cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b87h6
title: Data from: Managing trap-nesting bees as crop pollinators: spatiotemporal effects of floral resources and antagonists

description: 1. The decline of managed honeybees and the rapid expansion of
 mass-flowering crops increase the risk of pollination limitation in crops
 and raise questions about novel management approaches for wild pollinators
 in agroecosystems. Adding artificial nesting sites, such as trap nests,
 can promote cavity-nesting bees in agroecosystems, but effectiveness could
 be limited by the availability of floral resources in the surrounding
 landscape and by natural antagonists. 2. In two European regions, we
 exposed artificial trap nests in paired field boundaries adjacent to
 oilseed rape (OSR) fields or non-flowering crops for two years within 32
 landscapes covering two independent gradients of OSR cover and
 semi-natural habitat (SNH) cover in the landscape. We analysed the effects
 of local and landscape-wide floral resource availability, land-use
 intensity, landscape complexity and natural antagonists on community
 composition and population dynamics of trap-nesting bees. 3. Number of
 brood cells showed a strong, three-fold increase in response to the
 additional nesting sites. Species richness and abundance of cavity-nesting
 bees that were active during OSR flowering increased significantly with
 increasing amount of early-season landscape-wide floral resource
 availability, such as the cultivation of OSR. Later foraging species
 benefited instead from the availability of late-season alternative flower
 resources or SNH cover once the mass-flowering had ceased.
 Density-dependent parasitism increased following mass-flowering, while no
 density-dependent effect was found during mass-flowering. 4. Structural
 equation modelling revealed that the influence of floral resource
 availability on community growth rate was mediated by community size.
 Community size showed a strong negative effect on community growth rate.
 Despite positive density-dependent parasitism, antagonists had only weak
 regulating effects on community growth rate. 5. Synthesis and
 applications. Trap-nesting bee populations grow markedly with the
 increasing availability of food resources in the landscape and
 effectiveness of trap nests is only marginally limited by natural
 antagonists. Thus, trap nests could be a simple pollinator-supporting
 strategy to accompany the current expansion of mass-flowering crops, and
 to ensure pollination services for insect-pollinated crops. Trap nests
 benefit not only early season active generalist bees during oilseed rape
 flowering but also species with later phenology if accompanied by other
 pollinator-supporting practices.
description: TrapNest_Data_Dainese_etal_2017_JAPPLThe file contains all data used in the analyses of this paper.
DOI: 10.5061/dryad.46786
title: Data from: A robust and representative lower bound on object processing speed in humans

description: How early does the brain decode object categories? Addressing this
 question is critical to constrain the type of neuronal architecture
 supporting object categorization. In this context, much effort has been
 devoted to estimating face processing speed. With onsets estimated from 50
 to 150 ms, the timing of the first face-sensitive responses in humans
 remains controversial. This controversy is due partially to the
 susceptibility of dynamic brain measurements to filtering distortions and
 analysis issues. Here, using distributions of single-trial event-related
 potentials (ERPs), causal filtering, statistical analyses at all
 electrodes and time points, and effective correction for multiple
 comparisons, we present evidence that the earliest categorical differences
 start around 90 ms following stimulus presentation. These results were
 obtained from a representative group of 120 participants, aged 18-81, who
 categorized images of faces and noise textures. The results were reliable
 across testing days, as determined by test-retest assessment in 74 of the
 participants. Furthermore, a control experiment showed similar ERP onsets
 for contrasts involving images of houses or white noise. Face onsets did
 not change with age, suggesting that face sensitivity occurs within 100 ms
 across the adult lifespan. Finally, the simplicity of the face-texture
 contrast, and the dominant midline distribution of the effects, suggest
 the face responses were evoked by relatively simple image properties and
 are not face specific. Our results provide a new lower benchmark for the
 earliest neuronal responses to complex objects in the human visual system.
description: Face & noise
 single-trial ERPs from 194 recording sessionsftonsets.zip
DOI: 10.5061/dryad.sd8dp40
title: Data from: Early breeding females experience greater telomere loss

description: Annual reproductive success is often highest in individuals that initiate
 breeding early, yet relatively few individuals start breeding during this
 apparently optimal time. This suggests that individuals, particularly
 females who ultimately dictate when offspring are born, incur costs by
 initiating reproduction early in the season. We hypothesized that
 increases in the aging rate of somatic cells may be one such cost.
 Telomeres, the repetitive DNA sequences on the ends of chromosomes, may be
 good proxies of biological wear and tear as they shorten with age and in
 response to stress. Using historical data from a long-term study
 population of dark-eyed juncos (Junco hyemalis), we found that telomere
 loss between years was greater in earlier breeding females, regardless of
 chronological age. There was no relationship between telomere loss and the
 annual number of eggs laid or chicks that reached independence. However,
 telomere loss was greater when temperatures were cooler, and cooler
 temperatures generally occur early in the season. This suggests that
 environmental conditions could be the primary cause of accelerated
 telomere loss in early breeders.
description: TelomereCode.R code for analyses conducted in manuscriptDegradation.csv file with data for analysis of telomere degradation over time (ie., number of years sample was stored).FinalNestAge.csv file with all data for analyzing correlations of annual reproductive output, reproductive success, and age with seasonal nest initiation date.FinalTeloCode.csv file with all data for analyzing correlations of seasonal nest initiation, temperature, annual reproductive output, and reproductive success with change in telomere length.Repeatability.csv file with all data for analyzing repeatability of T/S ratio.DataColumnDescriptorsShort description of column titles in each .csv file.
DOI: 10.5061/dryad.th7kj
title: Data from: Genetic diversity and divergence in populations of the threatened grassland perennial Vincetoxicum atratum (Apocynaceae-Asclepiadoideae) in Japan

description: We examined the genetic diversity and structure in populations of the
 endangered grassland herb Vincetoxicum atratum using 11 polymorphic
 microsatellite loci. Although the populations were small and disconnected,
 our molecular data indicated that the species maintains relatively high
 levels of genetic diversity and connectivity among populations. Population
 clustering analyses detected two to three clusters and most of the
 populations of V. atratum comprised admixture of these genetic clusters.
 These admixtures likely formed during the process of colonizing habitats
 that had been disturbed by human activities. However, STRUCTURE clustering
 detected low-admixtures in populations occurring in rocky maritime sites,
 which may not be suitable for agriculture/rangeland activities. High
 genetic diversity and population connectivity suggested that loss of the
 remaining populations by grassland reduction might be an immediate threat
 for this species. Small grasslands populations managed by local farmers
 need appropriate conservation practices. Although our results showed
 genetic diversity and gene flow among populations of V. atratum were high,
 it is possible that this resulted from the historical continuous
 distribution of the species. To examine this hypothesis, further
 periodical monitoring of the genetic diversity and the genetic
 differentiation for the species is needed for a conservation action of the
 species.
description: atratum_primary_dataThis file contains Genepop and TESS formats of 11 micro satellite loci genotype on 13 Vincetoxicum atratum populations.
DOI: 10.15468/4d3neb
title: Redescription of the subgenus Rhithrogeniella Ulmer 1939 (Ephemeroptera, Heptageniidae, genus Ecdyonurus) based on reared specimens from India and Thailand

description: This dataset contains the digitized treatments in Plazi based on the original journal article Kluge, Nikita, Sivaruban, T., Srinivasan, Pandiarajan, Barathy, S., Isack, Rajasekaran (2023): Redescription of the subgenus Rhithrogeniella Ulmer 1939 (Ephemeroptera, Heptageniidae, genus Ecdyonurus) based on reared specimens from India and Thailand. Zootaxa 5319 (4): 501-523, DOI: 10.11646/zootaxa.5319.4.2, URL: http://dx.doi.org/10.11646/zootaxa.5319.4.2AbstractRhithrogeniella Ulmer 1939 is treated here as a subgenus of the genus Ecdyonurus Eaton 1868 (s. l.). The subgeneric name Rhithrogeniella is a senior synonym of Afghanurus Demoulin 1964 syn. n., Paracinygmula Bajkova 1975 syn. n. and Nixe Flowers 1980 syn. n. Additional description of Ecdyonurus (Rhithrogeniella) ornatus (Ulmer 1939) is given based on imagines and subimagines of both sexes reared from larvae in India and Thailand; lectotype of this species name is designated. Synonymy of E. (Rh.) ornatus and E. (Rh.) tonkinensis Soldán & Braasch 1986 is established (syn. n.). Male and female imagines and subimagines of an unnamed species of Rhithrogeniella are reported from India.
DOI: 10.5061/dryad.06575
title: Data from: Gametic selection, developmental trajectories, and extrinsic heterogeneity in Haldane's rule

description: Deciphering the genetic and developmental causes of the disproportionate
 rarity, inviability and sterility of hybrid males, Haldane's rule, is
 important for understanding the evolution of reproductive isolation
 between species. Moreover, extrinsic and pre-zygotic factors can
 contribute to the magnitude of intrinsic isolation experienced between
 species with partial reproductive compatibility. Here we use the nematodes
 Caenorhabditis briggsae and C. nigoni to quantify the sensitivity of
 hybrid male viability to extrinsic temperature and developmental timing,
 and test for a role of mito-nuclear incompatibility as a genetic cause. We
 demonstrate that hybrid male inviability manifests almost entirely as
 embryonic, not larval, arrest and is maximal at the lowest rearing
 temperatures, indicating an intrinsic-by-extrinsic interaction to hybrid
 inviability. Crosses using mitochondrial substitution strains that have
 reciprocally introgressed mitochondrial and nuclear genomes show that
 mito-nuclear incompatibility is not a dominant contributor to post-zygotic
 isolation and does not drive Haldane's rule in this system. Crosses
 also reveal that competitive superiority of X-bearing sperm provides a
 novel means by which post-mating pre-zygotic factors exacerbate the rarity
 of hybrid males. These findings highlight the important roles of gametic,
 developmental, and extrinsic factors in modulating the manifestation of
 Haldane's rule.
description: Mitochondrial
 replacement crosses (briggsae maternal)Total offspring &
 proportion male for all crosses where C. briggsae is the nuclear maternal
 parentBriggsaemtfinal.txtNigoni mitochondria replacement crossesMitochondrial replacement crosses. All crosses where the maternal nuclear genotype is C. nigoninigoni mt .txtTemperature & Haldane's ruleC. nigoni intraspecific crosses and C. nigoni x C. briggsae crosses at a range of temperatures. Columns show the paternal strain (AF16=briggsae, JU1421=nigoni). The total male offspring and female offspring produced each day is shown. e.g. D0_M shows the total male offspring laid on the first day after mating.Temperature & Haldanes rule.txtC. nigoni females x C. briggsae males. Development of hybrid offspringTotal hybrid offspring alive at different developmental stages. m=male, f=female. L1-L4 are the larval stages of development.6JuneDevelopment.txtC. briggsae hermaphrodites x C. nigoni males development of hybridsTotal hybrid offspring alive at different developmental stages. L1-L4 are the larval stages of development. No males were observed at any stage.bri_f_traj.txt
DOI: 10.5061/dryad.s1d25
title: Data from: Marker-dependent associations among oxidative stress, growth and survival during early life in a wild mammal

description: Oxidative stress (OS) is hypothesized to be a key physiological mechanism
 mediating life-history trade-offs, but evidence from wild populations
 experiencing natural environmental variation is limited. We tested the
 hypotheses that increased early life growth rate increases OS, and that
 increased OS reduces first-winter survival, in wild Soay sheep (Ovis
 aries) lambs. We measured growth rate and first-winter survival for four
 consecutive cohorts, and measured two markers of oxidative damage
 (malondialdehyde (MDA), protein carbonyls (PC)) and two markers of
 antioxidant (AOX) protection (total AOX capacity (TAC), superoxide
 dismutase (SOD)) from blood samples. Faster lamb growth was weakly
 associated with increased MDA, but not associated with variation in the
 other three markers. Lambs with higher SOD activity were more likely to
 survive their first winter, as were male but not female lambs with lower
 PC concentrations. Survival did not vary with MDA or total TAC. Key
 predictions relating OS to growth and survival were therefore supported in
 some OS markers, but not others. This suggests that different markers
 capture different aspects of the complex relationships between individual
 oxidative state, physiology and fitness, and that overarching hypotheses
 relating OS to life-history variation cannot be supported or refuted by
 studying individual markers.
description: RSPB-2016-1407
 DataData file used in
 analyses presented in this paper
DOI: 10.5061/dryad.7mt1t
title: Data from: Development of MHC-linked microsatellite markers in the domestic cat and their use to evaluate MHC diversity in domestic cats, cheetahs and Gir lions.

description: Diversity within the major histocompatibility complex (MHC) reflects the
 immunological fitness of a population. MHC-linked microsatellite markers
 provide a simple and inexpensive method for studying MHC diversity in
 large scale studies. We have developed six MHC-linked microsatellite
 markers in the domestic cat and used these, in conjunction with five
 neutral microsatellites, to assess MHC diversity in domestic mixed breed
 (n = 129) and purebred Burmese (n = 61) cat populations in Australia. The
 MHC of outbred Australian cats is polymorphic (average allelic richness =
 8.52) while the Burmese population has much significantly lower MHC
 diversity (average allelic richness = 6.81; P&lt;0.01). The MHC-linked
 microsatellites along with MHC cloning and sequencing demonstrated
 moderate MHC diversity in cheetahs (n = 13) and extremely low diversity in
 Gir lions (n = 13). Our MHC-linked microsatellite markers have potential
 future use in diversity and disease studies in other populations and
 breeds of cats as well as in wild felid species.
description: Cheetah MHC class I
 sequencesCheetah MHC class I
 alpha 1 domain sequencescheetahsequencesfordryad.txtLion MHC class I sequencesGir Lion MHC class I alpha 1 domain sequenceslionsequencesfordryad.txtDomestic cat microsatellite dataDomestic cat microsatellite data for 6 MHC-linked and 5 neutral microsatellites in two breeds, domestic mixed breed (DSH) and Burmese (BUR)Micosatellite_data.xlsxCheetah microsatellite dataCheetah microsatellite data for 3 MHC-linked microsatellite markers in two cheetah subspecies, jubatus and raineye.cheetah_microsatellite_data.xlsx
DOI: 10.5061/dryad.b43gf
title: Data from: Proportion of women presenters at medical grand rounds at major academic centres in Canada: a retrospective observational study

description: Objective: To assess the proportion of women who presented research or
 medical grand rounds at five major academic hospitals in Canada. Design: A
 cross sectional study. Setting: Five major university–affiliated hospitals
 in Toronto and Calgary. Results: Overall, at all sites and types of
 academic rounds, there were an average of 17% fewer women presenting than
 men (p &lt; 0.001). There were an average of 32% and 21% more men
 presenting at the city wide grand rounds in City A and B respectively (p
 &lt; 0.001, p = 0.002). There were more male speakers at 4 out of 5
 types of rounds. The proportion of women presenting on average was
 proportional to the Canadian workforce, but on average, below the
 proportion of female residents and medical students (median ratio 1.1, 0.7
 and 0.8 respectively). Conclusion: Our study demonstrated a lower
 proportion of females in an important outlet for academic recognition and
 role modeling. This provides a possible contributing factor to the under
 representation of women in academic medicine, and an area that can be
 systematically targeted to promote equity.
description: Female
 PresentersAll presenters gender,
 site and type of round by year between 2011 and 2015
DOI: 10.5061/dryad.gk7nh
title: Data from: Direct genetic evidence for reproductive philopatry and associated fine-scale migrations in female blacktip reef sharks (Carcharhinus melanopterus) in French Polynesia.

description: Conservation of top predators has been emphasised as essential in an
 ecosystem due to their role in trophic chain regulation. Optimization of
 conservation strategies for these endangered marine top predators requires
 direct estimates of breeding patterns and connectivity, which are
 essential to understand their population dynamics. While there have been
 some attempts to investigate breeding patterns of reef sharks from litter
 reconstruction using molecular analyses, direct fine-scale migrations of
 female sharks for parturition as well as connectivity at a medium scale,
 such as between islands, remain mostly unknown. We used microsatellite DNA
 markers and a likelihood-based parentage analysis to determine breeding
 patterns of female blacktip reef sharks in Moorea (Society Islands, French
 Polynesia). Such an approach demonstrates that while most females gave
 birth at their home island, some migrated to specific nursery areas
 outside their home range, sometimes going to another island (up to 50 km
 across deep ocean). Analysis also revealed that females migrated to the
 same nursery on every birthing event. Many offspring showed a high level
 of inbreeding indicating an overall reduced population size, restricted
 movements and dispersal, or specific mating behaviour. Females represent
 the vectors that transport the genes at nursery grounds, and their
 fidelity should thus define reproductive units. As females seem to be
 philopatric, males could be the ones dispersing genes between
 metapopulations. These results highlight the need for conservation of
 coastal zones where female reef sharks seems to exhibit philopatry during
 the breeding season.
description: Genotype_Raw_Data_Mourier_and_Planes_2012
DOI: 10.5061/dryad.f3kc0
title: Data from: A chemical-genomic screen of neglected antibiotics reveals illicit transport of kasugamycin and blasticidin S

description: Fighting antibiotic resistance requires a deeper understanding of the
 genetic factors that determine the antibiotic susceptibility of bacteria.
 Here we describe a chemical-genomic screen in Escherichia coli K-12 that
 was designed to discover new aspects of antibiotic resistance by focusing
 on a set of 26 antibiotics and other stresses with poorly characterized
 mode-of-action and determinants of resistance. We show that the screen
 identifies new resistance determinants for these antibiotics including a
 common signature from two antimicrobials, kasugamycin and blasticidin S,
 used to treat crop diseases like rice blast and fire blight. Following
 this signature, we further investigated the mechanistic basis for
 susceptibility to kasugamycin and blasticidin S in E. coli using both
 genetic and biochemical approaches. We provide evidence that these
 compounds hijack an overlapping set of peptide ABC-importers to enter the
 bacterial cell. Loss of uptake may be an underappreciated mechanism for
 the development of kasugamycin resistance in bacterial plant pathogens.
description: Metadata for the
 chemical genomics plates.Metadata for the plates
 used in the chemical genomics screen, including uid, image analysis
 filename, condition and concentration of antibiotic, source plate, flags,
 and plate opacity IQR.ImageKeyFinal.xlsIris Image Analysis FilesetTar ball of all Iris files generated in the current screen, see the image key for associated metadata.irisfile.tarimagefileTar ball of plate images, see image key for associated metadataInput Metadata for Statistical AnalysisThese files include the metadata for conditions and arrays used as input for the statistical analysis and generation of the fitness score.InputFiles.tar10C fitness-scoresGene deletions identified by ECK number. Ranked list of fitness-scores at 10C.10C.rnkCOG assignmentsCOG category assignments for KEIO genes, for use in GSEA analysiskeioCOG.gmx
DOI: 10.5061/dryad.2v4h6
title: Data from: Female social preference for males that have evolved via monogamy: evidence of a trade-off between pre- and post-copulatory sexually selected traits?

description: When females mate with multiple males both pre- and post-copulatory sexual
 selections occur. It has been suggested that females benefit from
 polyandry when better-quality males are successful in sperm competition
 and sire high-quality offspring. Indeed, studies of experimental evolution
 have confirmed that sperm competition selects for both increased ejaculate
 quality and elevated offspring viability. Fewer investigations have
 explored whether these fitness benefits are evident beyond early
 life-history stages. Here, I used house mice (Mus domesticus) from
 selection lines that had been evolving for 25 generations under either
 polygamy or monogamy to test whether females preferred males from lines
 that had evolved with sperm competition. Males from the polygamous lines
 had previously been shown to achieve a fitness advantage under
 semi-natural conditions, deeming them to be of high genetic quality and
 leading to the a priori expectation that females would prefer males that
 had evolved with sperm competition compared with males that had not.
 Contrary to expectation, the data showed that sexually receptive females
 spent more time associating with males from the monogamous lines. This
 unexpected but interesting result is discussed in relation to sperm
 competition theory that predicts a trade-off between male investment in
 pre- and post-copulatory sexually selected traits.
description: Firman Data Biol Lett
 2014Firman
 data Biol Lett 2014.xlsx