cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gmsbcc2m0
title: Data from: The comparative genomic landscape of adaptive radiation in Crater Lake cichlid fishes

description: Factors ranging from ecological opportunity to genome composition might
 explain why only some lineages form adaptive radiations. While being rare,
 particular systems can provide natural experiments within an identical
 ecological setting where the factors promoting increased species numbers
 and phenotypic divergence in two closely related lineages is notably
 different. We investigated one such natural experiment using two de novo
 assembled and 40 re-sequenced genomes and asked why two closely related
 Neotropical cichlid fish lineages, the Amphilophus citrinellus species
 complex (Midas cichlids; radiating) and Archocentrus centrarchus (Flyer
 cichlid; non-radiating), have resulted in such disparate evolutionary
 outcomes. Although both lineages inhabit many of the same Nicaraguan
 lakes, whole-genome inferred demography suggests that priority effects are
 not likely to be the only cause of the dissimilarities. Also, genome-wide
 levels of selection, transposable element dynamics, gene family expansion,
 major chromosomal rearrangements, and the number of genes under positive
 selection were not markedly different between the two lineages. To more
 finely investigate particular subsets of the genome that have undergone
 adaptive divergence in Midas cichlids, we also examined if there was
 evidence for molecular pre-adaptation in regions identified by QTL mapping
 of repeatedly diverging adaptive traits. Although most of our analyses
 failed to pinpoint substantial genomic differences, we did identify
 functional categories containing many genes under positive selection that
 provide candidates for future studies on the propensity of Midas cichlids
 to radiate. Our results point to a disproportionate role of local, rather
 than genome-wide factors underlying the propensity for these cichlid
 fishes to adaptively radiate.
description: The method for the genomes and transcriptomes assemblies was
 described in the paper "The Comparative Genomic Landscape of Adaptive
 Radiation in Crater Lake Cichlid Fishes".
DOI: 10.5061/dryad.fbg79cnt0
title: Data from: Multiple constraints cause positive and negative feedbacks limiting grassland soil CO2 efflux under CO2 enrichment

description: Terrestrial ecosystems are increasingly enriched with resources such as
 atmospheric CO2 that limit ecosystem processes. The consequences for
 ecosystem carbon cycling depend on the feedbacks from other limiting
 resources and plant community change, which remain poorly understood for
 soil CO2 efflux, JCO2, a primary carbon flux from the biosphere to the
 atmosphere. We applied a unique CO2 enrichment gradient (250 to 500 µL
 L-1) for eight years to grassland plant communities on soils from
 different landscape positions. We identified the trajectory of JCO2
 responses and feedbacks from other resources, plant diversity (effective
 species richness, exp(H)), and community change (plant species turnover).
 We found linear increases in JCO2 on an alluvial sandy loam and a lowland
 clay soil, and an asymptotic increase on an upland silty clay soil.
 Structural equation modelling identified CO2 as the dominant limitation on
 JCO2 on the clay soil. In contrast with theory predicting limitation from
 a single limiting factor, the linear JCO2 response on the sandy loam was
 reinforced by positive feedbacks from aboveground net primary productivity
 and exp(H), while the asymptotic JCO2 response on the silty clay arose
 from a net negative feedback among exp(H), species turnover, and soil
 water potential. These findings support a multiple resource limitation
 view of the effects of global change drivers on grassland ecosystem carbon
 cycling and highlight a crucial role for positive or negative feedbacks
 between limiting resources and plant community structure. Incorporating
 these feedbacks will improve models of terrestrial carbon sequestration
 and ecosystem services.
description: Data are from an 8 year (2007-2014) CO2 enrichment experiment of
 constructed communities of tallgrass prairie plants in central Texas, USA
 using the Lysimeter CO2 enrichment gradient facility (LYCOG)
DOI: 10.5061/dryad.v41ns1rtx
title: Clinical trial eligibility in COVID-19 patients

description: As the Coronavirus-2019 (COVID-19) pandemic continues, multiple therapies
 are rapidly being tested for efficacy in clinical trials. Clinical trials
 should be racially and ethnically representative of the population that
 will eventually benefit from these medications. There are multiple
 potential barriers to racial and ethnic minority enrollment in clinical
 trials, one of which could be that inclusion and exclusion criteria select
 for certain racial or ethnic groups disproportionately. In this
 observational cohort study at a single health care system, we examined if
 there were differences in eligibility for treatment with remdesivir based
 on clinical trial criteria for racial and ethnic minorities compared to
 non-Hispanic Whites. 201 electronic medical record charts were reviewed
 manually. Self-identified Whites were older than other racial or ethnic
 groups. At the time of presentation, Black, Latinx, and White participants
 met inclusion criteria for remdesivir at similar rates (72%, 80%, and 73%
 respectively), exclusion criteria at similar rates (43%, 38% and 49% for
 Black, Latinx and White participants respectively). In this study, there
 was no difference in eligibility for remdesivir based on race or ethnicity
 alone.
description: Data was manually extracted by 5 reviewers and then spot-checked
 and combined in Excel, cleaned then analyzed in R.
description: Missing value either a blanks pace or NAs. O2 scale key and
 ordinal severity are listed on separate tabs. Further information
 available on request. Age and gender were removed from this data set to
 preserve the anonymity of participants.
DOI: 10.5061/dryad.2547d7wpk
title: Effects of different concentrations of degradation products of magnesium and magnesium alloys on osteogenic precursor cells

description: Magnesium-based alloys have a great potential to become orthopedic
 degradable materials for internal fixation implants, and magnesium-based
 implants have been shown to influence the surrounding bone structure. To
 understand the effects of magnesium-based implants on bone healing and
 remodeling, we investigated the effects of the extracts of pure magnesium
 and three magnesium alloys on the proliferation and differentiation of
 osteogenic precursor cells in vitro. MC3T3-E1 cells were selected as the
 study objects. Cell culture medium was used to extract the aforementioned
 metal materials, and the degradation products and extracts were subjected
 to a compositional analysis. Subsequently, the extracts were diluted to
 different concentrations for cell proliferation/differentiation cultures.
 The MC3T3-E1 proliferation and differentiation were evaluated based on the
 cell viability, alkaline phosphatase activity, total protein content, and
 cellular ability to form calcified nodules in the extracellular matrix.The
 magnesium ions enhanced and opposed cell proliferation and differentiation
 in a concentration-dependent manner. Higher concentrations of metal
 extracts that degraded faster (indicating higher levels of Mg ions) had an
 adverse effect on cell proliferation, and extracts with a lower
 concentration or slower degradation promoted cell proliferation. When
 slightly elevated, the Mg ions in the extracts suppressed the osteogenic
 differentiation and extracellular matrix mineralization of the cells,
 while they promoted these processes when present beyond a certain
 concentration. In cases of similar Mg ion contents, the extracts that
 contained Zn ions were better in promoting cell proliferation and
 extracellular matrix mineralization.
DOI: 10.15468/dl.qqq2fu
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Crotalaria juncea",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 6 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002687-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.j6q573nch
title: Mountain's ecological and evolutionary variables

description: Aim.  High levels of species richness in mountains are associated
 with their hypothetical roles as cradles and/or museums of diversity but
 the generality of these roles remains unknown. To fill this gap, we tested
 these two hypotheses at a global scale and assessed the direct and
 indirect effects of abiotic regional features on the variation of montane
 amphibian richness worldwide. Location. Global Time period: Last 300
 million years Major taxa studied. Amphibians Methods. Using an amphibian
 phylogeny containing 7238 species, along with species distribution and
 climatic data, we estimated species richness, speciation rates,
 evolutionary time, terrain roughness, area, and climatic stability for 514
 of the world's mountain ranges. Then, we evaluated the direct and
 indirect effects of these variables on richness patterns across these
 mountains using structural equation models. Results. We found that most
 diverse mountain ranges for amphibians are concentrated in the Neotropics,
 but the fastest speciation rates are not restricted to this region.
 Instead, we found that evolutionary time, area and climatic stability
 better explained the global patterns of amphibian diversity in mountains.
 Species richness is higher in mountain regions with large and climatically
 stable areas, where early derived lineages originated/established and
 accumulated through time. Main conclusions. Mountains host and invaluable
 biodiversity shaped through deep time. Differences in speciation rates do
 not play a major role in explaining amphibian species richness across
 mountains. Instead, mountains experiencing milder historical climatic
 oscillations and having greater available areas for species persistence
 likely faced lower extinction rates leading to an increased accumulation
 of amphibian species through time.  This condition highlights the
 importance of mountains as museums of deep evolutionary legacies and
 speciose biotas
DOI: 10.5061/dryad.pzgmsbcjt
title: Beneficial wake-capture effect for forward propulsion with a restrained wing-pitch motion of a butterfly

description: Unlike other insects, a butterfly uses a small amplitude of the wing-pitch
 motion for flight. From an analysis of the dynamics of real flying
 butterflies, we show that the restrained amplitude of the wing-pitch
 motion enhances the wake-capture effect so as to enhance forward
 propulsion. A numerical simulation refined with experimental data shows
 that, for a small amplitude of the wing-pitch motion, the shed vortex
 generated in the downstroke induces air in the wake region to flow towards
 the wings, which enables a butterfly to capture this induced flow and to
 acquire an additional forward propulsion. When the amplitude of the
 wing-pitch motion exceeds 45o, the flow induced by the shed vortex drifts
 away from the wings; it attenuates the wake-capture effect and causes the
 butterfly to lose a part of its forward propulsion. Our results provide a
 physical elucidation for a butterfly adopting a small amplitude of the
 wing-pitch motion to enhance the wake-capture effect and forward
 propulsion. This work clarifies the variation of the flow field correlated
 with the wing-pitch motion, which is useful in the design of a
 micro-aerial vehicle.
description: The readme file contains an explanation of each of the variables
 in the dataset. The supporting data files include the experiment data of
 the kinematics and the flight speed of the butterfly and the simulation
 data of the aerodynamic forces.
DOI: 10.5061/dryad.qrfj6q5dj
title: Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle

description: Fourier-transform mid-infrared (FT-MIR) spectroscopy provides a
 high-throughput and inexpensive method for predicting milk composition and
 other novel traits from milk samples. Whilst there have been many
 genome-wide association studies (GWAS) conducted on FT-MIR predicted
 traits, there have been few GWAS for individual FT-MIR wavenumbers. Here
 we examine associations between genomic regions and individual FT-MIR
 wavenumber phenotypes within a population of 38,085 mixed-breed New
 Zealand dairy cattle with imputed whole-genome sequence. GWAS were
 conducted for each of 895 individual FT-MIR wavenumber phenotypes and
 three FT-MIR predicted milk composition traits, and gene annotation and
 mammary tissue gene expression datasets were employed to identify
 candidate causative genes and variants. This resulted in the
 identification of 38 co-locating, co-segregating expression QTL (eQTL),
 and 31 protein-sequence mutations for FT-MIR wavenumber phenotypes, the
 latter including a null mutation in ABO that has a potential role in
 changing milk oligosaccharide profiles. For the candidate causative genes
 implicated in these analyses, the strength of association between relevant
 loci and each wavenumber across the mid-infrared spectrum revealed shared
 association patterns for groups of genomically-distant loci, highlighting
 clusters of loci linked through their biological roles in lactation and
 their presumed impacts on the chemical composition of milk.
description: Adjusted FT-MIR spectra records for 38,085 multi-breed and
 crossbred New Zealand dairy cows were derived from 100,571 FT-MIR spectra
 records from individual milk samples collected as part of routine herd
 testing conducted by Livestock Improvement Corporation (LIC) in the
 2017/18 season. Imputed whole-genome sequence genotypes
 were generated using a stepwise imputation approach via panels of 50k and
 HD density.
description: <strong>phenotypic-data.txt.zip</strong> Mid-infrared spectra wavenumber phenotypes for 38,085 mixed breed New Zealand dairy cattle.   <strong>imputed-seq-genotypes-trait-qtl-output.vcf</strong> Imputed genotypes for variants representing significant trait QTL, for 38,085 animals.   <strong>eQTL-seq-model-outputs.zip</strong> Relevant 1Mbp cis-eQTL for 25 genes with co-locating trait and expression QTL peaks.   <strong>README file</strong> Description of files provided.
DOI: 10.5061/dryad.nvx0k6dr3
title: The visual ecology of Holocentridae, a nocturnal coral reef fish family with a deep-sea-like multibank retina

description: The visual systems of teleost fishes usually match their habitats and
 lifestyles. Since coral reefs are bright and colourful environments, the
 visual systems of their diurnal inhabitants have been more extensively
 studied than those of nocturnal species. In order to fill this knowledge
 gap, we conducted a detailed investigation of the visual system of the
 nocturnal reef fish family Holocentridae. Results showed that the visual
 system of holocentrids is well adapted to their nocturnal lifestyle with a
 rod-dominated retina. Surprisingly, rods in all species were arranged into
 6-17 well-defined banks, a feature most commonly found in deep-sea fishes,
 that may increase the light sensitivity of the eye and/or allow colour
 discrimination in dim-light. Holocentrids also have the potential for
 dichromatic colour vision during the day with the presence of at least two
 spectrally different cone types: single cones expressing the
 blue-sensitive SWS2A gene, and double cones expressing one or two
 green-sensitive RH2 genes. Some differences were observed between the two
 subfamilies, with Holocentrinae (squirrelfish) having a slightly more
 developed photopic visual system than Myripristinae (soldierfish).
 Moreover, retinal topography of both ganglion cells and cone
 photoreceptors showed specific patterns for each cell type, likely
 highlighting different visual demands at different times of the day, such
 as feeding. Overall, their well-developed scotopic visual systems and the
 ease of catching and maintaining holocentrids in aquaria, make them ideal
 models to investigate teleost dim-light vision and more particularly shed
 light on the function of the multibank retina and its potential for
 dim-light colour vision.
DOI: 10.5061/dryad.mkkwh70z1
title: Mating under climate change: impact of simulated heatwaves on the reproduction of model pollinators (Dataset)

description: Climate change is related to an increase in frequency and intensity of
 extreme events such as heatwaves. It is well established that such events
 may worsen the current worldwide biodiversity decline. In many organisms,
 heat stress is associated with direct physiological perturbations and
 could lead to a decrease of fitness. In contrast to endotherms, heat
 stress resistance has been poorly investigated in heterotherms; especially
 in insects, in which the internal physiological mechanisms available to
 regulate body temperature are almost negligible making them sensitive to
 extreme temperature variations. Wild bees are crucial pollinators for wild
 plants and crops. Among them, bumblebees are experiencing a strong decline
 across the world. Therefore, the ongoing global decline of these insect
 pollinators partly due to climate change could cause major economic
 issues. Here, we assess how simulated heatwaves impact fertility and
 attractiveness (key parameters of sustainability) of bumblebee males. We
 used three model species: Bombus terrestris, a widespread and warm-adapted
 species, B. magnus and B. jonellus, two declining and cold-adapted
 species. We highlight that heat shock (40°C) negatively affects sperm
 viability and sperm DNA integrity only in the two cold-adapted species.
 Heat shock can also impact the structure of cephalic labial glands and the
 production of pheromones only in the declining species. The specific
 disruption in key reproductive traits we identify following simulated
 heatwave conditions could provide one important mechanistic explanation
 for why some pollinators are in decline through climate change.
DOI: 10.5061/dryad.c866t1g5f
title: Data from: Heterozigosity-fitness correlations in a continental island population of Thorn-tailed Rayadito

description: Heterozygosity-fitness correlations (HFCs) have been used to monitor the
 effects of inbreeding in threatened populations. HFCs can also be
 useful to investigate the potential effects of inbreeding in isolated
 relict populations of long-term persistence, and to better understand the
 role of inbreeding and outbreeding as drivers of changes in genetic
 diversity. We studied a continental island population of thorn-tailed
 rayadito (Aphrastura spinicauda) inhabiting the relict forest of Fray
 Jorge National Park, north-central Chile. This population has experienced
 a long-term, gradual process of isolation since the end of the Tertiary.
 Using 10 years of field data in combination with molecular techniques, we
 tested for HFCs to assess the importance of inbreeding depression. If
 inbreeding depression is important, we predict a positive relationship
 between individual heterozygosity and fitness-related traits. We genotyped
 183 individuals at 12 polymorphic microsatellite loci, and used seven
 measures of reproductive success and estimates of apparent survival to
 calculate HFCs. We found weak to moderate statistical support (P-values
 between 0.05 and 0.01) for a linear effect of female multi-locus
 heterozygosity (MLH) on clutch size, and non-linear effects on laying date
 and fledging success. While more heterozygous females laid smaller
 clutches, non-linear effects indicated that females with intermediate
 values of MLH started laying earlier and had higher fledging success. We
 found no evidence for effects of MLH on annual fecundity or on apparent
 survival. Our results along with the long-term demographic stability of
 the study population contradict the hypothesis that inbreeding depression
 occurs in this population.
description: Details will be provided in the published paper.
description: Dataset: HFCs_Aspinicauda
 Heterozigosity-fitness correlations in a continental island
 population of Thorn-tailed Rayadito<br> MS Reference Number: esaa056
 (JOH-2020-108) The whole dataset contains data for
 evaluating the relationship between individual heterozygosity and fitness
 traits in a population of Thorn-tailed rayadito (Aphrastura spinicauda)
 located in Fray Jorge National Park (PNFJ; 30º38’S, 71º40’W),
 north-central Chile. The data set is divided into four
 spreadsheets. These datasets are described in detail in the ReadMe
 file.
DOI: 10.5061/dryad.zs7h44j79
title: Maternal provisioning and fluctuating thermal regimes enhance immune response in a reptile with temperature-dependent sex determination

description: The Charnov-Bull model of differential fitness is often used to explain
 the evolution and maintenance of temperature-dependent sex determination
 (TSD). Most tests of the model focus on morphological proxies of fitness,
 such as size traits, whereas early life physiological traits that are
 closely related to lifetime fitness might provide a framework for
 generalising the Charnov-Bull model across taxa. One such trait is the
 strength of early life immune response, which is strongly linked to early
 life survival and fitness. Here, we manipulate temperature, variance in
 temperature, and sex to test the Charnov-Bull model using a physiological
 trait, immune system strength, in the snapping turtle (Chelydra serpentina
 L. 1758). We find no evidence of sex-specific differences in bactericidal
 capacity of hatchling blood, and no evidence that mean temperature
 influences bactericidal capacity. However, we find that fluctuating
 incubation temperature (i.e., a more naturalized incubation regime) is
 associated with a greater bactericidal capacity compared to constant
 temperature incubation. We also find that egg mass, a proxy for maternal
 provisioning, is positively associated with bactericidal capacity. Our
 findings suggest that the evolution of temperature-dependent sex
 determination in reptiles is unrelated to our measure early-life innate
 immunity. Our study also underlines how immune response is
 condition-dependent in early life, and questions the biological relevance
 of constant temperature incubation in experimental studies on ectotherm
 development.
description: Snapping turtle eggs were collected soon after laying and were
 incubated in one of four temperature regimes (24C +/- 0C, 24C +/- 4C, 28C
 +/- 0C, 28C +/- 4C). Eggs in each temperature treatment were subjected to
 either an aromatase inhibitor or a control treatment creating eight total
 experimental groups.  On hatching, blood was extracted
 from hatchlings and this was subjected to a bacterial killing assay with
 <em>E.coli. </em>To determine the proportion of bacteria
 killed by hatchling plasma we measured absorbance with a
 spectrophotometer. Each hatchling BKA was run in duplicate. 
description: See ReadMe file for variable descriptions, abbreviations, and
 allowable values.