cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7m0cfxprs
title: Functional gene categories differentiate maize leaf drought-related microbial epiphytic communities

description: The phyllosphere epiphytic microbiome is composed of microorganisms that
 colonize the external aerial portions of plants. Relationships of plant
 responses to specific microorganisms–both pathogenic and beneficial–have
 been examined, but the phyllosphere microbiome functional and metabolic
 profile responses are not well described. Changing crop growth conditions,
 such as increased drought, can have profound impacts on crop productivity.
 Also, epiphytic microbial communities provide a new target for crop yield
 optimization. We compared Zea mays leaf microbiomes collected under
 drought and well-watered conditions by examining functional gene
 annotation patterns across three physically disparate locations each with
 and without drought treatment, through the application of short read
 metagenomic sequencing. Drought samples exhibited different functional
 sequence compositions at each of the three field sites. Maize phyllosphere
 functional profiles revealed a wide variety of metabolic and regulatory
 processes that differed in drought and normal water conditions and provide
 key baseline information for future selective breeding.
description: Experimental design, plant growth conditions, and leaf epiphytic
 microbial DNA collection is described in the manuscript methods section. 
 Full descriptions of computational methods are available in the R notebook
 in the drought-metagen folder. 
description: Metadata is included in the supplemental files folder; full
 details of code, simulations, and real data analysis are included in the
 drough-metagen folder.
DOI: 10.5061/dryad.rr4xgxd6m
title: Parallel ddRAD and genome skimming analyses reveal a radiative and reticulate evolutionary history of the temperate bamboos

description: Rapid evolutionary radiations are among the most challenging phylogenetic
 problems, wherein different types of data (e.g., morphology, molecular) or
 genetic markers (e.g., nuclear, organelle) often yield inconsistent
 results. The tribe Arundinarieae i.e., the temperate bamboos, is a clade
 of tetraploid originated 22 million years ago and subsequently radiated in
 East Asia. Previous studies of Arundinarieae have found conflicting
 relationships and/or low support. Here, we obtain nuclear markers from
 ddRAD data for 213 Arundinarieae taxa and parallel sampling of chloroplast
 genomes from genome-skimming for 147 taxa. We first assess the feasibility
 of using ddRAD-seq data for phylogenetic estimates of paleopolyploid and
 rapidly radiated lineages, optimize clustering thresholds and analysis
 workflow for orthology identification. Reference-based ddRAD data assembly
 approaches perform well and yield strongly supported relationships that
 are generally concordant with morphology-based taxonomy. We recover five
 major lineages, two of which are notable (the pachymorph and leptomorph
 lineages), in that they correspond with distinct rhizome morphologies. By
 contrast, the phylogeny from chloroplast genomes differed significantly.
 Based on multiple lines of evidence, the ddRAD tree is favored as the best
 species tree estimation for temperate bamboos. Using a time-calibrated
 ddRAD tree we find that Arundinarieae diversified rapidly around the
 mid-Miocene corresponding with intensification of the East Asian monsoon
 and the evolution of key innovations including the leptomorph rhizomes.
 Our results provide a highly resolved phylogeny of Arundinarieae, shed new
 light on the radiation and reticulate evolutionary history of this tribe,
 and provide an empirical example for the study of recalcitrant plant
 radiations.
DOI: 10.5061/dryad.59zw3r25c
title: Artificial night light helps account for observer bias in citizen science monitoring of an expanding large mammal population

description: 1. The integration of citizen scientists into ecological research is
 transforming how, where, and when data are collected, and expanding the
 potential scales of ecological studies. Citizen-science projects can
 provide numerous benefits for participants, while educating and connecting
 professionals with lay audiences, potentially increasing acceptance of
 conservation and management actions. However, for all the benefits,
 collection of citizen-science data is often biased towards areas that are
 easily accessible (e.g. developments and roadways), and thus data are
 usually affected by issues typical of opportunistic surveys (e.g. uneven
 sampling effort). These areas are usually illuminated by artificial light
 at night (ALAN), a dynamic sensory stimulus that alters the perceptual
 world for both humans and wildlife. 2. Our goal was to test whether
 satellite-based measures of ALAN could improve our understanding of the
 detection process of citizen scientist-reported sightings of a large
 mammal. 3. We collected observations of American black bears (Ursus
 americanus; n = 1,315) outside their primary range in Minnesota, USA, as
 part of a study to gauge population expansion. Participants from the
 public provided sighting locations of bears on a website. We used an
 occupancy modelling framework to determine how well ALAN accounted for
 observer metrics when compared to other commonly used metrics (e.g.
 housing density). 4. Citizen scientists reported 17% of bear sightings
 were under artificially-lit conditions and monthly ALAN estimates did the
 best job accounting for spatial bias in detection of all observations,
 based on AIC values and effect sizes (β ^ = 0.81, 0.71 – 0.90 95% CI).
 Bear detection increased with elevated illuminance; relative abundance was
 positively associated with natural cover, closer proximity to primary bear
 range and lower road density. Although the highest counts of bear
 sightings occurred in the highly illuminated suburbs of the
 Minneapolis-St. Paul metropolitan region, we estimated substantially
 higher bear abundance in another region with plentiful natural cover and
 low ALAN (up to 275% increased predicted relative abundance) where
 observations were sparse. 5. We demonstrate the importance of considering
 ALAN radiance when analyzing citizen scientist-collected data, and we
 highlight the ways that ALAN data provides a dynamic snapshot of human
 activity. 31-Jul-2020
description: This dataset contains all of the values used in occupancy models
 comparing the observations of bears by citizen scientists in Minnesota.
 Data need to be read into program R and converted to an unmarkedFrame
 object within the R package 'unmarked' (Fiske &
 Chandler, 2011; vers.0.13-0). Fiske, I., &
 Chandler, R. (2011). unmarked: An R package for fitting hierarchical
 models of wildlife occurrence and abundance. Journal of Statistical
 Software, 43(1), 1–23. doi: 10.18637/jss.v043.i10
DOI: 10.5061/dryad.bk3j9kd8c
title: CORE GREML: MTG2 code and instruction

description: Linear mixed models (LMMs) using genome-based restricted maximum
 likelihood (GREML) allow both fixed and random effects. Classic LMMs
 assume independence between random effects, which can be violated. To
 relax the assumption, we introduced a generalised GREML, named CORE GREML,
 that explicitly estimates the covariance between random effects. This
 dataset includes MTG2 code and instruction for CORE GREML.
description: The code was written in fortan program language.
DOI: 10.5061/dryad.79cnp5hsn
title: Kinetic data, oligomer data and binding data

description: The amyloid cascade hypothesis, according to which the self-assembly of
 amyloid-β peptide (Aβ) is a causative process in Alzheimer’s disease, has
 driven many therapeutic efforts for the past 20 years. Failures of
 clinical trials investigating Aβ-targeted therapies have been interpreted
 as evidence against this hypothesis, irrespective of the characteristics
 and mechanisms of action of the therapeutic agents, which are highly
 challenging to assess.  Here, we combine kinetic analyses with
 quantitative binding measurements to address the mechanisms of action of
 four clinical stage anti-Aβ antibodies, aducanumab, gantenerumab,
 bapineuzumab and solanezumab. We quantify the influence of these
 antibodies on the aggregation kinetics and on the production of oligomeric
 aggregates, and link these effects to the affinity and stoichiometry of
 each antibody for monomeric and fibrillar forms of Aβ.  Our
 results reveal that, uniquely amongst these four antibodies, aducanumab
 dramatically reduces the flux of Aβ oligomers.
description: Thioflavin T fluorescence, analysed uing Amylofit
 database Mass spectrometry after aggregation to t-half,
 centrifugation to remove fibrils and SEC to isolate oligomers
 Microfulidic diffusion sizing of Alexa647-labelled species with
 increaseing conenctration of ligand
DOI: 10.5061/dryad.qjq2bvqdg
title: Data from: Victims of ancient hyperthermal events herald the fates of marine clades and traits under global warming

description: Organismic groups vary non-randomly in their vulnerability to extinction.
 However, it is unclear whether the same groups are consistently
 vulnerable, regardless of the dominant extinction drivers, or whether
 certain drivers have their own distinctive and predictable victims. Given
 the challenges presented by anthropogenic global warming, we focus on
 changes in extinction selectivity trends during ancient hyperthermal
 events: geologically rapid episodes of global warming. Focusing on the
 fossil record of the last 300 million years, we identify clades and traits
 of marine ectotherms that were more prone to extinction under the onset of
 six hyperthermal events than during other times. Hyperthermals enhanced
 the vulnerability of marine fauna that host photosymbionts, particularly
 zooxanthellate corals, the reef environments they provide, and genera with
 actively burrowing or swimming adult life-stages. The extinction risk of
 larger-sized fauna also increased relative to non-hyperthermal times,
 while genera with a poorly buffered internal physiology did not become
 more vulnerable on average during hyperthermals. Hyperthermal-vulnerable
 clades include rhynchonelliform brachiopods and bony fish, whereas
 resistant clades include cartilaginous fishes, and ostreid and venerid
 bivalves. These extinction responses in the geological past mirror modern
 responses of these groups to warming, including range shift magnitudes,
 population losses, and experimental performance under climate-related
 stressors. Accordingly, extinction mechanisms distinctive to rapid global
 warming may be indicated, including sensitivity to warming-induced
 seawater deoxygenation. In anticipation of modern warming-driven marine
 extinctions, the trends illustrated in the fossil record offer an
 expedient preview.
description: Data were downloaded from the Paleobiology Database on
 25.05.2020. The R code for acquiring the basic results (i.e. Figure 1) are
 included. See Methods section in the full publication for
 description. Body size data (file
 'genus.sizes.ranges.rev.csv') are included from
 Payne & Heim (2020; Body size, sampling completeness,
 and extinction risk in the marine fossil record.
 <i>Paleobiology</i>, <b>46</b>(1),
 23–40).
DOI: 10.5061/dryad.vt4b8gtq2
title: Marine biomonitoring with eDNA: can metabarcoding of water samples cut it as a tool for surveying benthic communities?

description: In the marine realm, biomonitoring using eDNA of benthic communities
 requires destructive direct sampling or the setting-up of settlement
 structures. Comparatively much less effort is required to sample the water
 column, which can be accessed remotely. In this study we assess the
 feasibility of obtaining information from the eukaryotic benthic
 communities by sampling the adjacent water layer. We studied two different
 rocky-substrate benthic communities with a technique based on quadrat
 sampling. We also took replicate water samples at distances from a few
 centimetres to 20 m from the benthic habitat. Using as marker a fragment
 of the Cytochrome c oxidase subunit I gene with universal primers, we
 obtained a total of 3,543 molecular operational taxonomic units (MOTUs)
 from the samples. The structure obtained in the two environments was
 markedly different, with Metazoa, Archaeplastida Rhodophyta and
 Stramenopiles being the most diverse group in benthic samples, and
 HacrobiaAlveolata, Metazoa and Alveolata Rhizaria in the water. Only 265
 MOTUs (7.5%) were shared between benthos and water samples, and of these
 180 MOTUs (5.1%) were identified as benthic MOTUs that left their DNA in
 the water. Most of them were found immediately adjacent to the benthos,
 and their number decreased and The distribution of these benthic shared
 MOTUs showed a decrease both in number of MOTUs and in number of reads as
 we moved apart from the benthic habitat. It was concluded that water eDNA,
 even in the close vicinity of the benthos, was a poor proxy for the
 analysis of benthic structure, and that direct sampling methods are
 required for monitoring these complex benthic communities via
 metabarcoding.
DOI: 10.5061/dryad.7sqv9s4qp
title: Habitat deterioration relaxes resource competition and sexual selection in the threespine stickleback

description: The operation of sexual selection depends on ecological conditions. Thus,
 changes in environmental conditions because of human activities can alter
 the strength and direction of sexual selection, with implications for
 evolutionary trajectories and the viability of populations. We show that
 aquatic algal blooms can relax the operation of sexual selection by
 influencing which males are available to attract females. This is by
 influencing the ability of males to maintain a resource needed in mate
 attraction. When we exposed two competing threespine stickleback males
 (Gasterosteus aculeatus), whose attractiveness to females was known, to
 either clear or algal-turbid water, nest abandonment was more common in
 clear water, and it was usually the unattractive male that abandoned his
 nest. In turbid water, on the other hand, nest abandonments were less
 common and when they occurred, the probability increased that the
 attractive male abandoned his nest, and that the unattractive male
 subsequently occupied it. This change in the composition of nesting males
 increased the mating success of unattractive males. Thus, our results
 reveal a new mechanism through which habitat deterioration can influence
 sexual selection, by altering success in the competition for a resource
 critical in mate attraction, a territory with a nest in this case. This
 could be a common mechanism, considering the prevalence of resource
 competition in mate choice systems. On a broader level, our results
 emphasise the importance of considering the impact of environmental
 changes on the outcome of resource competition when investigating the
 influence that environmental disturbances have on the operation of sexual
 selection and thereby on evolutionary processes and population dynamics.
DOI: 10.5061/dryad.hx3ffbgc3
title: Rapid adaptive evolution to drought in a subset of plant traits in a large-scale climate change experiment

description: Rapid evolution of traits and of plasticity may enable adaptation to
 climate change, yet solid experimental evidence under natural conditions
 is scarce. Here, we imposed rainfall manipulations (+30%, control, -30%)
 for ten years on entire natural plant communities in two Eastern
 Mediterranean sites. Additional sites along a natural rainfall gradient
 and selection analyses in a greenhouse assessed whether potential
 responses were adaptive. In both sites, our annual target species
 Biscutella didyma consistently evolved earlier phenology and higher
 reproductive allocation under drought. Multiple arguments suggest that
 this response was adaptive: it aligned with theory, corresponding trait
 shifts along the natural rainfall gradient, and selection analyses under
 differential watering in the greenhouse. However, another seven candidate
 traits did not evolve, and there was little support for evolution of
 plasticity. Our results provide compelling evidence for rapid adaptive
 evolution under climate change. Yet, several non-evolving traits may
 indicate potential constraints to full adaptation.
description: The data table contains trait values for ten plant functional
 traits of 320 genotypes of Biscutella didyma, raised in the greenhouse
 under five water levels. Genotypes originated from four sites along a
 natural rainfall gradient: In the two intermediate sites (SA semi-arid, M
 Mediterranean) ten years Climate Change manipulations (dry -30%, control,
 wet +30% rainfall) had been imposed prior to seed collection; two
 additional control sites (A arid, MM mesic-Mediterranean) extended the
 span of the natural rainfall gradient.
DOI: 10.5061/dryad.qfttdz0f7
title: Data from: Concerted evolution reveals co-adapted amino acid substitutions in Na+K+ ATPase of frogs that prey on toxic toads

description: Gene duplication is an important source of evolutionary innovation, but
 the functional distinction between duplicates can be opposed by ongoing
 gene conversion between them. Here we document a tandem duplication of
 Na+,K+-ATPase subunit α1 (ATP1A1) sharedby frogs in the genus
 Leptodactylus,a group of species that feeds on toxic toads. One ATP1A1
 paralog evolved resistance to toad toxins while the other paralog retained
 ancestral susceptibility. Frequent non-allelic gene conversion homogenized
 most of the paralog sequences,yet the two Leptodactylusparalogs are
 distinguished by 12 amino acid substitutions that were maintained by
 strong selection that counteracted gene conversion. Protein-engineering
 experiments show that two substitutions substantially increase toxin
 resistance, whereas the 10 additional substitutions mitigate deleterious
 pleiotropic effects on enzyme function. Our results highlight how
 neofunctionalized gene duplicates can help pinpoint functional
 substitutions and their interactions with the genetic backgrounds on which
 they arise.
description: "NKA Enzyme Assays Raw Data" - raw plate reader data
 and downstream calculations for enzyme assays used in this study
 "Mohammadi_ATP1A1_alignment" - alignment of ATP1A1 gene
 sequences used to generate phylogenetic trees in this study
 "NKA_Enzyme_Assays_Raw_Data_Readme" - ReadMe file for
 the enzyme assay raw data
DOI: 10.5061/dryad.79cnp5hsp
title: Data from: Impact of a novel community testing pathway for people with suspected COVID-19 in Wales: a cost-minimisation analysis

description: Objective: To compare NHS organisations testing pathways for patients with
 suspected COVID-19 in the community versus standard hospital testing
 practices Perspective: NHS commissioners and services Methods: During the
 containment phase of the Covid-19 pandemic we developed a community model
 pathway for Covid-19 testing in Wales with testing teams undertaking
 swabbing for Covid-19 in individuals usual place of residence. We
 undertook a cost-minimisation analysis comparing the costs to the NHS in
 Wales of community testing for COVID-19 versus standard hospital testing
 practices and ambulance conveyancing. We analysed data from patients with
 suspected COVID-19 between January and February 2020 and applied
 assumptions of costs from national contractual and reference costs for
 ambulances, staffing and transportation with market costs at the time of
 publication. Results: 177 patients with suspected COVID-19 underwent
 community testing via local NHS organisations between January and February
 2020 with a mean age of 46.1 (IQR 27.5-56.3). This was 92% of total
 patients who were tested for Covid-19 during this period. We estimate,
 compared to standard hospital testing practices cash savings in improved
 productivity for the NHS of £152,190 during this time period, in addition
 to further non-monetised benefits for hospital and ambulance flow.
 Conclusions: Community testing for COVID-19 in Wales is now an established
 pathway and continues to bring benefits for patients, local healthcare
 organisations and the NHS. Further application of this model in other
 settings and to other infectious diseases may herald promising returns.
description: Data on numbers of people
 tested and their demographic and epidemiological information was
 maintained on a dataset held by the Public Health Wales Microbiology
 Division. This dataset additionally collated information on time to test,
 time to result, the result of common respiratory pathogen screen and
 reference laboratory results. We report here on data collected between
 17<sup>th</sup> January-17<sup>th</sup> February
 2020, excluding cases for which there was no sample collected (n=3) or no
 postcode recorded (n=4). We undertook a cost-minimisation analysis on the
 assumption that there was no significant difference in outcome of testing
 people with suspected COVID-19 in the community versus usual hospital
 care. Due to available data, we focus exclusively on the perspective of
 the health service provider and on health service costs and used then
 contemporary market prices. <br>
DOI: 10.5061/dryad.nvx0k6dq7
title: Vasohibin1, a new mouse cardiomyocyte IRES trans-acting factor that regulates translation in early hypoxia

description: Hypoxia, a major inducer of angiogenesis, triggers major changes in gene
 expression at the transcriptional level. Furthermore, under hypoxia,
 global protein synthesis is blocked while internal ribosome entry sites
 (IRES) allow specific mRNAs to be translated. Here, we report the
 transcriptome and translatome signatures of (lymph)angiogenic genes in
 hypoxic HL-1 mouse cardiomyocytes: most genes are induced at the
 translatome level, including all IRES-containing mRNAs. Our data reveal
 activation of (lymph)angiogenic factor mRNA IRESs in early hypoxia. We
 identify vasohibin1 (VASH1) as an IRES trans-acting factor (ITAF) that is
 able to bind RNA and to activate the FGF1 IRES in hypoxia, but which tends
 to inhibit several IRESs in normoxia. VASH1 depletion has a wide impact on
 the translatome of (lymph)angiogenesis genes, suggesting that this protein
 can regulate translation positively or negatively in early hypoxia.
 Translational control thus appears as a pivotal process triggering new
 vessel formation in ischemic heart.
description: The sequences of the different lentivector plasmids are
 provided.
DOI: 10.5061/dryad.69p8cz8zz
title: Temperature-mediated tradeoff between development and performance in larval wood frogs (Rana sylvatica)

description: Countergradient variation has been detected in diverse taxa. In a common
 manifestation, individuals from colder environments develop faster than
 conspecifics from warmer environments when placed in a common garden.
 Where such a pattern exists, it implies a tradeoff: individuals from
 warmer environments have intrinsic rates of development lower than those
 demonstrated by other individuals of the same species. We explored a
 tradeoff between development rate and locomotor performance in the wood
 frog (Rana sylvatica), an amphibian for which countergradient variation
 has been well documented. We reared wood frogs from 10 populations under
 two temperature regimes, bracketing the temperatures observed in local
 natural ponds. Individuals reared under warmer conditions developed more
 rapidly but exhibited burst speeds 20% lower than individuals reared under
 colder conditions. The shape of the relationship was consistent across the
 10 populations and thus, we found no evidence of countergradient variation
 in performance. Burst speed assays of wild-caught tadpoles from the same
 populations showed a similar but nonsignificant trend, with greater
 variability among ponds. Overall, our findings support the existence of a
 tradeoff that may be of broad importance and which may help explain
 widespread occurrence of countergradient variation.
description: Please see the methods section of our manuscript for details on
 data collection. The README file includes details about processing for
 specific variables. For further questions, please contact the authors:
 kaija.gahm@aya.yale.edu.