cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5h01m0c
title: Data from: Molecular assessment of Pocillopora verrucosa (Scleractinia; Pocilloporidae) distribution along a depth gradient in Ludao, Taiwan

description: It can be challenging to identify scleractinian corals from the genus
 Pocillopora (Lamarck 1816) in the field because of their large range of
 inter- and intra-specific morphological variation that co-occur with
 changes in the physical environment. This task is made more arduous in the
 context of a depth gradient, where light and water current could greatly
 affect the morphology of the corallum. Pocillopora verrucosa (Ellis and
 Solander, 1786) in Taiwan was previously reported exclusively from shallow
 waters (&lt;10m in depth), but a recent observation of this species in
 the mesophotic zone (&gt;40m in depth) questions this bathymetric
 distribution. We used the mitochondrial open reading frame and the histone
 3 molecular markers to investigate the vertical and horizontal spatial
 distribution of P. verrucosa around Ludao (Green Island), Taiwan. We
 genotyped 101 Pocillopora verrucosa-like colonies collected from 4 depth
 zones, ranging from 7 to 45m, at 3 sites around the island. Of the 101
 colonies sampled, 85 were genotyped as P. verrucosa, 15 as P. meandrina,
 and one specimen as an undescribed Pocillopora species. P. verrucosa was
 found at all depths, while P. meandrina and the undescribed Pocillopora
 specimen were limited to 15m depth. P. verrucosa has a large bathymetric
 distribution around Ludao and could benefit from the refuge that the
 mesophotic zone offers. This study illustrates the difficulty of
 identifying Pocillopora corals in the field and emphasizes the relevance
 of molecular taxonomy as an important and complementary tool to
 traditional taxonomy for clarifying vertical and horizontal species
 distribution. Our results also illustrate the need in conservation biology
 to target species genetic diversity rather than just species diversity.
description: Histone FASTA
 alignmentHistone 3 region
 alignment for all haplotype H1 to H9mtORF FASTA alignment
 dataMitochondrial Open
 Reading Frame alignment data for all samples
DOI: 10.5061/dryad.8mp74
title: Data from: Effects of grain size and niche breadth on species distribution modeling

description: Scale is a vital component to consider in ecological research, and spatial
 resolution or grain size is one of its key facets. Species distribution
 models (SDMs) are prime examples of ecological research in which grain
 size is an important component. Despite this, SDMs rarely explicitly
 examine the effects of varying the grain size of the predictors for
 species with different niche breadths. To investigate the effect of grain
 size and niche breadth on SDMs, we simulated four virtual species with
 different grain sizes/niche breadths using three environmental predictors
 (elevation, aspect, and percent forest) across two real landscapes of
 differing heterogeneity in predictor values. We aggregated these
 predictors to seven different grain sizes and modeled the distribution of
 each of our simulated species using MaxEnt and GLM techniques at each
 grain size. We examined model accuracy using the AUC statistic, Pearson’s
 correlations of predicted suitability with the true suitability, and the
 binary area of presence determined from suitability above the maximum True
 Skill Statistic (TSS) threshold. Habitat specialists were more accurately
 modeled than generalist species, and the models constructed at the grain
 size from which a species was derived generally performed the best. The
 accuracy of models in the homogenous landscape deteriorated with
 increasing grain size to a greater degree than models in the heterogenous
 landscape. Variable effects on the model varied with grain size, with
 elevation increasing in importance as grain size increased while aspect
 lost importance. The area of predicted presence was drastically affected
 by grain size, with larger grain sizes over predicting this value by up to
 a factor of 14. Our results have implications for species distribution
 modeling and conservation planning, and we suggest more studies include
 analysis of grain size as part of their protocol.
description: Code for Creating and
 Modeling Virtual SpeciesThe R code for
 simulating and then modeling a virtual species across landscape in
 Scandinavia. This is the code for the habitat generalist in the
 heterogeneous landscape - the same analysis was used for other created
 species (except for parameters changed described in
 paper).Virtual_Species_Creation_and_Modeling.R
DOI: 10.5061/dryad.h7d843j6
title: Data from: Genetic variation for antibiotic persistence in Escherichia coli

description: Bacterial persistence describes a heterogenous response to antibiotics in
 clonal populations of bacteria due to phenotypic variation within the
 population, with a small proportion of cells surviving treatment even at
 very high concentrations of drug. The aim of this study was to determine
 whether different natural isolates of E. coli, selected at random from a
 collection representing the spectrum of genetic diversity in the species,
 generate different fractions of persister cells. Despite comparable
 minimum inhibitory concentrations (MICs) to the antibiotics between the
 different strains, highly significant variation was observed in persister
 fractions following exposure to ampicillin, streptomycin or norfloxacin.
 Survival following treatment with one drug did not, however, correlate
 with survival against another. Finally, using competition assays we
 quantify fitness benefits of persistence. These results show that
 different strains of E. coli vary markedly in their response to
 antibiotics despite comparable genetic susceptibility and indicate
 different mechanisms of evolved persistence to different antibiotics.
description: Stewart and
 RozenTime-kill data organized
 by strain and drug.Stewart&Rozen_archived_data.xls
DOI: 10.15468/dl.umak88
title: Occurrence Download

description: A dataset containing 64488 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2026-01-01",
 "EventDate is less than or equal to 2026-01-31",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 },
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 64488 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000923-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4k2t3
title: Data from: Spatiotemporal variation of host use in a brood parasite: the role of the environment

description: Avian brood parasites should target the most profitable host species, but
 current conditions might locally influence their choice, producing
 geographic mosaics of coevolution. Throughout Europe, the magpie Pica pica
 has been invariably reported as the primary host of the great spotted
 cuckoo Clamator glandarius, whereas the carrion crow Corvus corone is the
 secondary one. However, we found that this pattern reversed in northern
 Spain, where up to 70% of carrion crow nests were parasitized versus 20%
 of magpie nests. In southern Spain, conversely, parasitism increased
 proportionally in both hosts (up to approximately 90% of available nests)
 throughout the 3 years of study. Surprisingly, magpies provided the best
 reproductive output for cuckoos in both areas, in contrast with cuckoo’s
 preference for the crow host in the north. Genetic data ruled out the
 presence of different host-specific races in this brood parasite,
 dismissing the hypothesis that a prevalence of different gentes at the 2
 sites explained the observed variability in host choice. Instead, we found
 that magpie nests in the south were easier to reach and more scattered
 than in the north, where cuckoos preferentially targeted nests that were
 less concealed and more isolated. We suggest that the habitat constraints
 parasitism on magpies in the north, driving cuckoo host choice toward the
 crows. The coevolutionary scenario therefore includes a 3-way interaction,
 where the pressure that the parasite puts on a host species in a given
 place critically depends on the environmentally mediated interaction
 between the same parasite and a different host.
description: genetic
 databaseGenotypes of all great
 spotted cuckoos that have been sampled at the two study
 sites.parasitism
 rateParasitism by great
 spotted cuckoo (0 = non parasitized nest; 1 = parasitized nest) on magpies
 (M) and crows (C), at the two studied populations (GR = Guadix, LE =
 Sobarriba). "Nest" idenitfy territory identity within this
 file.Number cuckoo
 eggsNumber of cuckoo eggs in
 magpie and crow nests in the two studied populations. See previous file
 for further description.reproductive
 successCuckoo reproductive
 success in crow and magpie nest. Cuckooo clutch = number of hatched cuckoo
 chicks; Cuckoo fledged = number of cuckoo chicks that survived untill
 fledging; Cuckoos dead = number of cuckoo chicks that died before
 fledging. See previous file for further description.Magpie nest
 distancesDistance to the nearest
 neighbour nest ("Distance") in magpies, in the two studied
 populations. See previous file for further description.
DOI: 10.5061/dryad.dc7s2
title: Data from: A rapid and cost-effective quantitative microsatellite genotyping protocol to estimate intraspecific competition in protist microcosm experiments

description: High levels of intra-specific variation are commonly observed in natural
 microbial populations, yet the consequences of this variation for
 ecological and evolutionary processes remains poorly understood. Protists
 are excellent experimental models for investigating fundamental and
 applied questions in ecology and evolution, but studying intra-specific
 variation remains a challenge due to a lack of molecular resources to aid
 in quantifying and distinguishing strains during experiments. Here we
 present a molecular method, quantitative microsatellite genotyping, to
 accurately quantify strain specific frequencies from microcosm experiments
 of the marine flagellate Oxyrrhis marina, both between many pairs of
 strains and between strains in a multi-strain mixture. We find that for
 pairs of strains the method is effective for relative frequencies as low
 as 0.02 and with around 99% accuracy. The method is able to quantify four
 strains reasonably well, though less accurately than for pairs (range
 92%-97% accuracy). This makes accessible a cheap and easy to implement
 method for quantifying strain (or allele) frequencies, and is suitable for
 use in a broad range of single celled eukaryotes (Protists) where copy
 number should correlate well with number of individuals (i.e. cells). This
 opens up the possibility of examining the role of intra-specific variation
 using experimental protist microcosms.
description: MS calibration data DNA
 PairsThis file contains data
 for extracted and mixed nDNA (i.e. black data in Fig.1), and shows
 microsatellite peak heights and peak areas for each of two strains. DNA is
 mixed in known ratios, and peak height and peak area ratios are
 calculated.MS calibration data CELL
 PairsThis data contains
 calibrations for mixtures of cells from pairs of strains (i.e. red data in
 Fig.1).MS calibration data CELL
 MultiThis data file contains
 calibration data for multistrain testing of the genotyping assay (i.e.
 data analysed in SI 1).Dynamics example
 dataExample dynamics from a
 microcosm experiment of two strains of Oxyrrhis over 13 days under two
 pCO2 levels, using the method for strain frequency determination described
 here.
DOI: 10.5061/dryad.v1q8j
title: Data from: Molecular analysis reveals high compartmentalisation in aphid-primary parasitoid networks and low parasitoid sharing between crop and non-crop habitats.

description: The ecosystem service of insect pest regulation by natural enemies, such
 as primary parasitoids, may be enhanced by the presence of uncultivated,
 semi-natural habitats within agro-ecosystems, although quantifying such
 host–parasitoid interactions is difficult. Here, we use rRNA 16S gene
 sequencing to assess both the level of parasitism by Aphidiinae primary
 parasitoids and parasitoid identity on a large sample of aphids collected
 in cultivated and uncultivated agricultural habitats in Western France. We
 used these data to construct ecological networks to assess the level of
 compartmentalization between aphid and parasitoid food webs of cultivated
 and uncultivated habitats. We evaluated the extent to which uncultivated
 margins provided a resource for parasitoids shared between pest and
 nonpest aphids. We compared the observed quantitative ecological network
 described by our molecular approach to an empirical qualitative network
 based on aphid–parasitoid interactions from traditional rearing data found
 in the literature. We found that the molecular network was highly
 compartmentalized and that parasitoid sharing is relatively rare between
 aphids, especially between crop and noncrop compartments. Moreover, the
 few cases of putative shared generalist parasitoids were questionable and
 could be due to the lack of discrimination of cryptic species or from
 intraspecific host specialization. Our results suggest that apparent
 competition mediated by Aphidiinae parasitoids is probably rare in
 agricultural areas and that the contribution of field margins as a source
 of these biocontrol agents is much more limited than expected. Further
 large-scale (spatial and temporal) studies on other crops and noncrop
 habitats are needed to confirm this.
description: 16S New species
 identifiedThis fasta file displays
 the 16S DNA sequences of new species identified in this study. This
 sequences are also deposited in Genbank16S New
 species.fasRaw_dataThis is the raw dataset. This file contains the sampling data (date and location), the aphids analysed, the parasitism rate and the parasitoid detected with the molecular tool. This file was used to perform the statistical tests (with R) and to build figure 1.Figure2_dataThis file contains all the aphid-parasitoid interactions identified with the molecular tool. This file was used to build the figure 2 with R.Figure3_dataThis file contains all the aphid-parasitoid interaction record in Europe found in the literature. This file was used to build the figure 3 with R.
DOI: 10.5061/dryad.gg610
title: Data from: Limited emigration from an outbreak of a forest pest insect

description: Population density and individual dispersal behaviour affect species´
 distribution dynamics. Population densities vary over time, and some
 species occasionally increase to very high numbers, for example during
 outbreaks. In such situations populations are expected to expand into new
 areas due to density-dependent dispersal and sometimes even result in
 range expansion. A local population of the northern pine processionary
 moth Thaumetopoea pinivora has recently reached outbreak densities at the
 edge of its northern range at the southern tip of Gotland Island in the
 Baltic Sea. We first investigated if the outbreak had resulted in
 establishment of populations in suitable habitats on Gotland Island
 outside of the outbreak area. Six small populations were found that could
 potentially have originated from the outbreak area. However, data from 12
 microsatellite markers strongly suggest that these populations did not
 originate from the recent outbreak. Genetic variability was not reduced in
 these small, isolated populations and there were several unique alleles,
 indicating instead a different population history and that there has been
 no recent range expansion. In addition, there was apparent genetic
 isolation by geographic distance, implying that despite that the outbreak
 population reached a high enough density to cause density-dependent
 dispersal, significant gene flow has not occurred.
description: T_pinivora
DOI: 10.5061/dryad.dc976
title: Data from: Comparison of Natural and Nonnative Two-Species Communities of Anolis Lizards

description: Human-mediated colonizations present an informative model system for
 understanding assembly of organismal communities. However, it is unclear
 whether communities including naturalized species are accurate analogs of
 natural communities or unique combinations not present in nature. I
 compared morphology and phylogenetic structure of natural and naturalized
 two-species communities of Anolis lizards. Natural communities are
 phylogenetically clustered, whereas naturalized communities show no
 significant phylogenetic structure. This result likely reflects
 differences in colonization pools for these communities—that is, invasion
 from anywhere for naturalized communities but from proximal and thus
 phylogenetically close lineages in natural communities. Both natural and
 naturalized communities each include pairs of species that are
 significantly similar to each other in morphology, and both sets of
 communities are composed of species that possess traits of good
 colonizers. These similarities suggest that the formation of natural and
 naturalized communities may be at least partially governed by similar
 processes. Human-mediated invasions may be credibly viewed as modern
 incarnations of natural colonizations in this case.
description: Poe.supplTable
DOI: 10.5061/dryad.js1gm
title: Data from: Niche partitioning in a sympatric cryptic species complex

description: Competition theory states that multiple species should not be able to
 occupy the same niche indefinitely. Morphologically, similar species are
 expected to be ecologically alike and exhibit little niche
 differentiation, which makes it difficult to explain the co-occurrence of
 cryptic species. Here, we investigated interspecific niche differentiation
 within a complex of cryptic bumblebee species that co-occur extensively in
 the United Kingdom. We compared the interspecific variation along
 different niche dimensions, to determine how they partition a niche to
 avoid competitive exclusion. We studied the species B. cryptarum, B.
 lucorum, and B. magnus at a single location in the northwest of Scotland
 throughout the flight season. Using mitochondrial DNA for species
 identification, we investigated differences in phenology, response to
 weather variables and forage use. We also estimated niche region and niche
 overlap between different castes of the three species. Our results show
 varying levels of niche partitioning between the bumblebee species along
 three niche dimensions. The species had contrasting phenologies: The
 phenology of B. magnus was delayed relative to the other two species,
 while B. cryptarum had a relatively extended phenology, with workers and
 males more common than B. lucorum early and late in the season. We found
 divergent thermal specialisation: In contrast to B. cryptarum and B.
 magnus, B. lucorum worker activity was skewed toward warmer, sunnier
 conditions, leading to interspecific temporal variation. Furthermore, the
 three species differentially exploited the available forage plants: In
 particular, unlike the other two species, B. magnus fed predominantly on
 species of heather. The results suggest that ecological divergence in
 different niche dimensions and spatio-temporal heterogeneity in the
 environment may contribute to the persistence of cryptic species in
 sympatry. Furthermore, our study suggests that cryptic species provide
 distinct and unique ecosystem services, demonstrating that morphological
 similarity does not necessarily equate to ecological equivalence.
description: Data for phenology,
 weather sensitivity and niche overlap anlaysesData for forage use
 analyses
DOI: 10.5061/dryad.f9n48
title: Data from: Intracoronary delivery of human mesenchymal/stromal stem cells: insights from coronary microcirculation invasive assessment in a swine model

description: Background: Mesenchymal stem/stromal cells have unique properties
 favorable to their use in clinical practice and have been studied for
 cardiac repair. However, these cells are larger than coronary microvessels
 and there is controversy about the risk of embolization and
 microinfarctions, which could jeopardize the safety and efficacy of
 intracoronary route for their delivery. The index of microcirculatory
 resistance (IMR) is an invasive method for quantitatively assessing the
 coronary microcirculation status. Objectives: To examine heart
 microcirculation after intracoronary injection of mesenchymal stem/stromal
 cells with the index of microcirculatory resistance. Methods: Healthy
 swine were randomized to receive by intracoronary route either 30x106 MSC
 or the same solution with no cells (1% human albumin/PBS) (placebo).
 Blinded operators took coronary pressure and flow measurements, prior to
 intracoronary infusion and at 5 and 30 minutes post-delivery. Coronary
 flow reserve (CFR) and the IMR were compared between groups. Results: CFR
 and IMR were done with a variance within the 3 transit time measurements
 of 6% at rest and 11% at maximal hyperemia. After intracoronary infusion
 there were no significant differences in CFR. The IMR was significantly
 higher in MSC-injected animals (at 30 minutes, 14.2U vs. 8.8U, p = 0.02)
 and intragroup analysis showed a significant increase of 112% from
 baseline to 30 minutes after cell infusion, although no
 electrocardiographic changes or clinical deterioration were noted.
 Conclusion: Overall, this study provides definitive evidence of
 microcirculatory disruption upon intracoronary administration of
 mesenchymal stem/stromal cells, in a large animal model closely resembling
 human cardiac physiology, function and anatomy.
description: Research
 DATA_SETTables with research
 results