cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.w3r2280pp
title: Data from: Burrowing by translocated boodie (Bettongia lesueur) populations alters soils but has limited effects on vegetation

description: Digging and burrowing mammals modify soil resources, creating shelter for
 other animals and influencing vegetation and soil biota. The use of
 conservation translocations to reinstate the ecosystem functions of
 digging and burrowing mammals is becoming more common. However, in an
 increasingly altered world, the roles of translocated populations, and
 their importance for other species, may be different. Boodies (Bettongia
 lesueur), a commonly translocated species in Australia, construct
 extensive warrens, but how their warrens affect soil properties and
 vegetation communities is unknown. We investigated soil properties,
 vegetation communities, and novel ecosystem elements (specifically
 non-native flora and fauna) on boodie warrens at three translocation sites
 widely distributed across the species’ former range. We found that soil
 moisture and most soil nutrients were higher, and soil compaction was
 lower, on warrens in all sites and habitat types. In contrast, there were
 few substantial changes to vegetation species richness, cover, composition
 or productivity. In one habitat type, the cover of shrubs less than 1 m
 tall was greater on warrens than control plots. At the two sites where
 non-native plants were present, their cover was greater, and they were
 more commonly found on boodie warrens compared to control plots. Fourteen
 species of native mammals and reptiles were recorded using the warrens,
 but, where they occurred, the scat of the non-native rabbit (Oryctolagus
 cuniculus) was also more abundant on the warrens. Together our results
 suggest that translocated boodie populations may be benefiting both native
 and non-native flora and fauna. Translocated boodies, through the
 construction of their warrens, substantially alter the sites where they
 are released, but this does not always reflect their historic ecosystem
 roles.
DOI: 10.5061/dryad.c866t1g5s
title: Mangrove diversity enhances plant biomass production and carbon storage in Hainan Island, China

description: Mangrove forests, one of the highest carbon density ecosystems, are very
 different from other forests as they occupy saline and tidal habitats.
 Although previous studies in forests, shrublands, and grasslands have
 shown a positive effect of biodiversity on plant biomass and carbon
 storage, it remains unclear whether this relation to biodiversity also
 exists in mangrove forests. Here, we evaluate the possible effects of
 mangrove species diversity, structural characteristics, and environmental
 factors on mangrove biomass production and carbon storage, using survey
 data from 234 field plots of 30 transects in the mangrove forests along
 the coastlines of Hainan Island, China, during 2017 and 2018.We found that
 mangrove species diversity had a positive effect, not only on mangrove
 biomass production, but also on soil carbon storage. This positive effect
 was more strongly evident in the forest communities than in either the
 shrub communities or forest-shrub mixed communities, with the forests type
 having the biggest mangrove biodiversity and carbon storage. In addition,
 the diversity effect was affected by structural characteristics, namely,
 mangrove biomass increased exponentially with tree stem diameter and
 decreased with tree density. Furthermore, we observed a resource-dependent
 mediation of the mangrove ecosystem when linking diversity to biomass. The
 areas with high soil Nitrogen content and Mean annul precipitation (MAP)
 showed higher mangrove biomass and carbon storage. This suggests that the
 spatial pattern of mangrove carbon storage and diversity was driven by
 both climate factors (MAP) and soil fertility (soil N).Our findings
 suggest that mangrove forests with greater diversity also have higher
 carbon storage capacities and conservation potential. Thus, biodiversity
 conservation is crucial for mangrove to mitigate the greenhouse effect.
 Our findings strengthen the understanding of the diversity effects on
 mangrove ecosystem services and have important implications for mangrove
 restoration and conservation.
description: We collected data based on
 an intensive field survey from 234 field plots of 30 transects in the
 mangrove forests along the coastlines of Hainan Island, China, during 2017
 and 2018. We
 calculated the mangrove species diversity, structural parameters, mangrove
 biomass production, and carbon storage based on the breast-height
 diameter, species, height, tree density from field plots.
DOI: 10.5061/dryad.0rxwdbrzb
title: Source data of main figures of the effect of splicing inhibition on antigen presentation

description: The success of cancer immunotherapy relies on the induction of an
 immunoprotective response targeting tumor antigens (TAs) presented on
 MHC-I molecules. We demonstrated that the splicing inhibitor isoginkgetin
 and its water-soluble and non-toxic derivative IP2 act at the production
 stage of the Pioneer Translation Products (PTPs). We showed that IP2
 increases PTP-derived antigen presentation in cancer cells in vitro and
 impairs tumor growth in vivo. IP2 action is long-lasting and dependent on
 the CD8+ T cell response against TAs. We observed that the antigen
 repertoire displayed on MHC-I molecules at the surface of MCA205
 fibrosarcoma is modified upon treatment with IP2. In particular, IP2
 enhances the presentation of an exon-derived epitope from the tumor
 suppressor nischarin. The combination of IP2 with a peptide vaccine
 targeting the nischarin-derived epitope showed a synergistic antitumor
 effect. These findings identify the spliceosome as a druggable target for
 the development of epitope-based immunotherapies.
DOI: 10.5061/dryad.h9w0vt4gw
title: Data from: Predation favours Bicyclus anynana butterflies with fewer forewing eyespots

description: There are fewer eyespots on the forewings versus hindwings of nymphalids
 but the reasons for this uneven distribution remain unclear. One
 possibility is, in many butterflies, the hindwing covers part of the
 ventral forewing at rest and there are fewer forewing sectors to display
 eyespots (covered eyespots are not continuously-visible and are less
 likely to be under positive selection). A second explanation is that
 having fewer forewing eyespots confers a selective advantage against
 predators. We analysed wing overlap at rest in 275 nymphalid species with
 eyespots and found that many have exposed forewing sectors without
 eyespots: i.e. wing overlap does not constrain the forewing from having
 more eyespots than the hindwing. We performed two predation experiments
 with mantids to compare the relative fitness of and attack damage patterns
 on two forms of Bicyclus anynana butterflies, both with seven hindwing
 eyespots, but with two (in wildtype) or four (in Spotty) ventral forewing
 eyespots. Spotty experienced more intense predation on the forewings, were
 shorter-lived and laid fewer eggs. These results suggest that forewing
 eyespot number in B. anynana is limited by predation pressure. This may
 occur if attacks on forewing eyespots have more detrimental consequences
 for flight than attacks on hindwing eyespots.
description: Please find this information in the ReadMe file
 ("Chan_et_al_-_Readme.txt") and in the Proceedings B publication
 (https://doi.org/10.1098/rspb.2020.2840).
description: Please find this information in the ReadMe file
 ("Chan_et_al_-_Readme.txt") and in the Proceedings B publication
 (https://doi.org/10.1098/rspb.2020.2840).
DOI: 10.5061/dryad.bcc2fqzbk
title: Data from: Kin relationships in cultural species of the marine realm: case study of a matrilineal social group of sperm whales off Mauritius Island, Indian Ocean

description: Understanding the organization and dynamics of social groups of marine
 mammals through the study of kin relationships is particularly
 challenging. Here we studied a stable social group of sperm whales off
 Mauritius, using underwater observations, individual-specific
 identification, non-invasive sampling, and genetic analyses based on
 mitochondrial sequencing and microsatellite profiling. Twenty-four sperm
 whales were sampled between 2017 and 2019. All individuals except one
 adult female shared the same mtDNA haplotype—one that is rare in the
 Western Indian Ocean—thus confirming with near certainty the
 matrilineality of the group. All probable first- and second-degree kin
 relationships were depicted in a sperm whale social group: 13 first-degree
 and 34 second-degree relationships were identified. Notably, we highlight
 the likely case of an unrelated female having been integrated into a
 social unit, in that she presented a distinct mtDNA haplotype and no close
 relationships with any members of the group. Investigating the possible
 matrilineality of sperm whale cultural units (i.e., vocal clans) is the
 next step in our research program to elucidate and better apprehend the
 complex organization of sperm whale social groups.
DOI: 10.5061/dryad.m63xsj416
title: Metadata for the characterization of Platynereis dumerilii cephalic and non-cephalic sensory cell types

description: Rhabdomeric Opsins (r-Opsins) serve as light-sensory molecules in cephalic
 eye photoreceptors of many invertebrates, but also play roles in
 additional sensory organs. This has prompted questions on the evolutionary
 relationship of the cell types, specifically if ancient r-Opsins cells
 possessed non-photosensory functions. By extracting and profiling cephalic
 and non-cephalic r-opsin1-expressing cell types of the marine bristleworm
 Platynereis dumerilii, we find evidence for shared and distinct identities
 between these two cell types. We establish that non-cephalic cells possess
 a mechanosensory signature, but also a full set of phototransduction
 components. Using cell-culture-based second messenger assays, we determine
 that Platynereis r-Opsin1 is a Gαq-coupled blue-light receptor. Profiling
 of cells in r-opsin1 mutant animals, and comparing cells under dim and
 bright light conditions reveals that in the non-cephalic cell type,
 light – mediated by r-Opsin1 – adjusts the expression
 level of a calcium transporter relevant for auditory mechanosensation in
 vertebrates. We finally establish a supervised, deep learning-based
 quantitative behavioral analysis pipeline to assess animal trunk
 movements. We identify light-dependent differences in the fine-tuning of
 the worms’ undulatory movements in mutant vs. wildtype headless trunks,
 which are known to require mechanosensory feedback. Altogether, our
 results provide support for an evolutionary concept in which r-Opsins act
 as ancient, light-dependent modulators of mechanosensation. Our findings
 refine the reconstruction of sensory cell type evolution, and suggest that
 light-independent mechanosensory roles of r-Opsins likely result from
 secondary evolutionary processes.
DOI: 10.5061/dryad.q573n5thf
title: Leaf litter mixture experiment in a tropical montane rainforest

description: In this dataset are included values of mass loss, microbial
 biomass, basal respiration, metabolic quotient, and the slope of microbial
 growth after glucose addition, as well as the abundance of microarthropods
 (Acari and Collembola) of a litter mixture experiment in a tropical
 montane rainforest Ecosystem. In the experiment leaves of six
 native tree species (Cecropia andina, Dictyocaryum lamarckianum, Myrcia
 pubescens, Cavendishia zamorensis, Graffenrieda emarginata, and
 Clusia spp.) were used to fill litterbags and were incubated in
 monocultures and all possible two and four species combinations in the
 field for 6 and 12 months.
description: <strong>Abbreviations</strong> P: <em>Dictyocaryum lamarckianum</em>  G: <em>Graffenrieda emarginata</em> A: <em>Cecropia andina </em> C: <em>Clusia </em>spp. V: <em>Cavendishia zamorensis</em> M: <em>Myrcia pubescens</em> ab: abundance Mloss: mass loss (% from the initial) BR: Basal respiration (μl O<sub>2 </sub>g<sup>-1</sup> dry weight h<sup>-1</sup>) Cmic: microbial biomass (mg g<sup>-1 </sup>dry weight) qO2: metabolic quotient (μl O<sub>2</sub> mg<sup>−1</sup> Cmic h<sup>−1</sup>) C: Total carbon (%) N: Total nitrogen (%)
DOI: 10.5061/dryad.905qfttjx
title: Data on paternal age and sperm production of the progeny

description: Parental age has profound consequences for offspring’s phenotype. However,
 whether patrilineal age affects offspring sperm production is unknown,
 despite the importance of sperm production for male reproductive success
 in species facing post-copulatory sexual selection. Using a longitudinal
 dataset on ejaculate attributes of the houbara bustard, we showed that
 offspring sired by old fathers had different age-dependent trajectories of
 sperm production compared to offspring sired by young fathers.
 Specifically, they produced less sperm (-48%) in their first year of life,
 and 14% less during their lifetime. Paternal age had the strongest effect,
 with weak evidence for grandpaternal or great grandpaternal age effects.
 These results show that paternal age can affect offspring reproductive
 success by reducing sperm production, establishing an intergenerational
 link between aging and sexual selection.
DOI: 10.5061/dryad.8cz8w9gpb
title: Large scale virtual screening for finding inhibitor against the main protease from herbal medicine for SARS-Cov2 therapy

description: The pandemic COVID-19 caused by SARS-CoV-2 has raised global health
 concerns. However, there is still no targeted medicine available for
 treatment of this disease. It is reported that 3CLpro plays an important
 role for the life cycle of virus and this protein has also been proved as
 an effective drug target in the case of severe acute respiratory syndrome
 coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus
 (MERS-CoV). Medicinal plantsare important resource for drug discovery.
 Therefore, we executed large scale virtual screening on the herbal
 medicine library and hoped to find a potential drug againstthe main
 protease. As a result, we obtained three available compounds derived from
 Chinese herbal medicines through the docking and binding free energy
 calculation.Then 100 ns molecular dynamic (MD) were employed to uncover
 the potential mechanisms which is helpful for further drug optimization.
description: The figure_data was
 collected from the trajectory using the Cpptraj tool with the script
 ‘rmsd.in’, ‘rmsf.in’, ‘h_bond.in’ respectively. And the figures were drawn
 by the Orgin2020b software. The molecular data came from the
 database (ligand.zip) and the binding affinity was measured by Autodock
 vina. The
 trajectories of nine compounds with excellent binding affinity. The
 trajectories were produced by amber using the input file
 (md.in). The
 binding free energies were calculated by the script: mmpbsa.in.
DOI: 10.5061/dryad.2280gb5r0
title: Social consequences of energetically costly nest construction in a facultatively social bee

description: Social groups form when the costs of breeding independently exceed fitness
 costs imposed by group living. The costs of independent breeding can often
 be energetic, especially for animals performing expensive behaviors, such
 as nest construction. To test the hypothesis that nesting costs can drive
 sociality by disincentivizing independent nest founding, we measured the
 energetics of nest construction and inheritance in a facultatively social
 carpenter bee (Xylocopa sonorina Smith), which bores tunnel nests
 in wood. We measured metabolic rates of bees excavating wood and used
 computerized tomography (CT) images of nesting logs to measure excavation
 volumes. From these data, we demonstrate costly energetic investments in
 nest excavation of a minimum 4.3 kJ per offspring provisioned, an expense
 equivalent to nearly 7 hours of flight. This high, potentially prohibitive
 cost of nest founding may explain why females compete for existing nests
 rather than constructing new ones, often leading to the formation of
 social groups. Further, we found that nest inheritors varied considerably
 in their investment in nest renovation, with costs ranging more than
 twelve-fold (from 7.08 kJ – 89.1 kJ energy), likely reflecting
 differences in inherited nest quality. These results suggest that females
 may join social groups to avoid steep energetic costs, but that the
 benefits of this strategy are not experienced equally.
DOI: 10.5061/dryad.5hqbzkh51
title: Serological dataset and R code for: Patterns and processes of pathogen exposure in gray wolves across North America

description: The presence of many pathogens varies in a predictable manner with
 latitude, with infections decreasing from the equator towards the poles.
 We investigated the geographic trends of pathogens infecting a widely
 distributed carnivore: the gray wolf (Canis lupus). We compiled a large
 serological dataset of nearly 2000 wolves from 17 study areas, spanning
 80º longitude and 50º latitude. Generalized linear mixed models were
 constructed to predict the probability of seropositivity of four important
 viruses: canine adenovirus, herpesvirus, parvovirus, and distemper virus –
 and two parasites: Neospora caninum and Toxoplasma gondii. Canine
 adenovirus and herpesvirus were the most widely distributed pathogens,
 whereas N. caninum was relatively uncommon. Canine parvovirus and
 distemper had high annual variation, with western populations experiencing
 more frequent outbreaks than eastern populations. Seroprevalence of all
 infections increased as wolves aged, and denser wolf populations had a
 greater risk of exposure. Probability of exposure was positively
 correlated with human density, suggesting that dogs and synanthropic
 animals may be important pathogen reservoirs. Pathogen exposure did not
 appear to follow a latitudinal gradient, with the exception of N. caninum.
 Instead, clustered study areas were more similar: wolves from the Great
 Lakes region had lower odds of exposure to the viruses, but higher odds of
 exposure to N. caninum and T. gondii; the opposite was true for wolves
 from the central Rocky Mountains. Overall, mechanistic predictors were
 more informative of seroprevalence trends than latitude and longitude.
 Individual host characteristics as well as inherent features of ecosystems
 determined pathogen exposure risk on a large scale. Here we provide the
 serological dataset and the R code used in Brandell et al. 2021. See the
 README file for a description of the dataset and generalized linear mixed
 models (GLMM); see Brandell et al. 2021 main text and
 Supplementary Information for additional information about data
 collection and cleaning, research permits, and variable descriptions and
 rationales.
DOI: 10.5061/dryad.1vhhmgqrv
title: Relative impacts of gypsy moth outbreaks and insecticide treatments on forest resources and ecosystem: An experimental approach

description: Gypsy moth outbreaks cause severe defoliation in Holarctic forests, both
 in North America where it is invasive, and in its native range in Eurasia.
 Severe defoliation can hamper timber production and impact ecological
 communities and processes. Aerial insecticide applications are regularly
 performed in outbreak areas to mitigate economic losses. These operations
 can be financially costly and harmful to non-target species and may
 disrupt species interaction networks. However, replicated studies of the
 relative impacts of gypsy moth outbreaks and insecticide application on
 forest growth and animal communities are rare and have yet to be carried
 out in the species' indigenous range. Here, we review the pathways in
 which gypsy moth outbreaks and the chemical control of these outbreaks
 affect forest ecosystems. We then present an experimental design
 established in South Central Germany in early 2019, aiming to study the
 ecological and economic consequences of gypsy moth eruptions and
 insecticide application in oak forests. The study's full factorial
 design comprises forest stands with high and low defoliation risk, either
 treated with tebufenozide or left unsprayed, within 12 experimental
 blocks. Measurements of forest growth and structure, tree mortality, gypsy
 moth density, and composition of lepidopteran, bird, bat, ground beetle,
 and canopy arthropod communities will be conducted for several years.
 One-year intensive monitoring of gypsy moth populations and damage across
 the selected sites showed substantial differences in population density
 between plots with high and low defoliation risk and high efficacy of
 tebufenozide in suppressing gypsy moth populations in treated plots. In
 the first year of the experiment, gypsy moth density and defoliation in
 predicted outbreak plots differed strongly, confirming the importance of
 using many replicates and blocking to control spatial heterogeneity. The
 experiment will be running continuously during the coming years to produce
 short- and medium-term economic and ecological data to improve our
 understanding and management of gypsy moth outbreaks.
description: One-year monitoring of gypsy moth population and defoliation
 during an outbreak in German oak forests. Data collected from March to
 August 2019 at all life-stages of the gypsy moth (egg, larva, pupa,
 imago). Details on the sampling methods and timing and processing of the
 various data are provided in the associated article.
DOI: 10.5061/dryad.3n5tb2rg3
title: Data from: Compensatory growth in C. elegans is regulated by a thermosensitive TRP channel and increases reproductive fitness

description: Animals are often not growing at the maximum rate, but can compensate for
 a bad start of life by further increasing growth rate. While this
 compensatory growth is widespread, its direct fitness consequences are
 seldom investigated and its genetic basis is unknown. We investigated the
 genetic regulation, as well as fitness and lifespan consequences of
 compensatory growth in response to temperature, using C. elegans knockout
 of the thermo-sensitive TRP ion channel TRPA-1, involved in temperature
 recognition. We exposed juvenile worms to cold, normal or warm
 temperatures in order to delay or speed up development. After returning to
 normal temperature, we found that wild-type worms where early development
 was delayed, expressed compensatory growth and catched up in size, while
 juvenile exposure to warm temperatures expressed slowed-down growth and
 small size. Compensatory growth also altered the reproductive schedule
 towards early reproduction, so that rate-sensitive individual fitness
 increased even though total reproduction was unaffected. Surprisingly, no
 lifespan cost of compensatory growth was found. In contrast, juvenile
 temperature did not induce compensatory or slowed-down growth in the
 trpa-1 knockout mutants, and consequently did not affect fitness. We show
 that temperature-induced compensatory growth in C. elegans is regulated by
 the trpa-1 and can increase fitness.