cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0cfxpnw1p
title: Data for: Organic management and landscape heterogeneity combine to sustain multifunctional bird communities in European vineyards

description: Conserving functionally diverse bird communities in European farmland is
 becoming critical, with no exception for regions of wine production.
 Management intensification combined with the loss of semi-natural habitats
 in wine-growing landscapes has led to a long-term decline in birds of
 conservation concern, but also in once common insectivores and seed
 eaters. These declines are expected to threaten key ecological functions
 provided by vineyard birds, such as pest or weed control, but also their
 cultural significance. We analyzed how organic management and landscape
 heterogeneity affected taxonomic and functional diversity of 334 bird
 communities from 12 regions of the three main wine-producing European
 countries (France, Italy and Spain). We further modelled the responses of
 community-level metrics measuring mean habitat specialization and bird
 song attractiveness to humans, as well as cumulative abundances of
 functional insectivores, seed and grape eaters to account for individual
 avian functions. We found that organic viticulture enhanced bird
 functional diversity and individual functions, but that its positive
 effect partially depended on grass cover management in the inter-rows and
 landscape heterogeneity. Woodland cover and landscape compositional
 heterogeneity increased both taxonomic and functional diversity of bird
 communities, as well as functional insectivory. Landscape configurational
 heterogeneity also increased functional diversity and mean song
 attractiveness of bird communities. Overall, both bird diversity and
 functions were enhanced by higher landscape heterogeneity, especially in
 organic vineyards. However, mean habitat specialization decreased with
 woodland cover and configurational heterogeneity, meaning that open
 habitat specialists preferred more even landscapes with high vineyard
 cover. Synthesis and applications. Our study highlights the benefits of
 combining organic management and partial grass cover at the field level
 and promoting interfaces between vineyards and semi-natural habitats at
 the landscape level to sustain multifunctional bird communities in
 wine-producing European countries.
DOI: 10.5061/dryad.0gb5mkm0m
title: Genotyping-by-Sequencing data of weedy and domesticated Brassica rapa L.

description: The study of domestication contributes to our knowledge of evolution and
 crop genetic resources. Human selection has shaped wild Brassica rapa into
 diverse turnip, leafy, and oilseed crops. Despite its worldwide economic
 importance and potential as a model for understanding diversification
 under domestication, insights into the number of domestication events and
 initial crop(s) domesticated in B. rapa have been limited due to a lack of
 clarity about the wild or feral status of conspecific non-crop relatives.
 To address this gap and reconstruct the domestication history of B. rapa,
 we analyzed 68,468 genotyping-by-sequencing-derived SNPs for 416 samples
 in the largest diversity panel of domesticated and weedy B. rapa to date.
 To further understand the center of origin, we modeled the potential range
 of wild B. rapa during the mid-Holocene. Our analyses of genetic diversity
 across B. rapa morphotypes suggest that non-crop samples from the
 Caucasus, Siberia, and Italy may be truly wild, while those occurring in
 the Americas and much of Europe are feral. Clustering, tree-based
 analyses, and parameterized demographic inference further indicate that
 turnips were likely the first crop type domesticated, from which leafy
 types in East Asia and Europe were selected from distinct lineages. These
 findings clarify the domestication history and nature of wild crop genetic
 resources for B. rapa, which provides the first step toward investigating
 cases of possible parallel selection, the domestication and feralization
 syndrome, and novel germplasm for Brassica crop improvement.
DOI: 10.5061/dryad.vhhmgqnsg
title: Data from: Special care dentistry perception among dentists in Jakarta: an online survey study

description: Special Care Dentistry (SCD) or Special Needs Dentistry is a branch of
 dentistry concerned with the oral health of people with a variety of
 medical conditions or limitations that require more than routine delivery
 of care. There were reports on oral status of special care patients and
 special interest group for SCD dentists in Indonesia has existed. However,
 there was not perception report on SCD amongst dentists in Jakarta. This
 paper will describe the perception of dentists in Jakarta towards SCD. A
 cross-sectional questionnaire, translated and cross adapted to Indonesian,
 was distributed online through Whatsapp to dentists registered in Jakarta
 late 2019. Quantitative data was analyzed using statistical software for
 proportion and correlation using Chi-Square test. The questionnaire
 explored dentists’ perception towards SCD. A total of 250 dentists
 participated in this study, of them 173 general practitioners and 77
 specialist dentists. Most respondents reported that they did not have SCD
 component during undergraduate dental school and did not provide treatment
 to patients with special needs in their clinical practice. Most
 respondents have poor perception of SCD, however, most of the respondents
 showed motivation and interest towards SCD training. Dentists in Jakarta
 involved in this study had poor perception of SCD. More efforts should be
 performed to improve SCD education and awareness.
description: Survey was conducted using Google Form and distributed through
 Whatsapp messenger.
DOI: 10.5061/dryad.m0cfxpp34
title: Plant traits measured for Australian alpine plants

description: Rapid evolution is likely to be an important mechanism allowing native
 species to adapt to changed environmental conditions. Many northern
 hemisphere species have undergone substantial recent changes in phenology
 and morphology. However, we have little information about how native
 species in the southern hemisphere are responding to climate change. We
 used herbarium specimens from 21 native alpine plant species in Kosciuszko
 National Park, Australia to make over 1500 measurements of plant size,
 leaf thickness, leaf mass per area, leaf shape and leaf size across the
 last 126 years. Only two out of 21 species (9%) showed significant changes
 in any of the measured traits. The number of changes we observed was not
 significantly different to what we would expect by chance alone, based on
 the number of analyses performed. This lack of change is not attributable
 to methodology – an earlier study using the same methods found significant
 changes in 70% of species introduced to south-east Australia. Australia’s
 native alpine plants do not appear to be adapting to changed conditions,
 and because of the low elevation of Australia’s mountains, they do not
 have much scope for uphill migration. Thus, our findings suggest that
 Australia’s native alpine plants are at even greater risk in the face of
 future climate change than was previously understood. 
description: Plant trait data were measured from a combination of historic
 and modern herbarium specimens collected between 1890 and 2017. Specimens
 were sourced from the John T. Waterhouse Herbarium at UNSW Sydney (UNSW),
 Downing Herbarium at Macquarie University (MQU), National Herbarium of New
 South Wales at the Royal Botanic Gardens Sydney (NSW), and the Australian
 National Herbarium at CSIRO in Canberra (CANB). All modern and historic
 herbarium specimens used were collected within a five-kilometre radius
 from the summit of Mount Kosciuszko, and from sites above 1800m.
  
description: 1. Each sheet contains the values for the five plant traits
 measured; leaf length, leaf shape, growth form, leaf thickness, and leaf
 mass per unit area. 2. Units for leaf traits measured
 are present in the first tab (metadatatab) 3. Due to
 the varying conditions of herbarium specimens, it was not possible to
 measure every trait on every species. However, we measured all the
 possible traits available for each species.
DOI: 10.5061/dryad.cfxpnvx4j
title: Landscape composition mediates the relationship between predator body size and pest control

description: Understanding the mechanisms contributing to positive relationships
 between predator diversity and natural pest control is fundamental to
 inform more effective management practices to support sustainable crop
 production. Predator body size can provide important insights to better
 understand and predict such predator-pest interactions. Yet, most studies
 exploring the link between predator body size and pest control have been
 conducted in species-poor communities under controlled environmental
 conditions, limiting our ability to generalize this relationship across
 heterogeneous landscapes. Using the community of naturally occurring
 ground beetles in cabbage fields, we examined how landscape composition
 (percent cropland) influences the size structure (mean, variance, and
 skewness of body size distribution) of predator communities and the
 subsequent effects on pest control. We found that predator communities
 shifted their size distribution towards larger body sizes in
 agriculturally dominated landscapes. This pattern arose from increasing
 numerical dominance of a few large-bodied species rather than an
 aggregated response across the community. Such landscape-driven changes in
 community size structure led to concomitant impacts on pest control, as
 the mean body size of predators was positively related to predation rates.
 Notably, the magnitude of pest control depended not only on the size of
 the dominant predators but was also strongly determined by the relative
 proportion of small vs. large-bodied species (i.e., skewness). Predation
 rates were higher in predator assemblages with even representation of
 small and large-bodied species relative to communities dominated by either
 large or small-bodied predators. Landscape composition may therefore
 modulate the relationship between predator body size and pest control by
 influencing the body size distribution of co-occurring species. Our study
 highlights the need to consider agricultural practices that not only boost
 effective predators, but also sustain a predator assemblage with a diverse
 set of traits to maximize overall pest control.
description: <b>File description:
 </b>This file contains the activity density, species richness,
 species evenness, species diversity, and body size structure (i.e., mean,
 diversity and symmetry) of naturally occurring carabid communities
 collected in pitfall traps on 11 farms located across a gradient of
 landscape complexity in the Finger Lakes Region of New York State (USA),
 during the summers of 2014 and 2015.  <b>Date of data
 collection</b>: June-September 2014, June-October 2015.
 <b>Geographical
 location of data collection</b>: the field work was conducted in 43
 experimental fields in the Finger Lakes Region, NY, USA.
DOI: 10.5061/dryad.bcc2fqzbt
title: Data from: Suppression of a plant hormone gibberellin reduces growth of invasive plants more than native plants

description: Subsequent to escape from intense herbivory in the native range, invasive
 plants are expected to reduce allocation to costly anti-herbivory defences
 and have greater competitive ability than co-occurring native species.
 Given that invasive alien plants often occur in open habitats where light
 is less limited, it is reasonable to hypothesize that invasive plants
 should express high concentrations of gibberellins that enable them to
 allocate more biomass to roots, and thus have higher competitive ability
 than native plants. To test this prediction, we grew five congeneric pairs
 of invasive alien plants and native plants under two levels of nutrient
 availability (low versus high) and treated a half of the plants with a
 gibberellin biosynthesis inhibitor, paclobutrazol. Paclobutrazol
 significantly decreased aboveground, belowground, and total biomass of the
 test plants. Interestingly, the effects on belowground biomass were
 significantly stronger for invasive plants than for native plants. A
 similar pattern was found for total biomass (marginally significant effect
 p = 0.0592). Additionally, paclobutrazol decreased root mass fraction for
 invasive plants, but tended to increase it for native plants. Our findings
 suggest that plant hormones can differently regulate biomass allocation of
 invasive and native plants, and thus contribute to greater growth of
 invasive plants compared to native plants.
description: The dataset was collected from a greenhouse experiment.
description: The unit of biomass is g, and the unit of height is cm.
DOI: 10.5061/dryad.zkh189396
title: Protocol for safe, affordable, and reproducible isolation and quantitation of SARS-CoV-2 RNA from wastewater

description: The following protocol describes our workflow for processing wastewater
 with the goal of detecting the genetic signal of SARS-CoV-2. The steps
 include pasteurization, virus concentration, RNA extraction, and
 quantification by RT-qPCR. We include auxiliary steps that provide new
 users with tools and strategies that will help troubleshoot key steps in
 the process. This protocol is one of the safest, cheapest, and most
 reproducible approaches for the detection of SARS-CoV-2 RNA in wastewater.
 Owing to a pasteurization step, it is safe for use in a BSL1+ facility. In
 addition to making the protocol safe for the personnel involved,
 pasteurization had the added benefit of  increasing the
 SARS-CoV-2 genetic signal. Furthermore, the RNA obtained using this
 protocol can be sequenced using both Sanger and Illumina sequencing
 technologies. The protocol was adopted by the New York City Department of
 Environmental Protection in August 2020 to monitor SARS-CoV-2 prevalence
 in wastewater in all five boroughs of the city. In the future, this
 protocol could be used to detect a variety of other clinically relevant
 viruses in wastewater and serve as a foundation of a wastewater
 surveillance strategy for monitoring community spread of known and
 emerging viral pathogens.
description: Cts of SARS-CoV-2 RNA extracted from NYC wastewater processed
 using different techniques were converted to N1 copies/L using RT-qPCR
 standard curves. 
description: Rows represent independent samples obtained from different
 wastewater treatment plants on the same date. Columns under the same
 treatment heading represent repeated RT-qPCR assay measurements of the
 same sample.
DOI: 10.5061/dryad.ffbg79ctk
title: Circular dichroism spectroscopic and small-angle neutron scattering analysis of alpha-synuclein and bacteriorhodopsin in bicontinuous microemulsions

description: The membrane proteins (MPs) alpha-synuclein (ASYN) and bacteriorhodopsin
 (BR) were readily incorporated into bicontinuous microemulsions (BMEs)
 formed by two microemulsion systems: water/heptane/Aerosol-OT
 (AOT)/CK-2,13 and water/dodecane/sodium dodecyl sulfate (SDS)/1-pentanol.
 (CK-2,13 is an alkyl ethoxylate possessing two alkyl tail groups of carbon
 chain length 2 and 13 and an average degree of ethoxylation of 5.6.) MPs
 were encapsulated in BMEs through preparation of Winsor-III systems at
 optimal salinity, with the anionic surfactants AOT and SDS providing the
 driving force for extraction. Dissolution of ASYN in BMEs greatly
 increased the former’s alpha-helicity, similar to ASYN’s behavior in the
 presence of biomembranes, while BME- and vesicle-encapsulated BR possessed
 similar secondary structure. Small-angle neutron scattering (SANS) results
 clearly demonstrated the direct interaction of MPs with the surfactants,
 resulting in a decrease of surface area per volume for surfactant
 monolayers due to decreased surfactant efficiency. The SANS signal for
 ASYN was isolated through the use of neutron contrast matching for the
 surfactants through partial deuteration of water and oil, one of the first
 reports of contrast matching for BMEs in the literature. The SANS results
 of the contrast matched sample reflected similar aggregation for ASYN in
 BMEs as was reported previously for vesicles and SDS solution. This study
 demonstrates the potential use of BMEs as MP host systems for conducting
 biochemical reactions such as the conversion of sunlight into adenosine
 triphosphate (ATP) by BR and studying fundamental behavior of MPs, such as
 the role of ASYN dysfunction in Parkinson’s disease, as well as for
 isolation and purification of MPs via Winsor-III -based extraction.
description: Circular dichroism spectroscopic data reported herein was
 obtained directly from the instrument. The CONTIN program was used to fit
 the spectroscopic data, to obtain an estimate of the distribution of
 secondary structure for the proteins. Small-angle neutron scattering
 (SANS) data provided herein was obtained from the Bio-SANS instrument at
 Oak Ridge National Laboratory (Oak Ridge, TN, USA), and reduced and
 processed in a standard fashion. Microsoft Excel was employed to obtain
 linear fits to SANS data, as described in the spreadsheets and readme
 file.
DOI: 10.5061/dryad.0vt4b8gz2
title: Raw data for: Extreme climate shifts pest dominance hierarchy through thermal evolution and transgenerational plasticity

description: We conducted an 8-year field survey to link extreme high-temperature
 events to the shift in dominance hierarchy of two worldwide cereal aphid
 species (Rhopalosiphum padi and Sitobion avenae), which may respond
 rapidly through evolutionary or plastic responses to thermal extremes due
 to their short generation duration, clonal structure and high thermal
 sensitivity. To further understand the mechanism involved in this change
 in species’ dominance, we characterised aphid heat tolerance and
 demography of the 2 species sourced from relatively mild (Xinxiang) and
 hot (Wuhan) locations in a common garden design and compared the same
 measures in up- and down-selected lines of the two aphid species. All the
 datasets are the raw data for our three parts in this research,
 field survey, common garden test, and artificial selection experiment.
DOI: 10.15468/dl.qd4acj
title: Occurrence Download

description: A dataset containing 380 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Solanum nigrum"
 ]
}

 The dataset includes 380 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002789-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ns1rn8ps4
title: Non-adaptive evolutionary processes governed the diversification of a temperate conifer lineage after its migration into the tropics

description: Constructing phylogenetic relationships among closely related species is a
 recurrent challenge in evolutionary biology, particularly for long-lived
 taxa with large effective population sizes and uncomplete reproductive
 isolation, like conifers. Conifers further have slow evolutionary rates,
 which raises the question of whether adaptive or non/adaptive processes
 were predominantly involved when they rapidly diversified after migrating
 from temperate regions into the tropical mountains. Indeed, fine-scale
 phylogenetic relationships within several conifer genus remain under
 debate. Here, we studied the phylogenetic relationships of endemic firs
 (Abies, Pinaceae) discontinuously distributed in the montane forests from
 the Southwestern United States to Guatemala, and addressed several
 hypotheses related to adaptive and non-adaptive radiations. We derived
 over 80K SNPs from genotyping by sequencing (GBS) for 45 individuals of
 nine Mesoamerican species to perform phylogenetic analyses. Both Maximum
 Likelihood and quartets-inference phylogenies resulted in a well-resolved
 topology, showing a single fir lineage divided in four subgroups that
 coincided with the main mountain ranges of Mesoamerica; thus having
 important taxonomic implications. Such subdivision fitted a North-South
 isolation by distance framework, in which non-adaptive allopatric
 processes seemed the rule. Interestingly, several reticulations were
 observed within subgroups, especially in the central-south region, which
 may explain past difficulties for generating infrageneric phylogenies.
 Further evidence for non-adaptive processes was obtained from analyses of
 21 candidate-gene regions, which exhibited diminishing values of πa/πs and
 Ka/Ks with latitude, thus indicating reduced efficiency of purifying
 selection towards the Equator. Our study indicates that non-adaptive
 allopatric processes may be key generators of species diversity and
 endemism in the tropics.
description: Sample We sampled foliage from 45 individuals of genus <em>Abies</em> (Pinaceae) collected in 33 natural fir populations (1-2 indivs/pop) along a latitudinal gradient between the Southwestern USA and Guatemala. To root our networks and phylogenies, we used an individual of <i>A. lasiocarpa</i> as outgroup. We extracted DNA from frozen needles with either a DNeasy Plant Mini Kit (Qiagen) or a modified CTAB protocol. We double-digested individual DNA samples (200 ng) with enzymes <i>Msp</i>I (C|CGG) and <i>Pst</i>I (TGCA|G), and ligated unique barcodes and adapters to digestion products. Single end sequencing (100x1) was done in an Illumina Hiseq 2500 lane. Both library preparation and sequencing were performed at the Institute of Integrative Biology and Systems at Université Laval (http://www.ibis.ulaval.ca/en/services-2/genomic-analysis-platform/). We used a pyRAD (Eaton, 2014) pipeline (https://github.com/dereneaton/ipyrad) to process raw sequence reads.
description: Readme.txt describes each file.
DOI: 10.5061/dryad.b2rbnzsdp
title: The causes and ecological context of rapid morphological evolution in birds

description: Episodic pulses in morphological diversification are a prominent feature
 of evolutionary history, driven by factors that remain widely disputed.
 Resolving this question has proved challenging because comprehensive
 species-level data are generally unavailable at sufficient scale.
 Combining global phylogenetic and morphological data for birds, we show
 that pulses of diversification in lineages and traits tend to occur
 independently and in different contexts. Speciation pulses are preceded by
 greater differentiation in overall morphology and habitat niche, then
 followed by increased rates of beak evolution. Contrary to standard
 hypotheses, pulses of morphological diversification tend to be associated
 with habitat niche stability rather than adaptation to different diets and
 habitat types. These patterns suggest that the timing of diversification
 varies across traits according to their ecological function, and that
 pulses of morphological evolution may occur when successful lineages
 subdivide niche space within particular habitat types. Our results
 highlight the growing potential of functional trait data sets to refine
 macroevolutionary models.
description: Multivariate data sets were analyzed using BayesTraits with the
 posterior distribution of phylogenies provided.
DOI: 10.15468/dl.a5ucpf
title: Occurrence Download

description: A dataset containing 1408 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Desmanthus illinoensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1408 records from 99 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002790-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.