cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.5phvax
title: Occurrence Download

description: A dataset containing 89632 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Kenya Bird Map Occurrence Data"
 ]
}

 The dataset includes 89632 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003054-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.rfj6q57cf
title: Native- vs. introduced-range Polygonum cespitosum traits

description: In a common-garden experiment, Polygonum cespitosum plants
 (N=660) from native- and introduced-range populations
 were grown under uniform, favorable conditions in a glasshouse
 and their traits compared. Introduced-range populations were sampled from
 the eastern USA (N=17), and native-range populations were sampled
 from a climate-matched region in northern Japan (N=18). Parental growing
 conditions were standardized prior to the experiment.
description: Data are raw trait data collected for each individual plant.
description: MISSING VALUES Missing
 values are denoted with periods ("."). Missing values are values
 that have been excluded due to known issues during data collection (e.g.,
 loss of physical plant material, accidental failure to image a plant,
 etc.). COLUMN DEFINITIONS
 <em>Identitfying information/plant
 provenance</em> country = the geographic origin
 of source population; Japan = native range, USA = introduced
 range. pop = source population id; see "Polygonum
 cespitosum locality climates" dataset for source population location
 and climate data. line = genetic line/genotype; only
 one plant was grown per line, so column also serves as a unique identifier
 for each plant. <em>Plant
 traits</em> height = height (cm); the height of
 the bounding box containing aboveground tissue as measured from side-view
 images. canopy.area = canopy area (cm^2); a plant’s
 total leaf area as measured from overhead/aerial images.
 spread.area = spread area (cm^2); the area of the convex
 hull enclosing a plant as measured from overhead/aerial images.
 repro.onset = reproductive onset (no. days); the number of days
 from transplanting to first flower. ss.repro.out =
 short-season reproductive output (g); the total mass of reproductive
 tissue produced over a fixed 124/125 day period.
 es.repro.out = extended-season reproductive output (g); the total
 mass of reproductive tissue produced over individual lifetime.
 shoot.biomass = shoot biomass (g); the mass of aboveground
 vegetative tissue. allo.repro = allocation to
 reproduction (%); calculated as 100 x [(extended-season reproductive
 output) / (shoot biomass + extended-season reproductive
 output)]. sparseness = sparseness index; a unitless
 measure of growth form calculated as spread area divided by canopy
 area. leaf.area = individual leaf area (cm^2); the area
 of the most recent fully expanded leaf.
DOI: 10.5061/dryad.76hdr7sz8
title: GWAS pyrethroid-resistant Aedes aegypti

description: Genome-wide association studies (GWAS) use genetic polymorphism across the
 genomes of individuals with distinct characteristics to identify
 genotype-phenotype associations. In mosquitoes, complex traits such as
 vector competence and insecticide resistance could benefit from GWAS use.
 We used the Ae. aegypti 50k SNP chip to genotype
 populations with different levels of pyrethroid resistance from Northern
 Brazil. Pyrethroids are widely used worldwide to control mosquitoes and
 other agricultural pests, and their intensive use led to the selection of
 resistance phenotypes in many insects including mosquitoes.
 For Ae. aegypti, resistance phenotypes are mainly associated with
 several mutations in the voltage-gated sodium channel, known as knockdown
 resistance (kdr). We phenotyped those populations with the WHO insecticide
 bioassay using deltamethrin impregnated papers, genotyped
 the kdr alleles using qPCR, and the whole genomic
 regions with the SNP chip. We identified single-nucleotide polymorphisms
 (SNPs) directly associated with resistance and one epistatic SNP pair. We
 also observed that the novel SNPs correlated with the
 known kdr genotypes, although on different chromosomes
 or not in close physical proximity to the voltage-gated sodium channel
 gene. In addition, a pairwise comparison of resistance and susceptible
 mosquitoes from each population revealed differentiated genomic regions
 not associated with pyrethroid resistance. These new bi-allelic markers
 can be used to genotype other populations along
 with kdr alleles to understand their worldwide
 distribution. The functional roles of the genes near the newly discovered
 SNPs require new studies to determine if they act synergistically
 with kdr alleles or reduce the fitness cost of
 maintaining resistant alleles.
description: We used the custom-designed SNP chip for <i>Ae.
 aegypti </i>to genotype all mosquitoes (Evans<i> et
 al.</i> 2015).Once we selected the mosquitoes with the desired
 phenotype, we removed the DNA samples from the −20 °C freezer to
 concentrate and purify them using Amicon<sup>R</sup> Ultra 30k
 centrifugal filter devices (Millipore) according to the manufacturer
 instructions. We obtained approximately 23 µL of eluting. Next, we checked
 the genomic DNA concentration using Qubit (Invitrogen). Finally, we
 normalized the DNA concentrations to 20 ng/µL and sent approximately 200
 ng of genomic DNA from individual mosquitoes to the Functional Genomics
 Core at the University of North Carolina, Chapel Hill, for hybridization
 with the Axiom aegypti1 SNP chip (Life Technologies Corporation
 CAT#550481). We used the Affymetrix Genotyping Console v.3.1.51.0
 (Affymetrix) to generate and process the genotype calls (Evans<i> et
 al.</i> 2015). Briefly, we used the default parameters outlined as
 best practice for non-human samples, except for the call threshold set to
 90%, and by using the off-target variant correction.
DOI: 10.5061/dryad.4qrfj6qc0
title: Data supporting: Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions

description: Although the use and development of molecular biomonitoring tools based on
 environmental nucleic acids (eDNA and eRNA; collectively known as eNAs)
 have gained broad interest for the quantification of biodiversity in
 natural ecosystems, studies investigating the impact of site-specific
 physicochemical parameters on eNA-based detection methods (particularly
 eRNA) remain scarce. Here, we used a controlled laboratory microcosm
 experiment to comparatively assess the environmental degradation of eDNA
 and eRNA across an acid-base gradient following complete removal of the
 progenitor organism (Daphnia pulex). Using water samples collected over a
 30-day period, eDNA and eRNA copy numbers were quantified using a droplet
 digital PCR (ddPCR) assay targeting the mitochondrial cytochrome c oxidase
 subunit I (COI) gene of D. pulex. We found that eRNA decayed more rapidly
 than eDNA at all pH conditions tested, with detectability­—predicted by an
 exponential decay model—for up to 57 hours (eRNA; neutral pH) and 143 days
 (eDNA; acidic pH) post organismal removal. Decay rates for eDNA were
 significantly higher in neutral and alkaline conditions than in acidic
 conditions, while decay rates for eRNA did not differ significantly among
 pH levels. Collectively, our findings provide the basis for a predictive
 framework assessing the persistence and degradation dynamics of eRNA and
 eDNA across a range of ecologically relevant pH conditions, establish the
 potential for eRNA to be used in spatially and temporally sensitive
 biomonitoring studies (as it is detectable across a range of pH levels),
 and may be used to inform future sampling strategies in aquatic habitats.
description: This dataset was assembled as described in the resulting
 publication and in the README file. 
description: See the README file for a detailed account of the content of the
 uploaded file.
DOI: 10.5061/dryad.dz08kprzx
title: Genetic variance in contrasting environments

description: The evolutionary response of a trait to directional selection depends upon
 the level of additive genetic variance. It has been long argued that
 sustained selection will tend to deplete additive genetic variance as
 favoured alleles approach fixation. Non-additive genetic variance, due to
 interactions among alleles within and between loci, does not immediately
 contribute to an evolutionary response, although shifts in the allele
 frequencies within and between interacting loci may convert interaction
 variance into additive variance. Here we consider the possibility that an
 environmental shift may alter allelic interactions in ways that convert
 nonadditive into additive genetic variance. Specifically, we performed
 experiments that used a Bayesian implementation of the animal model to
 estimate the additive, dominance, and maternal components of variance for
 a pedigreed population of Brassica rapa. One experiment was performed in a
 field that mimicked agricultural conditions from which the base population
 was drawn, while the other was performed in the benign conditions of a
 greenhouse. Although the additive genetic variance was elevated in the
 greenhouse condition, no consistent pattens emerged that would indicate a
 conversion of dominance variance. The unusually low genetic variance and
 broad confidence intervals for the variance estimates obtained through
 this analysis preclude definitive interpretations. Thus, we promote
 further investigation to determine if between-environment changes in
 additive genetic variance can be traced to conversion of nonadditive
 variance.
description: Usage notes are detailed in the README files (separate files for
 data and R scripts).
DOI: 10.5061/dryad.8931zcrsg
title: Climate oscillations drive millennial-scale changes in seabird colony size

description: Seabird population size is intimately linked to the physical, chemical,
 and biological processes of the oceans. Yet, the overall effects of
 long-term changes in ocean dynamics on seabird colonies are difficult to
 quantify. Here, we used dated lake sediments to reconstruct ~10,000-years
 of seabird dynamics in the Northwest Atlantic to determine the influences
 of Holocene-scale climatic oscillations on colony size. On Baccalieu
 Island (Newfoundland and Labrador, Canada) – where the world’s largest
 colony of Leach’s storm-petrel (Hydrobates leucorhous Vieillot 1818)
 currently breeds – our data track seabird colony growth in response to
 warming during the Holocene Thermal Maximum (ca. 9,000 to 6,000 BP). From
 ca. 5,200 BP to the onset of the Little Ice Age (ca. 550 BP), changes in
 colony size were correlated to variations in the North Atlantic
 Oscillation (NAO). By contrasting the seabird trends from Baccalieu Island
 to millennial-scale changes of storm-petrel populations from Grand
 Colombier Island (an island in the Northwest Atlantic that is subjected to
 different ocean climate), we infer that changes in NAO influenced the
 ocean circulation, which translated into, among many things, changes in
 pycnocline depth across the Northwest Atlantic basin where the
 storm-petrels feed. We hypothesize that the depth of the pycnocline is
 likely a strong bottom-up control on surface-feeding storm-petrels through
 its influence on prey accessibility. Since the Little Ice Age, the effects
 of ocean dynamics on seabird colony size have been altered by
 anthropogenic impacts. Subsequently, the colony on Baccalieu Island grew
 at an unprecedented rate to become the world’s largest resulting from
 favourable conditions linked to climate warming, increased vegetation
 (thereby nesting habitat), and attraction of recruits from other colonies
 that are now in decline. We show that although ocean dynamics were an
 important driver of seabird colony dynamics, its recent influence has been
 modified by human interference.
DOI: 10.5061/dryad.5x69p8d4q
title: Data on transit history and anti-fouling practices for ships arriving to the Canadian Arctic

description: Ship biofouling is a major vector for the introduction and spread of
 harmful marine species globally, however, its importance in Arctic coastal
 ecosystems is understudied. The objective of this study was to provide
 insight regarding the extent of biofouling (i.e., percent cover,
 abundance, and species richness) on commercial ships operating in the
 Canadian Arctic. A questionnaire was used to collect information on
 transit history, anti-fouling practices, and self-reported estimates of
 biofouling extent from a sample of ships operating in the region during
 2015 – 2016.
description: A questionnaire was
 distributed electronically to all commercial ships entering the Northern
 Canada Vessel Traffic Services zone by the Canadian Coast Guard as part of
 the standard entry clearance communications, though participation in the
 survey was voluntary. Information was collected on ships’ operational
 profile (travel history, typical sailing speed, port residence time, and
 time at sea), information on antifouling systems installed, general
 characteristics (ship type, year built, gross tonnage, length, and wetted
 surface area), and self-reported estimates of percent cover of biofouling.
 The travel history of ships was requested for the last 10 ports-of-call
 preceding arrival at a Canadian Arctic port as well as the planned stops
 in the Arctic. The last 10 ports-of-call were categorized into
 biogeographic realms following the largest spatial units in the Marine
 Ecoregions of the World (MEOW) system; the Laurentian Great Lakes was
 included as an additional biogeographic realm. Self-reported estimates of
 percent cover of biofouling were based on a Captain’s general knowledge of
 the ship (i.e., best guess) and results from the latest underwater
 inspection (i.e. opportunistic observations on biofouling from the most
 recent underwater inspection as part of regular cleaning, repair, and/or
 maintenance of the hull conducted by ship owners).
description: Data are self-reported by vessel Captains that participated in
 the voluntary study. Missing values (marked as 'N/A') were not
 submitted by vessel Captains. Self-reported data have not been verified
 against any independent dataset.
DOI: 10.5061/dryad.98sf7m0kp
title: Datasets and R code for: Brood as booty: The effect of colony size and resource value in social insect contests

description: From the Manuscript: Animals engage in contests for access to resources
 like food, mates, and space. Intergroup contests between groups of
 organisms have received little attention, and it remains unresolved what
 information groups might use collectively to make contest decisions. We
 staged whole-colony contests using ant colonies (Temnothorax rugatulus),
 which perceive conspecific colonies as both a threat and resource from
 which to steal brood. We recorded individual behaviors and used
 demographic characteristics as proxies for resource value (number of brood
 items) and fighting ability (number of workers). We found that ants
 altered their fighting effort depending on the relative number of workers
 of their opponent. While the proximate mechanism for this ability remains
 uncertain, we found that colonies increased fighting when their opponent
 had relatively more brood, but not if opposing colonies had relatively
 many more workers. This suggests that ant colonies can use information
 about opposing colonies that shapes contest strategies. Further, the
 behavior of opposing colonies were strongly correlated with each other
 despite colony size differences ranging from 4-51%, consistent with the
 hypothesis that colonies can use opponent information. The behavior of a
 distributed, collective system of many individuals, like a eusocial insect
 colony, thus fits several predictions of contest models designed for
 individuals if we consider the gain and loss of worker ants analogous to
 energetic costs accrued during typical dyadic contests.
description: Data was collected and processed per the associate
 publication: Chapin KJ, Paat V, Dornhaus A. 2022.
 "Brood as booty: the effect of colony size and resource value in
 social insect contests". Behavioral Ecology
description: Please see README.txt for metadata.
DOI: 10.5281/zenodo.18386037
title: A zoonotic Streptococcus equi subsp. zooepidemicus strain survives in activated blood neutrophils of pigs through SzM expression

description: Streptococcus equi subsp. zooepidemicus (SEZ) causes disease in various animals and humans. In pigs, it is an emerging pathogen causing septicemia and other severe pathologies. SEZ expresses the M-like protein SzM which recruits host proteins such as fibrinogen to the bacterial surface. The objective of this study was to investigate mechanisms of survival of a zoonotic SEZ strain in porcine blood. The zoonotic SEZ C33 strain proliferated in porcine blood of 10-week-old piglets in vitro despite comparable high levels of IgM binding to the bacterial surface. Comparison with the isogenic szm deletion mutant showed that SzM_C33 expression is crucial for survival in porcine blood. Flow cytometry analysis revealed that SEZ C33 is associated with porcine blood granulocytes exhibiting prominent generation of reactive oxygen species. Cytochalasin D inhibited this association significantly. Furthermore, we found viable intracellular SEZ C33 in a penicillin/streptomycin protection assay in porcine blood and in purified porcine granulocytes in agreement with microscopic detection of streptococci in neutrophils. Experimental infection with SEZ C33 confirmed virulence of this strain in pigs including one case of fibrino-suppurative meningoencephalitis and tarsitis. In conclusion, SEZ C33, originally isolated from a diseased human, demonstrates SzM-mediated, intracellular survival in porcine blood granulocytes in vitro which is most likely involved in the pathogenesis of disease such as meningitis and arthritis in vivo.
DOI: 10.5281/zenodo.18386036
title: A zoonotic Streptococcus equi subsp. zooepidemicus strain survives in activated blood neutrophils of pigs through SzM expression

description: Streptococcus equi subsp. zooepidemicus (SEZ) causes disease in various animals and humans. In pigs, it is an emerging pathogen causing septicemia and other severe pathologies. SEZ expresses the M-like protein SzM which recruits host proteins such as fibrinogen to the bacterial surface. The objective of this study was to investigate mechanisms of survival of a zoonotic SEZ strain in porcine blood. The zoonotic SEZ C33 strain proliferated in porcine blood of 10-week-old piglets in vitro despite comparable high levels of IgM binding to the bacterial surface. Comparison with the isogenic szm deletion mutant showed that SzM_C33 expression is crucial for survival in porcine blood. Flow cytometry analysis revealed that SEZ C33 is associated with porcine blood granulocytes exhibiting prominent generation of reactive oxygen species. Cytochalasin D inhibited this association significantly. Furthermore, we found viable intracellular SEZ C33 in a penicillin/streptomycin protection assay in porcine blood and in purified porcine granulocytes in agreement with microscopic detection of streptococci in neutrophils. Experimental infection with SEZ C33 confirmed virulence of this strain in pigs including one case of fibrino-suppurative meningoencephalitis and tarsitis. In conclusion, SEZ C33, originally isolated from a diseased human, demonstrates SzM-mediated, intracellular survival in porcine blood granulocytes in vitro which is most likely involved in the pathogenesis of disease such as meningitis and arthritis in vivo.
DOI: 10.5061/dryad.n5tb2rbxf
title: Data from: Corn grain and stover nutrient uptake responses from sandy soil treated with designer biochars and compost

description: This is digital research data corresponding to a published
 manuscript,  Corn grain and stover nutrient uptake responses from
 sandy soil treated with designer biochars and compost. 2021. Agronomy.
 11(5):942. https://doi.org/10.3390/agronomy11050942. Biochars are used for
 soil fertility improvement because they may contain certain elements that
 plants use as nutrients, however, few studies have demonstrated enhanced
 crop nutrient uptake. Our study examined nutrient uptake responses of corn
 (Zea Mays L.) grain and stover over 4 years (Y) after a Goldsboro loamy
 sand (Fine-loamy, siliceous, sub-active, thermic Aquic Paleudults)
 received different designer biochars and a compost. The designer biochars
 were produced from lodgepole pine (Pinus contorta) chip (PC), poultry
 litter (PL), blends with switchgrass (SG; Panicum virgatum), and a SG
 compost alone.
description: Methods are described in
 the manuscript  https://doi.org/10.3390/agronomy11050942
description: Descriptions corresponding to each data table in the manuscript
 are placed on separate tabs in the Excel file to clarify abbreviations and
 summarize the data headings and units.
DOI: 10.5061/dryad.44j0zpcg2
title: Do experimental drought stress and species' drought sensitivity influence herbivory in tropical tree seedlings?

description: In tropical forests, drought and herbivory represent two potent stresses
 on seedlings. Climate change is expected to increase the frequency of
 severe droughts in many tropical forests, which may influence seedling
 vulnerability to herbivores if drought stress affects seedling
 palatability. Furthermore, contrasting selective pressures in wetter vs
 drier forests could mean that species well-adapted to herbivores are less
 drought resistant and vice versa. In this study, we measured seedling
 performance and herbivory in a common garden experiment where seedlings of
 15 tree species were subjected to irrigation or rainfall exclusion
 treatments across two dry seasons in Panama. Water-manipulation had no
 effects on foliar herbivory during the experiment for all species combined
 and for 14 of the 15 focal species when analyzed separately. There was
 large variation among species in herbivore damage, but no relationship
 between the sensitivity of species to drought and the amount of herbivory
 they experienced. Altogether, our findings suggest that increasing drought
 stress is unlikely to directly alter tropical tree seedling susceptibility
 to herbivore attack in this forest. Additional studies are needed to
 determine whether drought alters tropical plant-herbivore interactions via
 other mechanisms, such as through changes in herbivorous insect
 communities and/or increases in fitness costs of herbivory.