cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.92pd3
title: Data from: Analytical and clinical validation of a digital sequencing panel for quantitative, highly accurate evaluation of cell-free circulating tumor DNA

description: Next-generation sequencing of cell-free circulating solid tumor DNA
 addresses two challenges in contemporary cancer care. First this method of
 massively parallel and deep sequencing enables assessment of a
 comprehensive panel of genomic targets from a single sample, and second,
 it obviates the need for repeat invasive tissue biopsies. Digital
 SequencingTM is a novel method for high-quality sequencing of circulating
 tumor DNA simultaneously across a comprehensive panel of over 50
 cancer-related genes with a simple blood test. Here we report the analytic
 and clinical validation of the gene panel. Analytic sensitivity down to
 0.1% mutant allele fraction is demonstrated via serial dilution studies of
 known samples. Near-perfect analytic specificity (&gt; 99.9999%)
 enables complete coverage of many genes without the false positives
 typically seen with traditional sequencing assays at mutant allele
 frequencies or fractions below 5%. We compared digital sequencing of
 plasma-derived cell-free DNA to tissue-based sequencing on 165 consecutive
 matched samples from five outside centers in patients with stage III-IV
 solid tumor cancers. Clinical sensitivity of plasma-derived NGS was 85.0%,
 comparable to 80.7% sensitivity for tissue. The assay success rate on
 1,000 consecutive samples in clinical practice was 99.8%. Digital
 sequencing of plasma-derived DNA is indicated in advanced cancer patients
 to prevent repeated invasive biopsies when the initial biopsy is
 inadequate, unobtainable for genomic testing, or uninformative, or when
 the patient’s cancer has progressed despite treatment. Its clinical
 utility is derived from reduction in the costs, complications and delays
 associated with invasive tissue biopsies for genomic testing.
description: patient_tableTable providing patient-level concordance information.Lanman_2015This file is a zipped folder containing the variants tables for each of the 165 matched tumor and liquid biopsy samples.
DOI: 10.5061/dryad.gv234
title: Data from: Dynamics of cough frequency in adults undergoing treatment for pulmonary tuberculosis

description: Background: Cough is the major determinant of tuberculosis transmission.
 Despite this, there is a paucity of information regarding characteristics
 of cough frequency throughout the day and in response to tuberculosis
 therapy. Here we evaluate the circadian cycle of cough; cough frequency
 risk factors; and the impact of appropriate treatment on cough and
 bacillary load. Methods: We prospectively evaluated HIV-negative adults
 (n=64) with a new diagnosis of culture-proven, drug-susceptible pulmonary
 tuberculosis immediately prior to treatment and repeatedly until treatment
 day 62. At each time-point, participant cough was recorded (n=670) and
 analyzed using the Cayetano Cough Monitor. Consecutive coughs at least
 2-seconds apart were counted as separate cough episodes. Sputum samples
 (n=426) were tested with microscopic-observation drug-susceptibility broth
 culture, and in culture-positive samples (n=252) the time to culture
 positivity was used to estimate bacillary load. Results: The highest cough
 frequency occurred from 1-2 p.m., and the lowest from 1-2 a.m. (2.4 versus
 1.1 cough episodes/hour, respectively). Cough frequency was higher among
 participants who had higher sputum bacillary load (p&lt;0.01).
 Pre-treatment median cough episodes/hour was 2.3 (IQR=1.2-4.1), which at
 14 treatment days decreased to 0.48 (IQR=0.0-1.4) and at the end of the
 study decreased to 0.18 (IQR=0.0-0.59), both reductions p&lt;0.001. By
 14 treatment days, the probability of culture conversion was 29% (95%
 CI=19-41%). Conclusions: Coughs were most frequent during daytime. Two
 weeks of appropriate treatment significantly reduced cough frequency and
 made one-third of participants achieve culture conversion. Thus treatment
 by two weeks considerably diminishes but not eliminates the potential for
 airborne tuberculosis transmission.
description: 24-hour cough
 recordingsAll cough recordings
 that were complete to within 23.5 hours were included here and displayed
 per participant's treatment day.24hour.csvDaily report of cough and sputum resultsDaily results per participant's treatment day are reported here for cough recordings and sputum samples.coughsperday.csvHourly report of cough recordingsHourly report of all cough recordings per participant's treatment day are shown here.coughsperhour.csvOverview of participantsData for HIV-negative participants with culture-proven drug-susceptible tuberculosis are reported here.participants.csv
DOI: 10.5061/dryad.kn3d0
title: Data from: Origin and in situ diversification in Hemidactylus geckos of the Socotra Archipelago

description: The Socotra Archipelago is an ancient continental fragment of Gondwanan
 origin and one of the most isolated landforms on Earth and a biodiversity
 hotspot. Yet the biogeography and evolutionary history of its endemic
 fauna still remain largely overlooked. We investigate the origin, tempo
 and mode of diversification in the Hemidactylus geckos of the Socotra
 Archipelago. Concatenated and multilocus species coalescent analyses of
 Hemidactylus from Arabia and North Africa indicate that the Hemidactylus
 from Socotra do not form a monophyletic group and branch as three
 independent and well-supported clades instead. Both the chronogram
 inferred using the gene tree approach of BEAST and the age-calibrated
 multilocus species tree obtained using *BEAST suggest that the origin of
 Hemidactylus from Socotra may have involved a first vicariance event, that
 occurred in the Early Miocene, followed by two independent transoceanic
 dispersal events that occurred more recently, during the Pliocene. Within
 Socotra, we analyzed patterns of genetic diversity, the phylogeography and
 the demographic history in all seven non-introduced species of
 Hemidactylus. Results based on two mitochondrial and two nuclear loci from
 144 individuals revealed complex patterns of within-island diversification
 and high levels of intra-species genetic divergence. The interplay of both
 historical and ecological factors seems to have a role in the speciation
 process of this group of geckos. Interestingly, the case of H. forbesii
 and H. oxyrhinus, which inhabit the island of Abd al Kuri with an area of
 133 km², may represent one of the most extreme cases of intra-island
 speciation in reptiles ever reported.
description: GenBank accession
 numbersGenBank accession
 numbers of Hemidactylus specimens analyzed in the
 study.GenBank_Gómez-Díaz_MEC-12-0197.xlsxhemi_arb-soc_12S_starbeast12_So-14spSequence alingment for the gene 12S used in the *BEAST analysishemi_arb-soc_cyb_starbeast12_So-14spSequence alingment for the gene cyb used in the *BEAST analysishemi_arb-soc_mc1r_starbeast12_So-14spSequence alingment for the gene mc1r used in the *BEAST analysishemi_arb-soc_ND4_starbeast12_So-14spSequence alingment for the gene ND4 used in the *BEAST analysishemi_soc_12S_all-hapSequence alignment of Hemidactylus specimens from Socotra based on unique haplotype sequences of mitochondrial ribosomal gene 12Shemi_soc_cyb_all-hapSequence alignment of Hemidactylus specimens from Socotra based on unique haplotype sequences of mitochondrial gene cybhemi_soc_mc1r_all-hapSequence alignment of Hemidactylus specimens from Socotra based on unique haplotype sequences of nuclear protein coding gene mc1rhemi_soc_ND4_all-hapSequence alignment of Hemidactylus specimens from Socotra based on unique haplotype sequences of mitochondrial gene ND4hemi_soc_prdx4_all-hapSequence alignment of Hemidactylus specimens from Socotra based on unique haplotype sequences of nuclear intron prdx4
DOI: 10.5061/dryad.qm636
title: Data from: Niphargus–Thiothrix associations may be widespread in sulphidic groundwater ecosystems: evidence from southeastern Romania

description: Niphargus is a speciose amphipod genus found in groundwater habitats
 across Europe. Three Niphargus species living in the sulphidic Frasassi
 caves in Italy harbour sulphur-oxidizing Thiothrix bacterial
 ectosymbionts. These three species are distantly related, implying that
 the ability to form ectosymbioses with Thiothrix may be common among
 Niphargus. Therefore, Niphargus–Thiothrix associations may also be found
 in sulphidic aquifers other than Frasassi. In this study, we examined this
 possibility by analysing niphargids of the genera Niphargus and
 Pontoniphargus collected from the partly sulphidic aquifers of the
 Southern Dobrogea region of Romania, which are accessible through springs,
 wells and Movile Cave. Molecular and morphological analyses revealed seven
 niphargid species in this region. Five of these species occurred
 occasionally or exclusively in sulphidic locations, whereas the remaining
 two were restricted to nonsulphidic areas. Thiothrix were detected by PCR
 on all seven Dobrogean niphargid species and observed using microscopy to
 be predominantly attached to their hosts' appendages. 16S rRNA gene
 sequences of the Thiothrix epibionts fell into two main clades, one of
 which (herein named T4) occurred solely on niphargids collected in
 sulphidic locations. The other Thiothrix clade was present on niphargids
 from both sulphidic and nonsulphidic areas and indistinguishable from the
 T3 ectosymbiont clade previously identified on Frasassi-dwelling
 Niphargus. Although niphargids from Frasassi and Southern Dobrogea are not
 closely related, the patterns of their association with Thiothrix are
 remarkably alike. The finding of similar Niphargus–Thiothrix associations
 in aquifers located 1200 km apart suggests that they may be widespread in
 European groundwater ecosystems.
description: Alignment of 28S rRNA
 gene sequencesThe 28S rRNA gene
 sequences of Romanian niphargids obtained in the course of this study were
 aligned with other niphargid 28S sequences present in GenBank. Some
 individuals had more than one sequence type, hence the suffixes a, b and c
 appended to their names. Sequences were aligned using MAFFT's E-INS-i
 option.28S.fasAlignment of ITS sequencesThe ITS sequences of Romanian niphargids obtained in the course of this study were aligned using MAFFT's E-INS-i option. Some individuals had more than one sequence type, hence the suffixes a, b and c appended to their names.ITS.fasAlignment of COI sequencesThe COI sequences of Romanian niphargids obtained in the course of this study were aligned by hand.COI.fasAlignment of Thiothrix 16S rRNA gene sequencesThe Thiothrix 16S rRNA gene sequences isolated from Romanian niphargids in the course of this study were aligned with Thiothrix sequences present in GenBank using MAFFT's Q-INS-i option.16S.fas
DOI: 10.5061/dryad.1c88s
title: Data from: Hybridization occurs between Drosophila simulans and D. sechellia in the Seychelles archipelago

description: Drosophila simulans and D. sechellia are sister species that serve as a
 model to study the evolution of reproductive isolation. While D. simulans
 is a human commensal that has spread all over the world, D. sechellia is
 restricted to the Seychelles archipelago and is found to breed exclusively
 on the toxic fruit of Morinda citrifolia. We surveyed the relative
 frequency of males from these two species in a variety of substrates found
 on five islands of the Seychelles archipelago. We sampled different fruits
 and found that putative D. simulans can be found in a variety of
 substrates, including, surprisingly, M. citrifolia. Putative D. sechellia
 was found preferentially on M. citrifolia fruits, but a small proportion
 was found in other substrates. Our survey also shows the existence of
 putative hybrid males in areas where D. simulans is present in Seychelles.
 The results from this field survey support the hypothesis of current
 interbreeding between these species in the central islands of Seychelles
 and open the possibility for fine measurements of admixture between these
 two Drosophila species to be made.
description: Raw data and analytical
 codeThese files contain all
 the raw data for "Hybridization occurs between Drosophila simulans
 and D. sechellia in the Seychelles archipelago" by D. R. Matute and
 J. F. Ayroles. All datasets are in .csv format. The code and statistical
 results are also included in a single R file.sim_sech_hybrids_data.zip
DOI: 10.5061/dryad.hq4v0
title: Data from: Whole-body endothermy in a mesopelagic fish, the opah, Lampris guttatus

description: Endothermy (the metabolic production and retention of heat to warm body
 temperature above ambient) enhances physiological function, and whole-body
 endothermy generally sets mammals and birds apart from other animals.
 Here, we describe a whole-body form of endothermy in a fish, the opah
 (Lampris guttatus), that produces heat through the constant “flapping” of
 wing-like pectoral fins and minimizes heat loss through a series of
 counter-current heat exchangers within its gills. Unlike other fish, opah
 distribute warmed blood throughout the body, including to the heart,
 enhancing physiological performance and buffering internal organ function
 while foraging in the cold, nutrient-rich waters below the ocean
 thermocline.
description: Opah in situ
 temperatures (Table 1)Wegner et al in situ
 temperatures (Table 1).xlsxOpah in vivo
 temperatures (Table 1)Wegner et al in vivo
 temperatures (Table 1).xlsxOpah dive profile and
 temp measurements (Fig. 1)Wegner et al opah in vivo temp
 measurements (Fig. 1).xlsxOpah depth distribution
 (Fig. 3)Wegner et al opah depth
 distribution (Fig. 3).xlsxOpah fat thickness
 dataWegner
 et al opah fat thickness.xlsxOpah mass-length
 relationship data (Fig. S2)Wegner et al mass-length
 relationship (Fig. S2).xlsxOpah and
 king-of-the-salmon hematocrit data (Table S1)Wegner et al hematocrits (Table
 S1).xlsxOpah and
 king-of-the-salmon ventricular mass (Table S1)Wegner et al ventricle data
 (Table S1).xlsx
DOI: 10.5061/dryad.1bv6n
title: Data from: Towards a common methodology for developing logistic tree mortality models based on ring-width data

description: Tree mortality is a key process shaping forest dynamics. Thus, there is a
 growing need for indicators of the likelihood of tree death. During the
 last decades, an increasing number of tree-ring based studies have aimed
 to derive growth–mortality functions, mostly using logistic models. The
 results of these studies, however, are difficult to compare and synthesize
 due to the diversity of approaches used for the sampling strategy (number
 and characteristics of alive and death observations), the type of
 explanatory growth variables included (level, trend, etc.), and the length
 of the time window (number of years preceding the alive/death observation)
 that maximized the discrimination ability of each growth variable. We
 assess the implications of key methodological decisions when developing
 tree-ring based growth–mortality relationships using logistic
 mixed-effects regression models. As examples, we use published tree-ring
 datasets from Abies alba (13 different sites), Nothofagus dombeyi (one
 site), and Quercus petraea (one site). Our approach is based on a constant
 sampling size and aims at (1) assessing the dependency of growth–mortality
 relationships on the statistical sampling scheme used, (2) determining the
 type of explanatory growth variables that should be considered, and (3)
 identifying the best length of the time window used to calculate them. The
 performance of tree-ring-based mortality models was reasonably high for
 all three species (area under the receiving operator characteristics
 curve, AUC &gt; 0.7). Growth level variables were the most important
 predictors of mortality probability for two species (A. alba, N. dombeyi),
 while growth-trend variables need to be considered for Q. petraea. In
 addition, the length of the time window used to calculate each growth
 variable was highly uncertain and depended on the sampling scheme, as some
 growth–mortality relationships varied with tree age. The present study
 accounts for the main sampling-related biases to determine reliable
 species-specific growth–mortality relationships. Our results highlight the
 importance of using a sampling strategy that is consistent with the
 research question. Moving towards a common methodology for developing
 reliable growth–mortality relationships is an important step towards
 improving our understanding of tree mortality across species and its
 representation in dynamic vegetation models.
description: Ring-width
 dataYearly ring-width data
 (mm) for every studied treeRWdata.txtMetadataCharacteristics of every studied tree: code, site, species, reference article, contact person, status, age, dbh.Treedata.txt
DOI: 10.5061/dryad.qt745
title: Data from: Multivariate selection and intersexual genetic constraints in a wild bird population

description: When traits are genetically correlated between the sexes, the response to
 selection in one sex can be altered by indirect selection in the other
 sex, a type of genetic constraint commonly referred to as intralocus
 sexual conflict (ISC). While potentially common, ISC has rarely been
 studied in wild populations. In this study, we applied a multivariate
 framework to quantify the microevolutionary impacts of ISC over a set of
 morphological traits (wing length, tarsus length, bill depth, and bill
 length) in a wild population of great tits (Parus major) from Wytham
 Woods, UK. Specifically, we quantified the impact of cross-sex genetic
 covariances (the B matrix) on the additive genetic variance for relative
 fitness expected to be generated by directional selection and additive
 genetic (co)variance. Together, multivariate sex-specific selection and
 additive genetic (co)variance were expected to generate additive genetic
 variance for relative fitness that was uncorrelated between the sexes
 (cross-sex genetic correlation = -0.003, 95% CI = -0.83, 0.83). Gender
 load, defined as the expected reduction in additive genetic variance for
 relative fitness generated by the traits under study due to sex-specific
 effects, was estimated at 50% (95% CI = 13%, 86%). This study provides
 novel insights into the evolution of sexual dimorphism in great tits and
 illustrates how quantitative genetics and selection analyses can be
 combined in a multivariate framework to quantify the expected
 microevolutionary impacts of ISC.
description: pedigree
 filePedigree file for
 quantitative genetic analyses. Contains 3 columns: ID, Sire and
 Dam.poissant_animal_model_pedigree.pedPhenotypic and environmental data for quantitative genetic analysesPhenotypic and environmental data for quantitative genetic analyses. See readme file for description of columns.poissant_animal_model_phenotypic_data.asdPhenotypic and fitness data for selection analysesPhenotypic and fitness data for selection analyses. columns are: ID: Animal ID, sex: sex of individual, wing: wing length, tars: tarsus length, bd: bill depth, bl: bill length, LRS: Lifetime reproductive success, longevity: Longevity, MRS: Mean annual reproductive success. See article for details.selection_analysis_data.csv
DOI: 10.5061/dryad.130vb65
title: Data from: Temporal dynamics of the genetic clines of invasive European green crab (Carcinus maenas) in eastern North America

description: Two genetically distinct lineages of European green crabs (Carcinus
 maenas) were independently introduced to eastern North America, the first
 in the early 19th century and the second in the late 20th century. These
 lineages first came into secondary contact in southeastern Nova Scotia,
 Canada (NS), where they hybridized, producing latitudinal genetic clines.
 Previous studies have documented a persistent southward shift in the
 clines of different marker types, consistent with existing dispersal and
 recruitment pathways. We evaluated current clinal structure by quantifying
 the distribution of lineages and fine-scale hybridization patterns across
 the eastern North American range (25 locations, ~39-49°N) using
 informative single nucleotide polymorphisms (SNPs; n=96). In addition,
 temporal changes in the genetic clines were evaluated using mitochondrial
 DNA and microsatellite loci (n=9-11) over a 15-year period (2000-2015).
 Clinal structure was consistent with prior work demonstrating the
 existence of both northern and southern lineages with a hybrid zone
 occurring between southern New Brunswick (NB) and southern NS. Extensive
 later generation hybrids were detected in this region and in southeastern
 Newfoundland. Temporal genetic analysis confirmed the southward
 progression of clines over time; however, the rate of this progression was
 slower than predicted by forecasting models, and current clines for all
 marker types deviated significantly from these predictions. Our results
 suggest that neutral and selective processes contribute to cline dynamics,
 and ultimately, highlight how selection, hybridization, and dispersal can
 collectively influence invasion success.
description: Genepop file 96
 SNPGenepop file of all
 green crab samples genotyped at 96 informative single nucleotide
 polymorphisms (SNPs). Includes all individuals collected between 2011 and
 2015 from eastern North America. Samples are combined by location
 (population).crab2015-2011-all-genepop96.txtMicrosatellite genotypes for green crabs in 2011Genepop file of microsatellite data (11 loci) for green crabs collected in 2011.Genepop_2011_micro_crabs.txt
DOI: 10.5061/dryad.qp1nd
title: Data from: Species diversity can be overestimated by a fixed empirical threshold: insights from DNA barcoding of the genus Cletus (Hemiptera: Coreidae) and the meta-analysis of COI data from previous phylogeographical studies

description: The use of genetic distances to identify species within the framework of
 DNA barcoding has to some extent improved the development of biodiversity
 studies. However, using a fixed empirical threshold to delimit species may
 lead to overestimating species diversity. In this study, we use a new data
 set of COI sequences for 366 specimens within the genus of Cletus as well
 as conduct an analysis on the same genetic data for collected
 morphologically defined species from previous phylogeographical studies,
 to test whether high intraspecific genetic divergences are common with the
 premises of comprehensive sampling. The results indicate C. graminis Hsiao
 & Cheng 1964, is the same species with C. punctiger (Dallas, 1852)
 and should be synonymized and that the distributional record of C.
 pugnator (Fabricius, 1787) in China is correct. High intraspecific genetic
 differentiations (0%–4.35%) were found in C. punctiger. Furthermore, as to
 the mined data, the maximum intraspecific K2P distances of 186 species
 (48.44% of 384) exceed 3%, and 101 species (26.30%) can be divided into
 two or more clusters with a threshold of 3% in cluster analysis. If
 genetic distance is used to delimit species boundaries, the minimum
 interspecific K2P distance of the congeneric species should be considered
 rather than only using the fixed empirical value; otherwise, the species
 richness may be overestimated in some cases.
description: COI data from previous
 phylogeographical studiesData
 matricesCletuso.nexResulting trees