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1,037 results for “large-scale”
Large-scale metabolic interaction network of the mouse and human gut microbiota
<p>The role of our gut microbiota in health and disease is largely attributed to the collective metabolic activities of the inhabitant microbes. A system-level framework of the microbial community structure, mediated through metabolite transport, would provide important insights into the complex microbe-microbe and host-microbe chemical interactions. This framework, if adaptable to both mouse and human systems, would be useful for mechanistic interpretations of the vast amounts of experimental data from gut microbiomes in murine animal models, whether humanized or not. Here, we constructed a literature-curated, interspecies network of the mammalian gut microbiota for mouse and human hosts, called NJC19. This network is an extensive data resource, encompassing 838 microbial species (766 bacteria, 53 archaea, and 19 eukaryotes) and 6 host cell types, interacting through 8,224 small-molecule transport and macromolecule degradation events. Moreover, we compiled 912 negative associations between organisms and metabolic compounds that are not transportable or degradable by those organisms. Our network may facilitate experimental and computational endeavors for the mechanistic investigations of host-associated microbial communities.</p>
Modeling cannabinoids from a large-scale sample of Cannabis sativa chemotypes
<p>The widespread legalization of <i>Cannabis</i> 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 <i>Cannabis</i> 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 <i>Cannabis</i> cultivars.</p>
ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets
<p>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.</p> <p>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.<br> <br> Data:</p> <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> <p>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.</p> <p>Data:</p> <ul> <li>Drug Matrix (<a href="https://doi.org/10.5281/zenodo.3766569">https://doi.org/10.5281/zenodo.3766569</a>)</li> </ul>
ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets (TGGATEs rat dataset)
<p>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, <em>ToxicoGx</em> (<a href="https://github.com/bhklab/ToxicoGx">https://bioconductor.org/packages/devel/bioc/html/ToxicoGx.html</a>), and are available publicly in the <em>ToxicoDB </em>web application (<a href="http://www.toxicodb.ca">www.toxicodb.ca</a>).</p>
Data from: Robust inference on large-scale species habitat use with interview data: the status of jaguars outside protected areas in Central America
Evaluating range-wide habitat use by a target species requires information on species occurrence over broad geographic regions, a process made difficult by species rarity, large spatiotemporal sampling domains, and imperfect detection. We address these challenges in an assessment of habitat use for jaguars (Panthera onca) outside protected areas in Central America. Occurrence records were acquired within 12 putative corridors using interviews with knowledgeable corridor residents. We developed a Bayesian hierarchical occupancy model to gain robust inference, allowing for heterogeneity introduced in the sampling process over space and time, using records of jaguar occurrence prone to false positives and false negatives. Probability of false detection of jaguars increased with the number of interviews conducted per unit (from 5.42% to 7.74% given <4 and ≥4 observers per unit). True probability of detection (mean=0.58) increased with the number of days interviewees spent in a survey unit per year. Failing to account for false positives biased predicted habitat use high (˜1.8x), especially where occurrence records were sparse. Probability of site use by jaguars increased with greater forest cover, prey richness, and distance from human settlements, and decreased with greater agricultural cover, elevation, and distance from protected areas. Site use probabilities averaged 0.15-0.97 by corridor, providing relatively fine-scale resolution of predicted jaguar occurrence consistent with known patterns of jaguar gene flow across Central America. Model validation, accounting for both false positives and negatives in the observation process, indicated moderate correspondence between model-predicted observations and actual observations for withheld data (0.65, 95% CRI 0.59–0.71), with sensitivity and specificity rates of 0.69 (0.61 – 0.77) and 0.59 (0.50 – 0.68), respectively. These results demonstrate that reliable predictions can be achieved despite the complexity of large-scale, interview-based analyses of species occurrence. Synthesis and applications. Our Bayesian hierarchical occupancy model accommodated heterogeneity caused by typical sampling inequities and idiosyncrasies associated with interview data, yielding robust estimates of jaguar habitat use. Our approach is applicable to any wide-ranging and readily identifiable species and has particular utility for rare species in human-dominated landscapes where traditional survey techniques (e.g., camera traps) may be impractical.
ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets (TGGATEs human dataset)
<p>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, <em>ToxicoGx</em> (<a href="http://bioconductor.org/packages/devel/bioc/html/ToxicoGx.html">http://bioconductor.org/packages/devel/bioc/html/ToxicoGx.html</a>), and are available publicly in the <em>ToxicoDB </em>web application (<a href="http://www.toxicodb.ca">www.toxicodb.ca</a>).</p>
Drivers of large-scale geographical variation in sexual systems of woody plants
<p><b>Aim: </b>Sexual systems strongly influence angiosperm evolution, and play important roles in community assembly and species responses to climate change. However, geographical variation in proportions of different sexual systems (dioecy, monoecy, and hermaphroditism) in response to changes in climate, life-history traits and evolutionary age remains poorly understood. Here, we map the geographical variation in proportions of different sexual systems and hypothesize that the prevalence of hermaphrodites increases with aridity due to their advantages in colonizing harsh environment, whereas dioecy is most successful in humid regions with tall-canopy vegetation and old floras.</p> <p><b>Location: </b>China</p> <p><b>Time period: </b>Current</p> <p><b>Major taxa studied:</b> Woody angiosperms</p> <p><b>Methods: </b>Using data on sexual systems and distributions of 10,449 woody species in China, we estimated the proportions of different sexual systems in local floras (50 × 50 km grid cells). Spatial linear models, phylogenetic general linear models and structural equation models were used to compare the relative influences of climate, plant height and evolutionary age on geographical variation in proportions of different sexual systems.</p> <p><b>Results: </b>We found contrasting geographical patterns in the proportions of different sexual systems. The proportions of dioecy and monoecy increased with plant height and were highest in humid regions with older floras, while that of hermaphroditism decreased with plant height and was highest in arid regions with younger floras. Plant height was the strongest correlate of sexual system frequency. Climate influenced sexual system frequency both directly and indirectly via its effects on plant height.</p> <p><b>Main conclusions: </b>Our study provides the first continuous map of sexual system composition in woody floras over a large spatial scale. Our findings suggest that mature plant height, reflecting plant longevity, dominates geographical variation in sexual systems and that the proportions of different sexual systems in local floras may reflect their correlated evolution with traits in response to climate changes.</p>
Data from: Large-scale connectivity, cryptic population structure, and relatedness in Eastern Pacific olive ridley sea turtles (Lepidochelys olivacea)
<p>Endangered species are grouped into genetically discrete populations to direct conservation efforts. Mitochondrial Control Region (mtCR) haplotypes are used to elucidate deep divergences between populations, as compared to nuclear microsatellites that can detect recent structuring. When prior populations are unknown, it is useful to subject microsatellite data to clustering and/or ordination population inference. Olive ridley sea turtles (Lepidochelys olivacea) are the most abundant sea turtle, yet few studies have characterized olive ridley population structure. Recently, clustering results of olive ridleys in the Eastern Tropical Pacific Ocean suggested weak structuring (FST=0.02) between Mexico and Central America. We analyzed mtCR haplotypes, new microsatellite genotypes from Costa Rica, and pre-existing microsatellite genotypes from olive ridleys across the Eastern Tropical Pacific, to further explore population structuring in this region. We subjected inferred populations to multiple analyses to explore the mechanisms behind their structuring. We found 10 mtCR haplotypes from 60 turtles nesting at three sites in Costa Rica, but did not detect divergence between Costa Rican sites, or between Central America and Mexico. In Costa Rica, clustering suggested one population with no structuring, but ordination suggested four cryptic clusters with moderate structuring (FST=0.08, p<0.001). Across the Eastern Tropical Pacific, ordination suggested nine cryptic clusters with moderate structuring (FST=0.103, p<0.001) that largely corresponded to Mexican and Central American populations. All ordination clusters displayed significant internal relatedness relative to global relatedness (p<0.001) and contained numerous sibling pairs. This suggests that broadly dispersed family lineages have proliferated in Eastern Tropical Pacific olive ridleys and corroborates previous work showing basin-wide connectivity and shallow population structure in this region. The existence of broadly dispersed kin in Eastern Tropical Pacific olive ridleys has implications for management of olive ridleys in this region, and adds to our understanding of sea turtle ecology and life-history, particularly in light of the natal-homing paradigm.</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: Bat trait, genetic and pathogen data from large-scale investigations of African fruit bats (Eidolon helvum)
Bats, including African straw-coloured fruit bats (Eidolon helvum), have been highlighted as reservoirs of many recently emerged zoonotic viruses. This common, widespread and ecologically important species was the focus of longitudinal and continent-wide studies of the epidemiological and ecology of Lagos bat virus, henipaviruses and Achimota viruses. Here we present a spatial, morphological, demographic, genetic and serological dataset encompassing 2827 bats from nine countries over an 8-year period. Genetic data comprises cytochrome b mitochondrial sequences (n=608) and microsatellite genotypes from 18 loci (n=544). Tooth-cementum analyses (n=316) provide rare age-specific serologic data for a lyssavirus, a henipavirus and two rubulaviruses. This dataset contributes a substantial volume of data on the ecology of E. helvum and its viruses and will be valuable for a wide range of studies, including viral transmission dynamic modelling in age-structured populations, investigation of seasonal reproductive asynchrony in wide-ranging species, ecological niche modelling, inference of island colonisation history, exploration of relationships between island and body size, and various spatial analyses of demographic, morphometric or serological data.
Data from: Small- to large-scale patterns of ground-dwelling spider (Araneae) diversity across northern Canada
We examined how Arctic spider (Araneae) biodiversity is distributed at multiple spatial scales in Northern Canada using a standardized hierarchical sampling design. We investigated which drivers, environmental or spatial, influence the patterns observed. Spatial patterns of species richness and composition of Arctic spiders were assessed in 12 sites located in Arctic, Subarctic, and North-Boreal regions, across 30 degrees of latitude and 80 degrees of longitude. Variation of diversity was partitioned in relation to multiple environmental and spatial drivers of diversity patterns. Over 23, 000 adult spiders, representing 306 species in 14 families, were collected in Northern Canada, with 107 species (35% of the total species collected) representing new Territorial or Provincial records. Spider diversity was structured at the regional scale across ecoclimatic regions but not with latitude. Longitudinal patterns of spider diversity across Canada may be explained by post-glacial dispersal. At local scales, diversity was non-randomly distributed, and possibly limited by biotic interactions. We recommend the use of ecoclimatic regions as a framework for conservation of biodiversity in Northern Canada and spiders as useful bioindicators which can help us understand the effects of climate change across ecoclimatic regions of northern Canada.
Data from: Novel bird responses to successive large-scale, landscape transformations
Transformation of intact vegetation into new kinds and configurations of human-modified habitats is a well established driver of biodiversity loss. Following initial conversion, many human-dominated landscapes are then subject to further large-scale changes in land use. The impacts on biodiversity of repeated changes in land use remain poorly known, particularly how changes in the matrix interact with initial patterns of vegetation clearing. We used an 18-year study of birds in remnant patches of endangered temperate woodland in south-eastern Australia to quantify the spatial and temporal effects of successive land use transformation in the surrounding landscape. We examined bird response to: (1) initial patterns of landscape modification (creating semi-cleared grazing land dominated by pastures that surrounded remnant woodland patches), (2) subsequent establishment and maturation of exotic tree plantations on the pastures surrounding woodland patches, and (3) additive and interactive effects of both types of landscape transformation. The majority of the 57 bird species modelled responded to conversion of grazing land to exotic plantations, either independently from initial patterns of landscape transformation (20 species), or interactively (18 species) or additively (15 species) with initial landscape transformation. The occurrence of only one species (the Common Bronzewing) was related to patterns of initial transformation but not subsequent transformation due to plantation establishment. Thus, despite many characteristics of the woodland patches within the plantation remaining largely unaltered throughout our 18 year investigation, the matrix had a profound effect on the kinds of species inhabiting them, with such impacts often magnified over time as the matrix continued to change. Plantation establishment triggered new regional-level spatial processes with effects on birds detected in woodland patches up to 2 km away from the plantation. Matrix conversion selected for species with different traits (size, diet and movement patterns) compared to the initial transformation, suggesting it is acting as a different filter on the bird community. New kinds of landscape transformation (such as plantation establishment on previously cleared land) can radically affect the species that have persisted for many decades in previously modified landscapes. This highlights the challenges, but also opportunities, for conserving taxa in ever changing human-dominated environments.
Data from: An optimized protocol for large-scale in situ sampling and analysis of volatile organic compounds
Chemical ecology is an ever‐expanding field with a growing interest in population‐ and community‐level studies. Many such studies are hindered due to lack of an efficient and accelerated protocol for large‐scale sampling and analysis of chemical compounds. Here, we present an optimized protocol for such large‐scale study of volatiles. A large‐scale in situ study to understand role of semiochemicals in variation in mating success of lekking blackbuck was conducted. Suitable methods for sampling and statistical analysis were identified by testing and comparing the efficiencies of available techniques to reduce analysis time while retaining sensitivity and comprehensiveness. Solid‐phase extraction using polydimethylsiloxane, analysis using a semiautomated detection of retention time and base peak, and statistical analysis using random forest algorithm were identified as the most efficient methods for large‐scale in situ sampling and analysis of volatiles. The protocol for large‐scale volatile analysis can facilitate evolutionary and metaecological studies of volatiles in situ from all types of biological samples. The protocol has potential for wider application with the analysis and interpretation methods being suitable for all kinds of semiochemicals, including nonvolatile chemicals.
Data from: Large-scale genetic panmixia in the blue shark (Prionace glauca): a single worldwide population, or a genetic lag-time effect of the "grey zone" of differentiation?
The blue shark Prionace glauca, among the most common and widely studied pelagic sharks, is a top predator, exhibiting the widest distribution range. However, little is known about its population structure and spatial dynamics. With an estimated removal of 10 to 20 million individuals per year by fisheries, the species is classified as "Near Threatened" by International Union for Conservation of Nature. We lack the knowledge to forecast the long-term consequences of such a huge removal on this top predator itself and on its trophic network. The genetic analysis of more than 200 samples collected at broad scale (from Mediterranean Sea, North Atlantic and Pacific Oceans) using mtDNA and nine microsatellite markers allowed to detect signatures of genetic bottlenecks but a nearly complete genetic homogeneity across the entire studied range. This apparent panmixia could be explained by a genetic lag-time effect illustrated by simulations of demographic changes that were not detectable through standard genetic analysis before a long transitional phase here introduced as the "population grey zone". The results presented here can thus encompass distinct explanatory scenarios spanning from a single demographic population to several independent populations. This limitation prevents the genetic-based delineation of stocks and thus the ability to anticipate the consequences of severe depletions at all scales. More information is required for the conservation of population(s) and managements of stocks, which may be provided by large scale sampling not only of individuals worldwide, but also of loci genome-wide.
Data from: Small beetle, large-scale drivers: how regional and landscape factors affect outbreaks of the European spruce bark beetle
Unprecedented bark beetle outbreaks have been observed for a variety of forest ecosystems recently, and damage is expected to further intensify as a consequence of climate change. In Central Europe, the response of ecosystem management to increasing infestation risk has hitherto focused largely on the stand level, while the contingency of outbreak dynamics on large-scale drivers remains poorly understood. To investigate how factors beyond the local scale contribute to the infestation risk from Ips typographus (Col., Scol.), we analysed drivers across seven orders of magnitude in scale (from 103 to 1010 m²) over a 23-year period, focusing on the Bavarian Forest National Park. Time-discrete hazard modelling was used to account for local factors and temporal dependencies. Subsequently, beta regression was applied to determine the influence of regional and landscape factors, the latter characterized by means of graph theory. We found that in addition to stand variables, large-scale drivers also strongly influenced bark beetle infestation risk. Outbreak waves were closely related to landscape-scale connectedness of both host and beetle populations as well as to regional bark beetle infestation levels. Furthermore, regional summer drought was identified as an important trigger for infestation pulses. Large-scale synchrony and connectivity are thus key drivers of the recently observed bark beetle outbreak in the area. Synthesis and applications. Our multiscale analysis provides evidence that the risk for biotic disturbances is highly dependent on drivers beyond the control of traditional stand-scale management. This finding highlights the importance of fostering the ability to cope with and recover from disturbance. It furthermore suggests that a stronger consideration of landscape and regional processes is needed to address changing disturbance regimes in ecosystem management.
Data from: Patterns of local community composition are linked to large-scale diversification and dispersal of clades
At any location, a group of organisms may be represented by several clades. What determines which clades will dominate local communities in terms of their species richness? Here, this relatively neglected question is addressed by analyzing 166 local assemblages of snakes distributed globally. For most regions, local assemblages are dominated by clades with higher global-scale diversification rates and more frequent dispersal into each region, and not by clades that have been present in that region longer. This result contrasts with many other studies of local richness (in other organisms), which show strong impacts of regional colonization time on overall local species richness of clades. Furthermore, even though local assemblages are assembled independently on different continents, most regions have converged on similar patterns of proportional richness. Specifically, a few rapidly diversifying clades dominate most communities around the world. The high diversification rates of these clades are then linked to their high dispersal rates. Similar patterns may occur in many groups, such as plants, frogs, salamanders, birds, and mammals.
Data from: Template for using biological trait groupings when exploring large-scale variation in seafloor multifunctionality
Understanding large-scale spatial variation in ecosystem properties and associated functionality is key for successful conservation of ecosystems. This study provides a template for how to estimate differences in ecosystem functionality over large spatial scales by using groupings of biological traits. We focus on trait groupings that describe three important benthic ecosystem properties, namely bioturbation, community stability and juvenile dispersal. Recognizing that groups of traits interact and are constrained within an organism, we statistically define important functional trait subgroups that describe each ecosystem property. The sub-groups are scored according to their weighted ecological impact to gain an overall estimation of the cumulative expression of each ecosystem property at individual sites. Furthermore, by assigning each property a value relative to its observed maximum, and by summing up the individual property values, we offer an estimate of benthic ecosystem multifunctionality. Based on a spatially extensive benthic data set, we were able to identify coastal areas with high and low potential for the considered benthic ecosystem properties and the measure of ecosystem multifunctionality. Importantly, we show that a large part of the spatial variation in functional trait sub-groups and in benthic ecosystem multifunctionality was explained by environmental change. Our results indicate that through this simplification it is possible to estimate the functionality of the seafloor. Such information is vital in marine spatial planning efforts striving to balance the utilization with the preservation of natural resources.
Data from: The large-scale drivers of population declines in a long-distance migratory shorebird
Migratory species can travel tens of thousands of kilometers each year, spending different parts of their annual cycle in geographically distinct locations. Understanding the drivers of population change is vital for conserving migratory species, yet the challenge of collecting data over entire geographic ranges has hindered attempts to identify the processes leading to observed population changes. Here, we use remotely sensed environmental data and count data to investigate the factors driving variability in abundance in two subspecies of a long-distance migratory shorebird, the bar-tailed godwit (Limosa lapponica). We compiled a spatially and temporally explicit dataset of three environmental variables to identify the conditions experienced by each subspecies in each stage of their annual cycle (breeding, non-breeding and staging). We used a Bayesian N-mixture model to analyze 18 years of monthly count data from 21 sites across Australia and New Zealand in relation to the remote sensing datasets. We found that the abundance of one subspecies (L. l. menzbieri) in their non-breeding range was related to climate conditions in breeding grounds, and detected sustained population declines between 1995 and 2012 in both subspecies (L. l. menzbieri, -6.7% and L. l. baueri, -2.1% year-1). To investigate the possible causes of the declines, we quantified changes in habitat extent at 22 migratory staging sites in the Yellow Sea, East Asia, over a 25-year period and found -1.7% and -1.2% year-1 loss of habitat at staging sites used by L. l. menzbieri and L. l baueri, respectively. Our results highlight the need to identify environmental and anthropogenic drivers of population change across all stages of migration to allow the formulation of effective conservation strategies across entire migratory ranges.
Data from: Large-scale parentage analysis reveals reproductive patterns and heritability of spawn timing in a hatchery population of steelhead (Oncorhynchus mykiss)
Understanding life history traits is an important first step in formulating effective conservation and management strategies. The use of artificial propagation and supplementation as such a strategy can have numerous effects on the supplemented natural populations and minimizing life history divergence is crucial in minimizing these effects. Here, we use single nucleotide polymorphism (SNP) genotypes for large-scale parentage analysis and pedigree reconstruction in a hatchery population of steelhead, the anadromous form of rainbow trout. Nearly complete sampling of the broodstock for several consecutive years in two hatchery programmes allowed inference about multiple aspects of life history. Reconstruction of cohort age distribution revealed a strong component of fish that spawn at 2 years of age, in contrast to programme goals and distinct from naturally spawning steelhead in the region, which raises a significant conservation concern. The first estimates of variance in family size for steelhead in this region can be used to calculate effective population size and probabilities of inbreeding, and estimation of iteroparity rate indicates that it is reduced by hatchery production. Finally, correlations between family members in the day of spawning revealed for the first time a strongly heritable component to this important life history trait in steelhead and demonstrated the potential for selection to alter life history traits rapidly in response to changes in environmental conditions. Taken together, these results demonstrate the extraordinary promise of SNP-based pedigree reconstruction for providing biological inference in high-fecundity organisms that is not easily achievable with traditional physical tags.
The magnitude of large-scale tree mortality caused by the invasive pathogen Phytophthora ramorum
<p>Forest pathogens are important drivers of tree mortality across the globe but it is exceptionally challenging to gather and build unbiased quantitative models of their impacts, which has resulted in few estimates matching the scale of disease. Here we harness the rare dataset matching the spatial scale of pathogen invasion, host, and disease heterogeneity to estimate infection and mortality for the four most susceptible host species of <em>Phytophthora ramorum</em>, an invasive pathogen that drives the most important biological cause of tree mortality in a broad geographic region of coastal California and southwest Oregon. As of 2012, the most current field survey year, we estimate 17.5 (± 4.6 95% CI) million tanoak (<em>Notholithocarpus densiflorus)</em> stems were pathogen-killed with an additional 71 (± 21.5) million infected. We estimated 9.0 million (± 2.2) coast live oak (<em>Quercus agrifolia)</em> and 1.7 million (± 0.5) California black oak (<em>Quercus kelloggii</em>) stems are disease impacted (mortality and infection combined). Lastly, our estimates showed 95.23 million (± 8.6) million infected California bay laurel (<em>Umbellularia californica</em>), which does not suffer mortality from infection and represents a critical source of continued spread. Using an extensive dataset on mortality rates of infected individuals we estimate that cumulative mortality likely increased from 20.8 to 42.8 million individual stems between 2012 and 2019 for all species. While these impacts are substantial, the majority of host populations occur in a yet to be invaded region of northern California indicating that the disease will intensify in the coming decades.</p>
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.