cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2vf74
title: Data from: Regulation of thermal acclimation varies between generations of the short-lived mosquitofish (Gambusia holbrooki) that developed in different environmental conditions

description: 1. Environmental variability and perturbations can influence population
 persistence. It is therefore important to understand whether and how
 animals can compensate for environmental variability, and thereby increase
 resilience of natural populations. Evolutionary theory predicts that in
 fluctuating environments selection should favour developmental modifiers
 that reduce phenotypic expression of genetic variation. The expected
 result is that phenotypes are buffered from environmental variation across
 generations. 2. Our aim was to determine whether phenotypes of
 mosquitofish (Gambusia holbrooki) remain stable across generations in
 which individuals were born into different thermal environments. We
 predicted that the spring generation (cool environment) would acclimate by
 increasing the concentration of regulatory transcription factor mRNA and
 activities of rate-limiting enzymes (hierarchical regulation) to
 compensate for the negative thermodynamic effects of lower temperatures on
 metabolic and locomotor performance. In contrast, the summer-born
 generation (warm environment) would show less capacity for acclimation and
 hierarchical regulation. 4. We show that fish from both generations
 acclimated, but that there were significant differences in the phenotypic
 consequences of acclimation. The overall result was that sprint
 performance, metabolic scope, and the activities of cyctochrome c oxidase
 and lactate dehydrogenase were buffered from environmental change, and did
 not differ between spring and summer fish at their natural water
 temperatures of 15oC and 25oC, respectively. However, there were
 differences between generations in sustained swimming performance and
 citrate synthase activity. 5. We used metabolic control analysis to show
 that modes of regulation of metabolic scope and locomotor performance
 differed between generations. Spring fish showed primarily hierarchical
 regulation, but regulation in summer fish relied to a lesser extent on
 rate-limiting enzymes and transcription factors. 6. We suggest that
 developmental modifiers are favoured in fluctuating environments to
 maximise phenotypic fitness of each generation. We show that the
 interaction between developmental and reversible acclimation can render
 physiological performance of a natural population independent from climate
 variation.
description: All
 dataAll data presented in
 this ms: swimming, MO2, qRT-PCR, enzyme activitiesFE-2013-00104_data.xlsx
DOI: 10.15468/dl.w4n3zh
title: Occurrence Download

description: A dataset containing 136 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Türkiye",
 "TaxonKey is Cedrus libani"
 ]
}

 The dataset includes 136 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000601-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7n4h4
title: Data from: The distribution and numbers of cheetah (Acinonyx jubatus) in southern Africa

description: Assessing the numbers and distribution of threatened species is a central
 challenge in conservation, often made difficult because the species of
 concern are rare and elusive. For some predators, this may be compounded
 by their being sparsely distributed over large areas. Such is the case
 with the cheetah Acinonyx jubatus. The IUCN Red List process solicits
 comments, is democratic, transparent, widely-used, and has recently
 assessed the species. Here, we present additional methods to that process
 and provide quantitative approaches that may afford greater detail and a
 benchmark against which to compare future assessments. The cheetah poses
 challenges, but also affords unique opportunities. It is photogenic,
 allowing the compilation of thousands of crowd-sourced data. It is also
 persecuted for killing livestock, enabling estimation of local population
 densities from the numbers persecuted. Documented instances of persecution
 in areas with known human and livestock density mean that these data can
 provide an estimate of where the species may or may not occur in areas
 without observational data. Compilations of extensive telemetry data
 coupled with nearly 20,000 additional observations from 39 sources show
 that free-ranging cheetahs were present across approximately 789,700 km2
 of Namibia, Botswana, South Africa, and Zimbabwe (56%, 22%, 12% and 10%
 respectively) from 2010 to 2016, with an estimated adult population of
 3,577 animals. We identified a further 742,800 km2 of potential cheetah
 habitat within the study region with low human and livestock densities,
 where another ∼3,250 cheetahs may occur. Unlike many previous estimates,
 we make the data available and provide explicit information on exactly
 where cheetahs occur, or are unlikely to occur. We stress the value of
 gathering data from public sources though these data were mostly from
 well-visited protected areas. There is a contiguous, transboundary
 population of cheetah in southern Africa, known to be the largest in the
 world. We suggest that this population is more threatened than believed
 due to the concentration of about 55% of free-ranging individuals in two
 ecoregions. This area overlaps with commercial farmland with high
 persecution risk; adult cheetahs were removed at the rate of 0.3
 individuals per 100 km2 per year. Our population estimate for confirmed
 cheetah presence areas is 11% lower than the IUCN’s current assessment for
 the same region, lending additional support to the recent call for the
 up-listing of this species from vulnerable to endangered status.
description: Cheetah Distribution and
 Population Data
DOI: 10.5061/dryad.75252
title: Data from: Widespread generalist clones are associated with range and niche expansion in allopolyploids of Pacific Northwest Hawthorns (Crataegus L.)

description: Range and niche expansion are commonly associated with transitions to
 asexuality, polyploidy, and hybridity (allopolyploidy) in plants. The
 ability of asexual polyploids to colonize novel habitats may be due to
 widespread generalist clones, multiple ecologically specialized clones, or
 may be a neutral byproduct of multiple, independent origins of asexual
 polyploids throughout the range. We have quantified niche size and
 divergence for hawthorns of the Pacific Northwest using data from
 herbarium vouchers with known cytotypes. We find that all polyploid niches
 diverge from that of the diploid range, and allopolyploids have the
 broadest niches. Allotetraploids have the largest niche and the widest
 geographic distribution. We then assessed the genetic mechanism of range
 expansion by surveying the ecological and geographic distribution of
 genotypes within each cytotype from sites in which fine-scale habitat
 assessments were completed. We find no isolation by either geographic or
 ecological distance in allopolyploids, suggesting high dispersal and
 colonization ability. In contrast, autotriploids and diploids show
 patterns of isolation by geographic distance. We also compared the
 geographic and ecological distributions of clonal genotypes with those of
 randomly drawn sites of the most widespread cytotype. We found that most
 clones are geographically widespread and occur in a variety of habitats.
 We interpret these findings to suggest that patterns of range and niche
 expansion in Pacific Northwest Hawthorns may stem from these widespread,
 ecologically generalist clones of hybrid origin.
description: Crataegus subg
 Americanae + Sanguineae_localities and bioclim dataThis excel sheet
 represents the localities from which distributions and ecological climate
 niches were created for Pacific Northwest members of Crataegus subg.
 Sanguineae, and subg. Americanae. Alt= altitude, bio1-19 refer to Bioclim
 variables 1-19, available here:
 http://www.worldclim.org/bioclimCrataegus subg Americanae +
 sanguinae_localities and bioclim
 data.xlsxCrataegus subg.
 Sanguineae_collection sites + ecological variablesLocalities and climate,
 soil, and habitat variables which were collected from 2010-2013.
 Dist.to."X" refers to the distance from the site to the nearest
 agriculture, road, or aboveground water source, %"X" refers to
 the percent coverage of different substrates, and soil."X"
 refers to soil characteristics.Crataegus subg.
 Sanguineae_microsatellite data_binary form for genodiveMicrosatellite data,
 coded as binary (Present=7, Absent=9) in the format for GenoDive for all
 species and cytotypes sampled from Crataegus subg. Sanguineae. Column
 headers for the genetic data are coded with the name of the locus followed
 by a period followed by the allele size variant.
DOI: 10.5061/dryad.620jh
title: Data from: The relative risk of fatal poisoning by methadone or buprenorphine within the wider population of England & Wales

description: Objective: To examine the population-wide overdose risk emerging from the
 prescription of methadone and buprenorphine for opioid substitution
 treatment in England and Wales. Design: Retrospective administrative data
 study. Setting: National databases for England and Wales.
 Participants/cases: Drug-related mortality data were drawn from the Office
 for National Statistics, and prescription data for methadone and
 buprenorphine were obtained from the National Health Service for the years
 2007–2012. During this 6-year period, a total of 2366 methadone-related
 deaths and 52 buprenorphine-related deaths were registered, corresponding
 to 17 333 163 methadone and 2 602 374 buprenorphine prescriptions issued.
 The analysis encompassed poisoning deaths among members of the wider
 population of England and Wales who consumed, but were not prescribed
 these medications, in addition to patients prescribed methadone or
 buprenorphine. Main outcome measures :Mortality risk: substance-specific
 overdose rate per 1000 prescriptions issued; relative risk ratio of
 methadone in relation to buprenorphine. Results: During the years
 2007–2012, the pooled overdose death rate was 0.137/1000 prescriptions of
 methadone, compared to 0.022/1000 prescriptions of buprenorphine
 (including buprenorphine-naloxone). The analysis generated a relative risk
 ratio of 6.23 (95% CI 4.79 to 8.10) of methadone in relation to
 buprenorphine. UK Borders Agency data were taken into consideration and
 revealed that only negligible amounts of methadone and buprenorphine were
 seized on entering UK territory between 2007 and 2012, suggesting domestic
 diversion. Conclusions: Our analysis of the relative safety of
 buprenorphine and methadone for opioid substitution treatment reveals that
 buprenorphine is six times safer than methadone with regard to overdose
 risk among the general population. Clinicians should be aware of the
 increased risk of prescribing methadone, and tighter regulations are
 needed to prevent its diversion.
description: Marteau, McDonald &
 Patel_2015ZIP file containing
 Microsoft XLS and Adobe pdf files of data and calculations on:
 Prescriptions issued, deaths and drug seizuresMarteau_McDonald_Patel_2015.zip
DOI: 10.5061/dryad.s33p3
title: Data from: Population genetics of Wolbachia-infected, parthenogenetic and uninfected, sexual populations of Tetrastichus coeruleus (Hymenoptera: Eulophidae).

description: Wolbachia are endosymbiotic bacteria known to manipulate the reproduction
 of their hosts. These manipulations are expected to have consequences on
 the population genetics of the host, such as heterozygosity levels,
 genetic diversity and gene flow. The parasitoid wasp Tetrastichus
 coeruleus has populations that are infected with parthenogenesis-inducing
 Wolbachia and populations that are not infected. We studied the population
 genetics of T. coeruleus between and within Wolbachia-infected and
 uninfected populations, using nuclear microsatellites and mitochondrial
 DNA. We expected reduced genetic diversity in both DNA types in infected
 populations. However, migration and gene flow could introduce new DNA
 variants into populations. We therefore paid special attention to
 individuals with unexpected (genetic) characteristics. Based on nuclear
 and mitochondrial DNA, two genetic clusters were evident: a thelytokous
 cluster containing all Wolbachia-infected, parthenogenetic populations and
 an arrhenotokous cluster containing all uninfected, sexual populations.
 Nuclear and mitochondrial DNA did not exhibit concordant patterns of
 variation, although there was reduced genetic diversity in infected
 populations for both DNA types. Within the thelytokous cluster, there was
 nuclear DNA variation, but no mitochondrial DNA variation. This nuclear
 DNA variation may be explained by occasional sex between infected females
 and males, by horizontal transmission of Wolbachia, and/or by novel
 mutations. Several females from thelytokous populations were uninfected
 and/or heterozygous for microsatellite loci. These unexpected
 characteristics may be explained by migration, by inefficient transmission
 of Wolbachia, by horizontal transmission of Wolbachia, and/or by novel
 mutations. However, migration has not prevented the build-up of
 considerable genetic differentiation between thelytokous and arrhenotokous
 populations.
description: Dryad Data
 Microsatellite genotypesTcoer_ND1 incl internal
 F2 primer_reverse complement (reading frame 2)Tcoer_ND1 excl internal
 F2 primer_reverse complement (reading frame 2)Dryad README Tcoer_CO1
 (reading frame 2)Tcoer_CO1 (reading frame
 2).fasDryad README
 Tcoer_CO1aTcoer_CO1a.fasTcoer_CO1bTcoer_CO1ab
DOI: 10.5061/dryad.tm1k0
title: Data from: A molecular gut content study of Themisto abyssorum (Amphipoda) from Arctic hydrothermal vent and cold seep systems

description: The use of DNA as a marker for prey inside the gut of predators has been
 instrumental in further understanding of known and unknown interactions.
 Molecular approaches are in particular useful in unavailable environments
 like the deep-sea. Trophic interactions in the deep-sea are difficult to
 observe in situ, correct deep-sea experimental laboratory conditions are
 difficult to obtain, animals rarely survive the sampling, or the study
 organisms feed during the sampling due to long hauls. Preliminary studies
 of vent and seep systems in the Nordic Seas have identified the
 temperate-cold water pelagic amphipod Themisto abyssorum as a potentially
 important predator these chemosynthetic habitats. However, the prey of
 this deep-sea predator is poorly known, and we applied Denaturing High
 Performance Liquid Chromatography (DHPLC) to investigate the predator -
 prey interactions of T. abyssorum in deep-water vent and seep systems. Two
 deep-water hydrothermally active localities (The Jan Mayen and Loki's
 Castle vent fields) and one cold seep locality (The Håkon Mosby mud
 volcano) in the Nordic Seas were sampled, genomic DNA of the stomachs of
 T. abyssorum was extracted, and 18S rDNA gene was amplified and used to
 map the stomach content. We found a wide range of organisms including
 micro-eukaryotes, metazoans and detritus. Themisto abyssorum specimens
 from Loki's Castle had the highest diversity of prey. The wide range
 of prey items found suggests that T. abyssorum might be involved in more
 than one trophic level and should be regarded as an omnivore and not a
 strict carnivore as have previously been suggested.
description: OTU_best_rep_97_similarityBest representative sequences from each OTU based on 97% similarity.OTU_best_rep_98_similarityBest representative sequences from each OTU based on 98% similarity.OTU_best_rep_99_similarityBest representative sequences from each OTU based on 99% similarity.OTU_matrix_97_similarityA presence absence matrix for each OTU and specimen using 97% similarity to assign OTUsOTU_matrix_98_similarityA presence absence matrix for each OTU and specimen using 98% similarity to assign OTUs. See read me file in 'OTU_matrix_97_similarity.tab'OTU_matrix_99_similarityA presence absence matrix for each OTU and specimen using 99% similarity to assign OTUs. See read me file in 'OTU_matrix_97_similarity.tab'all_sequences_tab_delimitedAll sequences used in this studyTaxonomy_WORMSThe basis for the annotation of all OTUs in the study. Must be used together with the OTU matrixes to be able to get any geographical data from it.
DOI: 10.15468/dl.6xt7at
title: Occurrence Download

description: A dataset containing 370712801 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 GBIF_ISEA3HCODE(14, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000)) isea3hcellcode,
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, GBIF_ISEA3HCODE(14, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000)))) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, GBIF_ISEA3HCODE(14, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000)))) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, GBIF_ISEA3HCODE(14, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000)))) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, GBIF_ISEA3HCODE(14, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000)))) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, GBIF_ISEA3HCODE(14, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000)))) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, GBIF_ISEA3HCODE(14, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000)))) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.occurrencestatus = 'PRESENT'
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND (occurrence.classificationdetails['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c']['specieskey'] &lt;&gt; '' AND occurrence.hascoordinate = TRUE)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 GBIF_ISEA3HCODE(14, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000))

 The dataset's 370712801 records were derived from 66275 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000379-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.r1cr4
title: Data from: Plasmids and evolutionary rescue by drug resistance

description: Antibiotic resistance provides evolutionary rescue for bacterial
 populations under the threat of extinction through antibiotics. It can
 arise de novo through mutation in the population, or be obtained from
 other bacterial populations via the transfer of a resistance-conferring
 plasmid. We use stochastic modelling methods to establish whether the most
 likely source of rescue is via a plasmid or via the chromosome, and show
 that contrary to what is assumed plasmids are not necessarily beneficial
 locations for resistance genes. Competition at the plasmid level of
 selection is of great importance - the spread of a resistant plasmid in
 the population can be slowed or entirely stopped by a non-resistant
 version of the same plasmid. We suggest that future studies on
 antibiotic-resistant plasmids should explicitly consider competition at
 this level of selection.
description: RescueR file to run
 simulationsSimresultsExcel file with the results of the simulations.DataStuffMathematica file for plotting the results.
DOI: 10.5061/dryad.3gg62
title: Data from: A molecular phylogeny of Eumorpha (Lepidoptera: Sphingidae) and the evolution of anti-predator larval eyespots

description: Many insects possess conspicuous external circular ring markings that
 resemble the eye of a vertebrate. These ‘eyespots’ typically function to
 startle or otherwise deter predators, but few studies have examined how
 eyespots have evolved. We study the evolution of the posterior larval
 eyespot in the charismatic New World hawkmoth genus Eumorpha. While
 Eumorpha has a range of posterior larval eyespot shapes and sizes, little
 is known of how this trait has evolved because phylogenetic relationships
 of Eumorpha remain largely unknown. In this study, we included 62
 individuals from 23 of 26 described Eumorpha species, and sequenced four
 genes (CAD, EF-1α, Wingless and COI), totaling 3773 base pairs. Maximum
 likelihood and Bayesian phylogenetic methods produced largely congruent
 trees with well-supported relationships. Our analyses reveal that Eumorpha
 probably had an ancestor with a posterior larval eyespot and that the
 eyespot was subsequently lost in at least three lineages. Eumorpha appears
 to have originated in Central and South America and expanded its
 distribution to North America.
description: READMEList of files in the
 packagePonce_et_al_2014_taxa_listMicrosoft excel file that lists species names and the sample ID's used in nexus filesPonce_et_al_2014_Dataset1DNA data matrix Dataset1 of Ponce et al. 2014 in nexus format including charsets for each gene.Ponce_et_al_2014_Dataset2DNA data matrix Dataset2 of Ponce et al. 2014 in nexus format including charsets for each gene.
DOI: 10.15468/dl.jepdh3
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The InBIO Barcoding Initiative Database: Ypsolopha rhinolophi sp. nov. (Lepidoptera: Ypsolophidae), a new species from Portugal and France unveiled by bats"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000602-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b4b7tn
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The InBIO Barcoding Initiative Database: Ypsolopha milfontensis, a new species from the Portuguese coast (Lepidoptera: Ypsolophidae)"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000603-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.