cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.xd2547dkn
title: Data to accompany from: Effects of neonicotinoid seed treatments on wildbee populations and soybean and corn fields in eastern Ontario

description: Neonicotinoid-coated corn and soybean seeds are a common crop in Canada
 and the US. A growing body of research is demonstrating that, through
 various exposure routes, neonicotinoids can impact a suite of non-target
 organisms including beneficial insects such as bees. However, to date,
 only a few studies have examined the effects of neonicotinoids in field
 settings. We assessed the relationship between agricultural crop soil
 neonicotinoid levels and wild bee abundance and diversity at 16
 agricultural sites representing different soil neonicotinoid levels. We
 detected clothianidin at 11 sites, thiamethoxam at three sites;
 imidacloprid was not detected. Hedgerow and crop soils were consistent in
 terms of where clothianidin was detected; thiamethoxan was not detected in
 hedgerow soils. Based on model outcomes, fields with higher levels of soil
 neonicotinoids exhibited significantly lower wild bee abundance and
 diversity than those with low or no neonicotinoids detected. Crop soil
 neonicotinoid level, hedgerow floral resource abundance and crop type were
 consistent predictors of bee abundance across models; only neonicotinoid
 level and crop type were significant predictors of diversity. Our results
 are consistent with recent findings in the midwestern US, and underscore
 the potential risk of soil neonicotinoids to wild bee populations across
 regions and crop systems.
description: Field data (wild bee surveys with pan traps, soil samples).
 Pesticide tests were performed on the soil samples as per the methods in
 the paper.
DOI: 10.7272/q6dj5cwd
title: PhIP-Seq/VirScan Coronavirus phage display assay in maternal-infant dyads

description: We investigated antibody linear epitope binding and transplacental
 transfer using the PhIP-seq/VirScan SARS-CoV-2 Spike protein phage display
 array in mother-infant dyads at the time of birth. SARS-CoV-2
 antibody linear epitope binding after vaccination during pregnancy showed
 high levels of binding in carboxy terminal of N-terminal, S1/S2 cleavage
 site, and S2 — with multiple immunodominant regions found in the majority
 of mothers and infants.
description: Description of methods used for collection/generation of
 data: <strong>PhIP-Seq/VirScan Coronavirus phage
 display assay</strong> <em>Immunoprecipitation of phage-bound
 patient antibodies</em> Maternal
 plasma at delivery and cord plasma were evaluated by PhIP-Seq/Virscan
 Coronavirus phage display. Construction of the Coronavirus PhIP-Seq
 library and detailed methods for immunoprecipitation, sequencing, and
 bioinformatic processing of data are identical to what has previously been
 described. For the purposes of the analysis conducted in this study,
 analysis was restricted to sero-reactivity against the SARS-CoV-2 Spike
 protein. As previously described, a total of two rounds of amplification
 and selection were performed for all PhIP-Seq analyses.
 <em>Next Generation Sequencing library
 prep</em> Amplicon sequencing library preps were
 performed using the Labcyte Echo 525 and an Integra Via Flow 96 and were
 identical to what has previously been described. All libraries were pooled
 by equal volume, cleaned and size selected using Ampure XP beads at 1.0X
 per manufacturer’s protocol. Libraries were quantified by High Sensitivity
 DNA Qubit and quality-checked by High Sensitivity DNA Bioanalyzer.
 Sequencing was then performed on a NovaSeq S1 (300 cycle kit with 1.3
 billion clusters) aiming for sequencing depths of at least 1 million reads
 per sample. <em>Bioinformatic Analysis of
 PhIP-Seq Data</em> Sequencing reads were aligned
 to a Human coronavirus reference database of the full viral peptide
 library using the Bowtie2 aligner. For all VirScan libraries, the null
 distribution of each peptide’s log10(rpK) was modeled using a set of 95
 pre-pandemic, healthy control sera. All counts were augmented by 1 to
 avoid zero counts in the healthy control sera samples.
DOI: 10.5061/dryad.5dv41ns89
title: Microsatellite data for rufous-and-white wren population genetics

description: Among tropical organisms, heightened habitat specialization, limited natal
 dispersal, and strong philopatry suggest that many species may experience
 reduced rates of gene flow. Diverse forms of barriers, including
 geographic, ecological, and behavioural barriers, further promote genetic
 divergence among tropical bird populations. In this study, we extend our
 comprehension of gene flow in tropical birds by examining population
 genetic structure in a widespread insectivorous songbird of the
 neotropics: the Rufous-and-white Wren (Thryophilus rufalbus). We explore
 the effects of geographic distance and habitat connectivity on genetic
 structure using 10 microsatellite loci and nuclear and mitochondrial
 sequence data. We report high levels of genetic divergence and population
 structure with reduced contemporary gene flow between populations over a
 500 km transect in Nicaragua and Costa Rica. Mitochondrial DNA and nuclear
 sequence data indicate that two distinct mtDNA genetic groups came into
 contact in northwestern Costa Rica; molecular dating suggests that the
 genetic patterns arose as a result of Pleistocene glaciations. Geographic
 distance and habitat connectivity predicted genetic structure, but
 explained a relatively low proportion of the observed contemporary genetic
 variation. Patterns were similar for both males and females. Our research
 demonstrates the deep genetic divergence in tropical birds and that
 genetic differentiation can occur over a relatively short distance. For
 tropical birds, strong limits to gene flow likely arise as a result of
 limited dispersal from natal populations.
description: # Microsatellite data for rufous-and-white wren population genetics
 Dataset DOI: [10.5061/dryad.5dv41ns89](10.5061/dryad.5dv41ns89) ##
 Description of the data and file structure Microsatellite dataset that
 accompanies the article "Habitat connectivity, gene flow, and
 population genetic structure in a Neotropical understory insectivore, the
 Rufous-and-white Wren" in Ornithology:
 https://doi.org/10.1093/ornithology/ukac030. ### File: README.txt
 Abbreviated README describing the data. ### File:
 ORNITH-21-158_Dryad_Data_file.csv Dataset includes individuals
 identification for each sample, population that they were collected from,
 latitiude and longitude for each sampling site, and microsatellite
 genotyping at 10 microsatellite loci (labelled a and b as these loci are
 biallelic). #### Variables: * BirdID = individual name for each sample *
 Sex = male or female * Population = Nicaragua (NIC), Mointe Verde (MV),
 Rincon de la Vieja (RV), Central Valley (CV), and Santa Rosa (SR). *
 Latitude = Latitude * Long = Longitude * Loci = Tru20, Tru11, RWWR2,
 Tru18, Tru25, Tru08, Tru24, ThPl14, ThPl26, and ThPl30. * a = allele 1 * b
 = allele 2
DOI: 10.5061/dryad.63xsj3v54
title: Data from: Genomic regions associate with major axes of variation driven by gas exchange and leaf construction traits in cultivated sunflower (Helianthus annuus L.)

description: Stomata and leaf veins play an essential role in transpiration and the
 movement of water throughout leaves. These traits are thus thought to play
 a key role in the adaptation of plants to drought and a better
 understanding of the genetic basis of their variation and coordination
 could inform efforts to improve drought tolerance. Here, we explore
 patterns of variation and covariation in leaf anatomical traits and
 analyze their genetic architecture via genome-wide association (GWA)
 analyses in cultivated sunflower (Helianthus annuus L.). Traits related to
 stomatal density and morphology as well as lower order veins were manually
 measured from digital images while the density of minor veins was
 estimated using a novel deep learning approach. Leaf, stomatal, and vein
 traits exhibited numerous significant correlations that generally followed
 expectations based on functional relationships. Correlated suites of
 traits could further be separated along three major principal component
 (PC) axes that were heavily influenced by variation in traits related to
 gas exchange, leaf hydraulics, and leaf construction. While there was
 limited evidence of colocalization when individual traits were subjected
 to GWA analyses, major multivariate PC axes that were most strongly
 influenced by several traits related to gas exchange or leaf construction
 did exhibit significant genomic associations. These results provide
 insight into the genetic basis of leaf trait covariation and showcase
 potential targets for future efforts aimed at modifying leaf anatomical
 traits in sunflower.
description: Detailed methods can be found in the publication "Genomic
 regions associate with major axes of variation driven by gas exchange and
 leaf construction traits in cultivated sunflower
 (<em>Helianthus</em> <em>annuus</em> L.)" in
 The Plant Journal.
description: Data from paper entitled "Genomic regions associate with
 major axes of variation driven by gas exchange and leaf
 construction traits in cultivated sunflower (Helianthus annuus L.)"
 in <em>The Plant Journal.</em> Raw images are included for
 leaf scans, microscope images of stomata and veins and scanned images of
 cleared leaves. Spreadsheets are included for the experimental design,
 genotype averaged data, and a trait list.
DOI: 10.5061/dryad.3bk3j9knc
title: Individual growth of the Flathead Knobscaled Lizard, Xenosaurus platyceps, from tropical and temperate populations

description: Growth rates of ectotherms are frequently affected by environmental
 conditions, such as temperature, precipitation, and prey availability.
 However, local adaptation to environmental conditions could influence
 geographic variation in growth rates. We studied growth rates of the
 Flathead Knob-scaled Lizard, Xenosaurus platyceps, from a tropical
 population and a temperate population in Tamaulipas, Mexico. We used a
 field study and a common garden experiment to examine the extent and
 potential causes of variation in individual growth rates between these two
 populations from contrasting environments. Field-determined growth rates
 in the tropical population were greater than those in the temperate
 population. In a laboratory common garden experiment that manipulated food
 availability and temperature for neonates from each population, neonates
 from the tropical population grew faster than those from the temperate
 population. Neonates kept at higher temperatures grew faster than those
 kept at lower temperature. In addition, growth rates of neonates from
 temperate and tropical populations did not differ at low temperature, but
 neonates from the tropical population grew faster at the higher
 temperature than did the neonates from the temperate population. Food
 treatment did not affect individual growth rates in these lizards,
 although there was a trend for neonates grown with higher food
 availability to grow faster. Our results suggest that not only does the
 warm environment of the tropical population contribute to the observed
 differences in field growth rates, but there is a genetic difference in
 the ability of the tropical population to take advantage of the warmer
 temperatures to increase growth rates.
description: We used a field study and a
 common garden experiment to examine the extent and potential causes of
 variation in individual growth rates between tropical and temperate
 populations.
description: Data is in plain text files.
DOI: 10.5061/dryad.m63xsj44v
title: Switchgrass metabolomics reveals striking genotypic and developmental differences in specialized metabolic phenotypes

description: Switchgrass (Panicum virgatum L.) is a bioenergy crop that grows
 productively on lands not suitable for food production and is an excellent
 target for low-pesticide input biomass production. We hypothesize that
 resistance to insect pests and microbial pathogens is influenced by
 low-molecular-weight compounds known as specialized metabolites. We
 employed untargeted liquid chromatography–mass spectrometry, quantitative
 gas chromatography–mass spectrometry (GC–MS), and nuclear magnetic
 resonance spectroscopy to identify differences in switchgrass ecotype
 metabolomes. This analysis revealed striking differences between upland
 and lowland switchgrass metabolomes as well as distinct developmental
 profiles. Terpenoid- and polyphenol-derived specialized metabolites were
 identified, including steroidal saponins, di- and sesqui-terpenoids, and
 flavonoids. The saponins are particularly abundant in switchgrass extracts
 and have diverse aglycone cores and sugar moieties. We report seven
 structurally distinct steroidal saponin classes with unique steroidal
 cores and glycosylated at one or two positions. Quantitative GC–MS
 revealed differences in total saponin concentrations in the leaf blade,
 leaf sheath, stem, rhizome, and root (2.3 ± 0.10, 0.5 ± 0.01, 2.5 ± 0.5,
 3.0 ± 0.7, and 0.3 ± 0.01 μg/mg of dw, respectively). The quantitative
 data also demonstrated that saponin concentrations are higher in roots of
 lowland (ranging from 3.0 to 6.6 μg/mg of dw) than in upland (from 0.9 to
 1.9 μg/mg of dw) ecotype plants, suggesting ecotypic-specific biosynthesis
 and/or biological functions. These results enable future testing of these
 specialized metabolites on biotic and abiotic stress tolerance and can
 provide information on the development of low-input bioenergy crops.
DOI: 10.5061/dryad.9ghx3ffkx
title: Data of subjective poverty, public services supply, and livelihood capital

description: Poverty is not only an economic problem but also a social problem, and
 there are certain limitations of objective poverty based on the
 population's income. It does not reflect the residents' true
 feelings regarding education opportunities, pension and medical security,
 and participation in decision-making. Researchers have studied it
 intensively in different objective dimensions of Chinese poverty, and
 little attention has been paid to subjective poverty. This study analyzes
 how public services supply, livelihood capital, and livelihood strategies
 affect subjective perceptions of poverty.
DOI: 10.6078/d1f412
title: Solid-state nuclear magnetic resonance data from: Covalent organic frameworks for carbon dioxide capture from air

description: We report the first covalent incorporation of reactive aliphatic amine
 species into covalent organic frameworks (COFs). This was achieved through
 the crystallization of an imine-linked COF, termed COF-609-Im, followed by
 conversion of its imine linkage to base-stable
 tetrahydroquinoline linkage through aza-Diels-Alder
 cycloaddition, and finally, the covalent incorporation of
 tris(3-aminopropyl)amine into the framework. The obtained COF-609 exhibits
 a 1360-fold increase in CO2 uptake capacity compared to the
 pristine framework and a further 29% enhancement in the presence
 of humidity. We confirmed the chemistry of framework conversion and
 corroborated the enhanced CO2 uptake phenomenon with and without humidity
 through isotope-labeled Fourier transform infrared spectroscopy
 and solid-state nuclear magnetic resonance spectroscopy. With this study,
 we established a new synthetic strategy to access a class
 of chemisorbents characterized by high affinity to CO2 in dilute
 sources, such as the air.
description: Solid-state
 <sup>13</sup>C and <sup>15</sup>N NMR experiments were conducted on a
 Bruker AV-500 (500 MHz) or a Bruker Avance NEO 400 (400 MHz) spectrometer
 at 297–300 K. All samples were fully activated, packed, and sealed in
 zirconia rotors in an argon-filled glovebox before loading into the probe
 for measurements. Experiments on AV-500 spectrometer were
 performed using a Bruker 4-mm double resonance MAS probe
 (<sup>1</sup>H/X) operating at 125.75 MHz for
 <sup>13</sup>C and at 50.69 MHz for
 <sup>15</sup>N, and a magic angle spinning rate of 8
 kHz. Experiments on the NEO 400 spectrometer were performed using a 3.2-mm
 or 1.3-mm MAS probe (<sup>1</sup>H/X) operating at 100.65 MHz for
 <sup>13</sup>C and at 50.69 MHz for
 <sup>15</sup>N, and a magic angle spinning rate of 24
 kHz. The magic angle was calibrated by maximizing the number and intensity
 of rotational echoes for the <sup>79</sup>Br resonance for KBr under MAS.
 <sup>13</sup>C chemical shifts were externally
 referenced to the downfield resonance of adamantane at 38.48 ppm.
 <sup>15</sup>N chemical shifts were externally
 referenced to glycine at 33.4 ppm. <sup>13</sup>C multiple cross-polarization (multi-CP)
 experiments were performed using the compensated-multi-CP (compMulti-CP)
 sequence developed by Schmidt Rohr and coworkers. The data
 were read and processed with MestReNova such as polynominal background
 substraction for integration.
description: The spectrum files require MestReNova software to be opened and
 processed.
DOI: 10.6078/d19b0h
title: Data from: Limited role of generation time changes in driving the evolution of the mutation spectrum in humans

description: Recent studies have suggested that the human germline mutation rate and
 spectrum evolve rapidly. Variation in generation time has been linked to
 these changes, though its contribution remains unclear. We develop a
 framework to characterize temporal changes in polymorphisms within and
 between populations, while controlling for the effects of natural
 selection and biased gene conversion. Application to the 1000 Genomes
 Project dataset reveals multiple independent changes that arose after the
 split of continental groups, including a previously reported, transient
 elevation in TCC &gt;TTC mutations in Europeans and novel signals of
 divergence in C&gt;G and T&gt;A mutation rates among population
 samples. We also find a significant difference between groups sampled in
 and outside of Africa, in old T&gt;C polymorphisms that predate the
 out-of-Africa migration. This surprising signal is driven by TpG
 &gt;CpG mutations, and stems in part from mis--polarized CpG
 transitions, which are more likely to undergo recurrent mutations.
 Finally, by relating the mutation spectrum of polymorphisms to parental
 age effects on de novo mutations, we show that plausible changes in the
 generation time cannot explain the patterns observed for different
 mutation types jointly. Thus, other factors – genetic modifiers or
 environmental exposures – must have had a non-negligible impact on the
 human mutation landscape.
description: Relate output for SNPs in commonly accessible regions with
 additional annotation (one file for each population of YRI, LWK, CEU, TSI,
 CHB, JPT).
DOI: 10.5061/dryad.b8gtht7fz
title: Respirometry protocols for avian thermoregulation at high air temperatures: stepped and steady-state profiles yield similar results

description: Relationships between air temperature (Tair) and avian body temperature
 (Tb), resting metabolic rate (RMR) and evaporative water loss (EWL) during
 acute heat exposure can be quantified through respirometry using several
 approaches. One involves birds exposed to a stepped series of
 progressively increasing Tair setpoints for short periods (&lt; 20-30
 min), whereas a second seeks to achieve steady-state conditions by
 exposing birds to a single Tair for longer periods (&gt; 1-2 h). To
 compare these two approaches, we measured Tb, RMR and EWL over Tair = 28 C
 to 44 C in the dark-capped bulbul (Pycnonotus tricolor). The two protocols
 yielded indistinguishable values of Tb, RMR and EWL and related variables
 at most Tair values, revealing that both are appropriate for quantifying
 avian thermal physiology during heat exposure over the range of Tair in
 the present study. The stepped protocol, however, has several ethical and
 practical advantages. 
description: Body temperatures, resting metabolic rates and rates of
 evaporative water loss in Dark-capped bulbuls (Pycnonotus tricolor) were
 measured using two different protocols (stepped and steady-state) of
 flow-through respirometry at high air temperatures. These data were
 collected to determine whether conclusions regarding avian
 thermoregulation during acute heat exposure depend on the type of
 respirometry protocol used.
description: Microsoft Excel
DOI: 10.5061/dryad.573n5tb9r
title: Data associated to: Uncovering the genomic basis of an extraordinary plant invasion

description: Invasive species are a key driver of the global biodiversity crisis but
 the drivers of invasiveness, including the role of pathogens, remain
 debated. We investigated the genomic basis of invasiveness
 in Ambrosia artemisiifolia (ragweed), introduced to
 Europe in the late 19th century, by resequencing 655 ragweed genomes,
 including 308 herbarium specimens collected up to 190 years ago. In
 invasive European populations, we found selection signatures in defense
 genes and lower prevalence of disease-inducing plant pathogens. Together
 with temporal changes in population structure associated with
 introgression from closely related Ambrosia species,
 escape from specific microbial enemies likely favoured the plant’s
 remarkable success as an invasive species.
DOI: 10.5061/dryad.8pk0p2nqv
title: Data from: Terrigenous subsidies in lakes support zooplankton production mainly via a green food chain and not the brown food chain

description: Terrestrial organic matter (t-OM) has been recognized as an important
 cross-boundary subsidy to aquatic ecosystems. However, recent evidence has
 shown that t-OM contributes little to promote secondary production in
 lakes because it is low quality food for aquatic consumers. To resolve
 this conflict, we performed a field experiment using leaf litter as t-OM.
 In the experiment, we monitored zooplankton biomass in enclosures with and
 without addition of leaf litter under shaded and unshaded conditions and
 assessed food web changes with stable isotope analyses. We then examined
 whether or not leaf litter indeed stimulates lake secondary production
 and, if it does, which food chain, the detritus-originated food chain
 (“brown” food chain) or the algae-originated food chain (“green” food
 chain), contributes more to this increase. Analyses with stable isotopes
 showed a substantial importance of t-OM in supporting the secondary
 production under ambient lake conditions. However, addition of the leaf
 litter increased the zooplankton biomass under unshaded conditions but not
 under shaded conditions. We found that phosphorus was leached from leaf
 litter at much faster rate than organic carbon and nitrogen despite its
 low content in the leaf litter.  These results showed that leaf
 litter stimulated the increase of zooplankton biomass mainly through the
 green food chain rather than through the brown food chain, because the
 leaf litter supplied limiting nutrients (i.e., phosphorus) for primary
 producers. Our results indicate that the functional stoichiometry of the
 subsidized organic matter plays a crucial role in determining the relative
 importance of brown and green food chains in promoting production at
 higher trophic levels in recipient ecosystems.