cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.kka9ud
title: Occurrence Download

description: A dataset containing 125771 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Apis mellifera",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2026",
 "DecimalLatitude is greater than or equal to -60.0",
 "DecimalLatitude is less than or equal to 40.0",
 "DecimalLongitude is greater than or equal to -90.0",
 "DecimalLongitude is less than or equal to 55.0",
 "HasCoordinate is true"
 ]
}

 The dataset includes 125771 records from 197 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000665-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.h8017
title: Data from: Extreme genetic diversity in asexual grass thrips populations

description: The continuous generation of genetic variation has been proposed as one of
 the main factors explaining the maintenance of sexual reproduction in
 nature. However, populations of asexual individuals may attain high levels
 of genetic diversity through within-lineage diversification, replicate
 transitions to asexuality from sexual ancestors and migration. How these
 mechanisms affect genetic variation in populations of closely related
 sexual and asexual taxa can therefore provide insights into the role of
 genetic diversity for the maintenance of sexual reproduction. Here, we
 evaluate patterns of intra- and interpopulation genetic diversity in
 sexual and asexual populations of Aptinothrips rufus grass thrips. Asexual
 A. rufus populations are found throughout the world, whereas sexual
 populations appear to be confined to few locations in the Mediterranean
 region. We found that asexual A. rufus populations are characterized by
 extremely high levels of genetic diversity, both in comparison with their
 sexual relatives and in comparison with other asexual species. Migration
 is extensive among asexual populations over large geographic distances,
 whereas close sexual populations are strongly isolated from each other.
 The combination of extensive migration with replicate evolution of asexual
 lineages, and a past demographic expansion in at least one of them,
 generated high local clone diversities in A. rufus. These high clone
 diversities in asexual populations may mimic certain benefits conferred by
 sex via genetic diversity and could help explain the extreme success of
 asexual A. rufus populations.
description: Aptinothripsrufus_genotype fileThis worksheet contains genotypes of all individuals at eleven microsatellite loci as well as haplotypes of mitochondrial sequence markers COI-COII and pseudohaplotypes of the nuclear sequence markers H3 and Elongation factor.Arufus_genotypefile.xlsxElongation- factor (EF) sequencesThis fasta file contains sequences of EF nuclear sequence markers of all individuals. There is one sequence per individual and heterozygous positions are marked with IUPAC ambiguity code.eF_seqs.fasElongation- factor (EF) pseudohaplotypesThis fasta file contains 2 haploid sequences of EF marker per individual, obtained after phasing of raw sequences.eF_pseudohaplos.fasHistone3 (H3) pseudohaplotypesThis fasta file contains 2 haploid sequences of H3 marker per individual, obtained after phasing of raw sequences.H3_pseudohaplos.fas
DOI: 10.5061/dryad.6tn4h
title: Data from: Seasonal changes in plankton food web structure and carbon dioxide flux from Southern California reservoirs

description: Reservoirs around the world contribute to cycling of carbon dioxide (CO2)
 with the atmosphere, but there is little information on how ecosystem
 processes determine the absorption or emission of CO2. Reservoirs are the
 most prevalent freshwater systems in the arid southwest of North America,
 yet it is unclear whether they sequester or release CO2 and therefore how
 water impoundment impacts global carbon cycling. We sampled three
 reservoirs in San Diego, California, weekly for one year. We measured
 seasonal variation in the abundances of bacteria, phytoplankton, and
 zooplankton, as well as water chemistry (pH, nutrients, ions, dissolved
 organic carbon [DOC]), which were used to estimate partial pressure of CO2
 (pCO2), and CO2 flux. We found that San Diego reservoirs are most often
 undersaturated with CO2 with respect to the atmosphere and are estimated
 to absorb on average 3.22 mmol C m-2 day-1. pCO2 was highest in the winter
 and lower in the summer, indicating seasonal shifts in the magnitudes of
 photosynthesis and respiration associated with day length, temperature and
 water inputs. Abundances of microbes (bacteria) peaked in the winter along
 with pCO2, while phytoplankton, nutrients, zooplankton and DOC were all
 unrelated to pCO2. Our data indicate that reservoirs of semi-arid
 environments may primarily function as carbon sinks, and that carbon flux
 varies seasonally but is unrelated to nutrient or DOC availability, or the
 abundances of phytoplankton or zooplankton.
description: Time series data of
 Lakes Poway, Miramar, and MurrayThis data file contains
 both abiotic and biotic variables for each lake for each sampling date.
 The data included are described in the ReadMe file.Adamczyk_PLOSdata.csvWater chemistry data for Lakes Poway, Miramar, and MurrayWater chemistry parameters measured by YSI Professional Plus. Details are included in the ReadMe file.Adamczyk_YSI_PLOSdata.csvZooplankton lengths for Lakes Poway, Miramar, and MurrayZooplankton lengths for zooplankton samples counted (see other zooplankton data). These data were used to determine zooplankton biomass.Adamczyk_zooplankton_lengths_PLOSdata.csvZooplankton abundance for Lakes Poway, Miramar, and MurrayZooplankton were counted and then measured (see other zooplankton data) to determine community biomass. Details are included in the ReadMe file.Adamczyk_zooplankton_abundance_PLOSdata.csv
DOI: 10.5061/dryad.669r8
title: Data from: A few meters matter: local habitats drive reproductive cycles in a tropical lizard

description: Reproductive phenology often varies geographically within species, driven
 by environmental gradients that alter growth and reproduction. However,
 environments can differ between adjacent habitats at single localities. In
 lowland Puerto Rico, both open (sunny, warm) and forested (shady, cool)
 habitats may be only meters apart. The lizard Anolis cristatellus lives in
 both habitats: it thermoregulates carefully in the open but is a
 thermoconformer in the forest. To determine whether reproduction differs
 between habitats, we compared reproductive cycles of females in open
 versus forest habitats at two localities for over 2 years. Open females
 were more likely than forest females to be reproductive throughout the
 year, probably because open females were able to bask and thereby achieve
 warmer body temperatures. These between-habitat differences in
 reproduction were especially marked in cool months and are equivalent in
 magnitude to those between populations separated by elevation. Thus,
 environmental differences (even on a microlandscape scale) matter to
 reproduction and probably to demography.
description: Composite data file for
 Punta Salinas and MonagasExcel files. Ecological
 and reproductive data of Anolis cristatellus. Data collected in two field
 sites: Punta Salinas and Monagas, Puerto Rico. See 'Read me'
 files for more detailsCompositePuntaSalinasMonagasDRYAD.xlsx
DOI: 10.5061/dryad.dv4rg
title: Data from: Genetic correlations and little genetic variance for reaction norms may limit potential for adaptation to pollution by ionic and nanoparticulate silver in a whitefish (Salmonidae)

description: For natural populations to adapt to anthropogenic threats, heritable
 variation must persist in tolerance traits. Silver nanoparticles, the most
 widely used engineered nanoparticles, are expected to increase in
 concentrations in freshwaters. Little is known about how these particles
 affect wild populations, and whether genetic variation persists in
 tolerance to permit rapid evolutionary responses. We sampled wild adult
 whitefish and crossed them in vitro full factorially. In total, 2896
 singly raised embryos of 48 families were exposed to two concentrations
 (0.5 μg/L; 100 μg/L) of differently sized silver nanoparticles or ions
 (silver nitrate). These doses were not lethal; yet higher concentrations
 prompted embryos to hatch earlier and at a smaller size. The induced
 hatching did not vary with nanoparticle size and was stronger in the
 silver nitrate group. Additive genetic variation for hatching time was
 significant across all treatments, with no apparent environmental
 dependencies. No genetic variation was found for hatching plasticity. We
 found some treatment-dependent heritable variation for larval length and
 yolk volume, and one instance of additive genetic variation for the
 reaction norm on length at hatching. Our assessment suggests that the
 effects of silver exposure on additive genetic variation vary according to
 trait and silver source. While the long-term fitness consequences of
 low-level silver exposure on whitefish embryos must be further
 investigated to determine whether it is, in fact, detrimental, our results
 suggest that the evolutionary potential for adaptation to these types of
 pollutants may be low.
description: agnpExperimental treatments,
 parent IDs, and observations made on embryos raised individually in
 24-well plates.
DOI: 10.5061/dryad.q414b
title: Data from: Phylogenetic relationships of Trachylepis skink species from Madagascar and the Seychelles (Squamata: Scincidae)

description: Lizards of the genus Trachylepis are a species-rich group of skinks mainly
 inhabiting Africa, Madagascar, and several other islands in the western
 Indian Ocean. All except one probably introduced species of Madagascan
 Trachylepis are endemic. Two species groups have been distinguished on the
 basis of subocular scale shape but their phylogenetic relationships
 remained unclear. We inferred a multilocus phylogeny of the Madagascan
 Trachylepis species, based on a concatenated dataset of 3261 bp from 3
 mitochondrial and 4 nuclear genes with a dense Madagascan taxon sampling
 and find high support for the monophyly of the endemic Madagascan
 Trachylepis. The two species groups in Madagascar are highly supported as
 clades. The highland species T. boettgeri is nested in the T.
 aureopunctata species group of mainly arid-adapted species, suggesting a
 colonization of highland swamps by ancestors inhabiting dry western
 Madagascar. The Seychellois species were sister to the T. maculilabris/T.
 comorensis clade, suggesting their origin directly out of Africa as with
 Seychellois chameleons. In Madagascar, a high intraspecific molecular
 variation was confirmed for T. gravenhorstii, T. elegans, and T. vato,
 indicating a need for taxonomic revision.
description: Trachylepis_alignment_partition_scheme_P5Interleaved alignment of all genes in Nexus format, with exclusion settings and partition scheme (P5) as used in the partitioned Bayesian analysis.
DOI: 10.5061/dryad.s6h6b
title: Data from: A benign juvenile environment reduces the strength of antagonistic pleiotropy and genetic variation in the rate of senescence

description: 1. The environment can play an important role in the evolution of
 senescence because the optimal allocation between somatic maintenance and
 reproduction depends on external factors influencing life expectancy. 2.
 The aims of this study were to experimentally test whether environmental
 conditions during early life can shape senescence schedules, and if so, to
 examine whether variation among individuals or genotypes with respect to
 the degree of ageing differs across environments. 3. We tested
 life-history plasticity and quantified genetic effects on the pattern of
 senescence across different environments within a reaction norm framework
 by using an experiment on the three-spined stickleback (Gasterosteus
 aculeatus, Linnaeus) in which F1 families originating from a wild annual
 population experienced different temperature regimes. 4. Male sticklebacks
 that had experienced a more benign environment earlier in life
 subsequently reduced their investment in carotenoid-based sexual signals
 early in the breeding season, and consequently senesced at a slower rate
 later in the season, compared to those that had developed under harsher
 conditions. This plasticity of ageing was genetically determined. Both
 antagonistic pleiotropy and genetic variation in the rate of senescence
 were evident only in the individuals raised in the harsher environment. 5.
 The experimental demonstration of genotype-by-environment interactions
 influencing the rate of reproductive senescence provides interesting
 insights into the role of the environment in the evolution of
 life-histories. The results suggest that benign conditions weaken the
 scope for senescence to evolve, and that the dependence on the environment
 may maintain genetic variation under selection.
description: Kim et
 al_data1. Repeated measures
 data; 2. Individual-based data
DOI: 10.5061/dryad.gt223
title: Data from: The genetic architecture of hybridisation between two lineages of greenshell mussels

description: A multidisciplinary approach has identified sigmoidal genetic clines on
 the east and west coasts in central New Zealand where low-density
 ecological interactions occur between northern and southern lineages of
 the endemic greenshell mussel, Perna canaliculus. The sigmoidal clines
 indicate the existence of a mussel hybrid zone in a region of genetic
 discontinuities for many continuously distributed coastal taxa, in
 particular marine invertebrates. Examination of the genetic architecture
 of the hybrid zone revealed the differential contribution of individual
 microsatellite loci and/or alleles to defining the zone of interaction and
 no evidence of increased allelic richness or heterozygosity inside versus
 outside the hybrid zone. Genomics cline analysis identified one locus in
 particular (Pcan1–27) as being different from neutral expectations,
 thereby contributing to lineage differentiation. Estimates of contemporary
 gene flow revealed very high levels of within-lineage self-recruitment and
 a hybrid zone composed mostly (~85%) of northern immigrants. Broad scale
 interpretation of these results is consistent with a zone of genetic
 interaction that was generated between 0.3 and 1.3 million years before
 present at a time of pronounced global sea-level change. At that time, the
 continuous distribution of the greenshell mussel was split into northern
 and southern groups, which differentiated to become distinct lineages, and
 which have subsequently been reunited (secondary contact) resulting in the
 generation of the hybrid zone at ~42°S.
description: Perna
 canaliculus_Genotype data for GENEPOPMicrosatellite genotype
 data of 14 Perna canaliculus populations and 10 loci used for GENEPOP
 analysis. Can be transferred to other input data used for FSTAT, POPGENE,
 ARLEQUIN, MICROCHECHER analyses.Perna canaliculus_Clines
 analysis dataData used to fit
 sigmoidal cline plots [y = a0+a1/(1+exp(–(x–a2)/a3))] using SLIDEWRITE
 PLUS v3.Perna
 canaliculus_Geospatial dataLatitudes and longitudes
 of 14 Perna canaliculus populations used for Clines
 analysis.Perna
 canaliculus_Introgress_Four populationsMicrosatellite genotype
 data of four admixed populations and 10 loci used for INTROGRESS
 analysis.Perna
 canaliculus_Introgress_Six populationsMicrosatellite genotype
 data of six admixed populations and 10 loci used for INTROGRESS
 analysis.Perna
 canaliculus_BAYESASS_Four populationsMultilocus genotype data
 of four populations used for BAYESASS analysis (in population alpha
 order).Perna
 canaliculus_BAYESASS_Six populationsMultilocus genotype data
 of six populations used for BAYESASS analysis (in population alpha
 order).
DOI: 10.5061/dryad.9j92p2b
title: Data from: Diets of giants: the nutritional value of sauropod diet during the Mesozoic

description: A major uncertainty in estimating energy budgets and population densities
 of extinct animals is the carrying capacity of their ecosystems,
 constrained by net primary productivity (NPP) and its digestible energy
 content. The hypothesis that increases in NPP due to elevated atmospheric
 CO2 contributed to the unparalleled size of the sauropods has recently
 been rejected, based on modern studies on herbivorous insects that imply a
 general, negative correlation of diet quality and increasing CO2. However,
 the nutritional value of plants grown under elevated CO2 levels might be
 very different for vertebrate megaherbivores than for insects. Here we
 show plant species‐specific responses in metabolizable energy and nitrogen
 content, equivalent to a two‐fold variation in daily food intake estimates
 for a typical sauropod, for dinosaur food plant analogues grown under CO2
 concentrations spanning estimates for Mesozoic atmospheric concentrations.
 Our results potentially rebut the hypothesis that constraints on sauropod
 diet quality were driven by Mesozoic CO2 concentration.
description: Supporting Information
 1Estimated divergence
 times for orders represented by experimental taxa.Supporting Information
 2.1Figure S.1 Gas
 production data from in vitro fermentation experiments with experimental
 taxaSupp_info_fig_1.pdfSupporting Information 2.2ANOVA results for maximal gas production and gas production rateSupporting Information 2.docxSupporting Information 3Comparison of means for taxaSupporting Information 4Comparison of means for [CO2]Supporting Information 5Effect of CO2 growth concentration on gas production within taxaSupporting Information 6Effect of CO2 growth concentration on %N within taxaSupporting Information 7Regression equations for ME of individual taxa under varying CO2 growth concentrationsSupporting Information 8Daily food intake estimatesSupporting Information 9 - Reference listReferences cited in supplementary informationSupporting Information 9.docx
DOI: 10.5061/dryad.vb8r7
title: Data from: Patterns of host-parasite adaptation in three populations of monarch butterflies infected with a naturally occurring protozoan disease: virulence, resistance, and tolerance

description: Many studies have used host-parasite systems to study local adaptation but
 few of these studies have found unequivocal evidence for adaptation. One
 potential reason is that most studies have focused on limited measures of
 host and parasite fitness that are generally assumed to be under negative
 frequency-dependent selection. We have used reciprocal cross-infection
 experiments to test for local adaptation in Hawaiian, South Floridian, and
 eastern North American populations of monarch butterflies and their
 protozoan parasites. Sympatric host-parasite combinations did not result
 in greater host or parasite fitness, as would be expected under
 coevolutionary dynamics driven by negative frequency-dependent selection.
 Instead, we found that Hawaiian hosts were more resistant and carried more
 infective and virulent parasites, which is consistent with theoretical
 predictions for virulence evolution and coevolutionary arms race dynamics.
 We also found that Hawaiian hosts were more tolerant, particularly of
 Hawaiian parasites, indicating that increased resistance does not preclude
 increased tolerance within a population and hosts may be more tolerant of
 local parasites. We did not find a similar pattern in the South Floridian
 or eastern populations, possibly because host-parasite adaptation occurs
 within the context of the greater ecological community.
description: Hawaii versus Eastern
 Cross InfectionData from laboratory
 infections with monarchs and parasites from the eastern North American and
 Hawaiian populations. Additional details can be found in the ReadMe
 file.HawaiiEastern_CrossInfection.csvMiami versus Eastern CrossInfectionData from laboratory infections with monarchs and parasites from the eastern North American and Hawaiian populations. Additional details can be found in the ReadMe file.MiamiEastern_CrossInfection.csv
DOI: 10.5061/dryad.t2f47
title: Data from: Coverage of the 2011 Q fever vaccination campaign in the Netherlands, using retrospective population-based prevalence estimation of cardiovascular risk-conditions for chronic Q fever

description: Background: In 2011, a unique Q fever vaccination campaign targeted people
 at risk for chronic Q fever in the southeast of the Netherlands. General
 practitioners referred patients with defined cardiovascular
 risk-conditions (age &gt;15 years). Prevalence rates of those
 risk-conditions were lacking, standing in the way of adequate planning and
 coverage estimation. We aimed to obtain prevalence rates retrospectively
 in order to estimate coverage of the Q fever vaccination campaign.
 Methods: With broad search terms for these predefined risk-conditions, we
 extracted patient-records from a large longitudinal general-practice
 research-database in the Netherlands (IPCI-database). After validation of
 these records, obtained prevalence rates (stratified for age and sex)
 extrapolated to the Q fever high-incidence area population, gave an
 approximation of the size of the targeted patient-group. Coverage
 calculation addressed people actually screened by a pre-vaccination Q
 fever skin test and serology (coverage) and patients referred by their
 general practitioners (adjusted-coverage) in the 2011 campaign. Results:
 Our prevalence estimate of any risk-condition was 3.1% (lower-upper limits
 2.9-3.3%). For heart valve defects, aorta aneurysm/prosthesis, congenital
 anomalies and endocarditis, prevalence was 2.4%, 0.6%, 0.4% and 0.1%,
 respectively. Estimated number of eligible people in the Q fever
 high-incidence area was 11,724 (10,965-12,532). With 1330 people screened
 for vaccination, coverage of the vaccination campaign was 11%. For
 referred people, the adjusted coverage was 18%. Coverage was lowest among
 the very-old and highest for people aged 50–70 years. Conclusion: The
 estimated coverage of the vaccination campaign was limited. This should be
 interpreted in the light of the complexity of this target-group with much
 co-morbidity, and of the vaccine that required invasive pre-vaccination
 screening. Calculation of prevalence rates of risk-conditions based on the
 IPCI-database was feasible. This procedure proved an efficient tool for
 future use, when prevalence estimates for policy, implementation or
 surveillance of subgroup-vaccination or other health-care interventions
 are needed.
description: Risk-conditions chronic
 Q fever vaccination datasetsThe IPCI-dataset
 contains all extracted patients from a 5% sample of the population based
 general practice database, based on selection criteria described in the
 article. Patients age, sex and risk conditions are supplied with level of
 diagnostic certainty. The Q fever vaccination dataset contains accepted
 referrals and registered chronic Q fever risk conditions with sex, age and
 living area of patients. Code books are included.