cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h52h5t7
title: Data from: A phase 3 randomized study evaluating sialic acid extended-release for GNE myopathy

description: Objective: To investigate the efficacy and safety of aceneuramic acid
 extended-release (Ace-ER), a treatment intended to replace deficient
 sialic acid, in patients with GNE myopathy. Methods: UX001-CL301 was a
 Phase 3, double-blind, placebo-controlled, randomized, international study
 evaluating the efficacy and safety of Ace-ER in patients with GNE
 Myopathy. Participants who could walk ≥200 meters in a 6-minute walk test
 at screening were randomized 1:1, and stratified by sex, to receive Ace-ER
 6g/day or placebo for 48 weeks and assessed every 8 weeks. The primary
 endpoint was change in muscle strength over 48 weeks measured by Upper
 Extremity Composite (UEC) score. Key secondary endpoints included change
 in Lower Extremity Composite (LEC) score, knee extensor strength, and GNE
 myopathy-Functional Activity Scale (GNEM-FAS) mobility domain score.
 Safety assessments included adverse events (AEs), vital signs, and
 clinical laboratory results. Results: Eighty-nine patients were randomized
 (Ace-ER n = 45; Placebo n = 44). Change from baseline to week 48 for UEC
 score between treatments did not differ (least square mean [LSM] Ace-ER
 -2.25 kg vs Placebo -2.99 kg; LSM difference (confidence interval [CI])
 0.74 (-1.61, 3.09); p = 0.5387). At week 48, there was no significant
 difference between treatments for the change in key secondary endpoints:
 LEC LSM difference (CI) -1.49 (-5.83, 2.86); knee extension strength -0.40
 (-2.38, 1.58); and GNEM-FAS mobility domain score -0.72 (-2.01, 0.57).
 Gastrointestinal events were the most common AEs. Conclusions: Ace-ER was
 not superior to placebo in improving muscle strength and function in
 patients with GNE myopathy.
description: Lochmuller et al UX001
 CL301 MS supp materials protocol 13Dec2018Supplemental Material
 for Lochmuller et al Neurology: Table e-1. Change from Baseline to Week 48
 in UEC and LEC Individual Muscle Groups with Hand-Held Dynamometry; Figure
 e-1. UX001-CL301 CONSORT Flow Diagram; UX001-CL301
 Protocol
DOI: 10.5061/dryad.5sg5082
title: Data from: Population genomic analyses reveal a highly differentiated and endangered genetic cluster of northern goshawks (Accipiter gentilis laingi) in Haida Gwaii

description: Accurate knowledge of geographic ranges and genetic relationships among
 populations is important when managing a species or population of
 conservation concern. Along the western coast of Canada, a subspecies of
 the northern goshawk (Accipiter gentilis laingi) is legally designated as
 Threatened. The range and distinctness of this form, in comparison to the
 broadly distributed North American subspecies (Accipiter gentilis
 atricapillus), is unclear. Given this morphological uncertainty, we
 analyzed genomic relationships in thousands of single nucleotide
 polymorphisms identified using genotyping-by-sequencing of high-quality
 genetic samples. Results revealed a genetically distinct population of
 northern goshawks on the archipelago of Haida Gwaii and subtle structuring
 among other North American sampling regions. We then developed genotyping
 assays for ten loci that are highly differentiated between the two main
 genetic clusters, allowing inclusion of hundreds of low-quality samples
 and confirming that the distinct genetic cluster is restricted to Haida
 Gwaii. As the laingi form was originally described as being based in Haida
 Gwaii (where the type specimen is from), further morphological analysis
 may result in this name being restricted to the Haida Gwaii genetic
 cluster. Regardless of taxonomic treatment, the distinct Haida Gwaii
 genetic cluster along with the small and declining population size of the
 Haida Gwaii population suggests a high risk of extinction of an
 ecologically and genetically distinct form of northern goshawk. Outside of
 Haida Gwaii, sampling regions along the coast of BC and southeast Alaska
 (often considered regions inhabited by laingi) show some subtle
 differentiation from other North American regions. These results will
 increase the effectiveness of conservation management of northern goshawks
 in northwestern North America. More broadly, other conservation-related
 studies of genetic variation may benefit from the two-step approach we
 employed that first surveys genomic variation using high-quality samples
 and then genotypes low-quality samples at particularly informative loci.
description: NOGO_SNP_GenotypingThis "Nogo_SNP_Genotyping.zip" file contains the raw data from the genotyping of 10 ancestry informative SNPs from Geraldes et al. 2018. Within, there are twenty files. Each contains the results from one run on a Viia7 Real-Time PCR system. For each SNP two plates were genotyped. The SNP genotyping results reported in Supporting Table 6 and visualized in Supporting Figure 2 of Geraldes et al. 2018, were obtained by plotting columns "Allele 1 Delta Rn" and "Allele 2 Delta Rn" from the two files for each SNP. The column "Sample Name" in these files corresponds to the column "Irwin Code" in Supporting Table 1 of Geraldes et al. 2018.
DOI: 10.5061/dryad.8d44d4q
title: Data from: Lack of signal for the impact of conotoxin gene diversity on speciation rates in cone snails

description: Understanding why some groups of organisms are more diverse than others is
 a central goal in macroevolution. Evolvability, or the intrinsic capacity
 of lineages for evolutionary change, is thought to influence disparities
 in species diversity across taxa. Over macroevolutionary time scales,
 clades that exhibit high evolvability are expected to have higher
 speciation rates. Cone snails (family: Conidae, &gt;900 spp.) provide
 a unique opportunity to test this prediction because their toxin genes can
 be used to characterize differences in evolvability between clades. Cone
 snails are carnivorous, use prey-specific venom (conotoxins) to capture
 prey, and the genes that encode venom are known and diversify through gene
 duplication. Theory predicts that higher gene diversity confers a greater
 potential to generate novel phenotypes for specialization and adaptation.
 Therefore, if conotoxin gene diversity gives rise to varying levels of
 evolvability, conotoxin gene diversity should be coupled with
 macroevolutionary speciation rates. We applied exon capture techniques to
 recover phylogenetic markers and conotoxin loci across 314 species, the
 largest venom discovery effort in a single study. We paired a
 reconstructed timetree using 12 fossil calibrations with species-specific
 estimates of conotoxin gene diversity and used trait-dependent
 diversification methods to test the impact of evolvability on
 diversification patterns. Surprisingly, we did not detect any signal for
 the relationship between conotoxin gene diversity and speciation rates,
 suggesting that venom evolution may not be the rate-limiting factor
 controlling diversification dynamics in Conidae. Comparative analyses
 showed some signal for the impact of diet and larval dispersal strategy on
 diversification patterns, though detection of a signal depended on the
 dataset and the method. If our results remain true with increased
 taxonomic sampling in future studies, they suggest that the rapid
 evolution of conid venom may cause other factors to become more critical
 to diversification, such as ecological opportunity or traits that promote
 isolation among lineages.
description: PhuongSupplementaryFilesAll supplementary figures, tables, and supplementary doc on fossil calibration.
DOI: 10.25574/32108
title: Chandra X-ray Observatory ObsId 32108

description: AO-27 Big Dither Observation of Mkn421
DOI: 10.5061/dryad.jg1bn4s
title: Data from: Incorporating existing thermal tolerance into projections of compositional turnover under climate change

description: Aim: Observed, realized niche space often underestimates species’
 physiological tolerances due to interactions with other species, dispersal
 constraints, and because some combinations of influential environmental
 factors do not currently exist in the real world. Conversely, correlative
 ecological niche models rely on the assumption that the range of
 environmental conditions encompassed by a species’ geographic distribution
 accurately reflects their environmental tolerances, including
 community-level approaches like Generalised Dissimilarity Modelling (GDM).
 We extend GDM to better understand what effect broader environmental
 tolerances could have on compositional turnover under climate change.
 Innovation: We show how GDM can be adjusted as a function of
 best-available estimates of the average ratio between realized and
 potential niche widths to modify projected temporal turnover. We
 demonstrate this approach by using the estimated niche ratios of
 Australian plant species (n=7184) relative to thermal extremes, and the
 rate at which this ratio varied with temperature. The modified GDMs showed
 existing thermal tolerance could reduce the turnover predicted by standard
 models under climate change by up to 11%. We further show how the
 reduction in expected turnover by 2090 will influence where a greater
 proportion of the current community will persist in a region. Main
 conclusions: We suggest that standard spatial GDMs and their modified
 versions represent the extremes of ecological niche perspectives (i.e.
 realized and potential) and the range of tolerance communities may have
 when responding to environmental change. GDM projections therefore
 identify the range of uncertainty associated with a critical model
 assumption, and as climate change continues, ongoing community monitoring
 could be used to validate the balance between the two possibilities.
description: Supplementary_filesS1 provides R code to demonstrate how the i-splines fitted in a Generalized Dissimilarity Model can be used to estimate relative niche width, and thus subsequently be modified to account for evidence of broader potential tolerances than suggested by species' realized distributions. S2 provides R code and supporting data to implement a case study applying the potential-GDM concept to Australian plants.
DOI: 10.5061/dryad.c6t0470
title: Data from: Landscape genetic analyses of Cervus elaphus and Sus scrofa: comparative study and analytical developments

description: Red deer and wild boar are two major game species whose populations are
 managed and live in areas impacted by human activities. Measuring and
 understanding the impact of landscape features on individual movements and
 spatial patterns of genetic variability in these species is thus of
 importance for managers. A large number of individuals sampled across
 Wallonia (Belgium) for both species have been genotyped using
 microsatellite markers (respectively &gt;1700 and &gt;1200
 genotyped individuals) and some individuals have also been followed using
 a capture-mark-recapture (CMR) protocol. The combined data set represents
 an unprecedented opportunity to study and compare the environmental
 factors impacting the interconnectivity of these large mammals. The
 present study describes and uses a landscape genetic workflow to compare
 spatial patterns of genetic variability and the impact of environmental
 factors on genetic differentiation. For the latter analyses, we
 investigate the correlation between genetic and environmental distances
 (pairwise approach) and also between local genetic dissimilarity and
 environmental conditions (point approach). Preliminary analyses of CMR
 data confirm that motorways act as significant barriers to dispersal.
 However, analyses performed with the pairwise approach do not highlight
 any evidence of an impact of motorways on genetic differentiation, which
 is presumably due to their recent establishment. Complementary analyses
 performed with the point approach reveal that low altitude tends to be
 associated with higher genetic dissimilarity. From a methodological point
 of view, the present workflow illustrates the complementary application of
 both pairwise and point approaches as well as univariate and multivariate
 analyses.
description: Example files Appendix
 S1Example_files_Appendix_S1.zipCervus elaphus - CMR dataCervus_elaphus_CMR_data.txtSus scrofa - CMR dataSus_scrofa_CMR_data.txtCervus elaphus - microsatellites matrixCervus_elaphus_microsatellites.txtSus scrofa - microsatellites matrixSus_scrofa_microsatellites.txt
DOI: 10.5281/zenodo.18239131
title: US_CDC_ILI(influenze-like illness)
DOI: 10.5061/dryad.rc47tt4
title: Data from: Transcriptome-wide mining, characterization, and development of microsatellite markers in Lychnis kiusiana (Caryophyllaceae)

description: Background: Lychnis kiusiana Makino is an endangered perennial herb native
 to wetland areas in Korea and Japan. Despite its conservational and
 evolutionary significance, population genetic resources are lacking for
 this species. Next-generation sequencing has been accepted as a rapid and
 cost-effective solution for the identification of microsatellite markers
 in nonmodel plants. Results: Using Illumina HiSeq 2000 sequencing
 technology, we assembled 67,498,600 reads into 91,900 contigs and
 identified 11,403 microsatellite repeat motifs in 9,563 contigs. A total
 of 4,510 microsatellite-containing transcripts had Gene Ontology (GO)
 annotations, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis
 identified 124 pathways with significant scores. Many microsatellites in
 the L. kiusiana leaf transcriptome were linked to genes involved in the
 plant response to light intensity, salt stress, temperature stimulus, and
 nutrient and water deprivation. A total of 12,486 single-nucleotide
 polymorphisms (SNPs) were identified on transcripts harboring
 microsatellites. The analysis of nucleotide substitution rates for 2,389
 unigenes indicated that 39 genes were under strong positive selection. The
 primers of 6,911 microsatellites were designed, and 40 of 50 selected
 primer pairs were consistently and successfully amplified from 51
 individuals. Twenty-five of these were polymorphic, and the average number
 of alleles per SSR locus was 6.96, with a range from 2 to 15. The observed
 and expected heterozygosities ranged from 0.137 to 0.902 and 0.131 to
 0.827, respectively, and locus-specific FIS estimates ranged from -0.116
 to 0.290. Eleven of the 25 primer pairs were successfully amplified in
 three additional species of Lychnis: 56% in L. wilfordii, 64% in L.
 cognata and 80% in L. fulgens. Conclusions: The transcriptomic SSR markers
 of Lychnis kiusiana provide a valuable resource for understanding the
 population genetics, evolutionary history, and effective conservation
 management of this species. Furthermore, the identified microsatellite
 loci linked to the annotated genes should be useful for developing
 functional markers of L. kiusiana. The developed markers represent a
 potentially valuable source of transcriptomic SSR markers for population
 genetic analyses with moderate levels of cross-taxon portability.
description: Lychnis_ssrReadsThis files is the assembled contigs generated and analyzed during the current study
DOI: 10.5061/dryad.ns790j4
title: Data from: Thermal selection as a driver of marine ecological speciation

description: Intraspecific genetic structure in widely distributed marine species often
 mirrors the boundaries between temperature-defined bioregions. This
 suggests that the same thermal gradients that maintain distinct species
 assemblages also drive the evolution of new biodiversity. Ecological
 speciation scenarios are often invoked to explain such patterns, but the
 fact that adaptation is usually only identified when phylogenetic splits
 are already evident makes it impossible to rule out the alternative
 scenario of allopatric speciation with subsequent adaptation. We
 integrated large-scale genomic and environmental datasets along one of the
 world’s best defined marine thermal gradients (the South African
 coastline) to test the hypothesis that incipient ecological speciation is
 a result of divergence linked to the thermal environment. We identified
 temperature-associated gene regions in a coastal fish species that is
 spatially homogeneous throughout several temperature-defined
 biogeographical regions based on selectively neutral markers. Based on
 these gene regions, the species is divided into geographically distinct
 regional populations. Importantly, the ranges of these populations are
 delimited by the same ecological boundaries that define distinct
 infraspecific genetic lineages in co-distributed marine the species, and
 biogeographical disjunctions in species assemblages. Our results indicate
 that temperature-mediated selection represents an early stage of marine
 ecological speciation in coastal regions that lack physical dispersal
 barriers.
description: Teske_NeutralLociSelectively neutral SNPsTeske_gINLAnd_MinTempSNPs under thermal selection (minimum temperature data)Teske_gINLAnd_MaxTempSNPs under thermal selection (maximum temperature data)
DOI: 10.5061/dryad.p042h0c
title: Data from: Heterogeneous matrix habitat drives species occurrences in complex, fragmented landscapes

description: A fundamental tenet of modern ecology and conservation science is that
 species occurrence in habitat patches can be determined by patch area and
 isolation. But such island biogeographic models often poorly predict
 actual species occurrences in structurally complex landscapes that typify
 most ecosystems. Recent advances in circuit theory have enhanced estimates
 of species dispersal, and through integration with island biogeography,
 can provide powerful ways to predict landscape-scale distribution of
 species assemblages. Applying such an integrative analytical framework to
 43 bird species in Tanzania improved model fit by an average of 2.2-fold
 over models where patch isolation was estimated without accounting for
 landscape matrix heterogeneity. This approach also allowed us to assess
 species-specific dispersal rates and quantify differences among land cover
 types in their permeability to animal movement. These results reaffirm the
 utility of foundational island biogeographic principles, yet with an
 important caveat. Two-thirds of the variance in species occurrence in
 habitat fragments can be explained simply by patch area and isolation,
 conditional on isolation explicitly accounting for the spatial
 configuration of different land cover types in the landscape matrix.
description: 0_usambara1_sites2_isolation_occurrenceNodes_ENodes_WSitesspp_occurraster_east3raster_west3
DOI: 10.15468/dl.ygna9m
title: Occurrence Download

description: A dataset containing 432967 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-899.0",
 "Geometry POLYGON((-11.68833 35.65987,14.11904 35.65987,14.11904 51.3301,-11.68833 51.3301,-11.68833 35.65987))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Stylommatophora"
 ]
}

 The dataset includes 432967 records from 493 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001535-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.b2r160s
title: Data from: Variation in juvenile Chinook salmon (Oncorhynchus tshawytscha) transcription among and within eight population crosses from British Columbia, Canada

description: Phenotypic differences among populations within a species have been
 reported for a variety of traits, ranging from life history to physiology
 to gene transcription. Population-level phenotypic variation has been
 attributed to genetic differences resulting from genetic drift and/or
 local adaptation as well as environmental differences resulting from
 plasticity. We studied population- and family-level variation in gene
 transcription for 22 fitness-related genes, comprising immune, growth,
 metabolic, and stress processes in Chinook salmon (Oncorhynchus
 tshawytscha). We created hybrid Chinook salmon families from eight
 populations and treated them with an immune stimulus, a handling stress
 challenge, and held some as a no-treatment control group. Population
 effects, sire effects, and narrow-sense heritability (h2) were calculated
 for each candidate gene within each treatment group. We expected
 population to have a significant effect on gene transcription for many of
 our genes; however, we found a population effect for transcription at only
 one immune gene at rest. The limited number of significant population
 effects on gene transcription, combined with significant additive genetic
 variance within each population does not support the expectation of past
 strong selection pressures acting on heritable transcription profiles
 among populations. Instead, our results indicate that Chinook salmon
 likely adapt to their local environment through transcriptional plasticity
 rather than fixed differences. The expectation for fixed population-level
 differences in gene transcription at fitness-related genes, reflecting
 accepted models of local adaptation is high; however, comparisons among
 multiple populations using half-sib breeding designs are rare. Our work
 fills an important gap in our growing understanding of the process of
 among and within-population divergence.
description: READMEThis document defines
 all abbreviations within the other data files.Raw_qPCR_DataRaw qPCR data from a QuantStudio 12K Flex for all samples and candidate genes.Toews_2018_Raw_qPCR_Data_Chinook_Transcription.txtPCR_EfficienciesThis file contains the PCR efficiencies of all candidate genes used in the study. The efficiencies were calculated using LinRegPCR.Toews_2018_PCR_Efficiencies_Chinook_Transcription.txtProcessed_qPCR_DataThis file contains the information needed to normalize the Cq values from the raw data, as well as the final DCt values that were used in the manuscript.Toews_2018_Processed_qPCR_Data_Chinook_Transcription.txtSample_AnnotationThis file contains information for each sample in the study, including the individual sample's rearing tank, sire, population, weight, treatment group, etc.Toews_2018_Sample_Annotation_Chinook_Transcription.txtR_Source_CodeThis text file contains the R source code used for the analyses in the paper.Toews_2018_R_Source_Code_Chinook_Transcription.txt