cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pvmcvdnjn
title: Near-complete sequence of a novel reovirus genome identified from Callinectes sapidus

description: The Atlantic blue crab, Callinectes sapidus, is an estuarine keystone
 species that functions as both predator and prey in food webs and supports
 a multi-million dollar fishery along the western Atlantic coast from the
 US mid-Atlantic to southern Brazil. Throughout their range, blue crabs are
 host to viral, bacterial, fungal, protozoan, and metazoan pathogens.
 Reoviruses are non-enveloped icosahedral viruses with genomes comprised of
 9 to 12 segments of linear double-stranded RNA (dsRNA). They have been
 found in diverse host species including brachyuran
 crustaceans. This work describes the sequence of a novel reovirus
 genome, discovered in Callinectes sapidus. The double-stranded RNA genome
 of CsRV2 consists of 12 segments that encode 13 putative proteins. High
 nucleotide sequence identity with Eriocheir sinensis Reovirus 905 revealed
 this virus belongs to Cardoreovirus within the Reoviridae family.
description: Viral RNA was detected from total
 RNA isolated from the muscle of infected
 <i>C. sapidus</i>
 walking leg. DsRNA purified by CF11 cellulose
 chromatography, was used for cDNA synthesis with
 barcoded octamers (5’-GGCGGAGCTCTGCAGATATC-NNNNNNN-3’) and the resulting cDNA was amplified by PCR using the barcode primers (5’-GGCGGAGCTCTGCAGATATC-3’). PCR products of 250-500 bp were obtained by gel purification and DNA library preparation was performed using NEBNext Ultra DNA Library Prep kit following the manufacturer’s recommendations (Illumina, San Diego, CA, USA). The library was sequenced in a 2 × 250 paired-end configuration on the Illumina MiSeq platforms. After quality trimming and removal of barcode sequences, the reads were assembled into contigs using CLC Genomics Workbench 9.5.2 (Qiagen).  In total, 12 viral genomic contigs were constructed, integrating data from a total of 51,168 reads (67.1% of the total reads), generating a total of 21,109 nucleotides at 560-fold average coverage with a mean G+C content of 41.4%.
description: The two fastq files are raw sequence data of the CsRV2 genome,
 and the zip file contains the assembled nucleotide sequences of each 12
 segments of CsRV2.
DOI: 10.5061/dryad.dv41ns1wj
title: A three year trans-generational plasticity in life history traits

description: 1. Environmental conditions of maternal plants influence adaptive
 strategies of their progeny via the seed phenotype. Although
 traditionally, studies have explained patterns of reproduction traits in
 response to stresses, such as the changes in seed mass and seed
 germinability under different maternal conditions. However, it is still
 unclear how maternal effects affect progeny dispersal and germination
 strategy or how many generations plasticity persists. 2. Plants from
 diaspore types A and C of the diaspore-heteromorphic annual halophyte
 Atriplex centralasiatica were grown in low (favorable) vs. high
 (stressful) salinities over three generations in a fully factorial design.
 We measured life history traits and reproductive characteristics of
 progeny plants for a three-year transgenerational plasticity (TGP)
 experiment covering F0, F1, and F 3. TGP of plants grown in favorable vs.
 stressful salinities decreased from F2 → F1 → F0. Compared to the
 favorable condition, the stressful condition decreased the length of the
 vegetative period, extended length of reproductive time and increased
 reproductive allocation and size of progeny diaspores. Salinity tolerance
 and phenotypic plasticity were higher in plants from diaspore A than in
 those from diaspore C. In the stressful condition, plants produced less
 plant biomass, larger diaspores, a higher proportion of type C diaspores
 with dormancy and higher dispersal potential, but lower proportion of type
 A diaspores with nondormancy and lower dispersal potential. In addition,
 production of the proportion of type C diaspores increased with increase
 in number of previous generations that experienced stress. 4. Synthesis:
 The trade-off of reproductive allocation between diaspores A versus C
 enables plants to develop divergent strategies via both high diaspore C
 allocation to disperse progeny spatiotemporally across wide areas in
 stress conditions and high diaspore A allocation to limit progeny near
 maternal plants in favorable habitats. These findings provide evidence for
 the “escape strategy” by which the progeny of A. centralasiatica diffused
 spatially (dispersal) and temporally (dormancy) by TGP, thus allowing them
 to survive environmental heterogeneity in their cold desert habitats.
DOI: 10.5061/dryad.8931zcrph
title: Association of hemoglobin A1C with TDP-43 pathology: Supplemental materials

description: Objective. We tested the hypothesis that an inverse association exists
 between diabetes mellitus (DM) and hemoglobin A1C (A1C) with Transactive
 response DNA binding protein 43 (TDP-43) levels in older adults. Methods.
 We leveraged antemortem and postmortem data of decedents from three
 community-based clinical-pathological studies. DM status, A1C levels, and
 medications for DM were documented annually. TDP-43 cytoplasmic
 inclusions, evaluated in 6 brain regions using immunohistochemistry, were
 used to obtain a semiquantitative TDP-43 score (0-5) in each region, and
 scores were averaged across regions to obtain a TDP-43 severity score. We
 used linear regressions to test the association of DM and A1C with the
 TDP-43 severity score. Results. On average, participants (n=817) were 90
 years old at the time of death, three fourth were women, and one fourth
 had DM. The mean A1C was 6.0% (SD=0.6). TDP-43 was observed in 54% of
 participants, and the mean TDP-43 score was 0.7 (range 0-4.5). A higher
 level of A1C was associated with a lower TDP-43 score (estimate=-0.156,
 S.E.=0.060, p=0.009) while DM had a borderline inverse association with
 the TDP-43 score (estimate=-0.163, S.E.=0.087, p=0.060). The association
 of higher levels of A1C with lower TDP-43 scores persisted after further
 adjustment by Apolipoprotein ε4, vascular risk factors, stroke, and
 hypoglycemic medications. Exclusion of the oldest old participants did not
 change the results. Conclusion. Overall, the results suggest that a high
 level of A1C is associated with less TDP-43 proteinopathy in older persons
 while the relationship of DM with TDP-43 needs further study.
DOI: 10.15468/dl.kgzja9
title: Occurrence Download

description: A dataset containing 865 records in GBIF matching the query:
SELECT
 '445' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 41.89415215079384
 AND decimalLatitude &lt;= 46.479780028101516
 AND decimalLongitude &gt;= 53.94667277126278
 AND decimalLongitude &lt;= 62.94398091796209
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 865 records were derived from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002652-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6hdr7sqzk
title: Supplementary material for: Testing for a dietary shift in the Early Cretaceous ceratopsian dinosaur Psittacosaurus lujiatunensis

description: Many dinosaurs may have shown ecological differentiation between
 hatchlings and adults, possibly because of the great size differential.
 The basal ceratopsian Psittacosaurus lujiatunensis is known from thousands
 of specimens from the Early Cretaceous of China and these include many
 so-called ‘juvenile clusters’. During the early stages of ontogeny, P.
 lujiatunensis underwent a posture shift from quadrupedal to bipedal, and a
 dietary shift has also been postulated. In this study, we apply a 2D
 mechanical analysis of the jaws of a hatchling and an adult to determine
 the differences between the two systems and found some differences, but
 only modest. The adult was better suited to feeding on tough plant
 material than the hatchling, based on its higher values of absolute and
 relative bite forces and higher values of mechanical advantage, but there
 were no substantial shifts in jaw shape or function.
DOI: 10.5061/dryad.1g1jwsttw
title: Data from: Anthelmintic drugs modulate the acute phase immune response but not the microbiota in wild Song Sparrows

description: Co-infection with microparasites (e.g., bacteria) and macroparasites
 (e.g., helminths) is often the natural state for wild animals. Despite
 evidence that gut helminths can bias immune responses away from
 inflammatory processes, few field studies have examined the role that
 helminths, or their potential interactions with internal microbial
 communities, play in modulating immunity in free-living, wild birds. Here,
 we used anthelmintic drugs to treat wild Song Sparrows (Melospiza melodia)
 for helminth infections and measured markers of systemic inflammation
 (heterothermia and locomotor activity) in response to an immune challenge
 with lipopolysaccharide (LPS), a cell wall component of gram-negative
 bacteria. Using birds from a population that previously showed
 high helminth prevalence, we monitored skin temperature and activity
 remotely using automated radio telemetry. We also collected
 cloacal swabs to determine whether drug treatment was associated
 with changes in the cloacal microbiota, and whether cloacal microbial
 community structure was associated with the severity of birds’
 immune responses. Because helminths can reduce the severity of
 inflammatory immune responses in other species, we predicted that
 in comparison with untreated control birds, anthelmintic-treated
 birds would be more lethargic and display higher fevers when
 challenged with LPS. Consistent with these predictions,
 anthelmintic-treated birds expressed higher fevers in response to immune
 challenge. However, all LPS-challenged birds decreased locomotor activity
 to a similar degree, regardless of anthelmintic treatment.
 Although several individual indicator bacterial taxa were strongly
 associated with anthelmintic treatment, this treatment did not
 alter overall bacterial alpha- and beta- diversity. Similarly, we
 did not find evidence that bacterial community diversity influenced the
 severity of immune responses to LPS. These results suggest that
 under field conditions, natural helminth infection can reduce the
 severity of songbirds’ thermoregulatory responses (fever) during
 an immune challenge, without major impacts on internal microbial
 communities or behavioral responses to infection.
description: Data were collected during field work with automated
 radiotelemetry and hand measurements. Sequencing data were collected with
 Illumina MiSeq.
DOI: 10.15468/dl.gqfrww
title: Occurrence Download

description: A dataset containing 28823457 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 28823457 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002653-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6078/d1pt3w
title: Comparative transcriptomics of a monocotyledonous geophyte reveals shared molecular mechanisms of underground storage organ formation

description: Many species from across the vascular plant tree-of-life have modified
 standard plant tissues into tubers, bulbs, corms, and other underground
 storage organs (USOs), unique innovations which allow these plants to
 retreat underground. Our ability to understand the developmental and
 evolutionary forces that shape these morphologies is limited by a lack of
 studies on certain USOs and plant clades; Bomarea
 multiflora (Alstroemeriaceae) fills a key gap in our
 understanding of USO molecular development as the first monocot with
 tuberous roots to be the focus of this kind of research.  We take
 a comparative transcriptomics approach to characterizing the molecular
 mechanisms of tuberous root formation in B. multiflora and
 compare these mechanisms to those identified in other USOs across diverse
 plant lineages. We sequenced transcriptomes from the growing tip of four
 tissue types (aerial shoot, rhizome, fibrous root, and root tuber) of
 three individuals of B. multiflora.  We identify differentially
 expressed isoforms between tuberous and non-tuberous roots and test the
 expression of a priori candidate genes implicated in underground
 storage in other taxa. We identify 271 genes that are differentially
 expressed in root tubers versus non-tuberous roots, including genes
 implicated in cell wall modification, defense response, and starch
 biosynthesis. We also identify a phosphatidylethanolamine-binding protein
 (PEBP), which has been implicated in tuberization signalling in other taxa
 and, through gene-tree analysis, place this copy in a phylogenetic
 context. These findings suggest that some similar molecular processes
 underlie the formation of underground storage structures across flowering
 plants despite the long evolutionary distances among taxa and
 non-homologous morphologies (e.g., bulbs versus tubers).
description: This dataset includes the following files. Analysis information
 detailed in https://github.com/cmt2/bomTubers. 
 Trinity.fasta - the assembled consensus transcriptome for
 <em>Bomarea multiflora </em>of all tissue types
 trinotate_annotation_report.csv - the annotation report from the
 Trinotate pipeline for Trinity.fasta
 RSEM.isoform.counts.matrix - Quantification of 'genes'
 by tissue (aerial shoot = SAM, rhizome meristem = RHI, tuberous root tip =
 TUB, fibrous root tip = ROO)  pebp_genes.fasta -
 Alignment of PEBP genes used in gene tree analysis
 pebp_genes.tre - Gene tree file
DOI: 10.5061/dryad.sbcc2fr54
title: R code, spatial and tabular data to fully reproduce STEPS simulations of population change for common brushtail possum, grassland melomys and northern brown bandicoot in northern Australia

description: The development of effective fire management for biodiversity conservation
 is a global challenge. The highly dynamic nature of fire, the difficulty
 in replicating ‘real-world’ fire experiments, and the need to understand
 population changes at large spatiotemporal scales make computer
 simulations particularly useful for identifying optimal fire management
 regimes for biodiversity conservation. We aimed to develop a flexible
 modelling approach with which to investigate how the spatiotemporal
 application of fire (i.e. management scenarios) influences savanna
 biodiversity. We used existing data from a landscape-scale fire experiment
 to develop population simulations for the common brushtail possum
 (Trichosurus vulpecula), grassland melomys (Melomys burtoni) and northern
 brown bandicoot (Isoodon macrourus) across the Kapalga area of Kakadu
 National Park in northern Australia. We simulated how populations were
 expected to change between 1995 and 2015 in response to the fire patterns
 observed at Kapalga over this period, and under a hypothetical management
 scenario of extensive prescribed burning. Our models predicted a
 substantial decline in all three species in response to the observed fire
 regime at Kapalga, suggesting that the fire patterns observed at Kapalga,
 with the associated mechanisms and interactions with other ecological
 processes, were not conducive with the persistence of native mammal
 populations. Our prescribed burning scenario had little effect on the
 predicted population trajectory of the common brushtail possum and
 grassland melomys, but markedly improved the population trajectory of the
 northern brown bandicoot. These inconsistencies highlight the need for a
 nuanced approach to fire management across northern Australian savannas,
 that is tailored to local conditions and management objectives. Synthesis
 and applications. The modelling approach outlined here, provides a basis
 for identifying fire patterns that are beneficial for conserving
 biodiversity, thereby increasing our capacity to establish clear targets
 for prescribed fire management. Importantly, this approach is flexible and
 can be easily adapted to other taxa and fire-prone ecosystems.
DOI: 10.15468/dl.zgq6bd
title: Occurrence Download

description: A dataset containing 56 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Hopea hainanensis"
 ]
}

 The dataset includes 56 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002662-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7280/d1zt3d
title: Genome-wide architecture of adaptation in experimentally evolved Drosophila dataset

description: The molecular basis of adaptation remains elusive even with the current
 ease of sequencing the genome and transcriptome. Previous attempts to
 address this question have knocked out or knocked down genes, but these
 approaches are not applicable to populations with moderate to high genetic
 variation. By contrast, experimental evolution offers replicated outbred
 populations with well-defined selection regimes and known evolutionary
 histories. We used experimentally evolved populations of Drosophila in
 conjunction with statistical learning tools to explore interactions
 between the genome, the transcriptome, and phenotypes. Our results
 indicate that transcriptomic measures from adult samples can predict
 phenotypic characters at many adult ages, which is consistent with the
 presumed quiescence of the Drosophila transcriptome during adulthood.
 Importantly, when comparing the genome and transcriptome in predicting
 phenotypic characters, we find that the two types of data are comparably
 useful. When using genome sites as predictors for the expression of the
 transcriptome, we find that gene expression is influenced by genomic
 regions across all large chromosome arms. Conversely, we found many
 genomic regions influencing the expression of numerous genes, which is
 consistent with widespread pleiotropy. Our results also highlight the
 power of the combination of experimental evolution, next-generation
 sequencing, and statistical learning tools in exploring the molecular
 basis of adaptation.
DOI: 10.5061/dryad.j3tx95xcb
title: Quantifying capital vs. income breeding: new promise with stable isotope measurements of individual amino acids

description: 1. Capital breeders accumulate nutrients prior to egg development, then
 use these stores to support offspring. In contrast, income breeders rely
 on local nutrients consumed contemporaneously with offspring development.
 Understanding such nutrient allocations is critical to assessing wildlife
 reliance on different habitats. 2. Despite the contrast between these
 strategies, it remains challenging to trace nutrients from endogenous
 stores or exogenous food intake into offspring. Here, we tested a new
 solution to this problem. 3. Using tissue samples collected
 opportunistically from wild emperor penguins (Aptenodytes forsteri), which
 exemplify capital breeding, we hypothesized that the stable carbon (δ13C)
 and nitrogen (δ15N) isotope values of individual amino acids (AA) in
 endogenous stores (e.g., muscle) and in egg yolk and albumen reflect the
 nutrient sourcing that distinguishes capital versus income breeding.
 Unlike other methods, this approach does not require untested assumptions
 or diet sampling. 4. We found that over half of essential AA had δ13C
 values that did not differ between muscle and yolk or albumen, suggesting
 that most of these AA were directly routed from muscle into eggs. In
 contrast, almost all non-essential AA differed in δ13C values between
 muscle and yolk or between muscle and albumen, suggesting de novo
 synthesis. Over half of AA that have labile nitrogen atoms (i.e.,
 “trophic” AA) had higher δ15N values in yolk and albumen than in muscle,
 suggesting that they were transaminated during their routing into egg
 tissue. This effect was smaller for AA with less labile nitrogen atoms
 (i.e., “source” AA). 5. Our results indicate that the δ15N offset between
 trophic-source AA (Δ15Ntrophic-source) may provide an index of the extent
 of capital breeding. The value of emperor penguin Δ15NPro-Phe was higher
 in yolk and albumen than in muscle, reflecting the mobilization of
 endogenous stores; in comparison, the value of Δ15NPro-Phe was similar
 across muscle and egg tissue in previously-published data for
 income-breeding herring gulls (Larus argentatus smithsonianus). Our
 results provide a quantitative basis for using AA δ13C and δ15N, and
 isotopic offsets among AA (e.g., Δ15NPro-Phe), to explore the allocation
 of endogenous versus exogenous nutrients across the capital versus income
 spectrum of avian reproduction.
description: These are stable carbon isotope and stable nitrogen isotope
 values measured in amino acids from hydrolyzed proteins in samples of
 emperor penguin egg yolk, egg albumen, and skeletal muscle.