cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0k6djhb19
title: Do genetic differences in growth thermal reaction norms maintain genetic variation in timing of diapause induction?

description: An optimal timing for diapause induction through the sexual production of
 dormant propagules is expected in organisms with temporary populations.
 Yet, empirical studies often find high within-population genetic variation
 in the sexual production of such propagules, suggesting that this is a
 common feature of such organisms. Here, we hypothesize that genetic
 variation in the propensity to produce dormant propagules, Pd, is
 maintained by a genotype-by-environment interaction in clonal reproductive
 rates, where fast-growing genotypes within an environment should delay
 diapause relative to slow-growing genotypes. From this, we derive two
 predictions. First, if reaction norms of clonal reproduction cross between
 two environments, the genetic correlation of Pd between these environments
 should be negative. Second, the correlation between plasticity values of
 clonal reproduction and Pd should be negative. We tested these predictions
 by quantifying ephippia production in genotypes of a population of the
 facultative sexual cladoceran Daphnia magna at two temperatures. The
 population biomass at the onset of ephippia production was used as a
 measure of Pd, whereas juvenile somatic growth rate was used as a proxy
 for clonal reproductive rate. Plasticity for both measurements was derived
 from thermal reaction norms. Our results did not support either
 prediction, as neither the genetic correlation of Pd between environments,
 nor the correlation between plasticity values of growth and Pd were found
 to be significant. Our results suggest that genetic variation in the
 timing of diapause is not maintained by genetic differences in thermal
 clonal reproduction reaction norms. We propose as an alternative
 hypothesis that if there is across year variation in how stochastically
 the environment deteriorates, fluctuating selection may favor genotypes
 with different Pd between years.
description: Data from a laboratory experiment on the relationship
 between genetic variation in thermal growth performance and diapause
 induction.
DOI: 10.5061/dryad.2rbnzs7p5
title: Reference data and simulated communities for 16S rRNA GCN prediction

description: 16S rRNA gene has been widely used in microbial diversity studies to
 determine the community composition and structure. 16S rRNA gene copy
 number (16S GCN) varies among microbial species and this variation
 introduces biases to the relative cell abundance estimated using 16S rRNA
 read counts. To correct the biases, methods (e.g., PICRUST2) have been
 developed to predict 16S GCN. 16S GCN predictions come with inherent
 uncertainty, which is often ignored in the downstream analyses. However, a
 recent study suggests that the uncertainty can be so great that copy
 number correction is not justified in practice. Despite the significant
 implications in 16S rRNA-based microbial diversity studies, the
 uncertainty associated with 16S GCN predictions has not been well
 characterized. Here we develop a novel method to better model and capture
 the inherent uncertainty. Using cross-validation, we show that our method
 provides robust confidence estimates for the GCN predictions and
 outperforms PICRUST2 in both precision and recall. We found that 16S GCN
 correction should improve compositional and functional profiles estimated
 using 16S rRNA reads. On the other hand, we found that GCN variation has
 limited impacts on PCoA, PERMANOVA and random forest test, and 16S rRNA
 GCN correction is unnecessary in beta-diversity analyses. 
description: Reference genomes were downloaded from NCBI RefSeq database
 in April 2021. The annotated 16S rRNA genes were counted and one
 representative sequence was selected fro each genome. The reference
 phylogeny was inferred using RAxML version 8.2. The 16S rRNA GCN for SILVA
 non-redundant OTU99 was predicted using RasperGade16S. The simulated
 communities were generated using custom scripts.
description: The reference tree is provided in Newick format. The simulated
 communities are provided as binary RDS files that can be accessed through
 function readRDS() in R.
DOI: 10.5061/dryad.wpzgmsbnk
title: Potential risk zone for anthropogenic mortality of carnivores in Gandaki province, Nepal

description: Anthropogenic pressures in human-dominated landscapes often contribute to
 wildlife mortality. Carnivores are especially vulnerable to human-induced
 mortality due to the perceived threat to livestock and humans. Despite
 having widespread conservation implications, carnivore mortality data has
 been largely underutilized within Nepal. This study utilized Maxent to
 identify high-risk areas and explore the contribution of habitat
 attributes associated with carnivore mortality using the casualty database
 within the Gandaki province of central Nepal. We categorized the risk to
 carnivore species in three taxonomic groups: Felid, Viverridae, and
 Herpestidae, and identified a 3704 km2 area within the province at high
 risk for carnivore casualty. The middle mountains were the riskiest
 physiographic zone, and the Annapurna Conservation Area represented the
 largest risk zone among the four protected areas. Agricultural land was
 the most problematic area in terms of carnivore casualty. The human
 population was positively associated with high-risk areas and the number
 of casualties, whereas protected area cover had a negative association.
 This study identified that the common leopard was at the highest risk of
 mortality and therefore would benefit from the implementation of an action
 plan and species-specific conservation strategies, especially within
 identified high-risk zones. An expansion of protected areas in the middle
 mountain region would serve to greatly reduce carnivore casualty. Species
 distribution modeling can be further used with national-level spatial and
 temporal mortality data to identify the most prominent casualty times and
 pinpoint potential casualty locations throughout the country.
description: This data sheet was collected by visiting the division forest
 office, rescue center, and protected area offices within the
 province.
DOI: 10.15468/dl.8mgu7z
title: Occurrence Download

description: A dataset containing 4802 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is one of (North America, Europe)",
 "GbifRegion is one of (North America, Europe and Central Asia)",
 "TaxonKey is Hydrastis canadensis"
 ]
}

 The dataset includes 4802 records from 94 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002925-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.31166890
title: The synergistic effect of warming and nitrogen addition on carbon sequestration in a saline-alkaline grassland

description: The data support for the synergistic effect of warming and nitrogen addition on carbon sequestration in a saline-alkaline grassland.
DOI: 10.6084/m9.figshare.31166890.v1
title: The synergistic effect of warming and nitrogen addition on carbon sequestration in a saline-alkaline grassland

description: The data support for the synergistic effect of warming and nitrogen addition on carbon sequestration in a saline-alkaline grassland.
DOI: 10.5061/dryad.zpc866t90
title: Temporal variability of microparticles under the Seattle Aquarium, WA: Documenting the global Covid‐19 pandemic

description: Anthropogenic debris including microparticles (MP; &lt;5mm) are
 ubiquitous in marine environments. The Salish Sea experiences seasonal
 fluctuations in precipitation, river discharge, sewage overflow events,
 and tourism– all variables previously thought to have an impact on MP
 transport and concentrations. Our goals are two-fold: 1) Describe
 long-term MP contamination data including concentration, type, and size
 and 2) Determine if seasonal MP concentrations are dependent on
 environmental or tourism variables in Elliott Bay, Salish Sea. We sampled
 100 L of seawater at depth (~9 m) at the Seattle Aquarium approximately
 every two weeks 2019 – 2020 and used an oil extraction protocol to
 separate MP. We found MP concentrations ranged from 0 – 0.64 particles L⁻¹
 and fibers were the most common type observed. Microparticle concentration
 exhibited a breakpoint on April 10, 2020, where estimated slope and
 associated MP concentration significantly declined. Further, when
 considering both environmental as well as tourism variables, temporal MP
 concentration was best described by a mixed-effects model with tourism as
 the fixed effect and the person counting MP as the random effect. While
 monitoring efforts presented here set out to identify effects of
 seasonality and interannual differences in MP concentrations, it instead
 captured an effect of decreased tourism due to the global Covid-19
 pandemic. Long-term monitoring is critical to establish temporal MP
 concentrations and to help researchers understand if there are certain
 events, both seasonal and sporadic (e.g. rain events, tourism, or global
 pandemics), when the marine environment is more at risk from anthropogenic
 pollution.
DOI: 10.5061/dryad.x95x69pjz
title: Data from: Descriptive multi-agent epidemiology via molecular screening on Atlantic salmon farms in the northeast Pacific Ocean

description: Rapid expansion of salmon aquaculture has resulted in high-density
 populations that host diverse infectious agents, for which surveillance
 and monitoring are critical to disease management. Screening can reveal
 infection diversity from which disease arises, differential patterns of
 infection in live and dead fish that are difficult to collect in wild
 populations, and potential risks associated with agent transmission
 between wild and farmed hosts. We report results from a multi-year
 infectious-agent screening program of farmed salmon in British Columbia,
 Canada, using quantitative PCR to assess presence and load of 58 infective
 agents (viruses, bacteria, and eukaryotes) in 2931 Atlantic salmon (Salmo
 salar). Our analysis reveals temporal trends, agent correlations within
 hosts, and agent-associated mortality signatures. Multiple agents, most
 notably Tenacibaculum maritimum, were elevated in dead and dying salmon.
 We also report detections of agents only recently shown to infect farmed
 salmon in BC (Atlantic salmon calicivirus, Cutthroat trout virus-2),
 detection in freshwater hatcheries of two marine agents (Kudoa thyrsites
 and Tenacibaculum maritimum), and detection in the ocean of a freshwater
 agent (Flavobacterium psychrophilum). Our results provide information for
 farm managers, regulators, and conservationists, and enable further work
 to explore patterns of multi-agent infection and farm/wild transmission
 risk.
description: See published methods.
DOI: 10.6078/d1fm75
title: Supporting data for: Estimate of OH trends over one decade in North American cities

description: The hydroxyl radical (OH) is the most important oxidant on global and
 local scales in the troposphere. Urban OH controls the removal rate of
 primary pollutants and triggers the production of ozone. Interannual
 trends of OH in urban areas are not well documented or understood due to
 the short lifetime and high spatial heterogeneity of OH. We utilize
 machine learning with observational inputs emphasizing satellite remote
 sensing observations to predict surface OH in 49 North American cities
 from 2005 to 2014. We observe decadal changes in the summertime OH with
 wide variation among different cities. Compared to the summertime OH in
 2005, 3 cities show an significant increase of OH whereas in 27 cities OH
 decreases in 2014. The year to year variation of OH is mapped to the
 decline of the NO2 column. We conclude that these cities in this
 analysis are either in the NOx limited regime or at the transition from a
 NOx suppressed regime to a NOx limited regime. The result
 emphasizes that controlling NOx emissions will be most effective in
 regulating the ozone pollution over cities.
description: This dataset was produced by
 doi: 10.5281/zenodo.5296044 It contains machine
 learning inputs from both WRF-Chem and satellite observations.
description: The usage notes are described in README.docx file.
DOI: 10.5061/dryad.gxd2547mx
title: Manduca sexta experience high parasitoid pressures in the field but minor fitness costs of consuming plant secondary compounds

description: Plant-herbivore co-evolutionary interactions have led
 to a range of plant
 defenses that minimize insect damage and a suite of counter-adaptations that allow herbivores to feed on defended plants. Consuming plant secondary compounds results in herbivore growth and developmental costs but can have beneficial effects such as deterrence or harm of parasitoid enemies. Therefore, the role of secondary compounds on herbivore fitness must be considered in the context of the abundance and level of harm from natural enemies and the costs herbivores incur feeding on plant secondary compounds. In this study, I combined field measurements of Cotesia congregata wasp parasitism pressure with detailed measurements of the costs of plant secondary compounds across developmental stages in the herbivore host, Manduca sexta. I show that C. congregata parasitoids exert large negative selective pressures, killing 31-57% of M. sexta larvae in the field. Manduca sexta developed fastest during instars most at risk for parasitoid oviposition but growth was slowed by consumption of plant secondary compounds. The negative effects of consuming plant secondary compounds as larvae influenced adult size traits but there were no immune, survival, or fecundity costs. These results suggest that developmental costs experienced by M. sexta herbivores consuming defensive compounds are minor in comparison to the strong negative survival pressures from abundant parasitoid enemies.
DOI: 10.7291/d1209n
title: Effects of insect herbivory on seedling mortality in restored and remnant tropical forest

description: Insect herbivory is one of the major drivers of seedling mortality in the
 tropics and influences plant abundances and community composition.
 Anthropogenic disturbance can alter patterns of insect herbivory with
 potential consequences on plant communities in restored forests. We
 planted seedlings of early- and later-stage successional tree species in
 13–15-year-old restored and remnant tropical forests. We then either
 excluded insect herbivores or left seedlings exposed to examine how insect
 herbivory-affected seedling mortality. Early-successional seedlings
 experienced similar decreases in mortality when insect herbivores were
 excluded from both restored and remnant forest sites, but this effect was
 smaller and driven by only a few species in restored forests.
 Later-successional seedlings experienced a stronger decrease in mortality
 between open and insect-excluded treatments in remnant than restored
 sites. Our results suggest that herbivory-driven seedling mortality is
 lower in restored forests, particularly for later-successional seedlings.
 Results are encouraging from a restoration perspective because recruitment
 of later-successional seedlings is a key component of ecosystem recovery.
 However, if reductions in seedling mortality continue over the long term,
 this may affect tree community composition as succession progresses.
DOI: 10.5061/dryad.g79cnp5qd
title: Phenotypic, genetic, and epigenetic data from 29 Serratia marcescens strains from an evolution experiment

description: This dataset contains phenotypic, genetic, and epigenetic data from 29
 Serratia marcescens strains from an evolution experiment. In a previous
 study (https://doi.org/10.1111/evo.12148), the bacterium S. marcescens was
 left to evolve from a common ancestor culture in replicated populations
 kept under different temperature regimes, and evolved clones were isolated
 and their phenotypes measured. Here, we randomly selected 28 evolved
 clones from this experiment, as well as the original reference strain, and
 used PacBio single molecule real-time (SMRT) sequencing to obtain genetic
 and epigenetic (N6-methyladenine modifications, m6A) data. The goal of our
 study was to obtain a detailed description of the methylation landscape of
 S. marcescens and to examine the potential contributions of genetic and
 epigenetic changes to phenotypic adaptation.
description: A full description of the methods are available in Ketola et al.
 2013 (https://doi.org/10.1111/evo.12148) for phenotypic measurements (and
 for the original evolution experiment) and in Bruneaux et al. 2021
 (http://dx.doi.org/10.1080/15592294.2021.1966215) for the PacBio
 sequencing leading to the genetic and epigenetic data.
DOI: 10.5061/dryad.0k6djhb1b
title: Temperature perturbation of cellular host-microbe interactions explains continent-wide endosymbiont prevalence

description: Endosymbioses influence host physiology, reproduction, and fitness, but
 these relationships require efficient microbe transmission between host
 generations to persist. Maternally
 transmitted Wolbachia are the most common known
 endosymbionts, but their frequencies vary widely within and among host
 populations for unknown reasons. Here we integrate genomic, cellular, and
 phenotypic analyses with mathematical models to provide an unexpectedly
 simple explanation for
 global wMel Wolbachia prevalence
 in Drosophila melanogaster. Cooling temperatures
 decrease wMel cellular abundance at a key stage of host
 oogenesis, producing temperature-dependent variation in maternal
 transmission that plausibly explains latitudinal clines of wMel
 frequencies on multiple continents. wMel sampled from a
 temperate climate targets the germline more efficiently in the
 cold than a recently differentiated tropical variant (~2,200 years ago),
 indicative of rapid wMel adaptation to climate. Genomic analyses
 identify a very narrow list of wMel alleles—most notably,
 a derived stop codon in
 the major Wolbachia surface protein WspB—that
 underlie thermal sensitivity of cellularWolbachia abundance and
 covary with temperature globally. Decoupling temperate wMel and
 host genomes further reduces transmission in the cold, a pattern that is
 characteristic of host-microbe co-adaptation to a temperate
 climate. Complex interactions among Wolbachia, hosts,
 and the environment (GxGxE) mediate wMel cellular abundance and
 maternal transmission, implicating temperature as a key determinant
 of Wolbachia spread and equilibrium frequencies, in
 conjunction with Wolbachia effects on host fitness and
 reproduction. Our results motivate strategic use of locally
 selected wMel variants for Wolbachia-based biocontrol
 efforts, which currently protect millions of individuals from arboviruses
 that cause human disease.
DOI: 10.57841/casdc.0007114
title: 铁基超导线材性能调控实验数据
DOI: 10.5061/dryad.rr4xgxd8x
title: An abundance and morphology-based similarity index

description: Classic similarity indices measure community resemblance in terms of
 incidence (the number of shared species) and abundance (the extent to
 which the shared species are an equivalently large component of the
 ecosystem). Here we describe a general method for increasing the amount of
 information contained in the output of these indices and describe a new
 “soft” ecological similarity measure (here called soft Chao-Jaccard
 similarity). The new measure quantifies community resemblance in terms of
 shared species, while accounting for intraspecific variation in abundance
 and morphology between samples. We demonstrate how our proposed measure
 can reconstruct short ecological gradients using random samples of taxa,
 recognizing patterns that are completely missed by classic measures of
 similarity. To demonstrate the utility of our new index, we reconstruct a
 morphological gradient driven by river flow velocity using random samples
 drawn from simulated and real-world data. Results suggest that the new
 index can be used to recognize complex short ecological gradients in
 settings where only information about specimens is available. We include
 open-source R code for calculating the proposed index.
description: Author-created R code (DD), randomly generated data, and data
 pulled from published literature (see README document for more
 information).
DOI: 10.5061/dryad.tmpg4f504
title: Microbial diversity regulates ecosystem multifunctionality during natural secondary succession

description: Natural forest succession after disturbances is one of the most important
 restoration strategies. However, the responses of ecosystem
 multifunctionality during natural forest succession remains poorly
 understood in forest ecosystem. Here we evaluated how the ecosystem
 multifunctionality including nutrient cycling, carbon stocks, water
 regulation, decomposition, wood production and symbiosis develops using a
 chronosequence, and identified the key factors contributing to the
 variations in the ecosystem multifunctionality during natural forest
 succession. We provide evidence that the ecosystem multifunctionality
 gradually increased along with succession stages. The individual functions
 of carbon stocks and water regulation also exhibited increasing patterns
 with stand development. The microbial diversity were more principal
 factors than plant diversity and soil properties for the explanation of
 changes in the ecosystem multifunctionality. The regression analysis
 showed that the diversity of bacteria, general fungi, actinomycetes,
 nematodes, G+ bacteria and G- bacteria significantly and positively
 associated with ecosystem multifunctionality. Soil nematodes exhibited
 significantly positive correlation with most of the individual functions.
 Synthesis and Applications: Taken together, our results demonstrate that
 natural forest restoration plays a key role in promoting ecosystem
 multifunctionality, and emphasize the importance of soil microbial
 diversity for the maintenance of ecosystem functions and health.
DOI: 10.5061/dryad.2jm63xsq8
title: Richness, not evenness, of invasive plant species promotes invasion success into native plant communities via selection effects

description: Native plant communities are often invaded by multiple alien species. It
 is still unclear how increasing diversity of alien invasive species
 suppresses the growth of native species and thus contributes to invasion
 success. In the subtropical monsoon region of Southeast China, we
 experimentally created a native plant community with 18 herbaceous
 species. One week later, we let it be invaded by either zero (controls
 without invasion), one, two, four or eight alien plant species, with
 either high or low species evenness. After a four-month growth period we
 harvested the aboveground biomass of each species. We found that
 increasing invasive species richness significantly increased invasive
 plant biomass, the biomass of all invasive and native plant species within
 the community, and invasion success (the ratio of invasive plant biomass
 to the biomass of all native and invasive plants), but it did not
 significantly reduce native plant biomass. Experimentally manipulating
 invasive species evenness did not influence invasion success and did not
 show any differential suppression effects on native plants. One invasive
 species, Sesbania cannabina, became dominant in terms of plant biomass,
 irrespective of its proportion in the alien plant mixtures. Throughout
 this experiment, effects of invasive species richness on invasion success
 were mainly due to such selection effects among the invasive species. On
 the other hand, the unchanged biomass of native species under increasing
 invasive plant richness suggests the presence of at least partly
 complementary resource niches between invasive and native species.