cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.83bk3j9s2
title: Recommended fossil calibrators for time-scaled molecular phylogenies of Afrotheria

description: A phylogenetic framework provides the necessary evolutionary context for
 studies of comparative anatomy, life history, behavior, biogeography,
 systematics, and conservation. Time-scaled phylogenetic analyses require
 researchers to include calibration ages which are used to fit a model that
 transforms tree branch lengths into units of time. The inclusion of
 multiple calibration ages (if they are available) is a best practice that
 brings all the available evidence to bear on the temporal model. While
 selecting the appropriate ages of calibrating fossil taxa is obviously
 important, perhaps more relevant is where those calibrations are applied
 in the tree. A misattributed fossil calibrator (e.g., using a stem-taxon
 to set a minimum age on a tipward crown-node) can severely distort the
 results. Our aim is to provide a summary of fossil calibrators that can be
 used in molecular phylogenetic assessments of Afrotheria. The literature
 that documents these fossils, and discusses their ages and affiliations,
 is somewhat scattered. Included in this contribution are the oldest
 extinct species that are (in our opinion) securely attributable to stem
 lineages of afrotherian clades. Each informs a minimum age for the
 adjacent rootward tree node. We then assemble a large DNA supermatrix that
 includes 32 genes and 39 afrotherian genera – including recently extinct
 elephants and sea-cows. A time-scaled phylogenetic estimate is derived
 from this dataset with explicit inclusion of fossil taxa in the analysis.
DOI: 10.5061/dryad.0rxwdbs19
title: Diarrhea etiology prediction validation dataset - Bangladesh and Mali

description: Background: Diarrheal illness is a leading cause of antibiotic use for
 children in low- and middle-income countries. Determination of diarrhea
 etiology at the point-of-care without reliance on laboratory testing has
 the potential to reduce inappropriate antibiotic use. Methods: This
 prospective observational study aimed to develop and externally validate
 the accuracy of a mobile software application (“App”) for the prediction
 of viral-only etiology of acute diarrhea in children 0-59 months in
 Bangladesh and Mali. The App used previously derived and internally
 validated models using combinations of “patient-intrinsic” information
 (age, blood in stool, vomiting, breastfeeding status, and mid-upper arm
 circumference), pre-test odds using location-specific historical
 prevalence and recent patients, climate, and viral seasonality. Diarrhea
 etiology was determined with TaqMan Array Card using episode-specific
 attributable fraction (AFe) &gt;0.5. Results: Of 302 children with
 acute diarrhea enrolled, 199 had etiologies above the AFe threshold.
 Viral-only pathogens were detected in 22% of patients in Mali and 63% in
 Bangladesh. Rotavirus was the most common pathogen detected (16% Mali; 60%
 Bangladesh). The viral seasonality model had an AUC of 0.754 (0.665-0.843)
 for the sites combined, with calibration-in-the-large α=-0.393 (-0.455 –
 -0.331) and calibration slope β=1.287 (1.207 – 1.367). By site, the
 pre-test odds model performed best in Mali with an AUC of 0.783 (0.705 -
 0.86); the viral seasonality model performed best in Bangladesh with AUC
 0.710 (0.595 - 0.825). Conclusion: The app accurately identified children
 with high likelihood of viral-only diarrhea etiology. Further studies to
 evaluate the app’s potential use in diagnostic and antimicrobial
 stewardship are underway.
description: The dataset was collected in Bangladesh at the Dhaka Hospital of
 the International Center for Diarrhoeal Disease Research, Bangladesh
 (icddr,b) rehydration (short stay) unit and in Mali at the Centres de
 Santé de Référence (CSREF) and the Centres de Santé Communautaires (CSCOM)
 in Commune V and VI in Bamako, Mali. This dataset was used to produce a
 manuscript under review at eLife.
description: The readme file contains an explanation of each of the variables
 in the dataset and measurement units when applicable.
DOI: 10.5061/dryad.f7m0cfxx0
title: Activation of autophagy during normothermic machine perfusion of discarded livers is associated with improved hepatocellular function

description: We demonstrate that ischemia-reperfusion injury occurs in all livers
 during NMP, though there are notable differences in gene expression
 between functional and nonfunctional livers. We further demonstrate that
 activation of the liver’s repair and homeostasis mechanisms through
 autophagy plays a vital role in the graft’s response to injury and may
 impact liver function. These findings indicate that liver autophagy might
 be a key therapeutic target for rehabilitating the function of severely
 injured or untransplantable livers.
DOI: 10.5061/dryad.1rn8pk0v5
title: Data from: Protection mutualists affect colonization and establishment of host-associated species in a coral reef cryptofauna community

description: Protection mutualists display territorial behaviors that provide
 protective services for their host species. To investigate how protection
 mutualists impact the colonization and establishment
 of host-associated species, we conducted a two-stage experiment
 using a coral reef cryptofauna community as our study
 system. Pocillopora meandrina is a fairly
 common, branching coral species that forms habitat that is utilized by a
 variety of marine organisms. There is a guild of protection mutualists
 that associate with P. meandrina including Trapeziidae
 crabs and Alpheidae shrimp. We manipulated coral colonies to have
 Trapeziidae crabs, Alpheidae shrimp, both, or neither. For the
 first part of our experiment, we observed colonization of marine
 invertebrates to these colonies every other day for two months, while
 resetting the treatment levels every seven days. For the second part of
 our experiment, we surveyed the community composition weekly and then
 monthly for a total of six months without interference. During both
 experiments, we measured the initial and final size of the host coral
 colonies as a metric of fitness. Data are provided for observed
 marine decapods through time on each of forty experimental coral colonies
 for the colonization and the establishment experiments. Data are also
 provided for coral colony size at the beginning and end of each
 experiment.     
description: The community composition data were collected through visual
 surveys of the coral colonies conducted on SCUBA using a dive light to
 observe species in between the coral branches. For the colonization
 experiment (two month duration), surveys were done every other day and
 colonizers were removed from the corals every seven days. The colonization
 data includes community survey data and organism removal data. For the
 establishment experiment (six month duration), surveys were conducted
 weekly and then monthly with no interference to the community composition.
 Coral colony size was measured at the beginning and the end of the
 colonization experiment by transporting coral colonies into the lab and
 using buoyant weights. These weights have been processed to dry weights
 based on the density of the seawater when each colony was weighed. Coral
 colony size was measured at the beginning and the end of the
 establishment experiment through planar colony size measurements taken
 from top-down photographs of each colony. These photographs were scaled
 and aligned using the cement blocks to which each coral colony was
 secured. For more information on how these data were
 collected and how they have been analyzed, see Counsell and Donahue 2021
 in Oikos doi:  10.1111/oik.08282.
DOI: 10.5061/dryad.jq2bvq897
title: Genetic diversity and population structure of two endangered neotropical parrots inform In Situ and Ex Situ conservation strategies

description: A key aspect in the conservation of endangered populations is
 understanding patterns of genetic variation and structure, which can
 provide managers with critical information to support evidence-based
 status assessments and management strategies. This is especially important
 for species with small wild and larger captive populations, as found in
 many endangered parrots. We used genotypic data to assess genetic
 variation and structure in wild and captive populations of two endangered
 parrots, the blue-throated macaw, Ara glaucogularis, of Bolivia, and the
 thick-billed parrot, Rhynchopsitta pachyrhyncha, of Mexico. In the
 blue-throated macaw, we found evidence of weak genetic differentiation
 between wild northern and southern subpopulations, and between wild and
 captive populations. In the thick-billed parrot we found no signal of
 differentiation between the Madera and Tutuaca breeding colonies or
 between wild and captive populations. Similar levels of genetic diversity
 were detected in the wild and captive populations of both species, with
 private alleles detected in captivity in both, and in the wild in the
 thick-billed parrot. We found genetic signatures of a bottleneck in the
 northern blue-throated macaw subpopulation, but no such signal was
 identified in any other subpopulation of either species. Our results
 suggest both species could potentially benefit from reintroduction of
 genetic variation found in captivity, and emphasize the need for genetic
 management of captive populations.
description: Genotypes at 12 loci were obtained for the blue-throated
 macaw; alleles were scored in Geneious R8.1.7. Genotypes for 11 loci of
 the thick-billed parrot were scored using GeneMapper V3.5
description: Data stored as seperate Genepop formatted text files for
 each species.
DOI: 10.5061/dryad.15dv41nxz
title: Epigenetic mechanisms of partial dosage compensation in an avian, female heterogametic system

description: The evolution of genetic sex determination is often accompanied by
 degradation of one of the proto sex chromosomes. Male heterogametic
 systems have evolved convergent, epigenetic mechanisms restoring the
 resulting imbalance in gene dosage between diploid autosomes (AA) and the
 hemizygous sex chromosome (X). Female heterogametic systems (AAf ZWf, AAm
 ZZm) tend to only show partial dosage compensation (0.5 &lt; Zf:AAf
 &lt; 1) and dosage balance (0.5f:ZZm&lt;1). The underlying
 mechanism remains largely elusive. Here, we quantified gene expression for
 a total of 15 male and female Eurasian crows (Corvus (corone) spp.) raised
 under common garden conditions. In addition, we characterized aspects of
 the regulatory landscape quantifying genome-wide ATAC-seq and 5mC
 methylation profiles. Partial dosage compensation was explained by female
 upregulation of Z-linked genes accompanied by increased chromatin
 accessibility on the female Z chromosome. 5mC methylation was strongly
 reduced in open chromatin-regions and GC islands and showed chromosome-,
 but no sex-specific variation. With the exception of the pseudo-autosomal
 region (PAR), female upregulation of gene expression was evenly spread
 across the Z chromosome without evidence for regional epigenetic
 regulation, as has for example been suggested for the male hypermethylated
 region (MHM) in chicken. Our results support the hypothesis that partial
 dosage compensation in female heterogametic systems is subject to
 chromosome-wide, epigenetic control mediated by differential chromatin
 accessibility between the sexes.
description: Tables FM_Liver_PG_20kb_all.txt and FM_Spleen_PG_20kb_all.txt
  summarized the ATAC-seq and expression data utilized in this project.
 Peaks were called using MACS2 and FPKM values were calculated with
 cuffnorm. The more detailed description of the data can be found in the
 methods section of the manuscript The following tables
 describe the methylation data generated as described in the
 methods: 5mC_GW_FM.txt - methylation profile chromosome
 wide 5mC_PEAKS_FM.txt - methylation profile whithin
 called peaks 5mC_genes.20kb-5kbwin.FM.txt - methylation
 profile in expressed genes
 data_HeterozygosityFMChrZ_v5.6.txt - heterozygosity data on the Z
 chromosome used to identify the PAR
 D_Ko_C04_pooled_chr1.bg - bedgraph file of genome coverage on
 chr1 used for PAR identification
 D_Ko_C04_pooled_chr2.bg - bedgraph file of genome coverage on
 chr1 used for PAR identification
 D_Ko_C04_pooled_chrZ.bg - bedgraph file of genome coverage on
 chr1 used for PAR identification
 D_Ko_C20_pooled_chr1.bg - bedgraph file of genome coverage on
 chr1 used for PAR identification
 D_Ko_C20_pooled_chr2.bg - bedgraph file of genome coverage on
 chr1 used for PAR identification
 D_Ko_C20_pooled_chrZ.bg - bedgraph file of genome coverage on
 chr1 used for PAR identification
DOI: 10.15468/dl.9rp32h
title: Occurrence Download

description: A dataset containing 31592 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mimosa pudica"
 ]
}

 The dataset includes 31592 records from 726 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002915-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8931zcrrd
title: Genotype data of 1970 Pedunculate oak trees (Quercus robur L.) in 13 European countries at 381 gene loci covering the nuclear and organelle genome

description: The data set is the result of genetic inventory on 1970 Pedunculate oak
 trees from 197 locations in Europe. The samples are from the countries:
 Belarus, Bosnia, Bulgaria, Croatia, Finland, France, Germany, Hungary,
 Italy, Latvia, Poland, Russia and Ukraine. At each location ten individual
 trees were collected. The data set includes the location ID and geographic
 coordinates of each sampled tree (longitude and latitude in decimal
 degrees) and the genotype data. All samples were screened with a targeted
 sequencing approach on a set of 381 polymorphic loci (356 nuclear SNPs, 3
 nuclear InDels, 17 chloroplast SNPs and five mitochondrial SNPs). The
 genotype of each individual is one row in the csv-file “genotypes”. The
 genotypes at the nuclear markers are diploid and represented by two
 columns per gene marker. The genetic information at the organelle genome
 is haploid. For each of these gene markers one column is used. Genotypes
 are coded by Arabic numbers. The meaning of the numbers is explained in
 the table “coding genotypes” in a second csv-file.
description: The majority of the samples
 (188 locations) were collected in forest stands and for nine locations the
 material has been collected in provenance trials. For the sampling in the
 forests we set a minimum diameter of 20 cm at breast height and trees
 separated by a minimum of 50m to reduce the probability to collect related
 trees. At each location ten individual trees were collected.
 All samples were screened with a targeted sequencing approach on
 a set of 381 polymorphic loci (356 nuclear SNPs, 3 nuclear InDels, 17
 chloroplast SNPs and five mitochondrial SNPs). The details of the used
 gene markers are given by Degen et al. (2021).
description: The genotype of each
 individual is one row in the csv-table “genotypes”. The genotypes at the
 nuclear markers are diploid and represented by two columns per gene
 marker. The genetic information at the organelle genome is haploid. For
 each of these gene markers one column is used. Genotypes are coded by
 Arabic numbers. The meaning of the numbers is explained in the csv-table
 “coding genotypes”.
DOI: 10.5061/dryad.x69p8czjt
title: Vegetation responses to Soay sheep grazing on St Kilda

description: 1. The population of Soay sheep on the island of Hirta in the Outer
 Hebrides has been the subject of continuous study for more than 35 years.
 This paper focuses on the botanical aspects of the plant-herbivore
 interaction, showing how the vegetation affects and is affected by the
 sheep. 2. Grazing impacts on biomass and spatial structure varied across
 plant communities, with Holcus/Agrostis grasslands affected most and Wet
 Heath least, consistent with the hypothesis that herbivore impacts are
 proportional to plant productivity. 3. Within plant communities, the
 negative relationships between sheep numbers and plant abundance (sward
 height, gap/tussock cover and biomass) were significant in March but not
 significant in August, as expected if sheep numbers are limited by food
 supply in winter. 4. In most species, flower stem density declined with
 increasing sheep numbers. There were no examples where unpalatable plants
 showed increased flowering (e.g. from competitor release under selective
 grazing). 5. Plant production in temporary grazing exclosures (above
 ground net primary production) was greatest in Holcus/Agrostis grassland
 (12.6t/ha dry matter/year), lower in Nardus grassland (5.1t/ha/yr) and
 least in Plantago sward (1.3t/ha/yr) associated with differences in
 historical nutrient supply and microclimate.   6. The net effect
 of grazing on plant species richness was positive: a few highly palatable
 species were excluded, but small-scale coexistence of grazing tolerant
 species was enhanced by defoliation. 7. The Soay sheep population
 fluctuated from 908 (in 1988) to 2208 (in 2009), increasing by an average
 of 39 extra animals per year over the period 1985-2011. Between 2011 and
 2020, the population fluctuated less widely and showed no trend. 8.
 Population change (ln(N(t+1)/N(t)) was inversely density dependent but
 positively correlated with plant production in Holcus/Agrostis grassland
 which increased during the study. 9. This plant-herbivore interaction is
 highly resilient, and though some species (Festuca rubra and Ranunculus
 acris) declined in the Holcus/Agrostis grassland, there was no significant
 upward trend in the abundance of unpalatable plant species. 10.
 Implications for future studies and analyses of plant-herbivore data.
 Concentrating on estimating primary productivity and herbivore offtake,
 rather than simply measuring change in plant biomass, is likely to provide
 greatly improved explanatory power for understanding herbivore population
 dynamics.
description: Field work on St Kilda in March and August each year from 1993 to
 2017
description: Missing values are entered as NA
DOI: 10.5061/dryad.r4xgxd2d3
title: Data from: Local diversity in phenological responses of migratory lake sturgeon to warm winters

description: Rich intraspecific diversity in traits that shape responses to
 environmental conditions implies that effects of climate change will
 differ within species or even populations. Nevertheless, few studies
 investigate how different groups within species respond to climatic
 fluctuations, and most risk assessments rely upon species-wide
 generalizations. We studied effects of among-year variation in air
 temperature on the spring migratory phenology of a metapopulation of lake
 sturgeon (Acipenser fulvescens) within waters connecting Lake Huron and
 Lake Erie of the Laurentian Great Lakes. Sturgeon here express multiple
 migratory phenotypes that all spawn in either the St. Clair River or
 Detroit River but differ in their use after spawning of more than 86,000
 km2 of accessible lake and river habitat. Acoustic tracking over nine
 years (2012-2020) revealed mixed phenological responses to late-winter air
 temperatures, with three migratory groups arriving at rivers earlier
 during warm years and one whose arrival was consistent across years
 regardless of temperature. Notably, two groups that spawn in the same
 river but overwinter in different lakes entered the river with greater
 synchrony during warm years because one advanced its phenology while the
 other did not. The results indicated warm weather could alter the dynamics
 of the metapopulation and broader community, and exemplify the complexity
 hidden beneath broadscale generalizations of species’ response to climate
 change.
DOI: 10.5061/dryad.000000048
title: Decline in telomere length with increasing age across non‐human vertebrates: a meta‐analysis

description: The prediction that telomere length (TL) shortens with increasing age is a
 major element in considering the role of telomeres as a key player in
 evolution. While telomere attrition is found in humans both in vitro and
 in vivo, the increasing number of studies reporting diverse age-specific
 patterns of TL challenges the hypothesis of a universal decline of TL with
 increasing age. Here we performed a meta-analysis to estimate the
 relationship between TL and age across 175 estimates encompassing 98
 species of vertebrates. We found that, on average, TL does decline with
 increasing age during adulthood. However, this decline was weak and
 variable across vertebrate classes, and we also found evidence for a
 publication bias that might weaken our current evidence of decreasing TL
 with increasing age. We found no evidence for a faster decline in TL with
 increasing age when considering the juvenile stage (from birth to age at
 first reproduction) compared to the adult stage. Heterogeneity in TL
 ageing rates was explained by the method used to measure telomeres:
 detectable TL declines with increasing age were found only among studies
 using TRF with in-gel hybridisation and qFISH methods, but not in studies
 using qPCR and Southern blot-based TRF methods. While we confirmed that TL
 declines with increasing age in most adult vertebrates, our results
 identify an influence of telomere measurement methodology, which
 highlights the need to examine more thoroughly the effect of the method of
 measurement on TL estimates.
DOI: 10.5061/dryad.5qfttdz62
title: Data from: Environmental conditions during development affect sexual selection through trait-fitness relationships

description: Sexual selection can be shaped by spatial variation in environmental
 features among populations. Differences in sexual selection among
 populations generated through the effects of the environment could be
 shaped via four paths: differences in mean absolute fitness, differences
 in the means or variances of phenotypes, or differences in the absolute
 fitness-trait function relationship. Because sexual selection only occurs
 during the adult life stage, most studies have focused on identifying
 environmental features that influence these metrics of fitness and trait
 distributions among adults. However, these adult features could also be
 affected by environmental factors experienced in early life stages that
 then shape the trajectory for sexual selection during the adult life
 stage. Here we investigated how among-population variation in
 environmental conditions during the juvenile (larval) stage of two species
 of Enallagma damselflies shapes sexual selection on male
 body size. We found that environmental factors related to predation
 pressures, lake primary productivity, and habitat availability have a role
 in shaping spatial variation in sexual selection. This acts mainly through
 how the environment affects absolute fitness-body size associations, not
 spatial variation in mean fitness or body size means and variances. These
 results demonstrate that the underpinnings of sexual selection in the wild
 can arise from environmental conditions during pre-reproductive life
 stages.