cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.05qfttf0n
title: Fish mock community with 41 species from 13 orders

description: Tissue extracts of 41 North American fish species were obtained from the
 Ministère des Forêts, de la Faune et des Parcs (Québec). The selected
 species were chosen to represent a diversity of families within the
 Actinopterygii, and to include some species known to be present at the
 Experimental Lakes Area. Muscle or fin tissue was extracted using
 Qiagen Blood and Tissue kits and equimolarised to 15ng/µl. Library
 preparation and next-generation sequencing (NGS) was performed by
 equimolarising the DNA and combining two replicate mock community
 libraries which were then PCR amplified and sequenced. Sequencing
 was conducted using 2x300bp Illumina MiSeq at the McGill University and
 Génome Québec Innovation Centre, Montréal.  
description: Tissue extracts of 41 North American fish
 species were obtained from the Ministère des Forêts, de la Faune et des
 Parcs (Québec). The selected species were chosen to represent a diversity
 of families within the Actinopterygii. Tissues were stored in ethanol at
 -20C before extraction. Muscle or fin tissue was extracted using Qiagen
 Blood and Tissue kits according to the manufacturer’s instructions
 and equimolarised to 15ng/µl using the Quant-iT Picogreen dsDNA assay
 kit.<br> <br> <strong>Library preparation and
 next-generation sequencing (NGS) </strong><br> Equimolar
 amounts of DNA were combined to make two replicate mock communities. The
 mixture of mock community DNA was amplified in triplicate with the Leray
 primer with the following PCR chemistry: 7.875µl nuclease free water,
 1.25µl 10X buffer (Genscript), 1mM MgCl2 (ThermoFisher Scientific), 0.1mM
 GeneDirex dNTPs, 0.0125mg bovine serum albumen (ThermoFisher Scientific),
 0.2mM each 10mM primer, 1.25U taq (GenScript) and 2µl DNA in a final
 volume of 12.5µl. The thermocycling regime followed that of the original
 paper. Amplicons were run on 1% agarose gel stained with SYBR™ Safe DNA
 Gel Stain (Thermo-Fisher Scientific) and visualized with UV
 light. Triplicate PCR amplicons for each sample were combined, cleaned
 with AMPure beads in a 0.75 ratio and indexed with the Nextera
 DNA indexing kit for 96 samples (Illumina). A second clean-up with AMPure
 beads was performed, and libraries were quantified and normalised to
 5ng/ul. Sequencing was conducted using 2x300bp Illumina MiSeq at the
 McGill University and Génome Québec Innovation Centre, Montréal.<br>
 <br> Leray, M., Yang, J.Y., Meyer, C.P. et al. A new versatile
 primer set targeting a short fragment of the mitochondrial COI region
 for metabarcoding metazoan diversity: application for characterizing coral
 reef fish gut contents. Front Zool 10, 34
 (2013). https://doi.org/10.1186/1742-9994-10-34
DOI: 10.5061/dryad.44j0zpcbf
title: Data from: Sexually-selected male weapon is associated with lower inbreeding load but higher gender load in the bulb mite

description: Elaborate sexually selected ornaments and armaments are costly but
 increase the reproductive success of their bearers (usually males). It has
 been postulated that high-quality males can invest disproportionately more
 in such traits, making those traits honest signals of genetic quality.
 However, genes associated with such traits may have sexually antagonistic
 effects on fitness. Here, using a bulb mite Rhizoglyphus robini, a species
 in which a distinct dimorphism exists between males in the expression of a
 sexually selected weapon, we compare inbreeding and gender load between
 lines derived from armed fighters and unarmed scramblers. After four
 generations of sib-mating, inbreeding depression for female fitness was
 significantly lower in fighter-derived lines compared to scrambler-derived
 lines, suggesting that fighter males had significantly higher genetic
 quality. However, outbred females from fighter-derived lines had
 significantly lower fitness compared to outbred females from
 scrambler-derived lines, demonstrating significant gender load associated
 with the presence of a sexually selected male weapon. Our results imply
 that under outbreeding, genetic benefits of mating with bearers of
 elaborate sexually selected traits might be swamped by the costs of
 decreased fitness of female progeny due to sexually antagonistic effects.
DOI: 10.5061/dryad.nzs7h44p0
title: Populations of arable weed species show intra-specific variability in germination base temperature but not in early growth rate

description: Key plant traits affecting growth performance can differ among and within
 species, influencing competitive plant community dynamics. We determined
 the intra-specific variability of germination base temperature among 13
 arable weed species and the seedlings’ early post-emergence relative
 growth rate among 21 species in climate chamber and green house
 experiments. Intra-specific variability was quantified with two seed
 populations (originating from contrasting climate in Germany &
 France) for the germination base temperature of 6 species and for the
 early growth rate of 16 species. Inter-specific variability for both
 traits was always higher than intra-specific variability. Within a given
 species, we found that germination base temperatures were higher in seeds
 stemming from colder climate populations. Seedling relative growth rates
 did not differ between seed populations. Models simulating weed growth
 should reflect these differences in germination traits among populations,
 especially when they are used for weed community assembly studies in a
 local to regional extent.
description: Please see the published article for materials and methods of the
 experiments.
description: The file contains the raw data used in the analyses and for
 producing the figures in manuscript and supplementary material.
 "Fig1_temperatures" contains daily measurements of air and soil
 temperatures from Dijon-Epoisses (France) and Rostock-Warnemünde(Germany).
 "Table3_Basetemperature_counts" contains all counts of
 germinated seeds during germination experiments, together with timing of
 the observations (given as time since start of the experiment).
 "RelativeGrowth_perPot" contains all information on the
 regressions fitted on leaf area measurements vs. thermal time since
 emergence for each plant in the experiment. The two tables relating to
 "Fig5" contain the typical date ranges of crop management
 measures  as well as typical emergence periods of important weeds in the
 regions of Rostock and Dijon. For more detailed information see the
 published article.
DOI: 10.7280/d1hq2z
title: Data from: Analysis of southern California mitigation banks with implications for The Wildlands Conservancy's Sacred Lands Network and Bluff Lake Reserve

description: I conducted a qualitative analysis of mitigation banks in southern
 California, and from interviews with nine individuals associated with the
 banks or with mitigation tools, reveal the overall lack of cohesive
 understanding of the purpose and integrity of mitigation banks. This
 reveals the uncertainty in banking but also presents an opportunity to
 make recommendations on improvements to this prominent tool. This analysis
 also lends support to The Wildlands Conservancy as they establish their
 Sacred Lands Network, an alternative to mitigation banking. This dataset
 contains three .csv files: Bankers Groups'
 Coding_Declassified, Individuals Groups' Coding_Declassified, and RCD
 MWD Groups' Coding Declassified. The .csv files contain two
 tabs: descriptive coding and major bins. The descriptive codes were
 developed from the in vivo codes of the original interview transcript.
 These are organized according to participant and question they answer. The
 major bins are the pattern codes that arose for each participant and a
 brief code is listed below that gave rise to that pattern code. 
description: This dataset was collected through interviews, the review of
 interview transcripts, and the in vivo codes that were contained
 within.  For ease, this dataset also contains the .csv
 file, Interview_Questions. This file contains the interview
 questions. 
description: This dataset is declassified in order to protect the privacy of
 the participants. Information that was removed was replaced with
 "###." Participant names are pseudonyms.
DOI: 10.5061/dryad.v6wwpzgsf
title: Patterns of annual and seasonal immune investment in a temporal reproductive opportunist

description:             Historically, investigations of how organismal investments in immunity fluctuate in response to environmental and physiological changes have focused on seasonally breeding organisms that confine reproduction to seasons with relatively unchallenging environmental conditions and abundant resources. The red crossbill, Loxia curvirostra, is a songbird that can breed opportunistically if conifer seeds are abundant, on both short, cold, and long, warm days, providing an ideal system to investigate environmental and reproductive effects on immunity. In this study, we measured inter- and intra-annual variation in complement, natural antibodies, PIT54, and leukocytes in crossbills across four summers (2010-2013) and multiple seasons within one year (summer 2011-spring 2012). Overall, we observed substantial changes in crossbill immune investment among summers, with interannual variation driven largely by food resources, while variation across multiple seasons within a single cone year was less pronounced and lacked a dominant predictor of immune investment. However, we found weak evidence that physiological processes (e.g., reproductive condition, moult) or abiotic factors (e.g., temperature, precipitation) affect immune investment. Collectively, this study suggests that a reproductively flexible organism may be able to invest in both reproduction and survival-related processes, potentially by exploiting rich patches with abundant resources. More broadly, these results emphasize the need for more longitudinal studies of trade-offs associated with immune investment.
DOI: 10.15468/dl.k2kz6g
title: Occurrence Download

description: A dataset containing 750 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((18.82718 46.00639,19.15633 43.40621,19.9889 42.52781,20.56976 41.75255,21.28616 42.11265,22.42852 42.25612,23.06747 43.15249,22.81576 44.61763,22.44788 44.79652,22.15745 44.64519,21.55722 45.19359,20.84083 45.77729,20.37614 46.22115,19.5823 46.24793,18.82718 46.00639))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cinclus cinclus"
 ]
}

 The dataset includes 750 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002389-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.nk98sf7qx
title: New onset neurologic events in people with COVID-19 infection in three regions in China

description: Objective: To investigate new-onset neurologic impairments
 associated with coronavirus disease 2019 (COVID-19). Methods:  A
 retrospective multicenter cohort study conducted between 18 January and 20
 March 2020 including people with confirmed COVID-19 from 56 hospitals
 officially designated in three Chinese regions; data were extracted from
 medical records. New-onset neurologic events as assessed by neurology
 consultants based on manifestations, clinical examination and
 investigations, in which critical events included disorders of
 consciousness, stroke, CNS infection, seizures and status epilepticus.
 Results:  We enrolled 917 people with average age 48.7
 years and 55% were male. The frequency of new onset critical neurologic
 events was 3.5% (32/917) overall and 9.4% (30/319) among those with severe
 or critical COVID-19. These were impaired consciousness (n=25) or/and
 stroke (n=10). The risk of critical neurologic events was highly
 associated with age above 60 years and previous history of neurological
 conditions. Non-critical events were seen in less than 1% (7/917),
 including muscle cramp, unexplained headache, occipital neuralgia, tic and
 tremor. Brain CT in 28 people led to new findings in nine. Findings from
 lumbar puncture in three with suspected CNS infection, unexplained
 headache or severe occipital neuralgia were unremarkable.
 Conclusions:  People with COVID-19 aged over 60 and
 neurologic comorbidities were at higher risk of developing critical
 neurologic impairment, mainly impaired consciousness and cerebrovascular
 accidents. Brain CT should be considered when new-onset brain injury is
 suspected, especially in people under sedation or showing an unexplained
 decline in consciousness. Evidence of direct acute insult of SARS-COV-2 to
 the CNS is still lacking.
DOI: 10.5061/dryad.qjq2bvqcz
title: Mate-finding dispersal reduces local mate limitation and sex bias in dispersal

description: 1. Sex-biased dispersal (SBD) often skews the local sex ratio in a
 population. This can result in a shortage of mates for individuals of the
 less-dispersive sex. Such mate limitation can lead to Allee effects in
 populations that are small or undergoing range expansion, consequently
 affecting their survival, growth, stability and invasion speed. 2. Theory
 predicts that mate shortage can lead to either an increase or a decrease
 in the dispersal of the less-dispersive sex. However, neither of these
 predictions have been empirically validated. 3. To investigate how
 SBD-induced mate limitation affects dispersal of the less-dispersive sex,
 we used Drosophila melanogaster populations with varying dispersal
 propensities. To rule out any mate-independent density effects, we
 examined the behavioral plasticity of dispersal in presence of mates as
 well as same-sex individuals with differential dispersal capabilities. 4.
 In the presence of high-dispersive mates, the dispersal of both male and
 female individuals was significantly increased. However, the magnitude of
 this increase was much larger in males than in females, indicating that
 the former show greater mate-finding dispersal. Moreover, the dispersal of
 either sex did not change when dispersing alongside high- or
 low-dispersive individuals of the same sex. This suggested that the
 observed plasticity in dispersal was indeed due to mate-finding dispersal,
 and not mate-independent density effects. 5. Strong mate-finding dispersal
 can diminish the magnitude of sex bias in dispersal. This can modulate the
 evolutionary processes that shape range expansions and invasions,
 depending on the population size. In small populations, mate-finding
 dispersal can ameliorate Allee effects. However, in large populations, it
 can dilute the effects of spatial sorting. 28-May-2020
description: The data represents fly counts. No processing was done to the
 data.
description: No missing values. No outlier rejection.
DOI: 10.5061/dryad.nzs7h44p1
title: REV-ERBalpha mediates complement expression and circadian regulation of microglial synaptic phagocytosis

description: The circadian clock has been shown to regulate various aspects of brain
 health including microglial and astrocyte activation. Here we report that
 deletion of the master clock protein BMAL1 induces robust increases in the
 expression of complement genes such as C3, C4b and C1q in the hippocampus.
 Loss of downstream REV-ERBa-mediated transcriptional repression led to
 increases in C4b in neurons and astrocytes as well as C3 protein in
 microglia and astrocytes. REV-ERBa deletion induced complement C3/C4b gene
 expression and increased microglial phagocytosis of synapses in the CA3
 region of the hippocampus. Finally, we observed diurnal variation in the
 degree of microglial synaptic phagocytosis in wild type mice which was
 abrogated by REV-ERBα deletion. This work uncovers the BMAL1-REV-ERBa axis
 as a regulator of complement expression and synaptic phagocytosis in the
 brain, thereby illuminating a novel mechanism of synaptic regulation by
 the circadian clock.
description: The dataset is a GraphPad Prizm files with the raw data which
 constitutes each figure in the paper. The actual graphs are included in
 the file, along with the underlying data.  The data includes gene
 expression data (qPCR) from brain samples, as well as image quantification
 data. Raw images were confocal stacks (not included) which were analyzed
 with Imaris software, with the resulting data being put into the GraphPad
 file.
DOI: 10.15468/dl.tqc78z
title: Occurrence Download

description: A dataset containing 235975 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen)",
 "Geometry POLYGON((-74.18 43.34,-54.59 43.34,-54.59 48.25,-74.18 48.25,-74.18 43.34))",
 "HasCoordinate is true",
 "License is one of (CC-BY-NC 4.0, CC-BY 4.0, CC0 1.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Fungi"
 ]
}

 The dataset includes 235975 records from 191 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002333-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.hmgqnk9df
title: Data from: Hidden genetic variance contributes to increase the short-term adaptive potential of selfing populations

description: Standing genetic variation is considered a major contributor to the
 adaptive potential of species. The low heritable genetic variation
 observed in self-fertilising populations has led to the hypothesis that
 species with this mating system would be less likely to adapt. However, a
 non-negligible amount of cryptic genetic variation for polygenic traits,
 accumulated through negative linkage disequilibrium, could prove to be an
 important source of standing variation in self-fertilising species. To
 test this hypothesis we simulated populations under stabilizing selection
 subjected to an environmental change. We demonstrate that, when the
 mutation rate is high (but realistic), selfing populations are better able
 to store genetic variance than outcrossing populations through genetic
 associations, notably due to the reduced effective recombination rate
 associated with predominant selfing. Following an environmental shift,
 this diversity can be partially remobilized, which increases the additive
 variance and adaptive potential of predominantly (but not completely)
 selfing populations. In such conditions, despite initially lower observed
 genetic variance, selfing populations adapt as readily as outcrossing ones
 within a few generations. For low mutation rates, purifying selection
 impedes the storage of diversity through genetic associations, in which
 case, as previously predicted, the lower genetic variance of selfing
 populations results in lower adaptability compared to their outcrossing
 counterparts. The population size and the mutation rate are the main
 parameters to consider, as they are the best predictors of the amount of
 stored diversity in selfing populations. Our results and their impact on
 our knowledge of adaptation under high selfing rates are discussed.
DOI: 10.15468/dl.ak6qca
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "CatalogNumber" : [
 "is one of (K-M000773765, K-M000235257, K-M000193561, K-M000772199, K-M000769747, K-M000081495, K-M000202914, K-M000954750, K-M000770171, K-M000951276, K-M000974224, K-M000235255, K-M000122088, K-M001441830, K-M000202919, K-M000949144, K-M000235264, K-M000195450, K-M000822527, K-M000235258, K-M000949121, K-M000098650, K-M001441780, K-M000193560, K-M000193562, K-M000195452, K-M000819799)"
 ]
}

 The dataset includes 27 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002388-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d2547d80p
title: Data from: Host-induced genome instability rapidly generates phenotypic variation across Candida albicans strains and ploidy states

description: Candida albicans is an opportunistic fungal pathogen of humans that is
 typically diploid yet has a highly labile genome tolerant of large-scale
 perturbations including chromosomal aneuploidy and loss-of-heterozygosity
 events. The ability to rapidly generate genetic variation is crucial for
 C. albicans to adapt to changing or stressful environments, like those
 encountered in the host. Genetic variation occurs via stress-induced
 mutagenesis or can be generated through its parasexual cycle, in which
 tetraploids arise via diploid mating or stress-induced mitotic defects and
 undergo nonmeiotic ploidy reduction. However, it remains largely unknown
 how genetic background contributes to C. albicans genome instability in
 vitro or in the host environment. Here, we tested how genetic background,
 ploidy, and the host environment impacts C. albicans genome stability. We
 found that host association induced both loss-of-heterozygosity events and
 genome size changes, regardless of genetic background or ploidy. However,
 the magnitude and types of genome changes varied across C. albicans strain
 background and ploidy state. We then assessed if host-induced genomic
 changes resulted in fitness consequences on growth rate and nonlethal
 virulence phenotypes and found that many host-derived isolates
 significantly changed relative to their parental strain. Interestingly,
 diploid host-associated C. albicans predominantly decreased host
 reproductive fitness, whereas tetraploid host-associated C. albicans
 increased host reproductive fitness. Together, these results are important
 for understanding how host-induced genomic changes in C. albicans alter
 its relationship with the host. IMPORTANCE Candida albicans is an
 opportunistic fungal pathogen of humans. The ability to generate genetic
 variation is essential for adaptation and is a strategy that C. albicans
 and other fungal pathogens use to change their genome size. Stressful
 environments, including the host, induce C. albicans genome instability.
 Here, we investigated how C. albicans genetic background and ploidy state
 impact genome instability, both in vitro and in a host environment. We
 show that the host environment induces genome instability, but the
 magnitude depends on C. albicans genetic background. Furthermore, we show
 that tetraploid C. albicans is highly unstable in host environments and
 rapidly reduces in genome size. These reductions in genome size often
 resulted in reduced virulence. In contrast, diploid C. albicans displayed
 modest host-induced genome size changes, yet these frequently resulted in
 increased virulence. Such studies are essential for understanding how
 opportunistic pathogens respond and potentially adapt to the host
 environment.
DOI: 10.15468/dl.gmqvtt
title: Occurrence Download

description: A dataset containing 616 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "DatasetKey is one of (Wildlife diversity of the Dogo-Kétou forest (Benin, West Africa), iNaturalist Research-grade Observations, NRM-Mammals, Field Museum of Natural History (Zoology) Mammal Collection, RBINS DaRWIN, RBINS Mammal collection, Census of the threatened species of Benin., Observation.org, Nature data from around the World, AMNH Mammal Collections, Museum of Comparative Zoology, Harvard University)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Phacochoerus aethiopicus",
 "Year 1788-2026"
 ]
}

 The dataset includes 616 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002387-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.