cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n5tb2rbw9
title: Siliceous and non-nutritious: nitrogen limitation increases anti-herbivore silicon defenses in a model grass

description: Silicon (Si) accumulation alleviates a diverse array of environmental
 stresses in many plants, including conferring physical resistance against
 insect herbivores. It has been hypothesised that grasses, in particular,
 utilise ‘low metabolic cost’ Si for structural and defensive roles under
 nutrient limitation. While carbon (C) concentrations often negatively
 correlate with Si concentrations, the relationship between nitrogen (N)
 status and Si is more variable. Moreover, the impacts of N limitation on
 constitutive physical Si defences (e.g. silica and prickle cells) against
 herbivores are unknown. We determined how N limitation affected Si
 deposition in the model grass Brachypodium distachyon and how changes in
 these constitutive defences impacted insect herbivore (Helicoverpa
 armigera) growth rates. We used scanning electron microscopy (SEM) and
 energy dispersive X-ray spectrometry in conjunction with X-ray mapping
 (XRM) to quantify physical structures on leaves and determine Si
 deposition patterns. We also determined how N limitation and Si supply
 impacted the jasmonic acid (JA) pathway, the master-regulator of induced
 defences against arthropod herbivores. N limitation reduced shoot growth
 by over 40%, but increased root mass (+21%), leaf Si concentrations (+50%)
 and the density of silica (+28%) and flattened prickle (+76%) cells. EDS
 and XRM established that Si was being deposited in these structures,
 together with hooked prickle cells and macro-hairs. Herbivore relative
 growth rates (RGR) were more than 115% lower in Si supplied plants
 compared to plants without Si supply and negatively correlated with leaf
 Si concentration and silica cell density. RGR was further reduced by N
 limitation and positively correlated with leaf N concentrations. Increases
 in JA concentrations following induction of the JA pathway were at least
 doubled by N limitation. Si accumulation and deposition were
 highly regulated by N availability, with N limitation promoting both
 constitutive Si physical defences and induction of the JA defensive
 pathway, in line with the resource availability hypothesis. These results
 indicate that grasses use ‘low cost Si’ when resources are limited and
 suggests that plant productivity may benefit from optimising conventional
 fertilisers and Si fertilisation.
DOI: 10.5061/dryad.t4b8gtj2m
title: Supplementary datasets, data analysis code, and R tutorials for: Phylogenetic analysis of adaptation in comparative physiology and biomechanics: overview and a case study of thermal physiology in treefrogs

description: Comparative phylogenetic studies of adaptation are uncommon in
 biomechanics and physiology. Such studies require collecting data from
 many species, a challenge when data collection is experimentally
 intensive. Moreover, researchers struggle to employ the most biologically
 appropriate phylogenetic tools for identifying adaptive evolution. Here,
 we detail an established but greatly underutilized phylogenetic
 comparative framework—the Ornstein-Uhlenbeck process—that explicitly
 models long-term adaptation. We discuss challenges in implementing and
 interpreting the model, and we outline potential solutions. We demonstrate
 use of the model through studying the evolution of thermal physiology in
 treefrogs. Frogs of the family Hylidae have twice colonized the temperate
 zone from the tropics, and such colonization likely involved a fundamental
 change in physiology due to colder and more seasonal temperatures.
 However, which traits changed to allow colonization is unclear. We
 measured cold-temperature tolerance and characterized thermal performance
 curves in jumping for twelve species of treefrogs distributed from the
 Neotropics to temperate North America. We then conducted phylogenetic
 comparative analyses to examine how tolerances and performance curves
 evolved and to test whether that evolution was adaptive. We found that
 tolerance to low temperatures increased with the transition to the
 temperate zone. In contrast, jumping well at colder temperatures was
 unrelated to biogeography and thus did not adapt during dispersal.
 Overall, our paper shows how comparative phylogenetic methods can be
 leveraged in biomechanics and physiology to test the evolutionary drivers
 of variation among species.
description: Please see published paper.
description: Please see published paper.
DOI: 10.5061/dryad.q2bvq83kb
title: Fourteen morphological traits of three Japanese species of Arisaema sect. Pistillata (Araceae)

description: The Arisaema serratum group sensu
 stricto (Araceae) is a Japanese species complex characterized by
 a well-developed leaf rachis and long pseudostem. They were previously
 integrated into one species due to wide infraspecific variation,
 but were split into about 13 species again in
 recent monographs. In this group, A.
 maekawae and A.
 pseudoangustatum var. pseudoangustatum were
 recently divided from A. angustatum in the type
 localities (central Japan). A recent study found
 some sympatric populations of the three species in western
 Japan and distinguished them based on qualitative observation.
 However, there are no quantitative study to delimit the species
 boundaries objectively. The author collected this quantitative data set in
 these sympatric populations and found that principal component analysis
 with this data set can successfully delimit the species
 boundaries between the three sympatric species.
DOI: 10.5061/dryad.bzkh18997
title: Theoretical insights into the antiradical activity and copper-catalyzed oxidative damage of mexidol in the physiological environment

description: This dataset contains data from the calculations described in the paper:
 “Quan V. Vo*, Nguyen Thi Hoa, Mai Van Bay, Adam Mechler,
 Theoretical insights into the antiradical activity and copper-catalyzed
 oxidative damage of mexidol in the physiological environment. Royal
 Society Open Science. 2021. In this study, the hydroperoxyl radical
 scavenging activity of MD was studied to establish baseline antioxidant
 activity, followed by an investigation of the effect of MD on the
 copper-catalyzed oxidative damage in biological systems, using
 computational methods. It was found that MD exhibits moderate radical
 scavenging activity against HOO· in physiological environments. The
 activity in aqueous solution is defined by the single electron transfer
 mechanism of the anion state; however in nonpolar environments the formal
 hydrogen transfer pathway dominates at the O3-H bond. It was also
 confirmed that MD can chelate Cu (II), forming complexes that are much
 harder to reduce than free Cu (II): MD chelation completely quenches the
 Cu (II) reduction by ascorbic acid and suppresses the rate of reduction
 reaction by O2·- that are the main reductants of Cu (II) in biological
 environments. Therefore, MD exerts its anti- HO· activity primarily as an
 OIL-1 inhibitor.
description: The dataset was collected during the Gaussian 09 suite of
 programs at The University of Danang - University of Technology and
 Education, Vietnam, and La Trobe University, Australia.
 M06-2X/6-311++G(d,p) model chemistry was used for all calculations. It was
 demonstrated before that the M06-2X functional is one of the most reliable
 methods to study thermodynamics and kinetics of radical reactions,
 particularly in physiological environments. The solvation model density
 (SMD) method was used for including the effects of water and pentyl
 ethanoate in the computations. The kinetic calculations were performed
 following the quantum mechanics-based test for the overall free radical
 scavenging activity (QM-ORSA) protocol, using the conventional transition
 state theory (TST) and 1M standard state at 298.15 K.
description: The readme file contains the calculation methods (Table S1, SI),
 the calculated Gibbs free energy of reactions between MD and
 [Cu(H<sub>2</sub>O)<sub>4</sub>]<sup>2+</sup> in aqueous solution (Table S2, SI), the calculated BDE, PA, and IE (Table S3), the kinetic data (Table S4, SI), the calculated Gibbs free energy of reactions of the H<sub>2</sub>A<sup>+</sup> with HOO· following the FHT and SET mechanisms in the aqueous solution (Table S5, SI), the Cartesian coordinates of the transition states and complexes (Table S6, SI) and optimized geometries the selected complexes in aqueous solution (Figure 1) in all the studied environments, th draft data and input files. Information on how the calculations were done can also be found in the associated manuscript referenced above.
DOI: 10.5061/dryad.866t1g1r8
title: The genome data and annotation data of Rafetus swinhoei

description: The death of the only known female soft-shelled turtle (Rafetus swinhoei)
 in 2019 marked the imminent danger of
 the species’ permanent global extinction. To avoid it
 and facilitate the protection of R. swinhoei, we
 sequenced and assembled its chromosome-level genome
 and characterized its sex determination system. Population
 history analysis indicates R. swinhoei has the lowest
 heterozygosity among all turtles examined, and its population size has
 declined dramatically over the past ten million years. Many genes
 involved in autophagy and DNA damage response were shown to be
 under positive selection and fast evolution, suggesting their
 important contributions to the long lifespan and evolutionary adaptation
 of R. swinhoei. The loss of several tooth-related genes
 in turtle genomes explains the genetic basis of their toothless
 phenotype. These results provide genetic insights into the evolution
 of R. swinhoei, and will be useful for the potential
 identification of additional female individuals in the field.
DOI: 10.5061/dryad.r4xgxd2d0
title: Data-driven predictions of summertime visits to lakes across 17 US states

description: Using a dataset of more than 51,000 US lakes, we estimated the
 relationship between summertime lake visits, lake water quality, landscape
 features, and other amenities, where visitation was estimated using counts
 of geolocated photographs. Given the size and complexity of our dataset,
 we used a combination of machine learning techniques, imputation
 techniques, and a Poisson count model to estimate these relationships. We
 found that every additional meter of average summer-time Secchi depth was
 associated with at least 7% more summer-time lake visits, all else equal.
 Second, we found that lake amenities, such as beaches, boat launches, and
 public toilets, were more powerful predictors of visits than water
 quality. Third, we found that visits to a lake were strongly influenced by
 the lake’s accessibility and its distance to nearby lakes and the
 amenities the nearby lakes offered. Our research highlights the need for
 1) a better understanding of how representative social media data are of
 actual recreational behavior, 2) the development of best practices to
 account for non-random patterns in missing natural feature data, and 3) a
 better understanding of the potential reverse causality in the lake
 visit-water quality relationships.
DOI: 10.5061/dryad.76hdr7sx5
title: Data from: Finding common ground: Toward comparable indicators of adaptive capacity of tree species to a changing climate

description: Adaptive capacity, one of the three determinants of vulnerability to
 climate change, is defined as the capacity of species to persist in their
 current location by coping with novel environmental conditions through
 acclimation and/or evolution. Although studies have identified indicators
 of adaptive capacity, few have assessed this capacity in a quantitative
 way that is comparable across tree species. Yet, such multi-species
 assessments are needed by forest management and conservation programs to
 refine vulnerability assessments and to guide the choice of adaptation
 measures. In this paper, we propose a framework to quantitatively evaluate
 five key components of tree adaptive capacity to climate change:
 individual adaptation through phenotypic plasticity, population phenotypic
 diversity as influenced by genetic diversity, genetic exchange within
 populations, genetic exchange between populations and genetic exchange
 between species. For each component, we define the main mechanisms that
 underlie adaptive capacity and present associated metrics that can be used
 as indices. To illustrate the use of this framework, we evaluate the
 relative adaptive capacity of 26 northeastern North American tree species
 using values reported in the literature. Our results show adaptive
 capacity to be highly variable among species and between components of
 adaptive capacity, such that no one species ranks consistently across all
 components. On average, the conifer Picea glauca and the broadleaf Betula
 papyrifera show the greatest adaptive capacity among the 26 species we
 documented, whereas the conifers Picea rubens and Thuja occidentalis, and
 the broadleaf Ostrya virginiana possess the lowest. We discuss limitations
 that arise when comparing adaptive capacity among species, including poor
 data availability and comparability issues in metrics derived from
 different methods or studies. The breadth of data required for such an
 assessment exemplifies the multidisciplinary nature of adaptive capacity
 and the necessity of continued cross-collaboration to better anticipate
 the impacts of a changing climate.
description: Collected through metaanalysis
DOI: 10.5061/dryad.1vhhmgqt9
title: Data for: Strong phenotypic trait correlations between mating partners do not result from assortative mating in wild great tits (Parus major)

description: There is considerable debate about the occurrence of assortative mating
 between phenotypic traits measured within natural populations.
 Meta-analyses have implied that assortative mating occurs generally in
 natural populations but recent work indicates these conclusions largely
 result from biased data. Specifically, estimates of phenotypic
 correlations between mating partners do not solely result from non-random
 associations between individual-level traits of partners but also from
 other biological processes (joint phenotypic plasticity, indirect genetic
 effects), methodological practices (observer bias), and other unexplained
 residual correlations (e.g. correlated measurement error). This paper puts
 this critique to test. First, we estimated the overall phenotypic
 correlation between phenotypic traits of mating partners for a wild
 population of great tits. Second, we estimated various key variance
 components to reveal the extent to which phenotypic correlations between
 partners resulted from assortative mating, reversible plasticity, social
 partner effects, and methodological practices. We performed our analyses
 for a range of phenotypic traits (body mass, breathing rate, exploration
 behaviour, wing and tarsus length) to derive general conclusions not
 hinging on the specifics of the traits involved. Our analyses support the
 conclusion that patterns of assortative mating exist at first glance but
 occur because of the biasing effects of correlated residuals likely caused
 by a combination of phenotypic responses to unknown environmental factors
 or measurement error – not because of intrinsic patterns of assortative
 mating.
description: Between 2010 to 2019, we studied a great tit (<i>Parus
 major</i>) population breeding in 12 nest-box plots near the city of
 Starnberg in Southern Germany. Seven to 10 days after hatching, we caught
 the parents with a spring trap placed inside the nest-box and marked each
 individual, if not captured before, with a unique combination of one
 metal- and up to three colour rings. Immediately after ringing, birds were
 subjected to a cage-test to measure their exploration behaviour. After the
 test, we removed the focal bird from the cage and measured its breathing
 rate, tarsus and wing length, and body mass. We
 conducted all data analyses in <i>R</i> v. 4.0.2 (R Core Team,
 2020), and all models were fitted within a Bayesian framework using Markov
 chain Monte Carlo (MCMC) methods in the <i>MCMCglmm</i>
 package (Hadfield, 2010). Please also refer to the Methods section of the
 main manuscript for a detailed description of conducted
 analyses.  
 The data and accompanied R-script are included:
 1.
 Data_Holtmann_&_Dingemanse_JEB_Parus_major_assort_mating
 (including ReadMe file) 2.
 RScript_Holtmann_&_Dingemanse_JEB_Parus_major_assort_mating
DOI: 10.5061/dryad.f7m0cfxwr
title: 5′ modifications improve potency and efficacy of DNA donors for precision genome editing

description: Nuclease-directed genome editing is a powerful tool for investigating
 physiology and has great promise as a therapeutic approach to correct
 mutations that cause disease. In its most precise form, genome editing can
 use cellular homology-directed repair (HDR) pathways to insert information
 from an exogenously supplied DNA repair template (donor) directly into a
 targeted genomic location. Unfortunately, particularly for long
 insertions, toxicity and delivery considerations associated with repair
 template DNA can limit HDR efficacy. Here, we explore chemical
 modifications to both double-stranded and single-stranded DNA-repair
 templates. We describe 5′-terminal modifications, including in its
 simplest form the incorporation of triethylene glycol (TEG) moieties, that
 consistently increase the frequency of precision editing in the germlines
 of three animal models (Caenorhabditis elegans, zebrafish, mice) and in
 cultured human cells.
description: Regions of interest were
 amplified from genomic DNA and sequenced on an Illumina MiniSeq platform.
 PCR1 ((98° C- 2min, 24 cycles of (98° C- 15sec, 64° C- 20sec, 72° C-
 15sec), 72° C- 5min) was performed using 200ng gDNA, 1.25uL of 10uM
 forward and reverse primers that contain Illumina adapter sequences,
 12.5uL NEBNext UltraII Q5 Master Mix, and water to bring the total volume
 to 25uL. PCR2 (98° C- 2min, 10 cycles of (98° C- 15sec, 64° C- 20sec, 72°
 C- 15sec), 72° C- 5min) was done using 1uL of unpurified PCR1 reaction
 mixture, 1.25 uL of 10uM forward and reverse primers that contain unique
 barcode sequences, 12.5uL NEBNext UltraII Q5 Master Mix, and water to
 bring the total volume to 25uL. PCR2 products were first analyzed using 2%
 agarose gel electrophoresis, and then similar amounts were pooled based on
 the band intensities. Pooled PCR2 products were first purified by gel
 extraction (Qiagen) and purified again by PCR cleanup columns (Qiagen).
 Concentration of final purified library was determined by Qubit (High
 Sensitivity DNA assay). The integrity of library was confirmed by Agilent
 Tapestation using Agilent High Sensitivity D1000 ScreenTape kit. The
 library was then sequenced on an Illumina Miniseq platform according to
 the manufacturer’s instructions using MiniSeq Mid Output Kit (300-cycles).
 Sequencing reads were demultiplexed using bcl2fastq2 (Illumina) and
 CRISPResso2
 was used to align the reads and quantify editing
 efficiencies. Quantification window size was set as 30 to ensure the
 stringent analysis. HDR efficiency was calculated as percentage of
 (precise HDR reads) / (total reads). For Guide-Seq Experiments,
 two<b> </b>phosphorothioate linkages were incorporated between
 the first three and the last three nucleotides in the dsODN tags.
 Unmodified dsODN does not contain any further modifications whereas
 modified dsODN contains 5′ TEG (SP9) modification (Integrated DNA
 Technologies). Sequencing data was processed and analyzed using the
 GUIDE-seq analysis software.
DOI: 10.15468/dl.uw3tas
title: Occurrence Download

description: A dataset containing 1498 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Castanopsis fissa"
 ]
}

 The dataset includes 1498 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002903-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25349/d9fg8f
title: Variation in salinity tolerance and water use strategies in an introduced woody halophyte (Tamarix spp.)

description: 1. The form and function of terrestrial plants is largely governed by the
 availability of water, with plants in water limited environments
 expressing traits minimizing water loss and tissue damage during drought.
 Areas with high salinity are analogous to those with low water
 availability, even where water is abundant. We evaluated variation in
 salinity tolerance and water use strategies in an introduced halophytic
 shrub, Tamarix spp by measuring gas exchange rates, biomass accumulation,
 and turgor loss points. We hypothesized that salinity tolerance is not
 uniformly expressed, with high salinity ecotypes expressing more
 conservative water use traits that maximize hydraulic safety over high
 conductance rates. 2. We studied two populations of Tamarix spp. along the
 lower Colorado River where groundwater salinity differed by nearly
 six-fold. Cuttings collected from the sites were grown in a greenhouse
 with five salinity levels from 0 to 32 parts per thousand (ppt), imposing
 increasing water limitation. 3. In situ measurements of leaf water
 potentials () and branch xylem anatomy were taken on ecotypes sourced
 from high- and low-salinity sites. In the greenhouse, biomass and gas
 exchange rates were evaluated over the 0-32 ppt salinity gradient, and a
 separate dry down experiment was performed to determine turgor loss points
 and stomatal responses to drying soils. 4. In the greenhouse, the low
 salinity population accumulated 72% more biomass when grown at 4 ppt
 compared to 16 ppt, while the high salinity population produced 50% more
 biomass when grown at 16 ppt. Net carbon assimilation was greater at lower
 salinities in the low salinity population but independent of salinity in
 the high salinity population. The high salinity population had a lower
 turgor loss point and exhibited greater stomatal control relative to the
 low salinity population. 5. Synthesis. Results provide evidence for
 divergence of traits related to plant water use across salinity gradients
 in this recently introduced halophyte. Local adaptation to increased
 salinity has implications in aridland riparian ecosystems where water
 management or drought may lead to altered soil salinities. The interaction
 of trait variation within Tamarix spp. and increasing salinity is likely
 to favor its continued dominance.