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28 results for “Variational methods”
Graph construction method impacts variation representation and analyses in a bovine super-pangenome
<p>Pangenomes for minigraph, pggb, and cactus containing assemblies from</p> <ul> <li>Hereford (cattle reference genome)</li> <li>Highland</li> <li>Brown Swiss</li> <li>Angus</li> <li>Simmental</li> <li>Original Braunvieh</li> <li>Piedmontese</li> <li>Nellore</li> <li>Brahman</li> <li>Yak</li> <li>Bison</li> <li>Gaur</li> </ul> <p> </p> <p>Also contains the genomic region classifications for the ARS-UCD1.2 reference genome for</p> <ul> <li>Satellites</li> <li>Tandem repeats</li> <li>Low mappability</li> <li>Repetitive regions</li> <li>Normal (everything else)</li> </ul>
Data from: Apparent annual survival estimates of tropical songbirds better reflect life history variation when based on intensive field methods
Aim: Adult survival is central to theories explaining latitudinal gradients in life history strategies. Life history theory predicts higher adult survival in tropical than north temperate regions given lower fecundity and parental effort. Early studies were consistent with this prediction, but standard-effort netting studies in recent decades suggested that apparent survival rates in temperate and tropical regions strongly overlap. Such results do not fit with life history theory. Targeted marking and resighting of breeding adults yielded higher survival estimates in the tropics, but this approach is thought to overestimate survival because it does not sample social and age classes with lower survival. We compared the effect of field methods on tropical survival estimates and their relationships with life history traits. Location: Sabah, Malaysian Borneo. Time period: 2008–2016. Major taxon: Passeriformes. Methods: We used standard-effort netting and resighted individuals of all social and age classes of 18 tropical songbird species over 8 years. We compared apparent survival estimates between these two field methods with differing analytical approaches. Results: Estimated detection and apparent survival probabilities from standard-effort netting were similar to those from other tropical studies that used standard-effort netting. Resighting data verified that a high proportion of individuals that were never recaptured in standard-effort netting remained in the study area, and many were observed breeding. Across all analytical approaches, addition of resighting yielded substantially higher survival estimates than did standard-effort netting alone. These apparent survival estimates were higher than for temperate zone species, consistent with latitudinal differences in life histories. Moreover, apparent survival estimates from addition of resighting, but not from standard-effort netting alone, were correlated with parental effort as measured by egg temperature across species. Main conclusions: Inclusion of resighting showed that standard-effort netting alone can negatively bias apparent survival estimates and obscure life history relationships across latitudes and among tropical species.
Performance comparison of optimization methods on variational quantum algorithms
<p>This repository contains the code, data and notebooks to reproduce the plots from the manuscript "Performance comparison of optimization methods on variational quantum algorithms"</p>
Light and malaise traps tell different stories about the spatial variations in arthropod biomass and method-specific insect abundance
<p><span>1. Conclusions reached in meta-analyses of changes in insect communities may be influenced by method-specific sampling biases, which may lead to inappropriate conservation measures.</span></p> <p><span>2. </span><span>We argue that the contradictory conclusions regarding terrestrial insect biomass, abundance and richness patterns are, at least partly, due to methodological limitations that reflect taxon-specific responses to environmental changes.</span></p> <p><span>3. </span><span>In this study, light and Malaise traps were simultaneously deployed to sample insects at 52 plots in a temperate forest in Germany along gradients of elevation (> 1000 m) and canopy openness (3 - 100 %). These gradients were used as predictors in models of total arthropod biomass according to the two trapping methods, and in models of abundance and richness of three commonly targeted groups: nocturnal moths, sampled using light traps, and hoverflies and bees, collected with Malaise traps.</span></p> <p><span>4. </span><span>A comparison of the total arthropod biomass obtained with the two methods revealed contrary results along the canopy openness gradient. Biomass in light traps showed a decreasing trend with increasing canopy openness while biomass in Malaise traps increased. The same opposing pattern was found for the abundance of selected taxa.</span></p> <p><span>5. </span><span>The different patterns describing spatial variation of arthropod communities obtained using light and Malaise traps can be explained by differences in the taxa predominantly collected. Regarding the ongoing debate on insect decline, our results demonstrate that comparing different taxa from different taxon-specific traps is inappropriate. Thus, we recommend that future meta-analyses take into account the sampling methods and taxon-specific responses to environmental changes.</span></p>
Light and malaise traps tell different stories about the spatial variations in arthropod biomass and method-specific insect abundance
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Data from: Apparent annual survival estimates of tropical songbirds better reflect life history variation when based on intensive field methods
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Using spatial capture-recapture methods to estimate long-term spatiotemporal variation of a wide-ranging marine species
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Data from: Partitioning of genetic variation across the genome using multimarker methods in a wild bird population
The underlying basis of genetic variation in quantitative traits, in terms of the number of causal variants and the size of their effects, is largely unknown in natural populations. The expectation is that complex quantitative trait variation is attributable to many, possibly interacting, causal variants, whose effects may depend upon the sex, age and the environment in which they are expressed. A recently developed methodology in animal breeding derives a value of relatedness among individuals from high-density genomic marker data, to estimate additive genetic variance within livestock populations. Here, we adapt and test the effectiveness of these methods to partition genetic variation for complex traits across genomic regions within ecological study populations where individuals have varying degrees of relatedness. We then apply this approach for the first time to a natural population and demonstrate that genetic variation in wing length in the great tit (Parus major) reflects contributions from multiple genomic regions. We show that a polygenic additive mode of gene action best describes the patterns observed, and we find no evidence of dosage compensation for the sex chromosome. Our results suggest that most of the genomic regions that influence wing length have the same effects in both sexes. We found a limited amount of genetic variance in males that is attributed to regions that have no effects in females, which could facilitate the sexual dimorphism observed for this trait. Although this exploratory work focuses on one complex trait, the methodology is generally applicable to any trait for any laboratory or wild population, paving the way for investigating sex-, age- and environment-specific genetic effects and thus the underlying genetic architecture of phenotype in biological study systems.
Data from: A new method for testing evolutionary rate variation and shifts in phenotypic evolution
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Data from: Partitioning of genetic variation across the genome using multimarker methods in a wild bird population
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Evaluation datasets and pre-computed scores for: "CAPICE: a computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations"
<p>CAPICE is a computational method for predicting the pathogenicity of SNVs and InDels.</p> <p>This new repository added index for CAPICE v1.0 (build37) precomputed files.</p> <p><strong>Repository description:</strong></p> <p>1) "paper_datasets.tar.gz" contains all datasets used in the CAPICE paper;</p> <p>2) "capice_v1.0_build37_indels.tsv.gz" contains the precomputed scores for InDels in genome build 37</p> <p>3) "capice_v1.0_build37_indels.tsv.gz.tbi" contains the index for file"capice_v1.0_build37_indels.tsv.gz"</p> <p>4) "capice_v1.0_build37_snvs.tsv.gz" contains the precomputed scores for all possible SNVs in genome build 37</p> <p>5) "capice_v1.0_build37_snvs.tsv.gz.tbi" contains the index for file "capice_v1.0_build37_snvs.tsv.gz"</p> <p> </p>
Data from: A parametric method for assessing diversification rate variation in phylogenetic trees
Phylogenetic hypotheses are frequently used to examine variation in rates of diversification across the history of a group. Patterns of diversification-rate variation can be used to infer underlying ecological and evolutionary processes responsible for patterns of cladogenesis. Most existing methods examine rate variation through time. Methods for examining differences in diversification among groups are more limited. Here we present a new method, parametric rate comparison (PRC), that explicitly compares diversification rates among lineages in a tree using a variety of standard statistical distributions. PRC can identify subclades of the tree where diversification-rates are at variance with the remainder of the tree. A randomization test can be used to evaluate how often such variance would appear by chance alone. The method also allows for comparison of diversification-rate among a priori defined groups. Further, the application of the PRC method is not restricted to monophyletic groups. We examined the performance of PRC using simulated data which showed that PRC has acceptable false positive rates and statistical power to detect rate variation. We apply the PRC method to the well-studied radiation of North American Plethodon salamanders, and support the inference that the large-bodied P. glutinosus clade has a higher historical rate of diversification compared to other Plethodon salamanders.
Data from: How to measure maturation: a comparison of probabilistic methods used to test for genotypic variation and plasticity in the decision to mature
Maturation is a developmental trait that plays a key role in shaping organisms' life-history. However, progress in understanding how maturation phenotypes evolve has been held back by confusion over how best to model maturation decisions and a lack of studies comparing genotypic variation in maturation. Here, we fitted probabilistic maturation reaction norms (PMRNs) to data collected from five clones of Daphnia magna and five of Daphnia pulex collected from within and between different populations. We directly compared the utility of modeling approaches that assume maturation to be a process with an instantaneous rate with those that do not by fitting maturation rate and logistic regression models, and emphasize similarities and differences between them. Our results demonstrate that in Daphnia, PMRNs using a logistic regression approach were simpler to use and provided a better fit to the data. The decision to mature was plastic across a range of growth trajectories and dependent upon both body size and age. However, the age effect was stronger in D. magna than D. pulex and varied considerably between clones. Our results support the idea that maturation thresholds can evolve but also suggest that the notion of a threshold based on a single fixed state is an oversimplification that underestimates the adaptability of these important traits.
Data assessing survival variation between capture methods in white-tailed deer
<p>Understanding what variables affect ungulate neonate survival is imperative to successful conservation and management of the species. Predation is commonly cited as a cause-specific source of mortality and ecological covariates often influence neonate survival. However, variation in survival estimates related to capture methodology has been documented with opportunistically captured neonates generally displaying greater survival than those captured via aid of vaginal implant transmitters (VITs), likely because of increased left truncation observed in the opportunistically captured datasets. Our goal was to assess if 3- and 6-month survival estimates varied by capture method while simultaneously assessing if capture method affected model selection and interpretation of ecological covariates for white-tailed deer neonates captured from three study sites from 2014 to 2015 in North Dakota and South Dakota, USA. We found survival varied by capture method for 3-month neonate survival with opportunistically captured neonates displaying up to 26% greater survival than their counterparts captured via VITs; however, this relationship was not present for 6-month survival. We also found model selection and subsequent interpretation of ecological covariates varied when analyzing datasets comprised of neonates captured via VITs, neonates captured opportunistically, and all neonates combined regardless of capture method. When interpreting results from our VIT only analysis for 3-month survival, we found survival varied by three time intervals and was lowest in the first two weeks of life. Capture method did not affect 6-month survival, which was most influenced by total precipitation occurring during 3 – 8 weeks of a neonate's life and percent canopy cover found at a neonate's capture site. Our results support previous research that capture method must be accounted for when deriving survival estimates for ungulate neonates as it can impact derived estimates and subsequent interpretation of results. </p>
Data for "Quantum algorithm for the variational optimization of correlated electronic states with the linear method"
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Text-fig. 2. Methods of taking measurements. in An Exceptional Large Sample Of The Early Miocene Ctenodactyline Rodent Sayimys Giganteus, Specific Variation And Taxonomic Implications
Text-fig. 2. Methods of taking measurements.
Data assessing survival variation between capture methods in white-tailed deer
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Data from: A new Bayesian method for fitting evolutionary models to comparative data with intraspecific variation
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Data from: A parametric method for assessing diversification rate variation in phylogenetic trees
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Data from: How to measure maturation: a comparison of probabilistic methods used to test for genotypic variation and plasticity in the decision to mature
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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.