cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2rbnzs7s8
title: Fruits of Anacardiaceae from the Paleogene of the Paris Basin, France

description: Premise of research. The Anacardiaceae family is distributed throughout
 the vegetated continents. The fossil record indicates extensive
 diversification of the family during the Paleogene and, in particular,
 during the Eocene. Despite the abundant fossil record of this period,
 there are only a few reliable anacardiaceous fossils in the Paris Basin.
 Here, we aim to document newly recognized fossils of Anacardiaceae from
 the Paris Basin, understand their paleoecology, and discuss their
 biogeographic history. Methodology. Thirty-three lignite fruits were
 examined from two sites, one pre- and one post-the Paleocene-Eocene
 boundary, i.e., Petit Pâtis (Rivecourt) and Le Quesnoy (Houdancourt). The
 specimens were photographed and anatomy was studied using computed
 tomography and histological sections. Comparative analyses were undertaken
 using available descriptions of fossil and modern fruits of Anacardiaceae.
 Pivotal results. A new species is described, Cyrtocarpa biapertura sp.
 nov., based on a unilocular endocarp with two prominent apertures present
 on the ventral side, protruding into two lacunae surrounding the locule.
 Taphonomic analysis indicates that this plant grew close to river banks.
 Furthermore, a new record of Lannea europaea (Reid and Chandler) Chandler
 is reported from for the Eocene site. Conclusions. The occurrence of
 Cyrtocarpa in both the Paleocene and Eocene floras in the Paris Basin
 suggests similar vegetation during both time intervals. It is likely that
 both floras grew under similar subtropical climates. Moreover, it appears
 that the early Eocene shows an enrichment of the paleodiversity of
 Anacardiaceae and other plant families in the Paris Basin. The presence of
 Cyrtocarpa documents a rarely reported disjunction between the Paleogene
 of Europe and the recent tropical flora of South America.
description: CT-scan via the AST-RX
 platform of the Museum national d’Histoire naturelle (Paris, France, MNHN)
 was used for the Rivecourt specimen Riv-PPB 17 to reconstruct a 3D model,
 and gain access to the internal organization, the reconstruction was made
 using the software Mimics Innovation Suite.
DOI: 10.15468/dl.rrftff
title: Occurrence Download

description: A dataset containing 96 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "TaxonKey is Leptophlebia vespertina"
 ]
}

 The dataset includes 96 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003395-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.t1g1jwt61
title: Data: Upper thermal limits and risk of mortality of coastal Antarctic ectotherms

description: Antarctic marine animals face one of the most extreme thermal
 environments, characterized by a stable and narrow range of low seawater
 temperatures. At the same time, the Antarctic marine ecosystems are
 threatened by accelerated global warming. Determining the upper thermal
 limits (CTmax) is crucial to project the persistence and distribution
 areas of the Antarctic marine species. Using thermal death time curves
 (TDT), we estimated CTmax at different temporal scales
 from 1 minute to daily and seasonal, the predict vulnerability to the
 current thermal variation and two potential heatwave scenarios. Our
 results revealed that CTmax at 1 min are far from the
 temperature present in the marine intertidal area where our study species,
 showing Echinoderm species higher CTmax than the
 Chordata and Arthropods species. Simulations indicated that seasonal
 thermal variation from the intertidal zone contributed to basal mortality,
 which increased after considering moderate scenarios of heatwaves (+2 °C)
 in the Shetland Archipelago intertidal zone. Our finding highlighted the
 relevance of including exposure time explicitly on
 the CTmax estimates, which deliver closer and more
 realistic parameters according to the species that may be experiencing in
 the field.
DOI: 10.15468/dl.2xrsrd
title: Occurrence Download

description: A dataset containing 197521 records in GBIF matching the query:
SELECT
 '474' 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;= 46.479780028101516
 AND decimalLatitude &lt;= 51.21395264452012
 AND decimalLongitude &gt;= 12.588796183592416
 AND decimalLongitude &lt;= 20.04431404917282
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 197521 records were derived from 397 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003370-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.j6q573nj4
title: Data for: Phylogenetically controlled life history trait meta-analysis in cetaceans reveals unexpected negative brain size and longevity correlation

description: The identification of patterns in trait evolution is essential to
 understand the interaction of evolutionary forces, and provides useful
 information for species management. Cetaceans are a phylogenetically
 well-resolved infraorder that exhibit distinct trait variation across
 behavioural, molecular and life history dimensions, yet few researchers
 have applied a meta-analytic or comparative approach to these traits. To
 understand cetacean trait evolution, we used a phylogenetic generalised
 least squares approach to examine the cognitive buffer hypothesis (CBH). A
 large brain should buffer individuals against environmental challenges
 through increasing survival rates, and a longer lifespan should buffer
 individuals against the cost of extended development for larger brains
 according to the CBH, leading to an expected positive correlation between
 brain size and lifespan. In contrast to this expectation, previously
 observed in taxa including primates, we found a negative correlation
 between brain size and lifespan in cetaceans. This suggests cetaceans
 experience selective pressures different from most other mammals in these
 traits but may be more similar to some social mammalian carnivores that
 display alloparenting. We also provide a comprehensive dataset to explore
 additional aspects of trait evolution but which would greatly benefit from
 studies on behavioural ecology across cetaceans and increased focus on
 data-deficient species. 
description: Please see the associated paper.
DOI: 10.15468/dl.cd4tcb
title: Occurrence Download

description: A dataset containing 15857 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Royal Botanic Gardens, Kew - Herbarium Specimens",
 "Country is Sweden"
 ]
}

 The dataset includes 15857 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003394-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.cjsxksn9g
title: Canis lupus fecal metabarcoding dataset

description: Although wolves are wide-ranging generalist carnivores throughout their
 life cycle, during the pup-rearing season wolf activity is focused on
 natal den sites where pup survival depends upon pack members provisioning
 food. Because prey availability is influenced by habitat quality within
 the home range, we investigated the relative importance of prey species
 for adults and pups and further examined the relationship between habitat
 characteristics, wolf diet, and litter size on Prince of Wales Island
 (POW) in Southeast Alaska. During 2012–2020, we detected 13 active den
 sites within the home ranges of 9 wolf packs. We estimated minimum pup
 counts using motion-detecting cameras and individual genotypes from
 noninvasive samples (hair: n = 322; scat: n = 227), and quantified wolf
 diet composition using fecal DNA metabarcoding (n = 538). We assessed
 habitat composition, configuration, and connectivity within denning and
 annual home ranges estimated using wolf GPS-collar data. Contrary to
 expectations, wolves had a more constricted diet during denning season
 (April 15–July 31), and, within this season, pups had a narrower dietary
 niche (species richness [S] = 4) focused more on deer (relative frequency
 of occurrence [O/I] = 0.924) than adults (S = 15; deer O/I = 0.591).
 Litter size had a positive relationship with the relative frequency of
 deer in a wolf pack’s diet. Wolf consumption of deer was positively
 associated with the proportion of young-growth forest (≤25 years old)
 within denning and annual home ranges. High levels of vegetation patch
 interspersion and the density of closed logging roads were also important
 predictors, suggesting these habitat qualities were influential for
 increasing the availability of deer to wolves. Our results contrast with
 previous research indicating wolf pup diets included more alternate prey
 (i.e., beaver) than adults, and emphasize the importance of deer to wolf
 viability on POW, especially during denning season.
DOI: 10.6084/m9.figshare.30748301
title: Identification of the immunodominant regions of P1 protein of two genotypes of Mycoplasma pneumoniae through monoclonal antibodies

description: Mycoplasma pneumoniae (M. pneumoniae), is a significant human respiratory pathogen causing severe atypical pneumonia. Its pathogenicity critically depends on cell adhesion, primarily mediated by the large adhesin protein P1, which contains multiple immunodominant epitopes. However, a precise mapping of these epitopes, particularly in the context of prevalent genotypes I and II, is essential for advancing diagnostic and therapeutic strategies. This study aimed to address this gap by generating specific monoclonal antibodies (mAbs) and delineating the key immunodominant regions on the P1 protein. Sequence alignment of P1 from genotypes I and II revealed high homology, with bioinformatics predicting dominant epitopes clustered in the C-terminal region. Consequently, the C-terminal fragments of both genotypes were recombinantly expressed in a prokaryotic system and used to immunize BALB/c mice for mAb production. Guided by bioinformatic analysis, nine overlapping peptides spanning this region were synthesized. A systematic ELISA-based screening of five anti-P1 mAbs using these peptides. In summary, this study successfully produced genotype-specific mAbs against the P1 C-terminus and defined immunodominant epitopes. These findings provide crucial insights into the biological importance of the P1 protein in pathogenesis. Furthermore, the identified epitopes and specific mAbs establish a foundation for developing improved immunological detection methods and genotyping diagnostics for M. pneumoniae infections, potentially enhancing clinical management and epidemiological surveillance.
DOI: 10.6084/m9.figshare.30748301.v1
title: Identification of the immunodominant regions of P1 protein of two genotypes of Mycoplasma pneumoniae through monoclonal antibodies

description: Mycoplasma pneumoniae (M. pneumoniae), is a significant human respiratory pathogen causing severe atypical pneumonia. Its pathogenicity critically depends on cell adhesion, primarily mediated by the large adhesin protein P1, which contains multiple immunodominant epitopes. However, a precise mapping of these epitopes, particularly in the context of prevalent genotypes I and II, is essential for advancing diagnostic and therapeutic strategies. This study aimed to address this gap by generating specific monoclonal antibodies (mAbs) and delineating the key immunodominant regions on the P1 protein. Sequence alignment of P1 from genotypes I and II revealed high homology, with bioinformatics predicting dominant epitopes clustered in the C-terminal region. Consequently, the C-terminal fragments of both genotypes were recombinantly expressed in a prokaryotic system and used to immunize BALB/c mice for mAb production. Guided by bioinformatic analysis, nine overlapping peptides spanning this region were synthesized. A systematic ELISA-based screening of five anti-P1 mAbs using these peptides. In summary, this study successfully produced genotype-specific mAbs against the P1 C-terminus and defined immunodominant epitopes. These findings provide crucial insights into the biological importance of the P1 protein in pathogenesis. Furthermore, the identified epitopes and specific mAbs establish a foundation for developing improved immunological detection methods and genotyping diagnostics for M. pneumoniae infections, potentially enhancing clinical management and epidemiological surveillance.
DOI: 10.6084/m9.figshare.30748301.v2
title: Identification of the immunodominant regions of P1 protein of two genotypes of Mycoplasma pneumoniae through monoclonal antibodies

description: Mycoplasma pneumoniae (M. pneumoniae), is a significant human respiratory pathogen causing severe atypical pneumonia. Its pathogenicity critically depends on cell adhesion, primarily mediated by the large adhesin protein P1, which contains multiple immunodominant epitopes. However, a precise mapping of these epitopes, particularly in the context of prevalent genotypes I and II, is essential for advancing diagnostic and therapeutic strategies. This study aimed to address this gap by generating specific monoclonal antibodies (mAbs) and delineating the key immunodominant regions on the P1 protein. Sequence alignment of P1 from genotypes I and II revealed high homology, with bioinformatics predicting dominant epitopes clustered in the C-terminal region. Consequently, the C-terminal fragments of both genotypes were recombinantly expressed in a prokaryotic system and used to immunize BALB/c mice for mAb production. Guided by bioinformatic analysis, nine overlapping peptides spanning this region were synthesized. A systematic ELISA-based screening of five anti-P1 mAbs using these peptides. In summary, this study successfully produced genotype-specific mAbs against the P1 C-terminus and defined immunodominant epitopes. These findings provide crucial insights into the biological importance of the P1 protein in pathogenesis. Furthermore, the identified epitopes and specific mAbs establish a foundation for developing improved immunological detection methods and genotyping diagnostics for M. pneumoniae infections, potentially enhancing clinical management and epidemiological surveillance.
DOI: 10.5061/dryad.n2z34tn14
title: Data from: Geothermal stickleback populations prefer cool water despite multigenerational exposure to a warm environment

description: Given the threat of climate change to biodiversity, a growing number of
 studies are investigating the potential for organisms to adapt to rising
 temperatures. Earlier work has predicted that physiological adaptation to
 climate change will be accompanied by a shift in temperature preferences,
 but empirical evidence for this is lacking. Here, we test whether exposure
 to different thermal environments has led to changes in preferred
 temperatures in the wild. Our study takes advantage of a ‘natural
 experiment’ in Iceland, where freshwater populations of threespine
 sticklebacks (Gasterosteus aculeatus) are found in waters warmed by
 geothermal activity year-round (warm habitats), adjacent to populations in
 ambient-temperature lakes (cold habitats). We used a shuttle-box approach
 to measure temperature preferences of wild-caught sticklebacks from three
 warm-cold population pairs. Our prediction was that fish from warm
 habitats would prefer higher water temperatures than those from cold
 habitats. We found no support for this, as fish from both warm and cold
 habitats had an average preferred temperature of 13oC. Thus, our results
 challenge the assumption that there will be a shift in ectotherm
 temperature preferences in response to climate change. In addition, since
 warm-habitat fish can persist at relatively high temperatures despite a
 lower temperature preference, this suggests that preferred temperature
 alone may be a poor indicator of a population’s adaptive potential to a
 novel thermal environment.
DOI: 10.5061/dryad.866t1g1tw
title: TWIS meta-analyzed summary statistics

description: It remains unknown to what extent gene-gene interactions contribute to
 complex traits. Here, we introduce a new approach using predicted gene
 expression to perform exhaustive transcriptome-wide interaction studies
 (TWISs) for multiple traits across all pairs of genes expressed in several
 tissue types. Using imputed transcriptomes, we simultaneously reduce the
 computational challenge and improve interpretability and statistical
 power. We discover and replicate several interaction associations and find
 several hub genes with numerous interactions. We also demonstrate that
 TWIS can identify novel associated genes because genes with many or strong
 interactions have smaller single-locus model effect sizes. Finally, we
 develop a method to test gene set enrichment of TWIS associations
 (E-TWIS), finding numerous pathways and networks enriched in interaction
 associations. Epistasis is likely widespread, and our procedure represents
 a tractable framework for beginning to explore gene interactions and
 identify novel genomic targets.
description: We developed Transcriptome-Wide Interaction Study (TWIS), a new
 method that comprehensively tests associations of all pairwise gene-gene
 interactions with complex traits using imputed expression. We applied the
 method to 12 complex traits in humans across four tissues/cross-tissue
 expression measures. We applied the method to multiple datasets, then
 meta-analyzed the results using METAL.
description: Files are compressed using gzip.
 Transcriptome-wide interaction study (TWIS): code available at
 https://github.com/evanslm/TWIS.
DOI: 10.5061/dryad.0zpc86720
title: Main body part dominates crypsis in a flower-visiting spider

description: Camouflage is one of the most common defence strategies. Some crab spiders
 with uniform colouration have been demonstrated to camouflage on flowers
 via background matching. However, many more flower-visiting spiders do not
 have uniform body colour, and whether these species are cryptic on flowers
 needs more exploration. We investigated this question in a crab spider
 with a different-coloured abdomen and carapace, Ebrechtella tricuspidata,
 whose females and juveniles can normally be found on the flower petals of
 chamomile Matricaria recutita. We conducted predation experiments by using
 naive chicks as an avian predator of E. tricuspidata, to test
 whether avian predators could detect E. tricuspidata from flowers
 or leaves of M. recutita. We found that the probabilities of spiders that
 were detected and attacked were lower when the spider was on a flower
 petal than on a leaf, which supported the crypsis of E. tricuspidata.
 Furthermore, the visual modelling from the perspective of chicks showed
 that the spider abdomen matched the flower petal in both chromatic and
 achromatic contrast and was unlikely to be detected by avian predators.
 Taken together, our results indicate that E. tricuspidata is
 cryptic on chamomile flowers and has a much lower predation risk than on
 leaves. Importantly, E. tricuspidata is more representative than the
 species with uniform colouration. Thus, these findings highlight that
 camouflage may be widespread in flower-visiting spiders.
DOI: 10.5061/dryad.0vt4b8h39
title: Data from: Larger pollen loads increase risk of heat stress in foraging bumble bees

description: Global declines in bumblebee populations are linked to climate change, but
 specific mechanisms imposing thermal stress on these species are poorly
 known. Here we examine the potential for heat stress in workers foraging
 for pollen, an essential resource for colony development. Laboratory
 studies have shown that pollen foraging causes increased thoracic
 temperatures (Tth) in bees, but this effect has not been examined in
 bumblebees nor in real-world foraging situations. We examine the effects
 of increasing pollen load size on Tth of Bombus impatiens workers in the
 field while accounting for body size and microclimate. We found that Tth
 increased by 0.07°C for every mg of pollen carried (p = 0.007), resulting
 in a 2°C increase across the observed range of pollen load sizes. Bees
 carrying pollen were predicted to have a Tth 1.7–2.2°C hotter than those
 without pollen, suggesting that under certain conditions, pollen loads
 could cause B. impatiens workers to heat from a safe Tth to one within the
 range of critical thermal limits that we measured (41.3°C to 48.4°C).
 Bumblebees likely adopt behavioral or physiological strategies to
 counteract the thermal stress induced by pollen foraging and may have
 limited foraging opportunities as environmental temperatures continue to
 increase.
DOI: 10.15468/dl.w39qs9
title: Occurrence Download

description: A dataset containing 28470 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((3.39203 43.44612,3.48681 43.44612,3.48681 43.53656,3.39203 43.53656,3.39203 43.44612))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 28470 records from 346 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003396-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.gb5mkkwtd
title: Zebras of all stripes repel biting flies at close range

description: The best-supported hypothesis for why zebras have stripes is that stripes
 repel biting flies. While this effect is well-established, the mechanism
 behind it remains elusive. Myriad hypotheses have been suggested, but few
 experiments have helped narrow the field of possible explanations. In
 addition, the complex visual features of real zebra pelage and the natural
 range of stripe widths have been largely left out of experimental designs.
 In paired-choice field experiments in a Kenyan savannah, we found that
 hungry Stomoxys flies released in an enclosure strongly preferred to land
 on uniform tan impala pelts over striped zebra pelts but exhibited no
 preference between the pelts of the zebra species with the widest stripes
 and the narrowest stripes. Our findings confirm that zebra stripes repel
 biting flies under naturalistic conditions and do so at close range
 (suggesting that several of the mechanisms hypothesized to operate at a
 distance are unnecessary for the fly-repulsion effect) but indicate that
 interspecific variation in stripe width is associated with selection
 pressures other than biting flies.
description: Please see the Methods section of our open access paper in
 Scientific Reports (DOI: 10.1038/s41598-022-22333-7).
description: None are required to open the raw data provided in the ods file.
 However, R or RStudio are required to open the code provided, which loads
 the data in csv format (also provided).