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1,940 results for “data sample”
Sample of initial condition data for the ABC simplified atmospheric model and data assimilation system (vn1.4da)
<p>The file contains a link to a sample of initial condition data for use with the ABC simplified atmospheric model and data assimilation system (vn1.4da).</p>
Sample data of the CRCM5-LE for applications of the Latent Linear Adjustment autoencoder
<p>This is a sample of the CRCM5-LE (<a href="https://journals.ametsoc.org/jamc/article/58/4/663/336/The-ClimEx-Project-A-50-Member-Ensemble-of-Climate">Leduc et al. 2019</a>) for the applications of the Latent Linear Adjustment autoencoder as demonstrated in Heinze-Deml et al., 2020. The sample data set is a subset of the CRCM5-LE. The original data can be accessed at the <a href="https://www.climex-project.org/en/data-access">ClimEx data Access page</a>.</p> <p> </p> <p><strong>References</strong></p> <p>Heinze-Deml C., Sippel, S., Pendergrass, A. G., Lehner, F., and Meinshausen, N., 2020: Latent Linear Adjustment autoencoders: A novel method for estimating and emulating dynamic precipitation at high resolution. arXiV preprint</p> <p>Leduc, M., A. Mailhot, A. Frigon, J. Martel, R. Ludwig, G.B. Brietzke, M. Giguère, F. Brissette, R. Turcotte, M. Braun, and J. Scinocca, 2019: The ClimEx Project: A 50-Member Ensemble of Climate Change Projections at 12-km Resolution over Europe and Northeastern North America with the Canadian Regional Climate Model (CRCM5). J. Appl. Meteor. Climatol., 58, 663–693, <a href="https://doi.org/10.1175/JAMC-D-18-0021.1">https://doi.org/10.1175/JAMC-D-18-0021.1</a>.</p>
Data from: Bayesian analyses in phylogenetic palaeontology: interpreting the posterior sample
<p>Establishing hypotheses of relationships is a critical prerequisite for any macroevolutionary analysis, but different approaches exist for achieving this goal. Amongst palaeontologists using morphological data the Bayesian approach is increasingly preferred over parsimony, but this shift also alters the way we think about samples of trees. Here we revisit stratigraphic congruence as a comparator between Bayesian and parsimony samples, but in a new visual context: treespace. Such spaces represent an ordination of unique topologies that can also be extended to create a "landscape" where altitude represents some comparative measure (here congruence with stratigraphy). By co-opting existing visualization tools and applying them to a meta-analysis of 128 cladistic data sets we show that there is no consistent favouring of either Bayesian or parsimony according to stratigraphic congruence metrics, and further that empirical treespace visualizations suggest a complex variety of topological landscapes. We conclude by arguing that treespaces should become a standard exploratory tool in phylogenetic analysis.</p>
Data from msGBS: A new high-throughput approach to quantify the relative species abundance in root samples of multi-species plant communities
<p>Plant interactions are as important belowground as aboveground. Belowground plant interactions are however inherently difficult to quantify, as roots of different species are difficult to disentangle. Although for a couple of decades molecular techniques have been successfully applied to quantify root abundance, root identification and quantification in multi-species plant communities remains particularly challenging.</p> <p><span><span><span><span><span><span><span><span><span><span><span>Here we present a novel methodology, multi-species Genotyping By Sequencing (msGBS), as a next step to tackle this challenge. First, a multi-species meta-reference database containing thousands of gDNA clusters per species is created from GBS derived High Throughput Sequencing (HTS) reads. Second, GBS derived HTS reads from multi-species root samples are mapped to this meta-reference which, after a filter procedure to increase the taxonomic resolution, allows the parallel quantification of multiple species. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>The msGBS signal of 111 mock-mixture root samples, with up to 8 plant species per sample, was used to calculate the within-species abundance. Optional subsequent calibration yielded the across-species abundance. The within- and across-species abundances highly correlated (R<sup>2 </sup>range 0.72-0.94 and 0.85-0.98, respectively) to the biomass-based species abundance. Compared to a qPCR based method which was previously used to analyze the same set of samples, msGBS provided similar results. Additional data on 11 congener species groups within 105 natural field root samples showed high taxonomic resolution of the method. </span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><a>msGBS is highly scalable in terms of sensitivity and species numbers within samples, which is a major advantage compared to the qPCR method and advances our tools to reveal hidden belowground interactions.</a></span></span></span></span></span></span></span></span></span></span></span></p> <p>This dataset belongs to the article "<span><span><span><span><span><span><span><span><span><span><span><b>msGBS: A new high-throughput approach to quantify the relative species abundance in root samples of multi-species plant communities</b>". </span></span></span></span></span></span></span></span></span></span></span>msGBS is a technique that uses Genotyping By Sequencing on mixed plant species root samples which, after a filtering step to increase the taxonomic resolution and calibration, is able to estimate plant species abundances. </p> <p>The article uses data of two different experiment:</p> <ol> <li>the Jena field survay (13 plant species) and</li> <li>the Dutch field survay (120 plant species).</li> </ol>
Quantitative data from six years (2013-2018) of light trap sampling of macromoths (Lepidoptera) in Mt. Hallasan National Park, South Korea
This paper presents the results of long-term monitoring of macromoth communities in Mt. Hallasan National Park, South Korea. This mountain shows an altitudinal gradient of vegetation from evergreen deciduous to boreal trees, harbouring more than 550 species of vascular plants. The goal of this project was to investigate the changes in moth assemblages along the altitudinal gradient in this mountain ecosystem. We monitored macromoth communities at 11 sites in Mt. Hallasan National Park from 2013 to 2018, during which time moths were collected once a month from May to October, using an ultraviolet bucket trap. The generated dataset, which represented 587 species and 13,249 individuals from 14 families, can be adopted to establish a baseline for development of a network-orientated database to assess temporal and spatial changes of moths in temperate and tropical forests. This is the first long-term sampling-event dataset on macromoth assemblages in changing vegetation from evergreen deciduous to boreal tree zones, conducted in Mt. Hallasan National Park, the national park at the highest elevation and located on the largest volcanic island in South Korea. The aim of this study was to provide a description and a link to published data in the format of a peer-reviewed journal and to provide recognition of the effort in a scholarly article (based on data paper definition published at https://www.gbif.org/en/data-papers).
Identity-by-descent detection across 487,409 British samples reveals fine scale population structure and ultra-rare variant associations: data related to publication
<p>Data related to the following publication:</p> <p>"Identity-by-descent detection across 487,409 British samples reveals fine scale population structure and ultra-rare variant associations"</p>
Data from: Timing of vegetation sampling does not influence associations between visual obstruction and turkey nest survival in a montane forest
Evaluating relationships between ecological processes that occur concurrently is complicated by the potential for such processes to covary. Ground-nesting birds rely on habitat characteristics that provide concealment from predators; this protection often is provided by vegetation at the nest. Recently, researchers have raised concern that measuring vegetation at nest fate introduces a bias, as vegetation at successful nests is measured later in the growing season. This bias can lead to an erroneous conclusion that plant height is positively associated with nest survival. However, if the features that provide concealment are invariant during the incubation period, no bias should be expected, and the timing of measurement is less influential. We used data collected from 98 nests to evaluate whether there is evidence that such a bias exists in a study of wild turkey (Meleagris gallopavo) nesting in a forest ecosystem. We modelled nest survival as a function of visual obstruction and other covariates of interest. At unsuccessful nests, we collected visual obstruction readings at both the date of nest failure and the projected hatch date and compared survival estimates generated using both sets of vegetation data. In contrast to studies in other systems, we found little evidence that the timing of vegetation sampling influenced conclusions regarding the association between visual obstruction and survival; model selection and estimates of nest survival were similar regardless of when vegetation data were collected. The dominant hiding cover at most of our nests was provided by evergreen shrubs; slow growth of these plants likely prevent appreciable changes in visual obstruction during incubation. When considered with a growing body of literature, our results suggest that the influence of timing of sampling depends on the study system. When designing future studies, investigators should consider the structures that provide nest concealment and whether phenology is confounded with nest survival.
Data from: Spotting the pests of tomorrow - Sampling designs for detection of species associations with woody plants
Aim: Early warning against potentially harmful organisms of woody plant species can be achieved by sampling sentinel plants in exporting countries. However, it is unclear where sentinel plants can best be located, and how many samples are required and when and how often sampling optimally should take place for the adequate assessment of the biodiversity associated with the target plant species. We aimed to review spatial and temporal factors affecting associate biodiversity of single woody plant species and to develop guidance for the design of global biodiversity sampling studies. Location: Worldwide. Taxon: Insects and Fungi. Methods: Literature about factors affecting the diversity of insects and fungi in association with single plant species on global, regional, local and different temporal scales was reviewed. Case studies of insect and fungal diversity, primarily collected on single plant species, and the cost of collecting and analysing samples from locations around the world were analysed. Results: The review of the literature illustrated various factors affecting diversity, and the case studies allowed quantification of the relative impact of some spatial, temporal and financial aspects on captured biodiversity and, thus, illustrate the need to consider all possible factors that may affect the result of the sampling when deciding on a sampling design. Main conclusions: Our study illustrates the factors that should be considered when deciding on the location and timing of sampling for sentinel plants, which is important because of the trade-off between the number of samples and sampling locations needed to detect many of the species which may be potential pests, and the cost of (repeated) sampling in many locations. Decisions about the sampling design must be based on the objective of the sampling, but our recommendations apply irrespective of the targeted plant species or country.
Sample data of the 99 simulated brains dataset
<p>This archive is a supplement for the 99 simulated brains dataset <a href="http://dx.doi.org/10.6097/e230-20200511_1">http://dx.doi.org/10.6097/e230-20200511_1</a> and contains the data of one single sample subject created using MITK Diffusion [1]. It contains simulated MR images (T1, T2, dMRI) of 1 healthy subject as well as corresponding reference fiber tracts used for the MRI simulation. For more details, please refer to the full dataset [2]. If you are using this dataset in your work, please cite it and also cite the full dataset.</p> <p>[1] Neher, Peter. <em>MIC-DKFZ/MITK-Diffusion</em>. C++. 2019. Reprint, MIC-DKFZ, 2020. <a href="https://github.com/MIC-DKFZ/MITK-Diffusion">https://github.com/MIC-DKFZ/MITK-Diffusion</a>.</p> <p>[2] Neher, Peter, und Klaus Maier-Hein. „Simulated MRI Images and Reference Fiber Tracts of 99 Subjects.“ German Cancer Research Center, 2020. <a href="https://doi.org/10.6097/e230-20200511_1">https://doi.org/10.6097/e230-20200511_1</a>.</p> <p><strong>Acknowledgements:</strong></p> <p>Data were provided [in part] by the Human Connectome Project, WU-Minn Consortium (Principal Investigators: David Van Essen and Kamil Ugurbil; 1U54MH091657) funded by the 16 NIH Institutes and Centers that support the NIH Blueprint for Neuroscience Research; and by the McDonnell Center for Systems Neuroscience at Washington University.</p> <p>This work was supported by the Collaborative Research Center (SFB/TRR 125 Cognition-Guided Surgery) of the German Research Foundation (DFG) grant number INST 35/1120-1, DFG grant MA 6340/10-1, DFG grant MA 6340/12-1 and by the Helmholtz Association Initiative and Networking Fund under project number ZT-I-0003.</p>
Beyond 2022 Knowledge Graph Sample Data
<p>This dataset contains a CSV file and an RDF Turtle file. Both files contain information on a few people mentioned in the Irish Exchequer Payments 1270-1326, a book written by Connolly, P and published by the Irish Manuscripts Commission in 1998. A historian transcribed those people in a CSV file, subsequently transformed into RDF using an R2RML mapping. This dataset contains the records and the output of a handful of people transcribed in this way. This dataset illustrates how the Beyond 2022 project avails of CIDOC-CRM to populate its knowledge graph.</p> <p>Beyond 2022 is funded by the Government of Ireland, through the Department of Culture, Heritage and the Gaeltacht, under the Project Ireland 2040 framework. The project is also partially supported by the ADAPT Centre for Digital Content Technology under the SFI Research Centres Programme (Grant 13/RC/2106).</p>
Data from: Sampling beetle communities: trap design interacts with weather and species traits to bias capture rates
<p>Globally, many insect populations are declining, prompting calls for action. Yet these findings have also prompted discussion about sampling methods and interpretation of long-term datasets. As insect monitoring and research efforts increase, it is critical to quantify the effectiveness of sampling methods. This is especially true if sampling biases of different methods covary with climate, which is also changing over time. We assess the effectiveness of two types of flight intercept traps commonly used for beetles, a diverse insect group responsible for numerous ecosystem services, under different climatic conditions in Norwegian boreal forest. One of these trap designs includes a device to prevent rainwater from entering the collection vial, diluting preservatives and flushing out beetles. This design is compared to a standard trap. We ask how beetle capture rates vary between these traps, and how these differences vary based on precipitation levels and beetle body size, an important species trait. Bayesian mixed models reveal that the standard and modified traps differ in their beetle capture rates, but that the magnitude and direction of these differences change with precipitation levels and beetle body size. At low rainfall levels standard traps catch more beetles, but as precipitation increases the catch rates of modified traps overtake those of standard traps. This effect is most pronounced for large-bodied beetles. Sampling methods are known to differ in their effectiveness. Here, we present evidence for a less well-known but likely common phenomenon - an interaction between climate and sampling, such that relative effectiveness of trap types for beetle sampling differs depending on precipitation levels and species traits. This highlights a challenge for long-term monitoring programs, where both climate and insect populations are changing. Sampling methods should be sought that eliminate climate interactions, any biases should be quantified, and all insect datasets should include detailed methodological metadata.</p>
Raw data for predicting sample success for large-scale ancient DNA studies on marine mammals
<p>In recent years, non-human ancient DNA studies have begun to focus on larger sample sizes and whole genomes, offering the potential to reveal exciting and hitherto unknown answers to ongoing biological and archaeological questions. However, one major limitation to the feasibility of such studies is the substantial financial and time investments still required during sample screening, due to uncertainty regarding successful sample selection. This study investigates the effect of a wide range of sample properties including latitude, sample age, skeletal element, collagen preservation, and context on endogenous content and DNA damage profiles for 317 ancient and historic pinniped samples collected from across the North Atlantic. Using generalised linear and mixed-effect models, we found that a range of factors affected DNA preservation within each of the species under consideration. The most important findings were that endogenous content varied significantly according to context, the type of skeletal element, the collagen content and collection year. There also appears to be an effect of the sample's geographic origin, with samples from the Arctic generally showing higher endogenous content and lower damage rates. Both latitude and sample age were found to have significant relationships with damage levels, but only for walrus samples. Sex, ontogenetic age and extraction material preparation were not found to have any significant relationship with DNA preservation. Overall, the skeletal element and sample context were found to be the most influential factors and should therefore be considered when selecting samples for large-scale ancient genome studies.</p>
Data from: The theory of island biogeography, the sample-area effect, and the habitat diversity hypothesis: complementarity in a naturally fragmented landscape of lake islands
Aim: Investigate relationships between fragmentation and species diversity in the context of the theory of island biogeography, sample-area effect, and habitat diversity hypothesis. Location: Lake of the Woods, Canada. Taxon: Vascular plants Methods: Vascular plant species diversity was inventoried on 30 islands, organized into two island sets. Each island set contained four size classes that varied in degree of fragmentation while controlling for the sample-area effect (small island set: 8×0.1-ha, 4×0.2-ha, 2×0.4-ha, and 1×0.8-ha islands; large island set: identical pattern utilizing 1.0-ha to 8.0-ha islands). Fragmentation effects were then examined using SLOSS-based analyses, addressing whether single large or several small islands contained more species: (1) direct comparisons of species and habitat richness across size classes; (2) extrapolations of species-area relationships; and (3) analyses of species and habitat accumulation curves. Multigroup path analysis was next used to quantify effects of habitat diversity, island area, and isolation on species richness for both island sets. Finally, pairwise and multiple-site dissimilarity was estimated for both species and habitats across 0.1-ha and 1.0-ha islands to investigate whether: (1) variation in species composition was related to habitat composition; and (2) species dissimilarity increased with inter-island distance. Results: SLOSS-based analyses indicated that several small islands contained more species than single large islands in both island sets. This pattern was also observed for habitats, but only in the small islands set. Path analysis suggested that island area had significant direct and indirect effects (mediated by habitat diversity) on species richness. Habitat diversity and island isolation had significant positive and negative effects on species richness, respectively, independent of island area. Species and habitat dissimilarities were significantly related across 0.1-ha but not 1.0-ha islands, and showed no relationship to inter-island distance. Main Conclusions: The overall positive relationship between fragmentation and species richness may be attributed to greater habitat diversity and increased species dissimilarity across smaller islands relative to larger islands. However, negative isolation effects indicate that landscape configuration is still an important conservation consideration. These results each align with different predictions of the theory of island biogeography, sample-area effect, and habitat diversity hypothesis, questioning the exclusivity of these theoretical frameworks.
Data from: Assessing individual patterns of Echinococcus multilocularis infection in urban coyotes: non-invasive genetic sampling as epidemiological tool
1. In epidemiological studies of wildlife parasites, faecal genotyping has been introduced to prevent bias in estimates of parasite prevalence from faecal samples collected in the field. Such an approach could be particularly relevant in the study of Echinococcus multilocularis transmission in urban settings, where estimates of prevalence and patterns of infection in wild canid hosts are key parameters used in zoonotic risk assessment and management. However, no previous study has evaluated the reliability of E. multilocularis faecal prevalence, and individual patterns of infection in definitive hosts remain poorly understood. 2. We evaluated faecal genotyping as an epidemiological tool, using E. multilocularis in urban coyotes Canis latrans as our study system. Combining parasitological analysis and multilocus individual genotyping of coyote faeces, we compared faecal parasite prevalence with the prevalence obtained from genotyped faecal samples. Furthermore, we assessed patterns of individual infection, such as re-infection rates and phenology of parasite egg excretion. 3. Of 425 feces collected in five urban sites, we genotyped 142 samples (33.4%) corresponding to 60 unique individual coyotes. Number of genotyped samples per coyote ranged between 1 and 10 (mean = 2.3). Genotypes were obtained at 4–6 microsatellite loci and had a mean reliability of 0.9975. 4. Faecal prevalence of E. multilocularis in genotyped coyotes was 25.0%, and similar to results previously obtained from non-genotyped faeces. Faecal genotyping allowed estimating a re-infection rate of individual coyotes of 57.1%, and to observe temporal patterns of parasite infection that were not detected using non-genotyped faeces. 5. Synthesis and applications. If compared to independent data obtained through coyote post-mortem examination, our results suggest that reliable estimates of overall parasite prevalence in definitive host populations can be efficiently obtained through well-designed field collection and traditional faecal parasitological analysis. However, faecal genotyping allows assessing the dynamics of individual infections, which could otherwise only be estimated by using invasive techniques. Combining faecal genotyping with parasitology has a great potential in assessing zoonotic risk transmission in urban areas, as well as advancing the field of wildlife ecology, disease ecology and conservation.
Data from: Real-time assessment of hybridization between wolves and dogs: combining non-invasive samples with ancestry informative markers
Wolves and dogs provide a paradigmatic example of the ecological and conservation implications of hybridization events between wild and domesticated forms. However, our understanding of such implications has been traditionally hampered by both high genetic similarity and the difficulties in obtaining tissue samples (TS), which limit our ability to assess ongoing hybridization events. To assess the occurrence and extension of hybridization in a pack of wolf-dog hybrids in Northwestern Iberia, we compared the power of 52 nuclear markers implemented on TS with a subset of 13 ancestry informative markers (AIMs) typed in non-invasive samples (NIS). We demonstrate that the 13 AIMs are as accurate as the 52 markers that were chosen without regard to the power to differentiate between wolves and dogs, also having the advantage of being rapidly screened on NIS. The efficiency of AIMs significantly outperformed ten random sets of similar size and an additional commercial set of 18 markers. Bayesian clustering analysis implemented on AIMs and NIS identified nine hybrids, two wolves and two dogs. Four hybrids were unambiguously assigned to F1xWolf backcrosses. Our approach (AIMs + NIS) overcomes previous difficulties related to sample availability and informative power of markers, allowing a quick identification of wolf-dog hybrids in the first phases of hybridization episodes. This provides managers with a reliable tool to evaluate hybridization, and estimate the success of their actions. This approach may be easily adapted for other pairs of wild/domesticated species, thus improving our understanding of the introgression of domestication genes into natural populations.
Data from: Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes.
Rodentia is the largest order of placental mammals, with approximately 2,050 species divided into 28 families. It is also one of the most controversial with respect to its monophyly, relationships between families, and divergence dates. Here, we have analyzed and compared the performance of three nuclear genes (von Willebrand Factor, interphotoreceptor retinoid-binding protein, and Alpha 2B adrenergic receptor) for a large taxonomic sampling, covering the whole rodent and placental diversity. The phylogenetic results significantly support rodent monophyly, the association of Rodentia with Lagomorpha (the Glires clade), and a Glires + Euarchonta (Primates, Dermoptera, and Scandentia) clade. The resolution of relationships among rodents is also greatly improved. The currently recognized families are divided here into seven well-defined clades (Anomaluromorpha, Castoridae, Ctenohystrica, Geomyoidea, Gliridae, Myodonta, and Sciuroidea) that can be grouped into three major clades: Ctenohystrica, Gliridae + Sciuroidea, and a mouse-related clade (Anomaluromorpha, Castoridae + Geomyoidea, and Myodonta). Molecular datings based on these three genes suggest that the rodent radiation took place at the transition between Paleocene and Eocene. The divergence between rodents and lagomorphs is placed just at the K-T boundary and the first splits among placentals in the Late Cretaceous. Our results thus tend to reconcile molecular and morphological-paleontological insights.
Data from: Linking dung beetle mediated functions to interactions in the Atlantic Forest: sampling design matters
<p>Interactions between dung beetles and vertebrate dung are intimately linked to a suite of ecosystem functions in tropical forests. We show that the trapping method and the type of dung used affect the suite of beetles captured, with the potential to influence the outcome of experiments linking functions to interactions.</p>
Data from: Balancing sample accumulation and DNA degradation rates to optimize noninvasive genetic sampling of sympatric carnivores
Noninvasive genetic sampling, or noninvasive DNA sampling (NDS), can be an effective monitoring approach for elusive, wide-ranging species at low densities. However, few studies have attempted to maximize sampling efficiency. We present a model for combining sample accumulation and DNA degradation to identify the most efficient (i.e. minimal cost per successful sample) NDS temporal design for capture–recapture analyses. We use scat accumulation and faecal DNA degradation rates for two sympatric carnivores, kit fox (Vulpes macrotis) and coyote (Canis latrans) across two seasons (summer and winter) in Utah, USA, to demonstrate implementation of this approach. We estimated scat accumulation rates by clearing and surveying transects for scats. We evaluated mitochondrial (mtDNA) and nuclear (nDNA) DNA amplification success for faecal DNA samples under natural field conditions for 20 fresh scats/species/season from <1–112 days. Mean accumulation rates were nearly three times greater for coyotes (0.076 scats/km/day) than foxes (0.029 scats/km/day) across seasons. Across species and seasons, mtDNA amplification success was ≥95% through day 21. Fox nDNA amplification success was ≥70% through day 21 across seasons. Coyote nDNA success was ≥70% through day 21 in winter, but declined to <50% by day 7 in summer. We identified a common temporal sampling frame of approximately 14 days that allowed species to be monitored simultaneously, further reducing time, survey effort and costs. Our results suggest that when conducting repeated surveys for capture–recapture analyses, overall cost-efficiency for NDS may be improved with a temporal design that balances field and laboratory costs along with deposition and degradation rates.
Data from: Effects of spatial scale of sampling on food web structure
This study asks whether the spatial scale of sampling alters structural properties of food webs and whether any differences are attributable to changes in species richness and connectance with scale. Understanding how different aspects of sampling effort affect ecological network structure is important for both fundamental ecological knowledge and the application of network analysis in conservation and management. Using a highly resolved food web for the marine intertidal ecosystem of the Sanak Archipelago in the Eastern Aleutian Islands, Alaska, we assess how commonly studied properties of network structure differ for 281 versions of the food web sampled at five levels of spatial scale representing six orders of magnitude in area spread across the archipelago. Species (S) and link (L) richness both increased by approximately one order of magnitude across the five spatial scales. Links per species (L/S) more than doubled, while connectance (C) decreased by approximately two-thirds. Fourteen commonly studied properties of network structure varied systematically with spatial scale of sampling, some increasing and others decreasing. While ecological network properties varied systematically with sampling extent, analyses using the niche model and a power-law scaling relationship indicate that for many properties, this apparent sensitivity is attributable to the increasing S and decreasing C of webs with increasing spatial scale. As long as effects of S and C are accounted for, areal sampling bias does not have a special impact on our understanding of many aspects of network structure. However, attention does need be paid to some properties such as the fraction of species in loops, which increases more than expected with greater spatial scales of sampling.
Data from: Accuracy and precision of species trees: effects of locus, individual, and base-pair sampling on inference of species trees of the Liolaemus darwinii group (Squamata, Liolaemidae)
Molecular phylogenetics has entered a new era in which species trees are estimated from a collection of gene trees using methods that accommodate their heterogeneity and discordance with the species tree. Empirical evaluation of species trees is necessary to assess the performance (i.e., accuracy and precision) of these methods with real data, which consist of gene genealogies likely shaped by different historical and demographic processes. We analyzed 20 loci for 16 species of the South American lizards of the Liolaemus darwinii species group and reconstructed a species tree with *BEAST, then compared the performance of this method under different sampling strategies of loci, individuals, and sequence lengths. We found an increase in the accuracy and precision of species trees with the number of loci, but for any number of loci, accuracy decreased when using only one individual per species or 25% of the full sequence length. In addition, locus 'informativeness' was an important factor in the accuracy/precision of species trees when using a few loci, but it became increasingly irrelevant with additional loci. Our empirical results combined with previous simulation studies suggest that there is an optimal range of sampling effort of loci, individuals, and sequence lengths for a given speciation history and information content of the data. Future studies should be directed towards further assessment of other factors that can impact performance of species trees, including gene flow, data 'informativeness', tree shape, missing data, and uncertain species boundaries.
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.