Find research datasets worth reusing

Modeling cannabinoids from a large-scale sample of Cannabis sativa chemotypes

The widespread legalization of Cannabis has opened the industry to using contemporary analytical techniques for chemotype analysis. Chemotypic data has been collected on a large variety of oil profiles inherent to the cultivars that are commercially available. The unknown gene regulation and pharmacokinetics of dozens of cannabinoids offer opportunities of high interest in pharmacology research. Retailers in many medical and recreational jurisdictions are typically required to report chemical concentrations of at least some cannabinoids. Commercial cannabis laboratories have collected large chemotype datasets of diverse Cannabis cultivars. In this work a data set of 17,600 cultivars tested by Steep Hill Inc., is examined using machine learning techniques to interpolate missing chemotype observations and cluster cultivars into groups based on chemotype similarity. The results indicate cultivars cluster based on their chemotypes, and that some imputation methods work better than others at grouping these cultivars based on chemotypic identity. Due to the missing data and to the low signal to noise ratio for some less common cannabinoids, their behavior could not be accurately predicted. These findings have implications for characterizing complex interactions in cannabinoid biosynthesis and improving phenotypical classification of Cannabis cultivars.

Effect of ecological factors on fine-scale patterns of social structure in African lions

1. Environmental variations can influence the extent to which individuals interact with other individuals by changing the value of grouping. It is well known that many species can form and disband groups, often in response to the distribution and abundance of resources. 2. While previous studies showed that resources influence the broad-scale structure of animal groups, knowledge gaps remain on whether they affect fine-scale patterns of association among individuals within groups. 3. We quantify association patterns in African lions while simultaneously monitoring the abundance and distribution of prey. We test how social and ecological factors, including individual trait (age, sex, reproductive state) similarity and prey availability (prey abundance, dispersion, herd size and body size) affect within-pride social structure in African lions. 4. We found that individual decisions about associates depended on resource availability with individuals associating equally across all members of the pride when prey herds were scarce, aggregated or large bodied, and associating more exclusively (in subgroups of preferred associates) when prey herds were abundant, dispersed or small bodied. Individuals within lion prides seemed to be buffering against changes in prey availability by modulating their strength and density of connections with conspecifics when prides split into subgroups. The strength and density of connections among individuals within subgroups was greater when prey herds were large and lower when prey herds were dispersed or large bodied. 5. Our findings suggest that individual lions are making social decisions at both the subgroup level and the pride level, with decisions representing putatively fitness-enhancing strategies. Individuals were typically shifting between having few strong connections and having many weaker connections depending on prevailing ecological conditions, with prey abundance, dispersion and body size having the greatest impact on decisions about splitting into subgroups. The maintenance of connections within prides and subgroups in the face of ecological change suggests that the fission-fusion nature of lion prides might be essential for the long-term maintenance of social connections even when short-term conditions do not allow them. More broadly, our study reveals how fission-fusion dynamics and ecological factors can simultaneously have an effect on animals across multiple levels of sociality. 29-Jul-2020

Temperature and predator cues interactively affect ontogenetic metabolic scaling of aquatic amphipods

A common belief is that body-mass scaling of metabolic rate results chiefly from intrinsic body-design constraints. However, several studies have shown that multiple ecological factors affect metabolic scaling. The mechanistic basis of these effects is largely unknown. Here, we explore whether abiotic and biotic environmental factors have interactive effects on metabolic scaling. To address this question, we studied the simultaneous effects of temperature and predator cues on the ontogenetic metabolic scaling of amphipod crustaceans inhabiting two different aquatic ecosystems, a freshwater spring and a saltwater lagoon. We assessed effects of phenotypic plasticity on metabolic scaling by exposing amphipods in the laboratory to water with and without fish-cues at multiple temperatures. Temperature interacts significantly with predator cues to affect metabolic scaling. Our results suggest that metabolic scaling is highly malleable in response to short-term acclimation. The interactive effects of temperature and predators show the importance of studying effects of global warming in realistic ecological contexts.

Data from: Spatial scaling of beta diversity in the shallow marine fossil record

Beta diversity quantifies the spatial structuring of ecological communities and is a fundamental partition of biodiversity, central to understanding many macroecological phenomena in modern biology and paleobiology. Despite its common application in ecology, studies of beta diversity in the fossil record are limited, particularly at regional spatial scales that are important for understanding macroevolutionary processes. The spatial scaling of beta diversity in the fossil record is poorly understood, but has significant implications due to temporal variation in the spatial distribution of fossil collections and the large spatio-temporal scales typically employed. Here we test the spatial scaling of several common measures of beta diversity using the Cenozoic shallow marine molluscan fossil record of New Zealand, and derive a spatially standardized time series of beta diversity. To measure spatial scaling we use and compare grid cell occupancy based on an equal-area grid and summed minimum spanning tree length, both based on reconstructed paleocoordinates of fossil collections. We find that beta diversity is spatially dependent at local to regional scales, regardless of the metric or spatial scaling utilised, and that spatial standardization significantly changes apparent temporal trends of beta diversity and, therefore, inferences about processes driving diversity change.

Data from: Contrasting scales of local persistence between monsoonal and arid biomes in closely related, low-dispersal vertebrates

Aim: Focussing on pairs of sister species across three genera of scincid lizards, we use genomic evidence to test for larger-scale, late-Pleistocene changes in distributions of lizards in the Australian Arid Zone (AZ) than in the adjacent Monsoonal Tropics (MT). Location: Northern and central Australia. Taxon: Scincidae: Squamata. Methods: We sequenced ~ 2000 nuclear exons and one mitochondrial gene across the distributions of species with primarily MT or AZ distributions from three genera of lizards. Using phylogenetic analysis and population structure analyses we identified major phylogeographic lineages and then compared the spatial scale of structuring and tested for recent demographic expansions. Results: Two genera in particular, Proablepharus and Morethia, showed deeper and more geographically localised phylogeographic diversity in the MT than the AZ. In the MT, localised diversity was prevalent in the relatively mesic regions. By contrast, the AZ was characterised by widespread and often genetically uniform lineages and a higher proportion of these had signals of recent population expansion. Main conclusions: Consistent with other recent, but mostly less genetically extensive studies, our results point to deeper and more localised diversity in MT compared to AZ. In turn, this suggests higher local persistence in more mesic and topographically diverse biome through the late Quaternary climate fluctuations. For the AZ, geographically extensive range expansions have likely contributed to the low spatial turnover of this exceptionally rich lizard fauna.

Construction of a chromosome-scale long-read reference genome assembly for potato

Background: Worldwide, the cultivated potato, Solanum tuberosum L., is the number one vegetable crop and a critical food security crop. The genome sequence of DM1-3 516 R44, a doubled monoploid clone of S. tuberosum Group Phureja, was published in 2011 using a whole-genome shotgun sequencing approach with short read sequence data. Current advanced sequencing technologies now permit generation of near-complete, high-quality chromosome-scale genome assemblies at a minimal cost. Findings: Here, we present an updated version of the DM1-3 516 R44 genome sequence (v6.1) using Oxford Nanopore Technologies long reads coupled with proximity-by-ligation scaffolding (Hi-C) yielding a chromosome-scale assembly. The new (v6.1) assembly represents 741.6 Mb of sequence (87.8 %) of the estimated 844 Mb genome, of which, 741.5 Mb is non-gapped with 731.2 Mb anchored to the 12 chromosomes. Use of Oxford Nanopore Technologies full-length cDNA sequencing enabled annotation of 32,917 high-confidence protein-coding genes encoding 44,851 gene models that had a significantly improved representation of conserved orthologs compared to the previous annotation. The new assembly has improved contiguity with a 595-fold increase in N50 contig size, 99% reduction in the numbersof contigs, a 44-fold increase in N50 scaffold size, and an LTR Assembly Index score of 13.56, placing it in the category of reference genome quality. The improved assembly also permitted annotation of the centromeres via alignment to sequencing reads derived from CENH3 nucleosomes. Conclusions: Access to advanced sequencing technologies and improved software permitted generation of a high-quality, long-read, chromosome-scale assembly and improved annotation dataset for the reference genotype of potato that will facilitate research aimed at improving agronomic traits and understanding genome evolution.

Does conspicuousness scale linearly with colour distance? a test using reef fish

To be effective, animal colour signals must attract attention – and therefore need to be conspicuous. To understand signal function, it is useful to evaluate their conspicuousness to relevant viewers under various environmental conditions, including when visual scenes are cluttered by objects of varying colour. A widely used metric of colour difference (ΔS) is based on the Receptor Noise Limited (RNL) model, which was originally proposed to determine when two similar colours appear different from one another, termed the discrimination threshold (or JND, just noticeable difference). Estimates of the perceptual distances between colours that exceed this threshold – termed 'suprathreshold' colour differences – often assumes that a colour's conspicuousness scales linearly with colour distance, and that this scale is independent of direction in colour space. Currently, there is little behavioural evidence to support these assumptions. This study evaluated the relationship between ΔS and conspicuousness in suprathreshold colours using an Ishihara-style test with a coral reef fish, Rhinecanthus aculeatus. As our measure of conspicuousness, we tested whether fish, when presented with two colourful targets, preferred to peck at the one with a greater ΔS from the average distractor colour. We found the relationship between ΔS and conspicuousness followed a sigmoidal function, with high ΔS colours perceived as equally conspicuous. We found that the relationship between ΔS and conspicuousness varied across colour space (i.e. for different hues). The sigmoidal detectability curve was little affected by colour variation in the background or when colour distance was calculated using a model that does not correct for receptor noise. These results suggest that the RNL model may provide accurate estimates for perceptual distance for small suprathreshold distance colours, even in complex viewing environments, but must be used with caution with perceptual distances exceeding 10 ΔS.

opencc-by-4.0Sep 2020View details →

Identity-by-descent detection across 487,409 British samples reveals fine scale population structure and ultra-rare variant associations: data related to publication

Data related to the following publication: "Identity-by-descent detection across 487,409 British samples reveals fine scale population structure and ultra-rare variant associations"

Data from: Mortality, perception, and scale: understanding how predation shapes space use in a wild prey population

Attempts to assess behavioral responses of prey to predation risk are often confounded by depredation of prey. Moreover, the scale at which the response of prey is assessed has important implications for discovering how predation risk alters prey behavior. Herein, we assessed space use of wild Ring-necked Pheasants (Phasianus colchicus) in response to spatial and temporal variation in recreational hunting. We radio-marked pheasants and monitored space use at two spatial scales: short-term seasonal home range, and nightly resting locations. Additionally, we considered temporal variation in predation risk by monitoring space use prior to and during the pheasant hunting season. Although we found no change in nightly resting location, pheasants subjected to predation risk expanded their home range and shifted home range location even when invulnerable to predation. Home range formation was plastic, with home ranges expanding and contracting as risk fluctuated before and during the hunting season. Depredation reduced the measured response within the population, obscuring the potential importance of perceived predation risk in shaping prey communities, particularly when not measured at the appropriate scale. By assessing space use of a wild prey population at multiple scales, considering spatial and temporal variation in predation risk, we show that not only does predation risk affect space use, but that the effects at the population level may be challenging to assess when not measured at the appropriate ecological scale because of the direct effects of differential mortality on the same behaviors.

Scripts and files for "Small-scale population divergence is driven by local larval environment in a temperate amphibian"

Genomic variation within and among populations is shaped by the interplay between natural selection and the effects of genetic drift and gene flow. Adaptive divergence can be found in small scale natural systems even when population sizes are small and the potential for gene flow is high, suggesting that local environments exert selection pressures strong enough to counteract the opposing effects of drift and gene flow. Here, we investigated genomic differentiation in nine moor frog (Rana arvalis) populations in a small-scale network of local wetlands using 16 707 ddRAD-seq SNPs, relating levels of differentiation with local environments as well as with properties of the surrounding landscape. We characterized population structure and differentiation, and partitioned the effects of geographic distance, local larval environment and landscape features on total genomic variation. We also conducted gene-environment association studies using univariate and multivariate approaches. We found small-scale population structure corresponding to 6-8 clusters. Local larval environment was the most influential component explaining 2.3% of the total genetic variation followed by landscape features (1.8%) and geographic distance (0.8%), indicative of isolation-by-environment, -by-landscape and -by-distance, respectively. We identified 1000 potential candidate SNPs putatively under divergent selection mediated by the local larval environment. The candidate SNPs were involved in, among other biological functions, immune system function and development. Our results suggest that small scale environmental differences can exert selection pressures strong enough to counteract homogenizing effects of gene flow and drift in this small-scale system leading to observable population differentiation.

opencc-by-4.0Mar 2020View details →

ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets

This page links to the data associated with the publication "ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets ". The data have been curated and analyzed using our open-source R package, ToxicoGx (https://github.com/bhklab/ToxicoGx) and are available publicly in the ToxicoDB web application (www.toxicodb.ca). Please see the included DOIs below, or download the .csv file which contains the names, dates and DOIs of all datasets listed here. The TGGATES data was generated by Igarashi Y, Nakatsu N, Yamashita T, Ono A, Ohno Y, Urushidani T, Yamada H. Open TG-GATEs: a large-scale toxicogenomics database. Nucleic Acids Res [Internet]. 2015 Jan;43(Database issue):D921–7. Available from: http://dx.doi.org/10.1093/nar/gku955 PMCID: PMC4384023. Data: <ul> <li>TGGATEs humanldh (<a href="https://doi.org/10.5281/zenodo.3762812">https://doi.org/10.5281/zenodo.3762812</a>)</li> <li>TGGATEs humandna (<a href="https://doi.org/10.5281/zenodo.4024859">https://doi.org/10.5281/zenodo.4024859</a>)</li> <li>TGGATEs ratldh (<a href="https://doi.org/10.5281/zenodo.3762817">https://doi.org/10.5281/zenodo.3762817</a>)</li> <li>TGGATEs ratdna (<a href="https://doi.org/10.5281/zenodo.4024918">https://doi.org/10.5281/zenodo.4024918</a>)</li> </ul> This Drug Matrix data was generated by Ganter B, Snyder RD, Halbert DN, Lee MD. Toxicogenomics in drug discovery and development: mechanistic analysis of compound/class-dependent effects using the DrugMatrix database. Pharmacogenomics [Internet]. 2006 Oct;7(7):1025–1044. Available from: http://dx.doi.org/10.2217/14622416.7.7.1025 PMID: 17054413. Data: <ul> <li>Drug Matrix (<a href="https://doi.org/10.5281/zenodo.3766569">https://doi.org/10.5281/zenodo.3766569</a>)</li> </ul>

opencc-by-4.0Mar 2020View details →

ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets (TGGATEs rat dataset)

This data was generated by Igarashi Y, Nakatsu N, Yamashita T, Ono A, Ohno Y, Urushidani T, Yamada H. Open TG-GATEs: a large-scale toxicogenomics database. Nucleic Acids Res [Internet]. 2015 Jan;43(Database issue):D921–7. Available from: http://dx.doi.org/10.1093/nar/gku955 PMCID: PMC4384023. The data have been curated and analyzed using our open-source R package, ToxicoGx (<a href="https://github.com/bhklab/ToxicoGx">https://bioconductor.org/packages/devel/bioc/html/ToxicoGx.html</a>), and are available publicly in the ToxicoDB web application (<a href="http://www.toxicodb.ca">www.toxicodb.ca</a>).

opencc-by-4.0Sep 2020View details →

Open database of small-scale solar PV installations: a Citizen Science initiative

Presentation given at the European PV Solar Energy Conference 2020 about the development of a Citizen Science initiative related to PV installations, Generation Solar.

openmit-licenseSep 2020View details →

Data for Automated Mechanism Generation Using Linear Scaling Relationships and Sensitivity Analyses applied to Catalytic Partial Oxidation of Methane

Data, scripts, and plots for the preprint and article titled 'Automated Mechanism Generation Using Linear Scaling Relationships and Sensitivity Analyses applied to Catalytic Partial Oxidation of Methane'

opencc-by-4.0Sep 2020View details →

Automated Patch Assessment for Program Repair at Scale

In this package, we share  257 patches from Dcorrect and 381 patches from Doverfitting. We also a script used in our experiment for doing sanity checks and automated patch assessments.   If you use this dataset, please cite: <pre><code>@Article{Ye2021EMSE, author = {Ye, He and Martinez, Matias and Monperrus, Martin}, title = "Automated Patch Assessment for Program Repair at Scale", journal="Empirical Software Engineering", volume = "26", issn = "1573-7616", doi = "https://doi.org/10.1007/s10664-020-09920-w", year = "2021" } </code></pre>

Data from: Contrasting patterns of population structure at large and fine scales in an avian disturbance specialist of braided river ecosystems

Aim: To understand the population structure and its potential drivers at different spatial scales in a migratory bird, the black-fronted tern (Chlidonias albostriatus); a specialist of the spatially and temporally dynamic environments of braided rivers. Location: New Zealand Methods: We used a three-pronged approach based on 17 microsatellites, two mitochondrial loci (cytochrome b / control region), and phenotypic data (head-bill length, bill depth, wing length, weight). We determined large-scale genetic structure throughout the whole breeding range (approx. 150,000 km2), calculated genetic divergence of breeding populations, and tested for isolation-by-distance between populations. We investigated the level of fine-scale genetic structure based on spatial autocorrelation analyses and assessed the presence of a body size cline based on phenotypic data. Lastly, we compared phenotypic divergence (PST) and the level of divergence by genetic drift (FST) among breeding populations to test for underlying mechanisms of population differentiation. Results: Nuclear and mitochondrial DNA showed that across their range black-fronted terns were effectively panmictic, with low genetic divergence between breeding colonies overall and no isolation-by-distance. However, at fine geographical scales black-fronted terns accrued significant genetic structure for distances up to 75 km, primarily driven by males, indicating more frequent female dispersal. Furthermore, a phenotypic cline in accordance with Bergmann's rule was evident. PST exceeded FST in three traits, suggestive of local adaptation. Main conclusions: Significant fine-scale structure can be present in highly mobile, specialist species while not affecting spatial structures at larger scales. Hence, methodologies applied to both whole landscapes and local scales are important to appropriately estimate connectivity in dynamic metapopulations and investigate the processes behind connectivity. Conservation management will need to include protecting currently uninhabited patches to facilitate natural colonisation of suitable habitat. For black-fronted terns, managing whole catchments throughout the entire breeding range would be preferable to managing single patches.

Data from: Density-dependent offspring interactions do not explain macroevolutionary scaling of adult size and offspring size

Most lifeforms exhibit a correlated evolution of adult size (AS) and size at independence (SI), giving rise to AS-SI scaling relationships. Theory suggests that scaling arises because relatively large adults have relatively high reproductive output, resulting in strong density-dependent competition in early life, where large size at independence provides a competitive advantage to juveniles. The primary goal of our study is to test this Density Hypothesis, using large datasets that span the vertebrate tree of life (fishes, amphibians, reptiles, birds, and mammals). Our secondary goal is to motivate new hypotheses for AS-SI scaling, by exploring how subtle variation in life-histories among closely-related species is associated with variation in scaling. Our phylogenetically-informed comparisons do not support the Density Hypothesis. Instead, exploration of AS-SI scaling among life-history variants suggests that steeper AS-SI scaling slopes are associated with evolutionary increases in size at independence. We suggest that a positive association between size at independence and juvenile growth rate may represent an important mechanism underlying AS-SI scaling, a mechanism that has been underappreciated by theorists. If faster juvenile growth is a consequence of evolutionary increases in size at independence, this may help offset the cost of delayed maturation, leading to steeper AS-SI scaling slopes.

Data from: Nonlinear effects of intraspecific competition alter landscape-wide scaling up of ecosystem function

A major focus of ecology is to understand and predict ecosystem function across scales. Many ecosystem functions are only measured at local scales, while their effects occur at a landscape level. Here, we investigate how landscape-scale predictions of ecosystem function depend on intraspecific competition, a fine-scale process, by manipulating intraspecific density of shredding macroinvertebrates and examining effects on leaf litter decomposition, a key function in freshwater ecosystems. For two species, we found that per-capita leaf processing rates declined with increasing density following power functions with negative exponents, likely due to interference competition. To demonstrate consequences of this nonlinearity, we scaled up estimates of leaf litter processing from shredder abundance surveys in 10 replicated headwater streams. In accordance with Jensen's inequality, applying density-dependent consumption rates reduced estimates of catchment-scale leaf consumption by an order of magnitude relative to density-independent rates. Density-dependent consumption estimates aligned closely with metabolic requirements in catchments with large, but not small, shredder populations. Importantly, shredder abundance was not limited by leaf litter availability and catchment-level leaf litter supply was much higher than estimated consumption. Thus leaf litter processing was not limited by resource supply. Our work highlights the need for scaling-up which accounts for intraspecific interactions.

Data from: Helianthus maximiliani and species fine-scale spatial pattern affect diversity interactions in reconstructed tallgrass prairies

1. Biodiversity and Ecosystem Function analyses aim to explain how individual species and their interactions affect ecosystem function. With this study we asked in what ways do species interact, are these interactions affected by species planting pattern, and are initial (planted) proportions or previous year (realized) proportions a better reference point for characterizing grassland diversity effects? 2. We addressed these questions with experimental communities compiled from a pool of 16 tallgrass prairie species. We planted all species in monocultures and mixtures that varied in their species richness, evenness, and spatial pattern. We recorded species-specific biomass production over three growing seasons and fitted Diversity-Interactions (DI) models to annual plot biomass yields. 3. In the establishment season, all species interacted equally to form the diversity effect. In years 2 and 3, each species contributed a unique additive coefficient to its interaction with every other species to form the diversity effect. These interactions were affected by H. maximiliani and the species planting pattern. Models based on species planted proportions better-fit annual plot yields than models based on species previous contributions to plot biomass. 4. Outcomes suggest that efforts to plant tallgrass prairies to maximize diversity effects should focus on the specific species present and in what arrangement they are planted. Furthermore, for particularly diverse grasslands, the effort of collecting annual species biomass data may not be necessary when quantifying diversity effects with Diversity-Interactions models.