cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.afxtmq
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Barbantus Parr, 1951",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((26.9648 19.8496,17.9648 19.8496,17.9648 10.8496,26.9648 10.8496,26.9648 19.8496))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013828-250525065834625/datasets/export for details.
DOI: 10.15468/dl.8xnsvh
title: Occurrence Download

description: A dataset containing 242 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Stipa capillacea Keng",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 242 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013830-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a9rrvk
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Barbantus Parr, 1951",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((17.949 -34.5253,17.9648 -34.5378,17.9648 -34.1504,17.8905 -34.1504,17.949 -34.5253))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013831-250525065834625/datasets/export for details.
DOI: 10.15468/dl.t7yrwf
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euphorbia indica",
 "Country is Zimbabwe",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025100-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7db58
title: Data from: Molecular species-delimitation methods recover most song-delimited cicada species in the European Cicadetta montana complex

description: Molecular species delimitation is increasingly being used to discover and
 inform illuminate species level diversity and a number of methods have
 been developed. Here we compare the ability of two molecular species
 delimitation methods to recover song-delimited species in the Cicadetta
 montana cryptic species complex throughout Europe. Recent bioacoustics
 studies of male calling songs (pre-mating reproductive barriers) have
 revealed cryptic species diversity in this complex. Maximum likelihood and
 Bayesian phylogenetic analyses were used to analyze the mitochondrial
 genes COI and COII and the nuclear genes EF1α and period for thirteen
 European Cicadetta species as well as the closely related monotypic genus
 Euboeana. Two molecular species delimitation methods, general mixed
 Yule-coalescent (GMYC) and Bayesian Phylogenetics and Phylogeography
 (BPP), identified the majority of song-delimited species and were largely
 congruent with each other. None of the molecular delimitation methods were
 able to fully recover a recent radiation of four Greek species.
description: Specimen_Name_ExplanationExplains the naming scheme and species names for specimen IDs used in the alignment files.Gene_AlignmentsNexus alignment files for all four genes used in this study: COI, COII, EF1alpha, and period, as well as an alignment file with COI and COII concatenated.BPPThis folder contains the input files used in BPP analyses for this study, including the six ctl files used.Garli_filesThis folder contains Garli configuration files for EF1alpha, period, and the concatenated COI and COII datasets.BEASTThis folder includes the input files for BEAST and starBEAST analyses.
DOI: 10.5061/dryad.18nk2
title: Data from: The genetic architecture of growth rate in juvenile Takifugu species.

description: Closely related species have often evolved dramatic differences in body
 size. Takifugu rubripes (fugu) is a large marine pufferfish whose genome
 has been sequenced, whereas T. niphobles is the smallest species among
 Takifugu. We show that, unsurprisingly, the juvenile growth rate of T.
 rubripes is higher than that of T. niphobles in a laboratory setting. We
 produced F2 progenies of their F1 hybrids and found one quantitative trait
 locus (QTL) significantly associated with variation in juvenile body size.
 This QTL region (3.5 Mb) contains no known genes directly related to
 growth phenotype (such as IGFs) except Fgf21, which inhibits growth
 hormone signaling in mouse. The QTL in Takifugu spp. is distinct from the
 region previously known to control body size variations in stickleback or
 tilapia. Our results suggest that in the fish tested herein, genomic
 regions underlying body size evolution might have different genetic
 origins. They also suggest that many diverse traits in Takifugu spp. are
 amenable to genetic mapping.
description: SL of original
 speciesThis file includes
 original data for our Fig. 1-B. Standard length (mm) of each individuals
 of each species at 14, 28 and 56 days post hatch are
 listed.genetic
 mapIncludes 4 files (.qtx)
 that were used to create genetic map (Fig S2-A, S2-B).QTLThere are 2 files (.qtx)
 that were used for QTL analysis (Fig 2, and Fig S3).Allelic
 effectOriginal data for
 Table_2. Individuals were divided into 4 groups according to their
 genotypes at f198, and SL (mm) for each specimen were
 listed.
DOI: 10.5061/dryad.gg1fk
title: Data from: Rising variability, not slowing down, as a leading indicator of a stochastically driven abrupt transition in a dryland ecosystem

description: Complex systems can undergo abrupt state transitions near critical points.
 Theory and controlled experimental studies suggest that the approach to
 critical points can be anticipated by critical slowing down (CSD), i.e., a
 characteristic slowdown in the dynamics. The validity of this indicator in
 field ecosystems, where stochasticity is important in driving transitions,
 remains unclear. We analyzed long-term data from a dryland ecosystem in
 the Shapotou region in China and show that it underwent an abrupt
 transition from a nearly bare to a moderate grass-cover state. Prior to
 the transition, the system showed no (or weak) signatures of CSD, but
 exhibited expected increasing trends in the variability of the grass
 cover, quantified by variance and skewness. These surprising results are
 consistent with the theoretical expectation of stochastically driven
 abrupt transitions that occur away from critical points; indeed, a driver
 of vegetation - annual rainfall - showed rising variance prior to the
 transition. Our study suggests that rising variability can potentially
 serve as a leading indicator of stochastically driven transitions in real
 world ecosystems.
description: Time series of grass
 cover, annual rainfall, and data to trends of early warning signals for
 critical and stochastic transitions needed to produce Figure
 3"data_cn.csv"
 includes data of gras cover and annual rainfall.
 "Chenetal-theory-ews-cric-stochastic.nb" computes trends of
 early warning signals for critical and stochastic transitions needed to
 produce Figure 3 of the manuscript.data.zip
DOI: 10.5061/dryad.0039d
title: Data from: Fluctuations in neighbourhood fertility generate variable signaling effort

description: Studies of sexual signalling generally focus on interactions between
 dyadic pairs, yet communication in natural populations often occurs in the
 context of complex social networks. The ability to survey social
 environments and adjust signal production appropriately should be a
 critical component of success in these systems, but has rarely been
 documented empirically. Here, we used autonomous recording devices to
 identify 118 472 songs produced by 26 male common yellowthroats
 (Geothlypis trichas) over two breeding seasons, coupled with detailed
 surveys of social conditions on each territory. We found strong evidence
 that common yellowthroat males adjusted their total song production in
 response to both changes in within-pair social context and changes in the
 fertility of neighbouring females up to 400 m away. Within the social
 pair, males drastically reduced their song production when mated, but the
 magnitude of this reduction depended on both the time of day and on the
 fertility status of the social mate. By contrast, when fertile females
 were present on nearby territories, males increased their song output,
 especially during daytime singing. At this time, it is unclear whether
 males actively gathered information on neighbouring female fertility or
 whether the patterns that we observed were driven by changes in social
 interactions that varied with neighbourhood fertility. Regardless of the
 mechanism employed, however, subtle changes in the social environment
 generated substantial variation in signalling effort.
description: Data By
 MaleThis is the main data
 file used in the paper. It is described in detail in the associated
 'readme' file.ByMale.csvData By BinThis data file is used only for figure 1 in the paper. The column names are explained in the 'readme' file.ByBin.csvR CodeThis is the complete R code used for analyses presented in the paper and to generate figures in the paper. Comments within the code explain the functions. Additional relevant information can be found in the 'readme' file.Taff_R_Code.R
DOI: 10.5061/dryad.8h03j
title: Data from: Phylogeny of digitaria sections Trichachne and Trichophorae (Poaceae, Panicoideae, Paniceae): a morphological and molecular analysis. New circumscription and synopsis

description: The present study provides evidence for taxonomic delimitation of
 Digitaria sect. Trichachne based on morphological data (micro- and
 macromorphology) and molecular data. A phylogenetic analysis was performed
 using 121 morphological characters and ITS sequences of 22 species and one
 variety of Digitaria plus three outgroups. In all topologies (based on
 morphological, molecular, and combined data) Digitaria sect. Trichophorae
 was non-monophyletic and nested within D. sect. Trichachne. Digitaria
 sect. Trichophorae is thus synonymized under D. sect. Trichachne and the
 circumscription of D. sect. Trichachne is emended. Diagnostic
 morphological characters related to spikelet structure are described and
 documented with SEM. A key to taxa belonging to D. sect. Trichachne is
 provided, as well as a synopsis including synonymy, iconography,
 geographical distribution, and ecology. The neotype of Trichachne
 sacchariflora Nees is herein designated. Complete illustrations of
 Digitaria eggersii, D. hitchcockii, and D. patens are provided. The
 phylogenetic placement of the Australian species D. brownii differed among
 trees resulting from different data sets, thus it is provisionally not
 included in D. sect. Trichachne in spite of its morphological similarity.
 Furthermore, Megaloprotachne albescens is formally transferred to
 Digitaria, as Digitaria albescens .
description: TRICHACHNE Lo
 MedicoThis are the combined
 matrix data. It contains: *Continuous characters * Morphology characters *
 DNA MatrixTRICHACHNE q se subio a
 TreeBASE.NEXLo Medico et al.
 Supplementary MaterialThis is the list of
 herbarium specimens is presented, which were selected as reference
 material for documentation of the morphological characters. It includes
 species of Digitaria sections Trichachne and Trichophorae (one specimen
 from each province or department), D. brownii (three specimens), species
 from eight additional sections of Digitaria (three specimens in each
 case), and two specimens from A. lanata, P. repens, and M.
 albescens.
DOI: 10.5061/dryad.80vd7q6
title: Data from: Climate-warming alters the structure of farmland tri-trophic ecological networks and reduces crop yield

description: It is unclear how sustained increases in temperature and changes in
 precipitation, as a result of climate-change, will affect crops and their
 interactions with agricultural weeds, insect pests and predators, due to
 the difficulties in quantifying changes in such complex relationships. We
 simulated the combined effects of increasing temperature (by 1.4°C over a
 growing season) and applying additional rainwater (10% extra per week)
 using a replicated, randomized block experiment within a wheat crop. We
 examined how this affected the structure of 24 quantitative replicate
 plant-aphid-parasitoid networks constructed using DNA-based methods.
 Simulated climate-warming affected species richness, significantly altered
 consumer-resource asymmetries and reduced network complexity. Increased
 temperature induced an aphid outbreak but the parasitism rates of aphids
 by parasitoid wasps remained unchanged. It also drove changes in the crop,
 altering in particular the phenology of the wheat as well as its quality
 (i.e. fewer, lighter seeds). We discuss the importance of considering the
 wider impacts of climate change on interacting-species across trophic
 levels in agro-ecosystems.
description: Derocles et al
 DataData collected from the
 field at Stockbridge Technology Centre, UK in 2013.Derocles et al
 NetworksData collected in the
 field at Stockbridge Technology Centre, UK in 2013 to construct
 species-interaction networks.Derocles et al
 YieldYield data collected at
 Stockbridge Technology Centre, UK in 2013.
DOI: 10.5061/dryad.hp24b6f
title: Data from: Primary productivity is related to niche width in the Australian Wet Tropics

description: Aim: A key ecological debate is whether ecosystem functions are distinctly
 influenced by biological diversity across broad scales. Although recent
 work has emphasized the importance of links between ecosystem functions
 and measures of ecological specialization as proxies of biodiversity, few
 studies have analysed macroecological relationships empirically in diverse
 environments. We tested whether gross primary productivity (GPP) in the
 Australian Wet Tropics (WT) was distinctly related to community‐level
 measures of the ecological specialization of component tree species across
 climate space, after accounting for climate drivers. Location: Wet
 Tropics, Australia. Time period: 1976–2012. Major taxa studied: Nine
 hundred and forty‐eight WT tree species. Methods: Using all geographically
 valid herbarium records for WT trees, we quantified the realized climatic
 niche widths using continental surfaces for maximum temperature of the
 warmest period and total annual rainfall. The median realized niche width
 for all tree species occurring at 510 sites was used to approximate
 ecological specialization within communities. To separate climatic effects
 on GPP, we applied a novel analysis using the difference in GPP and the
 difference in median community realized niche width between site pairs
 with similar climatic conditions. Linear models were then run on the
 difference in GPP between site pairs (response) and the difference in
 climatic niche widths (predictor). Results: For climatically similar sites
 in drier areas, GPP was higher in sites composed of species with narrower
 temperature niches (average R2 = 0.087, average t‐statistic = −3.45).
 Conversely, for climatically similar sites in drier areas, GPP was lower
 in sites composed of species with narrower rainfall niches (average R2 =
 0.171, average t‐statistic = 5.06). Main conclusions: Wet Tropics sites
 with more thermal specialists had higher productivity, whereas sites with
 more moisture specialists had lower productivity. These findings suggest
 that physiological specialization across climate space can influence
 primary productivity at broad scales, but in inconsistent ways.
description: GPP_NICHE_WIDTHThis table contains the primary data used to create the results in the article "Primary productivity is related to niche width in the Australian Wet Tropics" in Global Ecology and Biology. It represents 510 ecological plot sites in the Wet Tropics. It contains columns for gross primary productivity (GPP_0112), rainfall (RAIN_0112), temperature (TEMP_0112) and the mean (MN), median (MD) and standard deviation (SD) in niche widths (NW) of tree species recorded at each site. See the methods sections in the GEB article for more details.
DOI: 10.5061/dryad.m4sn8
title: Data from: Distinguishing the effects of selection from demographic history in the genetic variation of two sister passerines based on mitochondrial-nuclear comparison

description: Determining the mechanisms responsible for the distribution of genetic
 diversity in natural populations has occupied a central role in molecular
 evolution. Our study was motivated by the unprecedented observation that a
 widespread Eurasian flycatcher, Ficedula albicilla, exhibited no variation
 at the mitochondrial DNA (mtDNA) ND2 gene in 75 individuals sampled over a
 5000-km distance. In contrast, its sister species, F. parva, had low but
 considerably higher levels of mtDNA variation. We assessed whether natural
 selection or demographic factors could explain the absence of mtDNA
 variation in F. albicilla. Eighteen nuclear genes were sequenced to
 estimate the two species’ phylogeographic histories, and for comparison to
 the mtDNA data. Multilocus coalescence analyses suggested that F.
 albicilla experienced a population expansion perhaps following a
 population bottleneck. Simulations based on this demographic history,
 however, did not replicate the extremely low level of mtDNA variation.
 Historical range changes based on ecological niche models also failed to
 explain the observed mtDNA patterns. Neutrality tests (DHEW and ML-HKA)
 suggested a non-neutral pattern in the mtDNA of F. albicilla. We found a
 transmembrane-skewed distribution of nonsynonymous substitutions between
 the two species, three of which caused functional change; the results
 implied that positive selection could have targeted mtDNA. Several lines
 of evidence support selection rather than demographic history as the main
 force influencing the patterns of mtDNA variation. Despite the influence
 of natural selection, many of the phylogeographic inferences derived from
 mtDNA were robust, including species limits and a high level of gene flow
 among populations within species.
description: Data deposit to DRYAD
 (Ficedula)
DOI: 10.5061/dryad.7r826
title: Data from: An invasive herbivore structures plant competitive dynamics

description: Species interactions are central to our understanding of ecological
 communities, but may change rapidly with the introduction of invasive
 species. Invasive species can alter species interactions and community
 dynamics directly by having larger detrimental effects on some species
 than others, or indirectly by changing the ways in which native species
 compete among themselves. We tested the direct and indirect effects of an
 invasive aphid herbivore on a native aphid species and two host milkweed
 species. The invasive aphid caused a 10-fold decrease in native aphid
 populations, and a 30% increase in plant mortality (direct effects). The
 invasive aphid also increased the strength of interspecific competition
 between the two native plant hosts (indirect effects). By investigating
 the role that indirect effects play in shaping species interactions in
 native communities, our study highlights an understudied component of
 species invasions.
description: Plant and aphid
 datasetsAphid population data
 for Aphis nerii and Aphis asclepiadis, and plant biomass, height and
 survival data for Asclepias syriaca and Asclepias tuberosa. Data are from
 competition experiments conducted in pots at the Koffler Scientific
 Reserve, in Southern Ontario. Column heading descriptions are provided in
 the first tab.Wong et al. -
 Data.xlsx
DOI: 10.5061/dryad.ms739
title: Data from: Spatio-temporal dynamics of a tree-killing beetle and its predator

description: Resolving linkages between local-scale processes and regional-scale
 patterns in abundance of interacting species is important for
 understanding long-term population stability across spatial scales.
 Landscape patterning in consumer population dynamics may be largely the
 result of interactions between consumers and their predators, or driven by
 spatial variation in basal resources. Empirical testing of these
 alternatives has been limited by the lack of suitable data. In this study,
 we analyzed an extensive network of spatially replicated time series to
 characterize the local and regional processes affecting spatio-temporal
 dynamics of a tree-killing bark beetle (Dendroctonus frontalis or SPB) and
 its key predator (Thanasimus dubius) across the southeastern United
 States. We first used a mechanistic model to evaluate factors affecting
 the stability of 95 predator-prey time series and then conducted spatial
 analyses to evaluate scale dependence in the factors affecting the
 geographical patterning of this system. Across the region, population
 fluctuations of both species were correlated in space beyond 400 km but
 there was notable spatial variation in the deterministic and stochastic
 processes influencing forest-scale (local) fluctuations. Time series
 analyses indicated that local dynamics of SPB and T. dubius are not
 cyclical. Instead, the abundance of T. dubius responded almost
 instantaneously to changes in SPB abundance. Spatial variation in
 long-term forest-scale abundance of both species was linked most strongly
 to the abundance of pine habitat indicating a stronger role for resource
 availability in SPB population dynamics than top–down effects. Our results
 are consistent with other studies indicating that animal populations tend
 to be synchronized in space via spatially correlated processes such as
 weather; yet local dynamics tend to be linked to smaller-scale host
 patterns. Our study provides a rare empirical assessment of how local
 processes scale up to produce landscape patterns that influence forest
 ecology and forest management.
description: ecog_dryad_dataPredator-prey time series at multiple forest locations across the southeastern USA.