cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pr1h0
title: Data from: Recurrent sublethal warming reduces embryonic survival, inhibits juvenile growth, and alters species distribution projections under climate change

description: The capacity to tolerate climate change often varies across ontogeny in
 organisms with complex life cycles. Recently developed species
 distribution models incorporate traits across life stages; however, these
 life-cycle models primarily evaluate effects of lethal change. Here, we
 examine impacts of recurrent sublethal warming on development and survival
 in ecological projections of climate change. We reared lizard embryos in
 the laboratory under temperature cycles that simulated contemporary
 conditions and warming scenarios. We also artificially warmed natural
 nests to mimic laboratory treatments. In both cases, recurrent sublethal
 warming decreased embryonic survival and hatchling sizes. Incorporating
 survivorship results into a mechanistic species distribution model reduced
 annual survival by up to 24% compared to models that did not incorporate
 sublethal warming. Contrary to models without sublethal effects, our model
 suggests that modest increases in developmental temperatures influence
 species ranges due to effects on survivorship.
description: output from
 'lethal' and 'sublethal' modelsThis Zip archive
 contains 14 netCDF files with the output from the lethal, sublethal, and
 age-at-maturity models. All file names indicate the time period
 ['contemp' = 1980-2000; 'future' = 2080-2100],
 variables ([survival' = embryo survival (percent decimal)
 'growth' = population growth (lizards/year),
 'maturity' = age at maturity (days), 'minmaxtemp' =
 minimum and maximum daily temperatures(°C)], and whether the output is
 from the 'lethal' or 'sublethal' model as described in
 the manuscript (or in the case of the age-at-maturity model, whether it
 includes the effect of slowed juvenile growth).Carloetal_EcolLett_model_output.zipCarloetal_EcolLett_labandfield_rearing_data2014and2015This .csv file contains data from the laboratory and field experiments described in the manuscript, including embryonic mortality and development times, maximum daily temperatures, hatchling sizes and body conditions, and juvenile growth rates estimated from von Bertalanffy growth models (for a subset of laboratory-reared lizards).
DOI: 10.5061/dryad.6f1t7
title: Data from: Identifying patterns of non-communicable diseases in developed eastern coastal China: a longitudinal study of electronic health records from 12 public hospitals

description: Objective: Few studies have examined the spectrum and trends of
 non-communicable diseases (NCDs) in inpatients in eastern coastal China,
 which is transforming from an industrial economy to a service-oriented
 economy and is the most economically developed region in the country. This
 study aimed to dynamically elucidate the spectrum and characteristics of
 severe NCDs in eastern coastal China by analysing patients’ longitudinal
 electronic health records (EHRs). Setting: To monitor the spectrum of NCDs
 dynamically, we extracted the EHR data from 12 general tertiary hospitals
 in eastern coastal China from 2003 to 2014. The rankings of and trends in
 the proportions of different NCDs presented by inpatients in different
 gender and age groups were calculated and analysed. Participants: We
 obtained a total sample of 1,907,484 inpatients with NCDs from 2003 to
 2014, 50.05% of whom were male and 81.53% were aged 50 years or older.
 Results: There was an increase in the number of total NCD inpatients in
 eastern coastal China from 2003 to 2014. However, the proportion of
 chronic respiratory diseases and cancer inpatients decreased over the
 12-year period. Compared with men, women displayed a significant increase
 in the proportion of mental and behavioural disorders (P&lt;0.001)
 over time. Additionally, digestive diseases and sensory organ diseases
 significantly decreased among men, but not women. The older group
 accounted for a larger and growing proportion of the NCD inpatients, and
 the most common conditions in this group were cerebral infarctions,
 coronary heart disease and hypertension. In addition, the proportion of
 21- to 50-year-old inpatients with diabetes, blood diseases or endocrine
 diseases skyrocketed from 2003 to 2014 (P&lt;0.001). Conclusions: The
 burden of inpatients' NCDs increased rapidly, particularly among
 women and younger people. The NCD spectrum observed in eastern coastal
 China is a good source of evidence for developing prevention guides for
 regions experiencing transition.
description: Data
DOI: 10.5061/dryad.689r9h2
title: Data from: Are we underestimating the occurrence of sympatric populations?

description: Sympatric populations are conspecific populations that co-exist spatially.
 They are of interest in evolutionary biology by representing the potential
 first steps of sympatric speciation and are important to identify and
 monitor in conservation management. Sympatric existence in freshwater
 habitats can be more easily defined than terrestrial ones, and a series of
 sympatric fish populations have been reported. Reviewing the literature
 pertaining to sympatric populations of salmonid fishes, we find that most
 cases of sympatry appear coupled to phenotypic divergence, implying ease
 of detection. In comparison, phenotypically cryptic, sympatric populations
 seem rarely documented. We explore the statistical power for detecting
 population mixtures from genetic marker data, using commonly applied tests
 for heterozygote deficiency (i.e., Wahlund effect) and the STRUCTURE
 software, through computer simulations. We find that both STRUCTURE and
 heterozygote deficiency tests are efficient at detecting population
 mixture only when genetic differentiation is high, sample size and number
 of genetic markers are reasonable, and the sympatric populations happen to
 occur in similar proportions in the sample. We present an approximate
 expression based on these experimental factors for the lower limit of FST,
 beyond which power for STRUCTURE collapses and only the heterozygote
 deficiency tests retain some, although low, power. The findings suggest
 that cases of cryptic sympatry may have passed unnoticed in population
 genetic screenings using number of loci typical of the pre-genomics era.
 Hence, cryptic sympatric populations may be more common than hitherto
 thought, and we urge more attention being diverted to their detection and
 characterization.
description: simulations_and_scriptsR-scripts for generating the figures presented in the paper.
DOI: 10.5061/dryad.16hc8
title: Data from: Whole genome sequencing reveals absence of recent gene-flow and separate demographic histories for Anopheles punctulatus mosquitoes in Papua New Guinea

description: Anopheles mosquitoes are the vectors of several human diseases including
 malaria. In many malaria endemic areas, several species of Anopheles
 coexist, sometimes in the form of related sibling species that are
 morphologically indistinguishable. Determining the size and organization
 of Anopheles populations, and possible ongoing gene flow among them is
 important for malaria control and, in particular, for monitoring the
 spread of insecticide resistance alleles. However, these parameters have
 been difficult to evaluate in most Anopheles species due to the paucity of
 genetic data available. Here, we assess the extent of contemporary gene
 flow and historical variations in population size by sequencing and de
 novo assembling the genomes of wild-caught mosquitoes from four species of
 the Anopheles punctulatus group of Papua New Guinea. Our analysis of more
 than 50 Mb of orthologous DNA sequences revealed no evidence of
 contemporary gene flow among these mosquitoes. In addition, investigation
 of the demography of two of the An. punctulatus species revealed distinct
 population histories. Overall, our analyses suggest that, despite their
 similarities in morphology, behaviour and ecology, contemporary sympatric
 populations of An. punctulatus are evolving independently.
description: Anopheles farauti 4 SNP
 informationThis file contains all
 the SNPs we identified from our genome assembly of Anopheles farauti 4,
 including information about the location, reference allele frequency, and
 coverage of each SNP.AF4_SNPs_1-26-15.xlsxAnopheles punctulatus SNP informationThis file contains all the SNPs we identified from our genome assembly of Anopheles punctulatus, including information about the location, reference allele frequency, and coverage of each SNP.AP_SNPs_1-26-15.xlsx
DOI: 10.5061/dryad.96712kh
title: Data from: Scaling up DNA barcoding - primer sets for simple and cost efficient arthropod systematics by multiplex PCR and Illumina amplicon sequencing

description: 1. The simplicity and cost efficiency of Illumina amplicon sequencing has
 greatly contributed to the advancement of DNA barcoding and metabarcoding
 applications. However, current amplicon sequencing based barcoding
 approaches are usually restricted to short, single-locus fragments,
 limiting their taxonomic and phylogenetic resolution. 2. Here, we
 establish a cost efficient and simple multiplex PCR protocol for arthropod
 systematics by Illumina amplicon sequencing. We introduce primer sets,
 including several new, generic primers, to reliably amplify nine loci
 across a wide range of arthropods. Using a diverse collection of arthropod
 species from 19 orders, we test loci for amplification efficiency and
 estimate the effect of cross-species amplification bias on taxon recovery
 from bulk community samples. We then explore the taxonomic and
 phylogenetic utility of the primer sets, focusing on a dataset of spiders
 that includes both deep and recent divergences. 3. The set of loci
 provides good phylogenetic support across a wide taxonomic spectrum,
 making it a useful addition to COI for resolving lineages within a
 comparative context. All loci recover sequences for the majority of
 arthropod taxa in separate PCRs. However, cross-species amplification bias
 in some primers prevents an exhaustive taxon recovery from bulk community
 samples. 4. Our protocol makes it possible to generate multilocus datasets
 for large numbers of arthropod taxa for a fraction of the price and
 workload of Sanger sequencing. This opens up the possibility for parallel
 phylogenetic and taxonomic analysis of large collections of arthropods,
 but also enables rapid exploratory analyses of target lineages. Primers
 for metabarcoding applications should be carefully evaluated for their
 performance in bulk community samples and chosen to minimize cross-species
 amplification bias.
description: All primer
 sequencesAll primer sequences
 tested to identify the selected primer set.All_Tested_Primers.xlsxGenetic DistancesIntraspecific and interspecific genetic distances within Hawaiian Tetragnatha species for 4 mitochondrial and 3 nuclear lociGeneticDistances.xlsxBlast results from specimen poolsBlast results and fold change values from specimen pools for all analyzed markersBLAST_Pools_All_Markers.xlsxMitochondrial genomes used for primer designMitochondrialGenomesPrimerDesign.fastaAlignments of nine loci for all spidersSpidersAlignments.rarSequence files for specimen pools for all lociSequences for all loci, which were amplified for the arthropod specimen poolsSpecimen_Pools.rarSequence files for nine loci for all seperate arthropod specimensSeperate_Specimens.rar
DOI: 10.5061/dryad.8sm32
title: Data from: Adaptive and non-adaptive divergence in a common landscape

description: Species in a common landscape often face similar selective environments.
 The capacity of organisms to adapt to these environments may be largely
 species specific. Quantifying shared and unique adaptive responses across
 species within landscapes may thus improve our understanding of
 landscape-moderated biodiversity patterns. Here we test to what extent
 populations of two coexisting and phylogenetically related
 fishes—three-spined and nine-spined stickleback—differ in the strength and
 nature of neutral and adaptive divergence along a salinity gradient.
 Phenotypic differentiation, neutral genetic differentiation and genomic
 signatures of adaptation are stronger in the three-spined stickleback.
 Yet, both species show substantial phenotypic parallelism. In contrast,
 genomic signatures of adaptation involve different genomic regions, and
 are thus non-parallel. The relative contribution of spatial and
 environmental drivers of population divergence in each species reflects
 different strategies for persistence in the same landscape. These results
 provide insight in the mechanisms underlying variation in evolutionary
 versatility and ecological success among species within landscapes.
description: Raeymaekers et
 al-NatCommun-2017Morphological, spatial
 and environmental data of populations of the three-spined stickleback
 (Gasterosteus aculeatus) and the nine-spined stickleback (Pungitius
 pungitius) from eight sites in the Belgian-Dutch
 lowlands.Raeymaekers et
 al-NatCommun-2017_three_spined_reference_based_genotypesReference-based SNP
 genotypes of the three-spined stickleback (VCF file). Individuals are
 labelled as Population_ID.Raeymaekers et
 al-NatCommun-2017_nine_spined_denovo_based_genotypesde novo-based SNP
 genotypes of the nine-spined stickleback (VCF file). Individuals are
 labelled as Population_ID.
DOI: 10.5061/dryad.h5p79
title: Data from: Nanoindentation analysis of the micromechanical anisotropy in mouse cortical bone

description: Studies investigating micromechanical properties in mouse cortical bone
 often solely focus on the mechanical behaviour along the long axis of the
 bone. Therefore, data on the anisotropy of mouse cortical bone is scarce.
 The aim of this study is the first-time evaluation of the anisotropy ratio
 between the longitudinal and transverse directions of reduced modulus and
 hardness in mouse femurs by using the nanoindentation technique. For this
 purpose, nine 22-week-old mice (C57BL/6) were sacrificed and all femurs
 extracted. A total of 648 indentations were performed with a Berkovich tip
 in the proximal (P), central (C) and distal (D) regions of the femoral
 shaft in the longitudinal and transverse directions. Higher values for
 reduced modulus are obtained for indentations in the longitudinal
 direction, with anisotropy ratios of 1.72 ± 0.40 (P), 1.75 ± 0.69 (C) and
 1.34 ± 0.30 (D). Hardness is also higher in the longitudinal direction,
 with anisotropic ratios of 1.35 ± 0.27 (P), 1.35 ± 0.47 (C) and
 1.17 ± 0.19 (D). We observed a significant anisotropy in the
 micromechanical properties of the mouse femur, but the correlation for
 reduced modulus and hardness between the two directions is low
 (r2 &lt; 0.3) and not significant. Therefore, we highly recommend
 performing independent indentation testing in both the longitudinal and
 transverse directions when knowledge of the tissue mechanical behaviour
 along multiple directions is required.
description: Load-depth
 curvesThe .zip file contains
 the load-depth curves of all indentations in .txt, .hys and .lfb format
 performed with the Hysitron TriboIndenter TI 900 (Hysitron Inc.,
 Minneapolis, MN, USA). The data files were loaded, viewed and analyzed
 with the software provided with the indenter (TriboScan, Hysitron Inc.,
 Minneapolis, MN, USA). The files are divided in two main folders. One
 folder contains all measurements performed in transverse direction
 (transverse) and the other contains all measurements in longitudinal
 direction (longitudinal). These folders contains subfolders named after
 the samples. They are subsequently divided in sub-subfolders, which
 contains a set of six indentations each. P: proximal region; C: central
 region; D: distal region. Mxx: mouse number and right or left femur (e.g.
 M1L: mouse no. 1, left femur).Load_depth_curves.zip
DOI: 10.15468/dl.y4q257
title: Occurrence Download

description: A dataset containing 304732 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((4.498074662042267 50.81224977627153, 4.496735466600527 50.82102017319961, 4.492719906720225 50.82945642631409, 4.486181042474845 50.83723407464415, 4.477369316851731 50.84405383656892, 4.466623060229313 50.84965317054918, 4.454355534708914 50.85381643483218, 4.441039008942522 50.85638324496356, 4.427186481999288 50.857254697158, 4.413331777985872 50.856397209209355, 4.40000880561664 50.853843825198645, 4.387730814387714 50.84969293169282, 4.376970479161808 50.844104436903415, 4.368141607809035 50.83729356574557, 4.361583194337124 50.829522518389304, 4.357546436998928 50.82109032362763, 4.356185213136613 50.812321287731585, 4.357550357051059 50.80355249177211, 4.36158793149265 50.795120823906686, 4.368141524874469 50.78735004704477, 4.37695845182777 50.78053839668977, 4.387699590109278 50.77494717946844, 4.3999524568291815 50.770790801430074, 4.41324701500102 50.768228598659455, 4.427073609926681 50.76735877351169, 4.440902365423574 50.76821466048932, 4.454203323213249 50.77076345924511, 4.466466585323722 50.77490748127693, 4.477221719263139 50.7804878644941, 4.486055709000639 50.787290618895405, 4.4926287812913115 50.79505478001288, 4.496687506206076 50.80348236741969, 4.498074662042267 50.81224977627153))",
 "KingdomKey is one of (Animalia, Fungi, Plantae)",
 "Year is one of (2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023, 2024, 2025, 2026)"
 ]
}

 The dataset includes 304732 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000428-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17894/ucph.7457f751-c7d5-4823-a372-9d365f5b46ca
title: Plasmid sequences of pACYC184 derivatives carrying sul and dfrA resistance genes

description: This dataset contains complete plasmid sequences of engineered pACYC184 derivatives carrying the antibiotic resistance genes sul1, sul2, sul3, dfrA1, dfrA5, and dfrA12. Plasmids were constructed using NEB HiFi DNA assembly and sequence verified by Sanger sequencing (Macrogen) using a multi-primer strategy to ensure full coverage of each construct. Sequencing reads were assembled into full-length consensus sequences representing the complete plasmids. The file is provided in multi-FASTA format. These plasmids are part of a study investigating conditionally essential genes for growth in the presence of sulfonamide and trimethoprim in sulfonamide- and trimethoprim-resistant Escherichia coli.
DOI: 10.5061/dryad.8140s
title: Data from: Spatially correlated extinctions select for less emigration but larger dispersal distances in the spider mite Tetranychus urticae

description: Dispersal is a central process to almost all species on earth, as it
 connects spatially structured populations and thereby increases population
 persistence. Dispersal is subject to (rapid) evolution and local patch
 extinctions are an important selective force in this context. In contrast
 to the randomly distributed local extinctions considered in most
 theoretical studies, habitat fragmentation or other anthropogenic
 interventions will lead to spatially correlated extinction patterns. Under
 such conditions natural selection is thought to lead to more long-distance
 dispersal, but this theoretical prediction has not yet been verified
 empirically. We test this hypothesis in experimental spatially structured
 populations of the spider mite Tetranychus urticae and supplement these
 empirical results with insights from an individual-based evolutionary
 model. We demonstrate that the spatial correlation of local extinctions
 changes the entire distribution of dispersal distances (dispersal kernel)
 and selects for overall less emigration but more long-distance dispersal.
description: data
 packageEvery file provides the
 data for the respective life-history trait or for the dispersal distances.
 Header lines describe the content of every column. Generally the first
 columns are explanatory variables and the last column(s) represent(s) the
 data of interest.data.zipsimulation packageThe simualtion package contains all simulated data. The folders indicate the scenarios. Both individual- and population level output is included.simulations.zip
DOI: 10.5066/p134q6k2
title: Developing a land change monitoring capability and supporting training data strategy for select international sites: First Outputs

description: The monitoring of landscape change is widely recognized as an important component towards understanding how the Earth changes and the impacts of, and to, human societies. The U.S. Geological Survey (USGS) Earth Resources Observation and Science (EROS) Center has been developing a monitoring capability suitable for monitoring land change along with climate-related factors towards the long-term goal of assessing impacts on human society such as food security, water availability, emerging infectious diseases, economic security, human health, and others. A prototype capability, developed from the design of the Land Change Monitoring, Assessment, and Projection (LCMAP) initiative, utilizes all available imagery in the USGS global Landsat 30-meter archive with the Continuous Change Detection and Classification (CCDC) time-series modeling approach to produce annual land cover and change outputs. Landscape change results are input into assessment of urban heat island effects using the Landsat Land Surface Temperature record and monitor changes in Surface Urban Heat Island (SUHI) over a 35-year period. Development of this capability includes a cloud-based computing infrastructure to draw input data directly from the USGS global Landsat archive, adoption of regional equal-area coordinate systems, assessment of existing sources of land cover training data to be harmonized and/or sampled from, and strategies for navigating the extreme variability in existing Landsat data cover prior to the launch of Landsat-7 in 1999. This presentation discusses the challenges, solutions, and lessons learned of building and applying this new land monitoring capability in two regions outside the USA; the 90,000 km2 regions surrounding Wuhan, China and Brasilia, Brazil – both regions which have been subject to rapid urban development and anthropogenic impact in recent decades. Initial results from these regions for landscape change and impacts on changing urban heat island effects will be discussed.