cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s4mw6m979
title: Do deaths from road traffic injuries follow a classical trimodal pattern in North West Ethiopia? A hospital based prospective cohort study

description: The data set contains information collected from road traffic injury
 victims. The data was collected from all traffic injury victims,
 regardless of age and sex except those who were dead on arrival, comatose,
 and had no attendant. The variables included in this data includes, crash
 characteristics, hospital arrival time, road user category, availability
 of pre-hospital first aid, type of transportation used to transfer the
 victim, clinical findings, the outcome in the emergency department, and
 decision after evaluation at the emergency department.  The
 primary outcome was time to death measured in hours between road traffic
 injury and the 30th day of injury. Accordingly, those victims who died
 between injury times to the 30th day of injury were events, and those who
 were still alive on the 30th day were censored cases.  Secondary
 outcomes were pre-hospital first aid, length of hospital stay, and
 hospital arrival time.  The exposure variable was having any
 degree of injury by any vehicle. The finding of the study showed, there
 were 80 deaths during the study time, (2.90 deaths per 10,000 person-hours
 of observation (95% CI: 2.77, 3.03). Being a driver, accidents at the
 inter urban locations, time from injury to hospital arrival time of 1 to 4
 hours, systolic blood pressure on admission of less than 90mmHG, GCS of
 less than 8 on admission and poly trauma were found to be independent
 predictors of time to death.
description: The
 dataset was collected from 01-May 2019 to 30-February 2020. The data has
 been processed by linear mixed model on STATA. The article produced is
 accepted by Journal of BMJ Open for publication.
description: The readme file contains
 description of each variable and recategorized variables. The units used
 in the data set were also described in the readme file.
DOI: 10.6078/d1rx3j
title: Selection on dispersal drives evolution of metabolic capacities for energy production in female wing‐polymorphic sand field crickets, Gryllus firmus

description: Life history and metabolism covary, but the mechanisms and individual
 traits responsible for these linkages remain unresolved. Dispersal
 capability is a critical component of life history that is constrained by
 metabolic capacities for energy production. Conflicting relationships
 between metabolism and life histories may be explained by accounting for
 variation in dispersal and maximal metabolic rates. We used female
 wing-polymorphic sand field crickets, Gryllus firmus, selected either for
 long wings (LW) and flight-capability or short wings (SW) and high early
 lifetime fecundity to test the hypothesis that selection on dispersal
 capability drives the evolution of metabolic capacities. While resting
 metabolic rates were similar, long-winged crickets reached higher maximal
 metabolic rates than short-winged crickets, resulting in improved running
 performance. We further provided insight into the mechanisms responsible
 for covariation between life history and metabolism by comparing
 mitochondrial content of tissues involved in powering locomotion and
 assessing function of mitochondria isolated from long- and short-winged
 crickets. Our results demonstrated that larger metabolic capacities in
 long-winged crickets were underpinned by increases in mitochondrial
 content of dorsoventral flight muscle and enhanced bioenergetic capacities
 of mitochondria within the fat body, a tissue responsible for fuel storage
 and mobilization. Thus, selection on flight-capability remodels metabolism
 in a trait and tissue-specific manner to enlarge metabolic capacities
 necessary for dispersal.
DOI: 10.5061/dryad.9s4mw6mhh
title: Interspecific trait variability and local soil conditions modulate grassland model community responses to climate

description:             High elevation grasslands provide critical services in agriculture and ecosystem stabilization. However, these ecosystems face elevated risks of disturbance due to predicted soil and climate changes. We experimentally exposed model grassland communities, comprised of three species grown on either local or reference soil, to varied climatic environments along an elevational gradient in the European Alps, measuring the effects on species and community traits. Although species-specific biomass varied across soil and climate, species’ proportional contributions to community-level biomass production remained consistent. Where species experienced low survivorship, species-specific biomass production was maintained through increased production of surviving individuals. Species responded directionally to climatic variation, segregating differentially by plant traits (including height, reproduction, biomass, survival, leaf dry weight, and leaf area) across all sites. Local soil variation drove stochastic trait responses across all species. This soil variability obscured climate-driven responses: we recorded no directional trait responses driven by climate. Our species-based approach contributes to our understanding of grassland community stabilization and suggests that these communities show some stability under climatic variation.
DOI: 10.5061/dryad.5mkkwh76v
title: Sporadic pseudohypoparathyroidism type 1B in monozygotic twins: insights into the pathogenesis of methylation defects

description: Context: Sporadic pseudohypoparathyroidism type 1B (sporPHP1B) is an
 imprinting disease without a defined genetic cause, characterized by broad
 methylation changes in differentially methylated regions (DMRs) of the
 GNAS gene. Objective: This work aims to provide insights into the
 causative event leading to the GNAS methylation defects through
 comprehensive molecular genetic analyses of a pair of female monozygotic
 twins concordant for sporPHP1B who were conceived naturally i.e., without
 assisted reproductive techniques. Methods: Using the leukocyte genome of
 the twins and family members, we performed targeted bisulfite sequencing,
 methylation-sensitive restriction enzyme (MSRE)-qPCR, whole-genome
 sequencing (WGS), high-density SNP array, and Sanger sequencing. Results:
 Methylation analyses by targeted bisulfite sequencing and MSRE-qPCR
 revealed almost complete loss of methylation at the GNAS AS, XL, and A/B
 DMRs and gain of methylation at the NESP55 DMR in the twins, but not in
 other family members. Except for the GNAS locus, we did not find apparent
 methylation defects at other imprinted genome loci of the twins. WGS, SNP
 array, and Sanger sequencing did not detect the previously
 described genetic defects associated with familial PHP1B. Sanger
 sequencing also ruled out any novel genetic alterations in the entire
 NESP55/AS region. However, the analysis of 28 consecutive SNPs could not
 exclude the possibility of paternal heterodisomy in a span of 22 kb
 comprising exon NESP55 and AS exon 5. Conclusion: Our comprehensive
 analysis of a pair of monozygotic twins with sporPHP1B ruled out all
 previously described genetic causes. Twin concordance indicates that the
 causative event was an imprinting error earlier than the timing of
 monozygotic twinning.
DOI: 10.5061/dryad.z34tmpgf8
title: Biodiversity-productivity relationships in a natural grassland community vary under diversity loss scenarios

description: Understanding the biodiversity-productivity relationship and underlying
 mechanisms in natural ecosystems under realistic diversity loss scenarios
 remains a major challenge for ecologists despite its importance for
 predicting impacts of rapid loss of biodiversity worldwide. Here we report
 the results of a plant functional group (PFG) removal experiment conducted
 on the Mongolian Plateau, the largest remaining natural grassland in the
 world. Our results demonstrated that the biodiversity-productivity
 relationship varied among positive linear, neutral, and unimodal forms
 under different PFG loss patterns. Moreover, the form of this relationship
 with the same PFG loss pattern sometimes changed through time. The
 abundance of the remaining PFG(s) before removal and their compensation
 following the loss of other PFGs were two major mechanisms affecting the
 biodiversity-productivity relationship under diversity loss scenarios. The
 abundance effect promoted positive responses of productivity to
 biodiversity, but the compensation effect caused several
 biodiversity-productivity relationships, hinging on its direction
 (positive or negative) and strength. As indicated by the values of the
 compensation index, negative, zero and partial compensations contributed
 to the positive relationships, while full compensation resulted in a
 neutral relationship. Over-compensation at intermediate PFG richness
 levels created a unimodal curve in our system, but it could also lead to a
 negative linear relationship. Synthesis. Our experiment provides a vivid
 picture of how the form of the biodiversity-productivity relationship
 varies among different diversity loss patterns in a natural ecosystem. We
 argue that compensation by the remaining species, which is not revealed by
 synthesized biodiversity experiments, plays a critical role in shaping the
 form of this relationship when diversity is lost from existing systems.
 The direction and strength of compensation are highly dependent on
 extirpation scenarios. Thus, impacts of biodiversity loss on natural
 ecosystems are likely more complex than predicted by the canonical
 positive saturating curve obtained from the synthesized biodiversity
 experiments. We suggest that models forecasting the consequences of
 biodiversity declines on natural ecosystems should take into account
 diversity loss patterns and the ensuing compensation.
DOI: 10.5061/dryad.83bk3j9s8
title: Data from: Consistency in the flight and visual orientation distances of habituated chacma baboons after an observed leopard predation: Do flight initiation distance methods always measure perceived predation risk?

description: Flight initiation distance (FID) procedures are used to assess the risk
 perception animals have for threats (e.g., natural predators, hunters) but
 it is unclear whether these assessments remain meaningful if animals have
 habituated to certain human stimuli (e.g., researchers, tourists). Our
 previous work showed that habituated baboons displayed individually
 distinct and consistent responses to human approaches, a tolerance trait,
 but it is unknown if the trait is resilient to life-threatening scenarios.
 If it were consistent, it would imply FIDs might measure specific human
 threat perception only and not generalise to other threats such as
 predators when animals have experienced habituation processes. We used FID
 procedures to compare baseline responses to the visual orientation
 distance, FID, and individual tolerance estimates assessed after a leopard
 predation on an adult male baboon (group member). All variables were
 consistent despite the predation event, suggesting tolerance to observers
 was largely unaffected by the predation and FID procedures are unlikely to
 be generalisable to other threats when habituation has occurred. FID
 approaches could be an important tool for assessing how humans influence
 animal behaviour across a range of contexts, but careful planning is
 required to understand the type of stimuli presented.
description: Flight initiation distances (FID) and Visual orientation
 distances (VOD) for 16 individuals from a group of habituated baboons, all
 data collected in the hours following a predation by a leopard on a group
 member. Also included are the same measures collected during less
 stressful scenarios. For each measure we include the individual's
 identity, trial number, time period, habitat, behaviour,
 looking/compatibility information, number of conspecifics within 5 meters,
 start distance, and calculations for the visual orientation distance delay
 and index.
DOI: 10.5061/dryad.wpzgmsbns
title: Predictors of genomic differentiation within a hybrid taxon

description: Hybridization is increasingly recognized as an important evolutionary
 force. Novel genetic methods now enable us to address how the genomes of
 parental species are combined in hybrid lineages. However, we still do not
 know the relative importance of admixed proportions, genome architecture
 and local selection in shaping hybrid genomes. Here, we take advantage of
 the genetically divergent island populations of Italian sparrow on Crete,
 Corsica and Sicily to investigate the predictors of genomic variation
 within a hybrid taxon. We test if differentiation is affected by
 recombination rate, selection, or variation in ancestry proportions. We
 find that the relationship between recombination rate and differentiation
 is less pronounced within hybrid lineages than between the parent species,
 as expected if purging of minor parent ancestry in low recombination
 regions reduces the variation available for differentiation. In addition,
 we find that differentiation between islands is correlated with
 differences in signatures of selection in two out of three comparisons.
 Signatures of selection within islands are correlated across all islands,
 suggesting that shared selection may mould genomic differentiation. The
 best predictor of strong differentiation within islands is the degree of
 differentiation from house sparrow, and hence loci with Spanish sparrow
 ancestry may vary more freely. Jointly, this suggests that constraints and
 selection interact in shaping the genomic landscape of differentiation in
 this hybrid species.
description: Genomic DNA was purified from blood samples. Double digestion of
 the genomic DNA for ddRAD using EcoR I and MseI restriction enzymes.
 Library pools were size selected for fragments between 500-600bp.
  Illumina Nextseq500 machine and the 1x75bp sequencing format. Vcftools,
 plink, bcftools, GATK, among others programes were use for filtering and
 generation of a final master VCF file. Here we provide
 scripts for processing raw data and for the statistical analysis in the
 study, VCF files and intermediate files used by the R script needed for
 the statistical analysis are also provided.
DOI: 10.5061/dryad.pzgmsbcn6
title: IUCN Red List protects avian genetic diversity

description: Despite well-established links between low genetic diversity and
 extinction processes, intra-specific genetic diversity is rarely
 considered in global conservation assessments, potentially leading to
 biased estimates of species’ extinction risk. We show that birds ranked as
 “threatened” by the IUCN Red List have lower intra-specific genetic
 diversity than “non-threatened” species, confirming that threat criteria,
 used by the IUCN, effectively protect genetically depleted species.
 However, some “non-threatened” species harbour low levels of genetic
 diversity, indicating an undetected vulnerability to global change. Global
 conservation assessments will benefit from explicitly integrating relevant
 genetic and genomic diversity-based measures in estimates of species’
 extinction risk.
description: The dataset contains a table with information about all the
 cytochrome-b (mtDNA) sequences of birds available in GenBank, corrected
 sequences alignments for each species and the code necessary to analyse
 the data.
description: The README.md file contains a detailed explanation of each file
 and variable in the dataset, including units. Information regarding the
 method used for the analyses can be found in the associated manuscript
 referenced above.
DOI: 10.5061/dryad.66t1g1k32
title: Comparative karyotype analysis in chickpea (Cicer arietinum L.) using oligo painting FISH

description: Chickpea (Cicer arietinum L.) is one of the main sources of plant proteins
 in the Indian subcontinent and West Asia, where two different morphotypes,
 desi and kabuli, are grown. Despite the progress in genome mapping and
 sequencing, the knowledge of chickpea genome at chromosomal level,
 including the long-range molecular chromosome organization is limited.
 Earlier cytogenetic studies in chickpea suffered from limited number of
 cytogenetic landmarks and did not permit to identify individual
 chromosomes in the metaphase spreads or to anchor pseudomolecules to
 chromosomes in situ. In this study, we developed a system for fast
 molecular karyotyping for both morphotypes of cultivated chickpea. We
 demonstrate that even draft genome sequences are adequate to develop
 oligo-FISH barcodes for identification of chromosomes and comparative
 analysis among closely related chickpea genotypes. Our results show the
 potential of oligo-FISH barcoding for identification of structural changes
 in chromosomes, which accompanied genome diversification among chickpea
 cultivars. Moreover, oligo-FISH barcoding in chickpea pointed out some
 problematic, most probably wrongly assembled regions of the
 pseudomolecules of both, kabuli and desi reference genomes. Thus, oligo
 painting appears as a powerful tool not only for comparative karyotyping,
 but also for validation of genome assemblies.
description: Four BAC clones (05E03, 10I13, 11K07 and 14M02) which gave
 chromosome specific cytogenetic position in desi accession WR315
 (Zatloukalová et al. 2011) were sequenced using Illumina. Sequencing
 libraries were prepared from 2 µg of fragmented DNA using
 TruSeq<sup>®</sup> DNA PCR-free kit (Illumina) and sequenced
 on the MiSeq Illumina platform with reads length 2 × 300 bp to achieve
 minimal sequence depth of 100×. Illumina sequences were processed using
 homemade perl script combining the assembly processes using MaSuRCA (Zimin
 et al. 2013) and identification of vector sequences flanking the chickpea
 assembles contigs/scaffolds.
DOI: 10.5061/dryad.8pk0p2np5
title: Social environment shapes female settlement decisions in a solitary carnivore

description: How and where a female selects an area to settle and breed is of central
 importance in dispersal and population ecology as it governs range
 expansion and gene flow. Social structure and organization have been shown
 to influence settlement decisions, but its importance in settlement of
 large, solitary mammals is largely unknown. We investigate how the
 identity of overlapping conspecifics on the landscape, acquired during the
 maternal care period, influences selection of settlement home ranges in a
 non-territorial, solitary mammal using location data of 56 female brown
 bears (Ursus arctos). We used a resource selection function to determine
 whether females’ settlement behavior was influenced by presence of their
 mother, related females, familiar females, and female population density.
 Hunting may remove mothers and result in socio-spatial changes prior to
 settlement. We compared overlap between settling females and their
 mother’s concurrent or most recent home ranges to examine the settling
 female’s response to the absence or presence of her mother on the
 landscape. We found that females selected settlement home ranges that
 overlapped their mother’s home range, familiar females, i.e. those they
 had previously overlapped with, and areas with higher density than their
 natal ranges. However, they did not select areas overlapping related
 females. We also found that when mothers were removed from the landscape,
 female offspring selected settlement home ranges with greater overlap of
 their mother’s range, compared with mothers who were alive. Our results
 suggest that females are acquiring and using information about their
 social environment when making settlement decisions
DOI: 10.5061/dryad.hqbzkh1h3
title: Performance tradeoffs and resource availability drive variation in reproductive isolation between sympatrically diverging crossbills

description: Theoretical models indicate that speciation, especially when the scope for
 gene flow is great (e.g., sympatric speciation), is most likely when
 strong performance tradeoffs coincide with reproduction. We tested this
 classic hypothesis using measures of the strength of three prezygotic
 reproductive isolating barriers (habitat isolation, reduced immigrant
 fecundity, and behavioral isolation) between two young (~2,000 yrs) and
 sympatric red crossbill (Loxia curvirostra) ecotypes. All three isolating
 barriers increased with increases in performance tradeoffs, with total
 reproductive isolation varying between 0.72 and 1 (0 represents random
 mating, 1 represents complete reproductive isolation). Strong tradeoffs
 led to strong habitat isolation, an inability to breed in the “wrong”
 habitat, and more assortative flocks, with the latter leading to stronger
 behavioral isolation. Reproductive isolation decreased as resource
 availability increased relative to the demands of breeding, with higher
 resource availabilities eliminating the positive relationship between
 reproductive isolation and performance tradeoffs. This latter result is
 consistent with previous work suggesting that increasing resource
 abundance dampens the effect of strong performance tradeoffs on
 evolutionary divergence. Because many organisms, with the notable
 exception of host-specific phytophagous insects, rely on abundant food
 resources with weak performance tradeoffs while breeding, our results may
 explain why sympatric speciation is uncommon.
DOI: 10.5061/dryad.9cnp5hqjv
title: Variation in plant carbon, nitrogen and phosphorus contents across the drylands of China

description: Determining large-scale patterns of plant elemental concentrations and
 stoichiometry along environmental gradients is critical for understanding
 plant adaptive strategies and predicting ecosystem biogeochemistry
 processes. However, it remains unclear as to how plant carbon (C),
 nitrogen (N), and phosphorus (P) concentrations and their stoichiometry in
 different organs (leaves, stems, and roots) respond to large-scale
 environmental gradients in drylands. We determined C, N, and P
 concentrations and their ratios in leaves, stems, and roots of plants
 growing in the dryland ecosystems of China. Using threshold indicator taxa
 analyses, we identified indicator species of plant C, N, and P responses
 to aridity and soil properties. The arithmetic averaged concentrations of
 C, N, and P in drylands were 414, 18.7, and 1.38 mg/g for leaves,
 respectively; 445, 12.1, and 1.08 mg/g for stems, respectively; and 418,
 10.5, and 0.89 mg/g for roots, respectively. The C : N, C : P, and N : P
 ratios were 25.2, 386, and 16.3 for leaves, respectively; 42.8, 592, and
 14.8 for stems, respectively; and 46.8, 658, and 15.6 for roots,
 respectively. Aridity and soil pH generally exerted positive effects on
 plant N and negative effects on C and P concentrations and, thus, were
 related negatively to C : N ratios and positively to C : P and N : P
 ratios. The C, N, and P concentrations in organs generally increased with
 increasing corresponding soil C, N, and P concentrations. Shrubs were
 mainly positive indicators of plant C, N, and P concentrations in response
 to aridity and soil pH, and negative indicators of soil nutrients. In
 contrast, herbaceous species were mainly positive indicators of soil
 nutrients and negative indicators of aridity and soil pH. These findings
 indicate that plants tend to accumulate N rather than C and P with
 increasing aridity and soil pH. The identification of indicator species
 for plant elements in response to aridity and soil traits informs our
 understanding of species-specific biogeographic patterns of organ elements
 and potential adaptive strategies of plants in drylands.