cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0k6djh9x4
title: Application of simultaneous selective pressures slows adaptation

description: Background and objectives: Beneficial mutations that arise in an evolving
 asexual population may compete or interact in ways that alter the overall
 rate of adaptation through mechanisms such as clonal or functional
 interference. The application of multiple selective pressures
 simultaneously may allow for a greater number of adaptive mutations,
 increasing the opportunities for competition between selectively
 advantageous alterations, and thereby reducing the rate of adaptation.
 Methodology: We evolved a strain of Saccharomyces cerevisiae that could
 not produce its own histidine or uracil for ~500 generations under one or
 three selective pressures: limitation of the concentration of glucose,
 histidine, and/or uracil in the media. The rate of adaptation was obtained
 by measuring evolved relative fitness using competition assays. Results:
 Populations evolved under a single selective pressure showed a
 statistically significant increase in fitness on those pressures relative
 to the ancestral strain, but the populations evolved on all three
 pressures did not show a statistically significant increase in fitness
 over the ancestral strain on any single pressure. Simultaneously limiting
 three essential nutrients for a population of S. cerevisiae effectively
 slows the rate of evolution on any one of the three selective pressures
 applied, relative to the single selective pressure cases. We identify
 possible mechanisms for fitness changes seen between populations evolved
 on one or three limiting nutrient pressures by high-throughput sequencing.
 Conclusions and implications: Adding multiple selective pressures to
 evolving disease like cancer and infectious diseases could reduce the rate
 of adaptation and thereby may slow disease progression, prolong drug
 efficacy and prevent deaths.
DOI: 10.5061/dryad.tmpg4f4w6
title: Clinical and genomic evaluation of 207 genetic myopathies in the Indian subcontinent

description: Objective Inherited myopathies comprise more than 200 different
 individually rare disease-subtypes but when combined together have a high
 prevalence of 1 in 6000 individuals across the world. Our goal was to
 determine for the first time the clinical- and gene-variant spectrum of
 genetic myopathies in a substantial cohort study of the Indian
 subcontinent. Methods In this cohort-study, we performed the first large
 clinical exome sequencing (ES) study with phenotype correlation on 207
 clinically well-characterized inherited myopathy-suspected patients from
 the Indian subcontinent with diverse ethnicities. Results
 Clinical-correlation driven definitive molecular diagnosis was established
 in 49% (101 cases; 95% CI, 42%-56%) of patients with the major
 contributing pathogenicity in either of three genes, GNE (28%;
 GNE-myopathy), DYSF (25%; Dysferlinopathy) and CAPN3 (19%; Calpainopathy).
 We identified 65 variant alleles comprising 37 unique variants in these
 three major genes. 78% of the DYSF patients were homozygous for the
 detected pathogenic variant suggesting the need for carrier-testing for
 autosomal-recessive disorders like Dysferlinopathy that are common in
 India. We describe the observed clinical spectrum of myopathies including
 uncommon and rare subtypes in India: Sarcoglycanopathies (SGCA/B/D/G),
 Collagenopathy (COL6A1/2/3), Anoctaminopathy (ANO5), telethoninopathy
 (TCAP), Pompe-disease (GAA), Myoadenylate-deaminase-deficiency-myopathy
 (AMPD1), myotilinopathy (MYOT), laminopathy (LMNA), HSP40-proteinopathy
 (DNAJB6), Emery-Dreifuss-muscular-dystrophy (EMD), Filaminopathy (FLNC),
 TRIM32-proteinopathy (TRIM32), POMT1-proteinopathy (POMT1), and
 Merosin-deficiency-congenital-muscular-dystrophy-type-1 (LAMA2). 13
 Patients harbored pathogenic variants in &gt;1 gene and had unusual
 clinical features suggesting a possible role of synergistic-heterozygosity
 / digenic-contribution to disease presentation and progression.
 Conclusions Application of clinically-correlated ES to myopathy diagnosis
 has improved our understanding of the clinical and genetic spectrum of
 different subtypes and their overlaps in Indian patients. This, in turn,
 will enhance the global gene-variant-disease databases by including data
 from developing countries/continents for more efficient clinically-driven
 molecular diagnostics.
description: In this cohort-study, we performed the first large clinical exome
 sequencing (ES) study with phenotype correlation on 207 clinically
 well-characterized inherited myopathy-suspected patients from the Indian
 subcontinent with diverse ethnicities.
DOI: 10.15468/dl.bge38g
title: Occurrence Download

description: A dataset containing 502328 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "GadmGid is MEX.28_1"
 ]
}

 The dataset includes 502328 records from 772 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002347-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8cz8w9gm9
title: Data from: Assessment of tumor treatment response using active contrast encoding (ACE)-MRI: comparison with conventional DCE-MRI

description: Purpose: To investigate the validity of contrast kinetic parameter
 estimates from Active Contrast Encoding (ACE)-MRI against those from
 conventional Dynamic Contrast-Enhanced (DCE)-MRI for evaluation of tumor
 treatment response in mouse tumor models. Methods: The ACE-MRI method that
 incorporates measurement of T1 and B1 into the enhancement curve washout
 region, was implemented on a 7T  MRI scanner to measure tracer
 kinetic model  parameters of 4T1 and GL261 tumors with treatment
 using bevacizumab and 5FU. A portion of the same ACE-MRI data was used for
 conventional DCE-MRI data analysis with a separately measured pre-contrast
 T1 map. Tracer kinetic model  parameters, such as Ktrans
 (permeability area surface product) and ve (extracellular space volume
 fraction), estimated from ACE-MRI were compared with those from DCE-MRI,
 in terms of  correlation and Bland-Altman analyses. 
 Results: A three-fold increase of the median Ktrans by treatment was
 observed in the flank 4T1 tumors by both ACE-MRI and DCE-MRI. In contrast,
 the brain tumors did not show a significant change by the treatment in
 either ACE-MRI or DCE-MRI. Ktrans and ve values  of the tumors
 from ACE-MRI were strongly correlated with those from DCE-MRI methods with
 correlation coefficients of 0.92 and 0.78, respectively, for the median
 values of 17 tumors. The Bland-Altman plot analysis showed a mean
 difference of -0.01 /min for Ktrans with the 95% limits of
 agreement of -0.12 /min to 0.09 /min, and -0.05 with -0.37 to
 0.26 for ve. Conclusion: The  tracer kinetic model parameters
 estimated from ACE-MRI and their changes by treatment closely matched
 those of DCE-MRI, which suggests that ACE-MRI can be used in place of
 conventional DCE-MRI for tumor progression monitoring and treatment
 response evaluation with a reduced scan time.
DOI: 10.5061/dryad.vq83bk3pz
title: Data from: Paleolimnological assessment of wildfire-derived atmospheric deposition of trace metal(loid)s and major ions to subarctic lakes (Northwest Territories, Canada)

description: Wildfires release terrestrial elements to the atmosphere as aerosols, and
 these events are becoming more frequent and intense in the Arctic boreal
 forest as the climate is warming. We quantified the impact of atmospheric
 deposition of aerosols from local wildfires on metal(loid) fluxes using
 macroscopic charcoal accumulation rates, historical fire mapping, and
 element concentrations in 210Pb‐dated lake sediment from five
 subarctic lakes with small catchments. Lake sediments showed small but
 significant increases in fluxes (median = 5–10%) for 22
 trace metals, metalloids, or major ions following fire events. The impact
 of wildfire aerosols on element fluxes was mostly due to short‐term
 (≤2 years) increasing sedimentation rate
 (6 ± 41% increase), whereas sediment element
 concentrations were not strongly impacted. Wildfire‐associated deposition
 to lake sediments was mainly composed of Ca, Al, Fe, Mg, K, Mn, and Na,
 which are major constituents of ash from burned biomass, but changes in
 sediment flux were greatest for Sb, As, Ni, Ba, Mn, Mo, and Sr compared to
 pre‐disturbance conditions. Compared to anthropogenic sources of
 pollution, wildfire‐associated atmospheric fluxes of metal contaminants to
 the lakes (e.g., Hg, Pb, As, Sb, and Cd) were low. This study provides
 quantitative estimates of wildfire impacts on atmospheric geochemical
 fluxes to subarctic lakes, which can be used for modeling larger‐scale
 impacts under changing fire regimes.
description: Information on the methods used to generate this dataset are
 provided in the citation below or please contact John Chételat
 (john.chetelat@canada.ca) for clarification. Pelletier,
 N., Chételat, J., Blarquez, O., & Vermaire, J.
 C. (2020). Paleolimnological assessment of wildfire‐derived atmospheric
 deposition of trace metal(loid)s and major ions to subarctic lakes
 (Northwest Territories, Canada). <i>Journal of Geophysical Research:
 Biogeosciences</i>, 125, e2020JG005720. https://doi.org/10.1029/2020JG005720
DOI: 10.6078/d11m62
title: Data from: Disentangling selection on genetically correlated polygenic traits using whole-genome genealogies

description: We present a full-likelihood method to estimate and quantify polygenic
 adaptation from contemporary DNA sequence data. The method combines
 population genetic DNA sequence  data and GWAS summary statistics
 from up to thousands of nucleotide sites in a joint likelihood function to
 estimate the strength of transient directional selection acting on a
 polygenic trait. Through population genetic simulations of polygenic trait
 architectures and GWAS, we show that the method substantially improves
 power over current methods. We examine the robustness of the method under
 uncorrected GWAS stratification, uncertainty and ascertainment bias in the
 GWAS estimates of SNP effects, uncertainty in the identification of causal
 SNPs, allelic heterogeneity, negative selection, and low GWAS sample size.
 The method can quantify selection acting on correlated traits, fully
 controlling for pleiotropy even among traits with strong genetic
 correlation (|rg|  = 80%; c.f. schizophrenia and bipolar
 disorder) while retaining high power to attribute selection to the causal
 trait. We apply the method to study 56 human polygenic traits for signs of
 recent adaptation. We find signals of directional selection on
 pigmentation (tanning, sunburn, hair, P=5.5e-15, 1.1e-11, 2.2e-6,
 respectively), life history traits (age at first birth, EduYears,
 P=2.5e-4, 2.6e-4, respectively), glycated hemoglobin (HbA1c, P=1.2e-3),
 bone mineral density (P=1.1e-3), and neuroticism (P=5.5e-3). We also
 conduct joint testing of 137 pairs of genetically correlated traits. We
 find evidence of widespread correlated response acting on these traits
 (2.6-fold enrichment over the null expectation, P=1.5e-7). We find that
 for several traits previously reported as adaptive, such as educational
 attainment and hair color, a significant proportion of the signal of
 selection on these traits can be attributed to correlated response, vs
 direct selection (P=2.9e-6, 1.7e-4, respectively). Lastly, our joint test
 uncovers antagonistic selection that has acted to increase type 2 diabetes
 (T2D) risk and decrease HbA1c (P=1.5e-5).
description: SNP likelihoods were calculated using PALM (github.com/35ajstern/palm); GWAS were curated from Price Lab, Neale Lab, and other GWAS (see S3 Table, https://www.biorxiv.org/content/10.1101/2020.05.07.083402v1).
description: See Wiki: https://github.com/35ajstern/palm/wiki
DOI: 10.5061/dryad.9zw3r22bf
title: Linked-read sequencing enables haplotype-resolved resequencing at population scale

description: The feasibility to sequence entire genomes of virtually any organism
 provides unprecedented insights into the evolutionary history of
 populations and species. Nevertheless, many population genomic inferences
 – including the quantification and dating of admixture, introgression and
 demographic events, and inference of selective sweeps – are still limited
 by the lack of high-quality haplotype information. The newest generation
 of sequencing technology now promises significant progress. To establish
 the feasibility of haplotype-resolved genome resequencing at population
 scale, we investigated properties of linked-read sequencing data of
 songbirds of the genus Oenanthe across a range of sequencing depths. Our
 results based on the comparison of downsampled (25x, 20x, 15x, 10x, 7x,
 and 5x) with high-coverage data (46-68x) of seven bird genomes mapped to a
 reference suggest that phasing contiguities and accuracies adequate for
 most population genomic analyses can be reached already with moderate
 sequencing effort. At 15x coverage, phased haplotypes span about 90% of
 the genome assembly, with 50 and 90 percent of phased sequences located in
 phase blocks longer than 1.25-4.6 Mb (N50) and 0.27-0.72 Mb (N90). Phasing
 accuracy reaches beyond 99% starting from 15x coverage. Higher coverages
 yielded higher contiguities (up to about 7 Mb/1Mb (N50/N90) at 25x
 coverage), but only marginally improved phasing accuracy. Phase block
 contiguity improved with input DNA molecule length; thus, higher-quality
 DNA may help keeping sequencing costs at bay. In conclusion, even for
 organisms with gigabase-sized genomes like birds, linked-read sequencing
 at moderate depth opens an affordable avenue towards haplotype-resolved
 genome resequencing at population scale.
description: 10X Genomics linked-reads (60x coverage) were assembled using the
 Supernova 2.1 assembler. To remove duplicate scaffolds of at least 99%
 identity from the pseudohaploid assembly, we ran the dedupe procedure in
 BBTools (https://sourceforge.net/projects/bbmap/) allowing up to 7,000
 edits. This reduced the assembly to 11,030 scaffolds. We then aimed to
 ensure that all duplicate scaffolds were removed and retain only scaffolds
 whose integrity can be confirmed by the presence of syntenic regions in
 another songbird genome. To this end, we performed a lastz alignment
 against the collared flycatcher assembly version 1.5, which is the
 highest-quality assembly available from the Muscicapidae family. For this
 we used lastz 1.04 with settings M=254, K=4500, L=3000, Y=15000, C=2, T=2,
 and --matchcount=10000. This resulted in 295 scaffolds with unique hits in
 the flycatcher assembly.
DOI: 10.5061/dryad.m0cfxpp10
title: Data from: Consistent scaling of inbreeding depression in space and time in a house sparrow metapopulation

description: Inbreeding may increase the extinction risk of small populations. Yet,
 studies using modern genomic tools to investigate inbreeding depression in
 nature have been limited to single populations, and little is known about
 the dynamics of inbreeding depression in subdivided populations over time.
 Natural populations often experience different environmental conditions
 and differ in demographic history and genetic composition; characteristics
 that can affect the severity of inbreeding depression. We utilised
 extensive long-term data on more than 3100 individuals from eight islands
 in an insular house sparrow metapopulation to examine the generality of
 inbreeding effects. Using genomic estimates of realised inbreeding, we
 discovered that inbred individuals had lower survival probabilities and
 produced fewer recruiting offspring than non-inbred individuals.
 Inbreeding depression, measured as the decline in fitness related traits
 per unit inbreeding, did not vary appreciably among populations or with
 time. As a consequence, populations with more resident inbreeding (due to
 their demographic history) paid a higher total fitness cost, evidenced by
 a larger variance in fitness explained by inbreeding within these
 populations. Our results are in contrast to the idea that effects of
 inbreeding generally depend on ecological factors and genetic differences
 among populations, and expand the understanding of inbreeding depression
 in natural subdivided populations.
description: Data has been collected from house sparrows on eight islands in
 the Helgeland archipelago in Norway. Datasets include SNP-genotypes for
 pedigree construction, pedigree, SNP-genotypes, fitness estimates and
 morphological data. Scripts include estimation of genomic and pedigree
 inbreeding coefficients and conducting analyses on the effects of
 inbreeding on fitness and morphological traits.
description: Description of the data and scripts are given in the Dryad_readme
 file.
DOI: 10.5061/dryad.70rxwdbv2
title: Data from: A new small, mesorostrine inioid (Cetacea, Odontoceti, Delphinida) from four late Miocene localities of the Pisco Basin, Peru

description: The moderately rich past diversity of the superfamily Inioidea (Cetacea,
 Odontoceti) in both the Atlantic and Pacific oceans contrasts with the
 present survival of a single genus (Inia, Amazon river dolphin, family
 Iniidae) in freshwater deposits of South America and of a single species
 (Pontoporia blainvillei, Franciscana, family Pontoporiidae) along the
 eastern coast of that continent. However, part of the late Miocene to
 Pliocene inioid fossil record is made of relatively fragmentarily known
 species, for which systematic affinities remain poorly understood. Based
 on a sample of six cranial specimens from early late Miocene (Tortonian,
 9.5-8.6 Ma) marine deposits of the Pisco Formation in four localities of
 the East Pisco Basin (southern coast of Peru), we describe a new genus and
 species of inioid, Samaydelphis chacaltanae. Bearing a proportionally
 short rostrum with an upper tooth count of about 30 teeth per row, this
 small-sized species is characterized by a moderately elevated vertex of
 the cranium displaying a long anteromedial projection of the frontals and
 interparietal, as well as by the plesiomorphic retention of a
 premaxilla-nasal contact. Recovered as a member of the family
 Pontoporiidae in our phylogenetic analysis, S. chacaltanae falls as
 sister-group to Meherrinia isoni, from the late Miocene of North Carolina
 (U.S.A.), which has previously been tentatively referred to the Iniidae or
 regarded as a stem Inioidea. Originating from the P1 allomember of the
 Pisco Formation, the mesorostrine S. chacaltanae was contemporaneous and
 sympatric with two other inioids, the brevirostrine pontoporiid
 Brachydelphis mazeasi and the longirostrine iniid Brujadelphis
 ankylorostris.
description: This dataset contains the character-taxon matrix (.nex file) and
 the constraint molecular tree (.nex file) for our phylogenetic analysis,
 as well as the complete strict consensus tree (.pdf file).
DOI: 10.82294/dvneqm0j5
title: Observaciones semiestructuradas. Territorio: Norte de Santander. Eje medular: Agenciamiento. Sector: Educación. Año: 2025

description: La capacidad de agencia o agenciamiento se entiende como las libertades y oportunidades que tiene un individuo para tomar decisiones y actuar en un contexto, transformando situaciones que afectan a su comunidad a nivel social y ambiental. Implica la capacidad de razonar críticamente y llevar a cabo acciones intencionales. En el ámbito de la educación artística y ambiental, esto se manifiesta en la capacidad de realizar el potencial creativo y de contribuir a la construcción de una realidad institucional o social (Maras, 2018; Katz-Buonicontro, 2018; García-Calvo y Garzón-Barragán, 2023).
DOI: 10.5061/dryad.h70rxwdg6
title: Transgressing Wallace´s Line brings hyperdiverse weevils down to earth

description: Wallace´s Line, located in the heart of the Indo-Australian archipelago,
 has historically been hypothesized to strongly inhibit dispersal. Taxa
 crossing this barrier are confronted with different biota of Asian or
 Australian origin, respectively, but the extent to which these conditions
 have affected the evolution of the colonizing lineages remains largely
 unknown. We examined the potential correlations of body size, lifestyle
 and biogeographical distribution in the weevil genus Trigonopterus. These
 beetles are highly diverse both on foliage and in litter east of Wallace´s
 Line but occur exclusively in leaf litter in the west. Based on a
 comprehensive, dated phylogeny of 303 species, we inferred nine crossing
 events of Wallace´s Line, all from east to west. Five previously
 foliage-dwelling lineages changed their lifestyle to leaf litter habitats
 after crossing this barrier. Our results indicate that dispersal is not
 more likely in edaphic lineages, but rather that, abiotic and/or biotic
 factors may be responsible for the exclusive leaf litter habitat of
 Trigonopterus in Sundaland. This includes differences in climate, and the
 different predatory faunas of Australia-New Guinea, Wallacea, and
 Sundaland. A mimicry complex in New Guinea with Trigonopterus species as
 presumable model may be of relevance in this context.
DOI: 10.15468/dl.4tnnd5
title: Occurrence Download

description: A dataset containing 9723 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Phacochoerus africanus",
 "Year 1788-2026"
 ]
}

 The dataset includes 9723 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002376-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.