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197 results for “time estimation”
Data from: A jungle tale: molecular phylogeny and divergence time estimates of the Desmopsis - Stenanona clade (Annonaceae) in Mesoamerica
The predominantly Asian tribe Miliuseae (Annonaceae) includes over 37 Neotropical species that are mainly distributed across Mesoamerica, from southern Mexico to northern Colombia. The tremendous ecological and morphological diversity of this clade, including ramiflory, cauliflory, flagelliflory, and clonality, suggests adaptive radiation. Despite the spectacular phenotypic divergence of this clade, little is known about its phylogenetic and evolutionary history. In this study we used a nuclear DNA marker and seven chloroplast markers, and maximum parsimony, maximum likelihood and Bayesian inference methods to reconstruct a comprehensive time-calibrated phylogeny of tribe Miliuseae, especially focusing on the Desmopsis-Stenanona clade. We also perform ancestral area reconstructions to infer the biogeographic history of this group. Finally, we use ecological niche modeling, lineage distribution models, and niche overlap tests to assess whether geographic isolation and ecological specialization influenced the diversification of lineages within this clade. We reconstructed a monophyletic Miliuseae that is divided into two strongly supported clades: (i) a Sapranthus-Tridimeris clade and (ii) a Desmopsis-Stenanona clade. The colonization of the Neotropics and subsequent diversification of Neotropical Miliuseae seems to have been associated with the expansion of the boreotropical forests during the late Eocene and their subsequent fragmentation and southern displacement. Further speciation within Neotropical Miliuseae out of the Maya block seems to have occurred during the last 15 million years. Lastly, the geographic structuring of major lineages of the Desmopsis-Stenanona clade seems to have followed a climatic gradient, supporting the hypothesis that morphological differentiation between closely related species resulted from both long-term isolation between geographic ranges and adaptation to environmental conditions.
Data from: Model misspecification confounds the estimation of rates and exaggerates their time dependency
While welcoming the comment of Ho et al. (2015), we find little that undermines the strength of our criticism, and it would appear they have misunderstood our central argument. Here we respond with the purpose of reiterating that we are (i) generally critical of much of the evidence presented in support of the time-dependent molecular rate (TDMR) hypothesis and (ii) specifically critical of estimates of μ derived from tip-dated sequences that exaggerate the importance of purifying selection as an explanation for TDMR over extended timescales. In response to assertions put forward by Ho et al. (2015), we use panmictic coalescent simulations of temporal data to explore a fundamental assumption for tip-dated tree shape and associated mutation rate estimates, and the appropriateness and utility of the date randomization test. The results reveal problems for the joint estimation of tree topology, effective population size and μ with tip-dated sequences using beast. Given the simulations, beast consistently obtains incorrect topological tree structures that are consistent with the substantial overestimation of μ and underestimation of effective population size. Data generated from lower effective population sizes were less likely to fail the date randomization test yet still resulted in substantially upwardly biased estimates of rates, bringing previous estimates of μ from temporally sampled DNA sequences into question. We find that our general criticisms of both the hypothesis of time-dependent molecular evolution and Bayesian methods to estimate μ from temporally sampled DNA sequences are further reinforced.
Data from: Among- and within-population variation in flowering time of Iberian Arabidopsis thaliana estimated in field and glasshouse conditions
The study of the evolutionary and population genetics of quantitative traits requires the assessment of within- and among-population patterns of variation. We carried out experiments including eight Iberian Arabidopsis thaliana populations (10 individuals per population) in glasshouse and field conditions. We quantified among- and within-population variation for flowering time and for several field life-history traits. Individuals were genotyped with microsatellites, single nucleotide polymorphisms and four well-known flowering genes (FRI, FLC, CRY2 and PHYC). Phenotypic and genotypic data were used to conduct QST–FST comparisons. Life-history traits varied significantly among- and within-populations. Flowering time also showed substantial within- and among-population variation as well as significant genotype × environment interactions among the various conditions. Individuals bearing FRI truncations exhibited reduced recruitment in field conditions and differential flowering time behavior across experimental conditions, suggesting that FRI contributes to the observed significant genotype × environment interactions. Flowering time estimated in field conditions was the only trait showing significantly higher quantitative genetic differentiation than neutral genetic differentiation values. Overall, our results show that these A. thaliana populations are genetically more differentiated for flowering time than for neutral markers, suggesting that flowering time is likely to be under divergent selection.
The implications of lineage-specific rates for divergence time estimation
<p>Rate variation adds considerable complexity to divergence time estimation in molecular phylogenies. Here, we evaluate the impact of lineage-specific rates—which we define as among-branch-rate-variation that acts consistently across the entire genome. We compare its impact to residual rates—defined as among-branch-rate-variation that shows a different pattern of rate variation at each sampled locus, and gene-specific rates—defined as variation in the average rate across all branches at each sampled locus. We show that lineage-specific rates lead to erroneous divergence time estimates, regardless of how many loci are sampled. Further, we show that stronger lineage-specific rates lead to increasing error. This contrasts to residual rates and gene-specific rates, where sampling more loci significantly reduces error. If divergence times are inferred in a Bayesian framework, we highlight that error caused by lineage-specific rates significantly reduces the probability that the 95% highest posterior density includes the correct value, and leads to sensitivity to the prior. Use of a more complex rate prior—which has recently been proposed to model rate variation more accurately—does not affect these conclusions. Finally, we show that the scale of lineage-specific rates used in our simulation experiments is comparable to that of an empirical data set for the angiosperm genus Ipomoea. Taken together, our findings demonstrate that lineage-specific rates cause error in divergence time estimates, and that this error is not overcome by analyzing genomic scale multilocus data sets.</p>
Data from: Population genetic and field ecological analyses return similar estimates of dispersal over space and time in an endangered amphibian
The explosive growth of empirical population genetics has seen a proliferation of analytical methods leading to a steady increase in our ability to accurately measure key population parameters, including genetic isolation, effective population size, and gene flow in natural systems. Assuming they yield similar results, population genetic methods offer an attractive complement to, or replacement of, traditional field ecological studies. However, empirical assessments of the concordance between direct field ecological and indirect population genetic studies of the same populations are uncommon in the literature. In this study, we investigate genetic isolation, rates of dispersal, and population sizes for the endangered California tiger salamander, Ambystoma californiense, across multiple breeding seasons in an intact vernal pool network. We then compare our molecular results to a previously published study based on multi-year, mark-recapture data from the same breeding sites. We found that field and genetic estimates of population size were only weakly correlated, but dispersal rates were remarkably congruent across studies and methods. In fact, dispersal probability functions derived from genetic data and traditional field ecological data were a significant match, suggesting that either method can be used effectively to assess population connectivity. These results provide one of the first explicit tests of the correspondence between landscape genetic and field ecological approaches to measuring functional population connectivity and suggest that even single-year genetic samples can return biologically meaningful estimates of natural dispersal and gene flow.
Data from: Accounting for heterogeneity when estimating stopover duration, timing and population size of red knots along the Luannan Coast of Bohai Bay, China
1. To successfully perform their long-distance migrations, migratory birds require sites along their migratory routes to rest and refuel. Monitoring the use of so-called stopover and staging sites provides insights into (1) the timing of migration and (2) the importance of a site for migratory bird populations. A recently developed Bayesian superpopulation model that integrates mark-recapture data and ring density data enabled the estimation of stopover timing, duration and population size. Yet, this model did not account for heterogeneity in encounter (p) and staying (ϕ) probabilities. 2. Here we extended the integrated superpopulation model by implementing finite mixtures to account for heterogeneity in p and ϕ. We used simulations and real data on red knots Calidris canutus staging in Bohai Bay, China, during spring migration to (1) show the importance of accounting for heterogeneity in encounter and staying probabilities to get unbiased estimates of stopover timing, duration and numbers of migratory birds at staging sites and (2) get accurate stopover parameter estimates for a migratory bird species at a key staging site that is threatened by habitat destruction. 3. Our simulations confirmed that heterogeneity in p affected stopover parameter estimates more than heterogeneity in ϕ. Bias was particularly severe when most birds had both low ϕ and p. Bias was largest for population size, intermediate for stopover duration and negligible for stopover timing. 4. 50,000-100,000 red knots were estimated to annually stop for 5-9 days in Bohai Bay between 10 and 30 May. This shows the key importance of this staging site for this declining species. There were no clear changes in stopover parameters over time. 5. Our study shows the importance of accounting for heterogeneity in both encounter and staying probabilities for accurately estimating stopover duration and population size and provides an appropriate modelling framework.
Data from: Using survival models to estimate invertebrate prey identification times in a generalist stream fish
Estimates of predator feeding rates are important for understanding trophic dynamics. One common method for quantifying feeding rates in fishes combine mass-based diet data with gastric evacuation times to estimate prey mass consumed per predator. An alternative approach is to estimate rates of prey individuals consumed using prey identification times − the time period over which prey remain identifiable in a predator's stomach. One challenge with the analysis of prey identification times, however, is that the response variable is likely to be censored because the 'true' prey identification time cannot be observed directly. Here, we applied survival analysis that can incorporate censored data to estimate the effects of predator body size, water temperature, and prey characteristics (type, count and body size) on identification times in reticulate sculpin (Cottus perplexus). We focused on seven types of prey that are common in this generalist predator's diet: mayflies (Ephemeroptera), caddisflies (Trichoptera), stoneflies (Plecoptera), flies (Diptera), beetles (Coleoptera), worms (Annelida), and sculpin eggs. An information-theoretic model comparison approach indicated that an accelerated failure-time Weibull model with all five covariates provided the best relative fit to the full dataset. Prey type had a strong effect on prey identification times, with annelid worms having the shortest times (< 1 hr) and caddisflies having the longest times (> 15 hrs). Water temperature decreased prey identification times (7.5% per 1°C increase), whereas prey count (i.e. meal size) increased prey identification times (15.5% per additional prey item). Sculpin body size had a weak negative effect on prey identification times (0.04% per 1 mm increase). Body sizes of some taxa, including mayflies, caddisflies, and stoneflies, increased prey identification times, leading to an interaction between prey type and prey size. Our study highlights the utility of survival analysis to quantify variation in prey identification times in the diets of generalist predators.
Data from: Repeatable, continuous and real-time estimates of coupled nitrogenase activity and carbon exchange at the whole-plant scale
1. Symbiotic nitrogen fixation (SNF) by higher plants and their bacterial symbionts is a globally important input of nitrogen. Our understanding of the mechanisms that control SNF and the timescales over which they operate has been constrained by limitations of the existing methods for measuring SNF. One method, Acetylene Reduction Assays by Cavity-ring down laser Absorption Spectroscopy (ARACAS), seems promising, as it is highly sensitive and gives rapid, continuous, repeatable and real-time measurements of nitrogenase activity. ARACAS has been used to study nitrogen fixation in lichens, mosses and asymbiotic bacteria, but adapting it to higher plants poses challenges because acetylene and ethylene can influence plant function. 2. Here we report modifications to ARACAS that allow it to be used on higher plants in an environmentally-controlled incubation chamber. The modifications include lower concentrations of acetylene (2%) and ethylene and concurrent measurements of whole chamber CO2 exchange, H2O exchange and nitrogenase activity, linking nitrogenase activity to whole-plant rates of photosynthesis and respiration. 3. After propagating the error terms from all sources, we establish the following parameters of the method: (A) The detection limit of our method was 2-3 ppbv C2H4 hr-1, although it rose substantially when we used tank-derived acetylene, which has much higher ethylene contamination; (B) Repeated measures at a frequency of 3 days or longer did not diminish nitrogenase activity or photosynthesis, although daily measurements diminished nitrogenase activity; (C) This method can detect changes at timescales as short as seconds; (D) Continuous measurement of nitrogenase activity is maintained above 90% of the maximum rate for 7.0 ± 1.3 (mean ± SD) hours. 4. This method has the potential to improve our understanding of the controls over SNF and therefore how SNF and global nitrogen and carbon cycling are likely to be affected by global change.
FIGURE 1 in Molecular phylogeny and divergence time estimates of Penaeid Shrimp Lineages (Decapoda: Penaeidae)
FIGURE 1. ML phylogeny for penaeidae family, reconstructed using 16S, COI and concatenated sequences. For 16S and COI phylogenies only ML bootstrap values are shown. For the concatenated sequence tree bootstrap support values for ML, BI, and NJ are shown near interior branches. Bootstrap values lower than 50 are not shown. Species with circles, triangles and squares belong respectively to Penaeini, Trachypenaeini, and Parapenaeini clades, following Burkenroad's (1953) traditional classification. The Penaeini clade (bold branches) was used in divergence times estimates. Letters A, B and C are references for the nodes where time constrains were set.
A Machine Learning Approach for Real-time Cortical State Estimation
<p>Data and code accompanying the following publication: Weiss, D. A., Borsa, A. M., Pala, A., Sederberg, A. J., & Stanley, G. B. (2024). A machine learning approach for real-time cortical state estimation. <em>Journal of neural engineering</em>, <em>21</em>(1), 10.1088/1741-2552/ad1f7b. https://doi.org/10.1088/1741-2552/ad1f7b</p>
CoUDlabs_TA_USFD_02_ANNULAR_Regueiro. Time series analysis of sewer temperatures in an annular flume to estimate sediment accumulation
<p>This dataset contains the results of the experimental campaign and how data were collected on the the <a href="https://co-udlabs.eu/">Co-UDlabs</a> Transnational Access project: <em>Temperature time series analysis for predicting sedimentation in sewer systems</em>, by Regueiro-Picallo et al. The Transnational Access project was funded under the European Union’s Horizon 2020 research and innovation programme under grant agreement No 101008626.</p> <p>The experiments were designed to further develop an innovative methodology for measuring sediment bed deposits in UDS based on temperature data analysis (<a href="https://doi.org/10.1039/D2EW00820C" target="_blank" rel="noopener">Regueiro-Picallo et al., 2023</a>; <a href="https://doi.org/10.1039/D3EW00825H" target="_blank" rel="noopener">Regueiro-Picallo et al., 2024</a>). Particularly, the aim of these experiments was to study the influence of the sewer hydrodynamics for estimating the sediment accumulation using temperature-based methods. Therefore, the main tasks of this project were the design of a temperature-control system for the ANNULAR flume to reproduce sewer temperature patterns, and the development of an experimental campaign including different flow, sediment depth and temperature pattern conditions. The purpose of these measurements is to prove the use of simplified systems to monitor sediment accumulation in sewer systems.</p> <p>The data are described so that others can use and reproduce.</p>
Estimating the time since admixture from phased and unphased molecular data
<p>After admixture, recombination breaks down genomic blocks of contiguous ancestry. The breakdown of these blocks forms a new `molecular clock', that ticks at a much faster rate than the mutation clock, enabling accurate dating of admixture events in the recent past. However, existing theory on the break down of these blocks, or the accumulation of delineations between blocks, so called `junctions', has mostly been limited to using regularly spaced markers on phased data. Here, we present an extension to the theory of junctions using the Ancestral Recombination Graph that describes the expected number of junctions for any distribution of markers along the genome. Furthermore, we provide a new framework to infer the time since admixture using unphased data. We demonstrate both the phased and unphased methods on simulated data and show that our new extensions have improved accuracy with respect to previous methods, especially for smaller population sizes and more ancient admixture times. Lastly, we demonstrate the applicability of our method on three empirical datasets, including labcrosses of yeast (Saccharomyces cerevisae) and two case studies of hybridization in swordtail fish and Populus trees.</p>
Estimating density of mountain hares using distance sampling: a comparison of daylight visual surveys, night-time thermal imaging and camera traps
<p><a name="_Hlk58254629"></a></p> <p><a name="_Hlk58254629">Surveying cryptic, nocturnal animals is logistically challenging. Consequently, density estimates may be imprecise and uncertain. Survey innovations mitigate ecological and observational difficulties contributing to estimation variance. Thus, comparisons of survey techniques are critical to evaluate estimates of abundance. We simultaneously compared three methods for observing mountain hare (<i>Lepus timidus</i>) using Distance sampling to estimate abundance. Daylight visual surveys achieved 41 detections, estimating density at 14.3 hares km<sup>-2</sup> (95%CI 6.3–32.5) resulting in the lowest estimate and widest confidence interval. Night-time thermal imaging achieved 206 detections, estimating density at 12.1 hares km<sup>-2 </sup>(95%CI 7.6–19.4). Thermal imaging captured more observations at furthest distances, and detected larger group sizes. Camera traps achieved 3,705 night-time detections, estimating density at 22.6 hares km<sup>-2 </sup>(95%CI 17.1–29.9). Between the methods, detections were spatially correlated, although the estimates of density varied. Our results suggest that daylight visual surveys tended to underestimate density, failing to reflect nocturnal activity. Thermal imaging captured nocturnal activity, providing a higher detection rate, but required fine weather. Camera traps captured nocturnal activity, and operated 24/7 throughout harsh weather, but needed careful consideration of empirical assumptions. </a>We discuss the merits and limitations of each method with respect to the estimation of population density in the field.</p>
Supplementary material for: nQMaker: estimating time non-reversible amino acid substitution models
<p><span>Amino acid substitution models are a key component in phylogenetic analyses of protein sequences. All commonly-used amino acid models available to date are time-reversible, an assumption designed for computational convenience but not for biological reality. Another significant downside to time-reversible models is that they do not allow inference of rooted trees without outgroups. In this paper, we introduce a maximum likelihood approach nQMaker, an extension of the recently published QMaker method, that allows the estimation of time non-reversible amino acid substitution models and rooted phylogenetic trees from a set of protein sequence alignments. We show that the non-reversible models estimated with nQMaker are a much better fit to empirical alignments than pre-existing reversible models, across a wide range of datasets including mammals, birds, plants, fungi, and other taxa, and that the improvements in model fit scale with the size of the dataset. Notably, for the recently published plant and bird trees, these non-reversible models correctly recovered the commonly estimated root placements with very high statistical support without the need to use an outgroup. We provide nQMaker as an easy-to-use feature in the IQ-TREE software (<a href="http://www.iqtree.org">http://www.iqtree.org</a>), allowing users to estimate non-reversible models and rooted phylogenies from their own protein datasets.</span></p>
Supplementary materials to "Brakenhoff et al., Application of time series analysis to estimate drawdown from multiple well fields."
<p>This repository contains the supplementary material that allow to reproduce all the results from the study submitted to Frontiers journal.</p> <p> </p>
Data from: Fossils matter: improved estimates of divergence times in Pinus reveal older diversification
Background: The taxonomy of pines (genus Pinus) is widely accepted and a robust gene tree based on entire plastome sequences exists. However, there is a large discrepancy in estimated divergence times of major pine clades among existing studies, mainly due to differences in fossil placement and dating methods used. We currently lack a dated molecular phylogeny that makes use of the rich pine fossil record, and this study is the first to estimate the divergence dates of pines based on a large number of fossils (21) evenly distributed across all major clades, in combination with applying both node and tip dating methods. Results: We present a range of molecular phylogenetic trees of Pinus generated within a Bayesian framework. We find the origin of pines is likely up to 30 Myr older (Early Cretaceous) than inferred in most previous studies (Late Cretaceous) and propose generally older divergence times for major clades within Pinus than previously thought. Our age estimates vary significantly between the different dating approaches, but the results generally agree on older divergence times. We present a revised list of 21 fossils that are suitable to use in dating or comparative analyses of pines. Conclusions: Reliable estimates of divergence times in pines are essential if we are to link diversification processes and functional adaptation of this genus to geological events or to changing climates. In addition to older divergence times in Pinus, our results also indicate that node age estimates in pines depend on dating approaches and the specific fossil sets used, reflecting inherent differences in various dating approaches. The sets of dated phylogenetic trees of pines presented here provide a way to account for uncertainties in age estimations when applying comparative phylogenetic methods.
Deaf individuals use compensatory strategies to estimate visual time events
<p>Dataset related to the manuscript entitled Deaf individuals use compensatory strategies to estimate visual time events</p>
Supplemental Video 1 to Vanzella et al paper: A passive, camera-based head-tracking system for real-time, three-dimensional estimation of head position and orientation in rodents
<p>This video shows how the head tracker described in the manuscript "<strong>A passive, camera-based head-tracking system for real-time, three-dimensional estimation of head position and orientation in rodents" </strong>can track in real time the pose of the head of rat engaged in a perceptual discrimination task.</p>
Figure 6 in A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Figure 6. Chronogram of Fulgoroidea estimated using the Bayesian phylogenetic by MCMCTREE in paml. Time units are in millions of years. Estimated divergence times are shown near nodes.
Figure 5 in A phylogeny with divergence-time estimation of planthoppers (Hemiptera: Fulgoroidea) based on mitochondrial sequences
Figure 5. BI analysis (PhyloBayes) based on PCG12R–ATP8. Numerals at nodes are Bayesian posterior probabilities (PP). '–' indicates different clades.
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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)
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.