cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zpc866t9r
title: Functional trait variation of Anemone nemorosa along macro‐ and microclimatic gradients close to the northern range edge

description: Climate warming is affecting ecosystems worldwide, and slow-colonizing
 forest under- storey species are particularly vulnerable if they are
 unable to track climate change. However, species’ responses to climatic
 conditions in terms of growth, reproduction and colonization capacity may
 vary with the distance to their distribution range edge. Anemone nemorosa
 is known to be a slow colonizing forest herb dependent on forest cover in
 the southern and central part of its distribution range, whereas at its
 northern distribution range (and at higher elevations) it also occurs in
 open habitats. Here, we investigated the response of plant functional
 traits of Anemone nemorosa in cen- tral Norway (close to its northern
 distribution range edge) to a macroclimatic gra- dient (elevation), two
 microclimatic gradients (forest density and distance to forest edge) and a
 competition treatment (removal of neighbouring vegetation). We aimed to
 identify which environmental conditions (light, temperature, soil pH
 and/or soil organic matter) drive A. nemorosa’s responses. In a total of
 90 plots, we measured six functional traits of A. nemorosa (plant height,
 biomass, specific leaf area, seed number, seed mass,and germination
 percentage). We found stronger variation in environmental conditions along
 the macroclimatic elevational gradient, than along the microclimatic
 gradients of forest density and distance to forest edge, and this was also
 reflected in A. nemorosa’s responses. Light availability, in interaction
 with temperature, was the key environmental variable driving plant
 performance, while soil conditions were less important. The competition
 release treatment had a negative effect on A. nemorosa in our study sites,
 indicating that the facilitative effect of the neighbouring vegetation may
 be stronger than the competitive effect. Our study suggests that A.
 nemorosa, close to its northern distribution range edge, has the capacity
 to cope with climate change through phenotypic responses, and that light
 and temperature are the key drivers of these responses.
DOI: 10.25625/kzrveg
title: Meta Data for "Visuomotor Mismatch Responses as a Hallmark of Explaining Away in Causal Inference"

description: Metadata for the publication. Simulation code to reproduce the figures can be found in the GitHub repository, see below.
DOI: 10.5061/dryad.34tmpg4mz
title: Historical biogeography and character-mapping of Hiptage (Malpighiaceae) corroborate Indochina's rainforests as one of the main sources of plant diversity in Southeastern Asia

description: In Malpighiaceae, Hiptage represents one of the seven past dispersal
 events from the Neotropics to the Paleotropical region, being by far the
 most widely diversified and distributed genus of Paleotropical
 Malpighiaceae. In this study, we tested the monophyly of the current
 infrageneric classification of Hiptage with a dated and calibrated
 molecular phylogeny. We also reconstructed ancestral areas to elucidate
 which route led to the colonization of Southeast Asia by the most recent
 common ancestor (MRCA) of this genus (Mainland or Indian routes). The
 pre-existing infrageneric classification of Hiptage was recovered as
 non-monophyletic due to being solely based on homoplasic morphological
 characters, such as the presence and number of sepal nectar glands.
 Regarding its biogeography, the MRCA of Hiptage arose in the rainforests
 of southeast Asia ca. 24.0 Mya and greatly diversified in this region. Few
 lineages have dispersed eastward to the pacific islands or westwards to
 India. Based on our results, we hypothesize that the MRCA of Hiptage did
 not take the Indian route to reach Southeastern Asia. Instead, it reached
 this region by past mainland forest connections between North
 America-Europe (Boreotropical hypothesis) and southeast Asia. Nonetheless,
 distribution ranges for the species of Hiptage must be carefully revised,
 and the five species of Hiptage endemic to India must also be sampled so
 we can properly test which route led the MRCA of Hiptage to reach
 Southeast Asia in the early Miocene.
description: Nexus matrixes and trees.
DOI: 10.5061/dryad.q2bvq83mq
title: Data from: Population genomics of Sitka black-tailed deer supports invasive species management and ecological restoration on islands

description: Invasive mammals represent a critical threat to island biodiversity;
 eradications can result in ecological restoration yet may fail in the
 absence of key population parameters. Over-browsing by invasive Sitka
 black-tailed deer (Odocoileus hemionus sitkensis) is causing severe
 ecological and cultural impacts across the Haida Gwaii archipelago
 (Canada). Previous eradication attempts demonstrate forest regeneration
 upon deer removal, but reinvasion reverses conservation gains. Here we use
 restriction-site associated DNA sequencing (12,947 SNPs) to investigate
 connectivity and gene flow of invasive deer (n=181) across 15 islands,
 revealing little structure throughout Haida Gwaii and identifying the
 large, central island of Moresby (&gt;2,600 km2) as the greatest
 source of migrants. As a result, the archipelago itself should be
 considered the primary eradication unit, with the exception of
 geographically isolated islands like SGang Gwaay. Thus, limiting
 eradications to isolated islands combined with controlled culling and
 enhanced biosecurity may be the most effective strategies for achieving
 ecological restoration goals.
description: deer_182ind_15pop_12961snp.vcf: genotypic data for 182
 individuals from 15 sample sites at 12,961 SNPs generated via
 RADseq. 12961_populations.loci.fa: fasta file
 containing sequences for 12,961 loci.
DOI: 10.5281/zenodo.17940431
title: The Mechanistic Universe: Direction-aware and topology-aware drug–protein interaction datasets

description:  

The purpose of this record is to provide structured, machine-readable data artifacts that support the analyses described in the associated manuscript.
DOI: 10.5281/zenodo.18399120
title: The Mechanistic Universe: Direction-aware and topology-aware drug–protein interaction datasets

description:  

The purpose of this record is to provide structured, machine-readable data artifacts that support the analyses described in the associated manuscript.
DOI: 10.5061/dryad.rbnzs7hcs
title: Entropy driven order in an array of nanomagnets

description: Long-range ordering, while typically understood as a decrease in entropy,
 can also be driven by increasing system entropy in certain special cases.
 We demonstrate that artificial spin ice arrays of single-domain
 nanomagnets can be designed to produce entropy-driven order. We probe
 thermally active tetris artificial spin ice, known to have a zero point
 Pauli entropy, both experimentally and through simulations. We find
 two-dimensional magnetic ordering in one subset of the nanomagnet moments,
 which we demonstrate to be induced by disorder (i.e., increased entropy)
 in another subset of moments. Contrasting with other entropy-driven
 systems, the degrees of freedom in artificial spin ice are both designable
 and directly observable at the microscale, and the entropy of the system
 is precisely calculable in simulations. This robust example, in which the
 system’s interactions and ground state entropy are well-defined,
 significantly expands the experimental landscape for the study of
 entropy-driven ordering.
DOI: 10.5061/dryad.547d7wm9x
title: Wilson Warbler molting and plumage observations

description: I made observations of a central California population of Wilson’s
 Warbler, Cardellina pusilla, on or after 1 July over ten breeding seasons.
 I sighted males in definitive prebasic molt as early as 4 July (in 2007)
 and as late as 1 September (in 1999). I determined that most territorial
 males at my study site molted on their breeding territories, and
 individual molt lasted a maximum of 46 days. Following prebasic molt,
 territorial males engaged in subdued “post-molt singing,” which appeared
 to last no more than seven days in most males, and which I first heard on
 13 August (in 1004), and last heard on 6 September (in 1999). I sighted no
 female in definitive prebasic molt, nor fresh basic plumage, during the
 study. Of 13 females sighted on or after 21 July, I confirmed that 11 were
 in late breeding season uniparental brood care, and I could not rule out
 late brood care for the other two. Most, and possibly all, females not
 engaged in late season uniparental brood care appear to have vacated their
 breeding territories before 21 July, as I saw just two possible after that
 date. This apparent early departure of the majority of resident females
 from their breeding grounds was much earlier than the departures of
 resident males, the last of which I sighted on 10 September (in 1999).
 Early-departing females presumably underwent prebasic molt after 21 July,
 and at locations not known. Remaining late-nesting females must have
 molted much later than did resident males, and also likely later than
 early-departing resident females, and at unknown locations. I last sighted
 two uniparental brood-tending females, still in worn plumage, on 26 and 29
 August respectively, whereas some males had completed prebasic molt as
 early as 13 August. Two unique findings of this study are a male/female
 difference in location of prebasic molt, and a likely dichotomy of
 prebasic molt timing between females which leave their breeding
 territories relatively early, and those which remain on their territories
 in uniparental brood care. Another finding, that most, and perhaps all,
 territorial male Wilson’s Warblers engaged in brief post-molt singing
 following prebasic molt, is a largely unrecognized behavior, but one
 previously reported in several other passerine species. Post-molt singing
 may be a reliable indicator that prebasic molt is complete.
description: Data collected through careful
 filed observation after 1 July over ten study seasons. Sightings of molt
 and plumage from the ten study seasons was divided into five day
 increments to obtain a record of the type of plumage (worn or basic) and
 the presence or absence of prebasic moltin in male and female
 Wilson's Warblers respecitively.
description: No missing values. Data used to develop a graph of the frequency
 of worn plumage, prebasic molt, and basic plumage sighted in male and
 female Wilson Warblers, and viewer could dublicate the progression of
 these stages after 1 July from the data.
DOI: 10.5061/dryad.cvdncjt62
title: Changes in the direction of the diversity-productivity relationship over fifteen years of stand development in a planted temperate forest

description: Experiments manipulating diversity in both forests and grasslands have
 often observed a positive diversity-productivity relationship (DPR) which
 tends to strengthen during plant community development. This pattern is
 generally attributed to an increase in niche complementarity or
 facilitation. Most analyses do not examine species dominance and density,
 which also change over time. Moreover, how neighbourhood scale
 interactions among tree species affect the DPR is not well understood. We
 analysed growth and mortality data from the Simplex experiment, a part of
 the BIOTREE tree diversity experiment. Simplex consists of 36 plots each
 planted with four common and commercially important tree species to create
 a gradient of tree species evenness at two tree densities (6667 and 3556
 trees ha-1). We test whether: i) the effect of evenness on total
 aboveground biomass productivity increase with stand development (year),
 ii) the effect of evenness on productivity is stronger in dense plots;
 iii) intra-specific competition from neighbours negatively affect the
 growth of dominant species more strongly compared to co-dominant species,
 and whether this negative effect is stronger in denser plots. The
 direction of DPR was initially negative because the fast-growing
 long-lived pioneer Douglas fir (Pseudotsuga menziesii (Mirb.) Franco)
 dominated. However, with time, shade tolerant Norway spruce (Picea abies
 (L.) Karst.) and European beech (Fagus sylvatica L.) increased in
 abundance (by biomass), and the relationship between evenness and biomass
 increment changed from negative to positive in high-density plots.
 Neighbourhood analyses revealed that for Douglas fir and Norway spruce,
 conspecifics reduced individual growth rates across density levels and
 years. Synthesis: We observed a shift in the diversity-productivity
 relationship over 15 years in our experiment. Over time, increasing
 intraspecific competition limited the increment of the abundant Douglas
 fir in uneven plots, and a persistent increase in the abundance (by
 biomass) of shade tolerant Norway spruce and European beech in even plots
 led to a higher community biomass increment, which led to a positive DPR.
 Emergence of a positive DPR in temperate forest plantations requires
 significant time and is importantly promoted by diversity at the
 neighbourhood scale (intimate mixtures) as well as higher density
 planting.
DOI: 10.5061/dryad.r7sqv9sdr
title: Understanding complex spatial dynamics from mechanistic models through spatio-temporal point processes

description: Landscape heterogeneity affects population dynamics, which determine
 species persistence, diversity and interactions. These relationships can
 be accurately represented by advanced spatially-explicit models (SEMs)
 allowing for high levels of detail and precision. However, such approaches
 are characterised by high computational complexity, high amount of data
 and memory requirements, and spatio-temporal outputs may be difficult to
 analyse. A possibility to deal with this complexity is to aggregate
 outputs over time or space, but then interesting information may be masked
 and lost, such as local spatio-temporal relationships or patterns. An
 alternative solution is given by meta-models and meta-analysis, where
 simplified mathematical relationships are used to structure and summarise
 the complex transformations from inputs to outputs. Here, we propose an
 original approach to analyse SEM outputs. By developing a meta-modelling
 approach based on spatio-temporal point processes (STPPs), we characterise
 spatio-temporal population dynamics and landscape heterogeneity
 relationships in agricultural contexts. A landscape generator and a
 spatially-explicit population model simulate hierarchically the
 pest-predator dynamics of codling moth and ground beetles in apple
 orchards over heterogeneous agricultural landscapes. Spatio-temporally
 explicit outputs are simplified to marked point patterns of key events,
 such as local proliferation or introduction events. Then, we construct and
 estimate regression equations for multi-type STPPs composed of event
 occurrence intensity and magnitudes. Results provide local insights into
 spatio-temporal dynamics of pest-predator systems. We are able to
 differentiate the contributions of different driver categories ( i.e.,
 spatio-temporal, spatial, population dynamics). We highlight changes in
 the effects on occurrence intensity and magnitude when considering drivers
 at global or local scale. This approach leads to novel findings in
 agroecology where, for example, we show that the organisation of
 cultivated patches and semi-natural elements play different roles for pest
 regulation depending on the scale considered. It aids to formulate
 guidelines for biological control strategies at global and local scale.
description: Data are numerically generated by model simulation in a
 previously published research (Zamberletti,
 Patrizia, et al. "More pests but less pesticide applications:
 Ambivalent effect of landscape complexity on conservation biological
 control." <em style="color:#222222;font-family:Arial , sans-serif;font-size:13px;background-color:#ffffff;">PLoS
 computational biology</em> 17.11
 (2021): e1009559.)
DOI: 10.15468/dl.3ed2wr
title: Occurrence Download

description: A dataset containing 1891 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Phragmites australis"
 ]
}

 The dataset includes 1891 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003049-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.r4xgxd2f6
title: Data from: Dispersion of SARS-CoV-2 in air surrounding COVID-19 infected individuals with mild symptoms

description: Since the beginning of the pandemic, the transmission modes of
 SARS-CoV-2—particularly the role of aerosol transmission—has been much
 debated. Accumulating evidence suggests that SARS-CoV-2 can be transmitted
 by aerosols, and not only via larger respiratory droplets. In this study,
 we quantified SARS-CoV-2 in air surrounding 14 test subjects in a
 controlled setting. All subjects had SARS-CoV-2 infection confirmed by a
 recent positive PCR test and had mild symptoms when included in the study.
 RT-PCR and cell culture analyses were performed on air samples collected
 at distances of one, two, and four meters from test subjects.
 Oronasopharyngeal samples were taken from consenting test subjects and
 analyzed by RT-PCR. Additionally, total aerosol particles were quantified
 during air sampling trials. Air viral concentrations at one-meter distance
 were significantly correlated with both viral loads in the upper airways,
 mild coughing, and fever. One sample collected at four-meter distance was
 RT-PCR positive. No samples were successfully cultured. The results
 reported here have potential application for SARS-CoV-2 detection and
 monitoring schemes, and for increasing our understanding of SARS-CoV-2
 transmission dynamics.
DOI: 10.5061/dryad.kh189327c
title: Data for Vijendravarma et al 2022: Drosophila females have an acoustic preference for symmetric males.

description: In many species, including humans and Drosophila, symmetric individuals
 secure more mating’s, suggesting that bilateral symmetry signals quality
 of potential mates and is subjected to sexual selection. However, this
 idea remains controversial, largely because obtaining conclusive
 experimental evidence has been hindered by confounding effects arising
 from methods used to increase asymmetry in test subjects. Here, we show
 that altering gravity during development increases asymmetry in Drosophila
 melanogaster without detrimental effect on survival, growth and behaviour.
 Testing males with altered gravity-induced asymmetry in female mate choice
 assays revealed symmetry-based discrimination of males via auditory cues.
 Females similarly discriminated against males with genetically-induced
 asymmetry, suggesting that their preference for symmetry is not specific
 to altered gravity. By segmenting male courtship song into left and right
 wing-generated song-bouts, we detected asymmetry in courtship song of
 altered gravity males with asymmetric wings that experienced rejection.
 Females experimentally evolved in absence of mate choice lacked this
 preference for symmetry, suggesting that symmetry is maintained by sexual
 selection. Our data provide evidence for the role of symmetry in sexual
 selection and reveals how non-visual cues can flag mate asymmetry during
 courtship.
description: The dataset collection methods have been completely discribed in
 the related manuscript
DOI: 10.5061/dryad.rfj6q57ck
title: Decreased ultraviolet radiation and decomposer biodiversity inhibit litter decomposition under continuous nitrogen inputs

description: Atmospheric nitrogen (N) deposition has altered biogeochemical cycles and
 ecosystem functioning. As a key process involved in carbon and nutrient
 cycles in terrestrial ecosystems, litter decomposition is sensitive to
 external N inputs. However, it remains unclear how the interactions of
 ultraviolet (UV) radiation, soil biodiversity (bacteria, fungi and
 invertebrates) and conventional drivers (e.g., litter chemistry and
 microbial activities) regulate the responses of litter decomposition to
 continuous N inputs. Based on an N-addition experimental platform, we
 conducted a two-year litter decomposition experiment to examine the
 relative importance of N-induced changes in biotic and abiotic factors in
 mediating changes in the decomposition rates of four litter types (three
 representative species and their mixture) along an experimental N gradient
 in a Tibetan alpine steppe. Our results showed that litter decomposition
 rates exhibited a consistent decrease in response to N enrichment among
 all species and their mixture. The slowed decomposition rates with
 increasing N addition were associated with N-induced reductions in UV
 radiation and soil bacterial diversity. An additional UV radiation
 manipulative experiment further confirmed that photodegradation had strong
 effects on plant litter decomposition at our study site. These results
 demonstrated that N-induced declines in UV radiation and soil bacterial
 diversity inhibited litter decomposition, challenging the traditional view
 that changes in litter chemistry and microbial activities determine the
 responses of litter decomposition to external N inputs.
DOI: 10.5061/dryad.g4f4qrfs7
title: The ecological function of insect egg micropyles

description: Insect egg micropyles are openings through the chorion allowing sperm
 entry for fertilisation. Micropyles are diverse structures showing
 remarkable variation in number, spatial arrangement and physical structure
 across extant insect orders. Despite being almost ubiquitous across
 insects, they have received little attention. As key morphological
 features of an immobile life stage, it is plausible that part of the
 diversity exihibited by micropyles is adaptive supporting other egg
 structures during embryo development. So whilst egg fertilization is the
 primary function of micropyles, they could aid embryo development and be
 shaped by natural, as well as sexual selection. Here I first used
 ancestral reconstruction to investigate micropyle presence, number and
 variation in primitive insects. Then, I used phylogenetic comparative
 analyses to explore the ecological function of micropyle number. I
 hypothesised that micropyle number correlated with: (i) aeropyle presence
 facilitating oxygen exchange; (ii) aquatic oviposition supporting
 development in water; and is influenced by (iii) critical bioclimatic
 variables. Across 24 hexapod orders the most likely ancestral state was
 one or two micropyles, interspecific variation was high and intraspecific
 variation low. Mean micropyle number ranged from zero in Entognatha,
 Strepsiptera and Thysanoptera to 120 in Panstrongylus geniculatus,
 Hemiptera, and over 100 on average for Apidae, Hymenoptera. Micropyle
 number was strongly positively related to: i) egg size, with larger eggs
 having more micropyles; ii) the presence of aeropyles; iii) annual
 precipitation, with eggs developing in habitats with low annual
 precipitation exhibiting fewer micropyles; and iv) negatively related to
 micropyle width, insect eggs having fewer larger micropyles or numerous
 smaller ones. However, aquatic oviposition did not affect micropyle
 number. Overall these findings point to an adaptive ecological function of
 egg micropyles in addition to their primary fertilisation function. This
 is consistent with the hypothesis that micropyles aid embryo survival, and
 so this almost-ubiquitous trait across insects is shaped by sexual and
 natural selection pressures during this critical life stage.
description: Data on micropyle number collated from published literature.
 Micropyle width mainly extracted and measured from images within the
 reference sources. Geolocation extracted from reference sources were
 possible. Bioclimatic data dowloaded from Bioclim.org. Species taxonomic
 names and synonyms verified using GBIF and the National Center for
 Biotechnology Information Taxonomy Browser. Please see Read Me file and
 main article for more information.
description: Missing values as NA.