of molecular evolution in crustaceans inhabiting continental saline habitats as compared with freshwaters, but it is unclear whether this trend is pervasive or whether it applies to the marine environment. We employ the phylogenetic comparative method to investigate relative molecular evolutionary rates between 148 pairs of marine or continental saline vs. freshwater lineages representing disparate eukaryote groups, including bony fish, elasmobranchs, cetaceans, crustaceans, mollusks, annelids, algae, and other eukaryotes, using available protein-coding and non-coding genes. Overall, we observed no consistent pattern in nucleotide substitution rates linked to habitat across all genes and taxa. However, we observed some trends of higher evolutionary rates within protein-coding genes in freshwater taxa—the comparisons mainly involving bony fish—compared with their marine relatives. The results suggest no systematic differences in substitution rate between marine and freshwater organisms.
Data from: Body mass-corrected molecular rate for bird mitochondrial DNA
Mitochondrial DNA remains one of the most widely used molecular markers to reconstruct the phylogeny and phylogeography of closely related birds. It has been proposed that bird mitochondrial genomes evolve at a constant rate of ~0.01 substitution per site per million years, that is that they evolve according to a strict molecular clock. This molecular clock is often used in studies of bird mitochondrial phylogeny and molecular dating. However, rates of mitochondrial genome evolution vary among bird species and correlate with life history traits such as body mass and generation time. These correlations could cause systematic biases in molecular dating studies that assume a strict molecular clock. In this study, we overcome this issue by estimating corrected molecular rates for birds. Using complete or nearly complete mitochondrial genomes of 475 species, we show that there are strong relationships between body mass and substitution rates across birds. We use this information to build models that use bird species' body mass to estimate their substitution rates across a wide range of common mitochondrial markers. We demonstrate the use of these corrected molecular rates on two recently published data sets. In one case, we obtained molecular dates that are twice as old as the estimates obtained using the strict molecular clock. We hope that this method to estimate molecular rates will increase the accuracy of future molecular dating studies in birds.
Data from: The local-clock permutation test: a simple test to compare rates of molecular evolution on phylogenetic trees
Rates of molecular evolution vary substantially between lineages, and a growing research effort is directed at uncovering the causes and consequences of this variation. Comparing local-clocks (rates of molecular evolution estimated from sets of branches of a phylogenetic tree) is a common tool in this research effort. Here, I show that a commonly used test (the Likelihood Ratio Test, LRT) will not be statistically valid for comparing local-clocks in most cases. Instead, I propose the local-clock permutation test (LCPT), a simple test which can be used to test the significance of differences between local-clocks. The LCPT could also be used to test for differences between any parameter that can be assigned to individual branches on a phylogenetic tree. Using simulated data, I show that the LCPT has good power to detect differences between local-clocks.
Supplementary material 1 from: Konvičková H, John V, Konvička M, Rindoš M, Hrček J (2024) High hymenopteran parasitoid infestation rates in Czech populations of the Euphydryas aurinia butterfly inferred using a new molecular marker. Journal of Hymenoptera Research 97: 29-42. https://doi.org/10.3897/jhr.97.113231
List of sampled colonies of E. aurinia
Figure 1 from: Konvičková H, John V, Konvička M, Rindoš M, Hrček J (2024) High hymenopteran parasitoid infestation rates in Czech populations of the Euphydryas aurinia butterfly inferred using a new molecular marker. Journal of Hymenoptera Research 97: 29-42. https://doi.org/10.3897/jhr.97.113231
Figure 1 The distribution of Euphydryas aurinia in the Czech Republic, historic records included, based on Beneš et al. (2002), with actualisations. The inset in upper right corner shows the position of the country in Europe.
Figure 3 from: Konvičková H, John V, Konvička M, Rindoš M, Hrček J (2024) High hymenopteran parasitoid infestation rates in Czech populations of the Euphydryas aurinia butterfly inferred using a new molecular marker. Journal of Hymenoptera Research 97: 29-42. https://doi.org/10.3897/jhr.97.113231
Figure 3 Per-site hymenopteran parasitoids infestation rates in colonies of the butterfly Euphydryas aurinia in two consecutive years (2019–20), with information of caterpillar web counts in the respective colonies in 2018–2021 (above), and illustration of the relationship between hymenopteran parasitoids infestation rates and E. aurinia caterpillar web counts in the previous year (below).
Figure 2 from: Konvičková H, John V, Konvička M, Rindoš M, Hrček J (2024) High hymenopteran parasitoid infestation rates in Czech populations of the Euphydryas aurinia butterfly inferred using a new molecular marker. Journal of Hymenoptera Research 97: 29-42. https://doi.org/10.3897/jhr.97.113231
Figure 2 Electrophoresis gels used to assess whether the primers used can discriminate lepidopteran hosts and hymenopteran parasitoids a various adult hymenopteran parasitoids (PCRs are positive) and positive (P) and negative (N) samples of E. auriniab four species of adult butterflies; PCRs are negative. The adult specimens of Hymenoptera and Lepidoptera were identified by M. Rindoš, M. Konvička, and Z. Faltýnek Fric.
Data from: Body mass-corrected molecular rate for bird mitochondrial DNA
Open the record for dataset details and reuse information.
Data from: The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms
Open the record for dataset details and reuse information.
Data from: Heterogeneous rates of molecular evolution and diversification could explain the Triassic age estimate for angiosperms
Open the record for dataset details and reuse information.
Data from: The local-clock permutation test: a simple test to compare rates of molecular evolution on phylogenetic trees
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.