cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dv41ns1wv
title: Genomic variation data for the wagtail hybrid zone

description: Genome-wide variation in introgression rates across hybrid zones offers a
 powerful opportunity for studying population differentiation. One poorly
 understood pattern of introgression is the geographic displacement of a
 trait implicated in lineage divergence from genome-wide population
 boundaries. While difficult to interpret, this pattern can facilitate the
 dissection of trait genetic architecture because traits become uncoupled
 from their ancestral genomic background. We studied an example of trait
 displacement generated by the introgression of head plumage coloration
 from personata to alba subspecies of
 the white wagtail. A previous study of the wagtail hybrid zone in Siberia
 revealed that the geographic transition in this sexual signal that
 mediates assortative mating was offset from other traits and genetic
 markers. We show that head plumage is associated with two small genetic
 regions. Despite having a simple genetic architecture, head plumage
 inheritance is consistent with partial dominance and epistasis, which
 could contribute to its asymmetric introgression.
DOI: 10.15468/dl.bznujt
title: Occurrence Download

description: A dataset containing 969 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Syzygium jambos"
 ]
}

 The dataset includes 969 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002696-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.hqbzkh1f6
title: RNA-seq data from TAS4464, a NEDD8-activating enzyme inhibitor, activates both intrinsic and extrinsic apoptotic pathways via c-Myc-mediated regulation in acute myeloid leukemia

description: TAS4464, a potent, selective small molecule NEDD8-activating enzyme (NAE)
 inhibitor, leads to inactivation of cullin-RING E3 ubiquitin ligases
 (CRLs) and consequent accumulations of its substrate proteins. Here, we
 investigated the antitumor properties and action mechanism of TAS4464 in
 acute myeloid leukemia (AML). TAS4464 induced apoptotic cell death in
 various AML cell lines. TAS4464 treatments resulted in the
 activation of both the caspase-9-mediated in intrinsic apoptotic pathway
 and caspase-8-mediated extrinsic apoptotic pathway in AML cells; combined
 treatment with inhibitors of these caspases markedly diminished
 TAS4464 induced apoptosis. In each apoptotic pathway, TAS4464
 induced the mRNA transcription of the intrinsic proapoptotic factor NOXA
 and decreased that of the extrinsic antiapoptotic factor c-FLIP.
 RNA-sequencing analysis showed that the signaling pathway of the CRL
 substrate c-Myc was enriched after TAS4464 treatment. Chromatin
 immunoprecipitation (ChIP) assay revealed that TAS4464 induced
 c-Myc bound to the PMAIP1 (encoding NOXA)
 and CFLAR (encoding c-FLIP) promoter regions, and
 siRNA-mediated c-Myc knockdown neutralized both TAS4464-mediated NOXA
 induction and c-FLIP downregulation. TAS4464 activated both caspase-8 and
 caspase-9 along with an increase in NOXA and a decrease in c-FLIP,
 resulting in complete tumor remission in a human AML xenograft model.
 These findings suggest that NAE inhibition leads to anti-AML activity via
 a novel c-Myc-dependent apoptosis induction mechanism.
description: HL-60 cells were either not treated (control) or treated with
 TAS4464 (0.1 μmol L<sup>-1</sup>) for 24 or 48 hours. Then,
 RNA was isolated from the cell samples using a phenol-guanidinium
 isothiocyanate (P/GTC) reagent according to the manufacturer’s
 protocol [45]. RNA was precipitated from the aqueous phase with
 isopropanol, and proteins were precipitated from the phenol/ethanol phase
 by the addition of acetone. A total of single-end-read RNA-seq tags were
 generated using a HiSeq 2000 sequencer according to the standard protocol.
 The generated sequence tags were mapped onto the human genome sequence
 (hg19 from the University of California Santa Cruz Genome Browser) using
 the Eland program (Illumina).
DOI: 10.5061/dryad.5x69p8d21
title: The allometry of plant height explains species loss under nitrogen addition

description: Light asymmetry, with a higher light acquisition per unit biomass for
 larger plants, has been proposed as a major mechanism of species loss
 after nitrogen addition. However, solid evidence for this has been scarce.
 We measured the allometric size-height relationships of 25 plant species
 along a nitrogen addition gradient manipulated annually for eight years in
 a speciose alpine meadow and found that the positive relationship between
 species relative abundance and the height scaling exponent in natural
 conditions disappeared after nitrogen addition. Those species with lower
 height scaling exponents increased in relative abundance after nitrogen
 addition, thereby decreasing the community weighted mean and dispersion of
 the height scaling exponent and ultimately the species richness. Our
 results provided some unique evidence for light asymmetry induced species
 loss after nitrogen addition and a new insight from the perspective of
 allometric scaling to explain biodiversity maintenance in the face of
 global changes.
DOI: 10.5061/dryad.tx95x69wr
title: Predator presence and recent climatic warming raise body temperatures of island lizards

description: In ectothermic predator-prey relationships, evasion of predation by prey
 depends on physiological and behavioural responses relating to the thermal
 biology of both predator and prey. On Japan’s Izu Islands, we investigated
 a prey lizard’s physiological and thermal responses to the presence of a
 snake predator over geologic time in addition to recent climatic warming.
 Foraging lizard body temperatures increased by 1.0°C from 1981 to 2019
 overall, yet were 2.9°C warmer on snake islands relative to snake-free
 islands. We also detected snake predator-induced selection on hind leg
 length, which in turn is a major determinant for sprint speed only in
 lizard populations exposed to predation by snakes. Accordingly, we found
 that warmer prey body temperatures result in faster sprint speeds by the
 prey at temperatures suboptimal for the snake predator, and therefore
 contribute to escaping predation. Given recent climatic change, further
 warming could irrevocably alter this and other ectothermic predator-prey
 relationships.
DOI: 10.5061/dryad.pvmcvdnjw
title: Spatial heterogeneity in soil pyrogenic carbon mediates tree growth and physiology following wildfire

description: Pyrogenic carbon (PyC) is a ubiquitous legacy of wildfire in terrestrial
 soils, yet how it affects the growth and function of regenerating plants
 has received little research attention. We examined responses to a natural
 gradient of PyC deposition five years following a severe fire in a
 northern boreal forest, based on measurements of growth (height, basal
 area increment, and leader extension), physiological performance (Fv/Fm),
 and foliar nutrition (foliar C, N, P, K, Mg) of Pinus banksiana Lamb. We
 determined the concentration of PyC, expressed as a dosage (t·ha-1), in
 mineral soils collected from the rhizospheres of each sapling and used it
 as an independent factor to model trait responses to increasing PyC
 levels, in conjunction with measurements of soil physio-chemical
 properties (pH, EC, VOC, Ash, N, P, K, Ca, and Mg). Quantification and
 spatial analysis of PyC reveals heterogeneous deposition across the
 landscape with fine-grained patchiness at scales &lt;0.5 m. In
 response to this heterogeneity, phenotypic and nutritional adjustments
 followed dose-dependent response patterns. Beneficial effects of PyC on
 sapling growth occurred to an optimum point of ~30-60 t·ha-1, while
 declining patterns were found for trees in dosages exceeding 100 t·ha-1.
 Some traits were positively and negatively related to soil K and N,
 respectively, and shared strong negative associations with soil pH and
 volatile matter. Synthesis. This study supports the longstanding
 hypothesis that soil PyC enhances growth and physiological function of
 fire-adapted plants, but indicates that responses are highly
 dosage-dependent, with natural levels of PyC deposition commonly exceeding
 an optimum point. These results also suggest that the main mechanisms for
 observed responses to PyC include: i) enhanced supply of base cations, ii)
 immobilization of N, and iii) pronounced liming. Future changes in climate
 are expected to increase fire frequency, particularly in circumpolar
 boreal forests. We predict shifts in PyC to frequently exceed the
 threshold resulting in reduced plant growth and ultimately ecosystem
 productivity.
DOI: 10.5061/dryad.prr4xgxkg
title: Shifts in plant composition mediate grazing effects on carbon cycling in grasslands

description:   Carbon cycling in grasslands can be impacted by livestock
 grazing, partially as an indirect result of herbivory-induced
 compositional shifts in the plant community. However, the underlying
 mechanisms of how these shifts impact carbon cycling are not well
 documented. We conducted a long-term grazing experiment with four sheep
 stocking rates in the semi-arid grasslands of Inner Mongolia, China, to
 examine grazing effects on the ratio of C3 to C4 species (C3:C4), shoot
 biomass, root biomass, root:shoot, soil respiration, soil C, soil N, and
 soil C:N between 2014 and 2018. We explored the responses of these carbon
 metrics to C3:C4 under different grazing treatments and the mechanisms
 driving grazing-induced carbon loss using structural equation models.
 Livestock grazing directly shifted plant community composition (i.e.,
 increasing C3:C4) and reduced vegetation carbon (i.e., shoot biomass),
 whereas grazing effects on belowground carbon were mediated by the
 interactions of the soil profile (i.e., depth-dependence) and year-to-year
 variation (e.g., rainfall regulation). Grazing-induced increases in C3:C4
 suppressed soil carbon loss by inhibiting the rate of soil respiration.
 Furthermore, grazing intensity indirectly altered these relationships.
 Specifically, C3:C4 was positively related to shoot biomass and negatively
 associated with root:shoot, soil C, and soil N, whereas these
 relationships were only significant in no-grazed plots. Meanwhile, soil
 respiration was negatively associated with C3:C4, soil C, soil N, and soil
 C:N, but a positive relationship with shoot biomass; these relationships
 were significant only in grazed-plots. Synthesis and applications. Our
 findings emphasize the functional linkages between community
 characteristics and ecosystem processes, i.e. shifts in plant community
 composition play a key role in regulating grassland carbon cycling. These
 results provide a useful field-observed resource for model development and
 could improve the guidelines for livestock management and policies
 regarding climate mitigation.  
description: Details of the methods can be found in the manuscripts.
DOI: 10.5061/dryad.b2rbnzsd4
title: Fossilization processes have little impact on tip-calibrated divergence time analyses

description: The importance of palaeontological data in divergence time estimation has
 increased with the introduction of Bayesian Total-Evidence Dating methods
 which utilise fossil taxa directly for calibration, facilitated by the
 joint analysis of morphological and molecular data. Fossil taxa are
 invariably incompletely known as a consequence of taphonomic processes,
 resulting in the decidedly non-random distribution of missing data. The
 impact of non-random missing data on the accuracy and precision of clade
 age estimation is unknown. In an attempt to constrain the impact of
 taphonomy on tip-calibrated dating analyses, we compared clade ages
 estimated from a very complete morphological matrix to ages estimated from
 the same matrix permuted to simulate the progressive loss of anatomical
 information resulting from taphonomic processes. We demonstrate that
 systematically distributed missing data negatively influence clade age
 estimates, but that successive stages within the taphonomic process
 introduce greater differences in age estimates, when compared to estimates
 obtained from untreated data. Despite these effects, the general influence
 of missing data is weak, presumably due to the compensatory effect of
 extensive morphological data from extant taxa. We suggest that, in the
 absence of models that can explicitly account for taphonomic processes,
 morphological datasets should be constructed to minimise the impact of
 taphonomy on divergence time estimation.
description: These datasets consist of simulated fossilisation of
 morphological data. They have been produced under two different models of
 fossilisation, with the degree of fossilisation altered across different
 scaling factors. 
description: The morphological matrices are in Nexus format.
DOI: 10.5061/dryad.1rn8pk0sd
title: Data from: Arthropod assemblages on small mammal carrion of the Kansas Flint Hills: an ecological approach

description: Arthropods are critical to the decomposition of carrion, but little is
 known about the biodiversity of arthropods attracted to carrion or
 environmental factors that shape communities. This research described
 carrion beetle (Coleoptera: Silphidae) and dung beetle (Coleoptera:
 Scarabaeidae: Scarabaeinae and Aphodiinae) community assemblages
 on rat carrion across a full annual cycle (twelve contiguous
 months, 2016-2017). Abiotic data (light availability, wind speed, soil
 surface humidity, soil surface temperature) complement the beetle
 biodiversity data. Together, these data allow investigation of the
 conditions that drive necrophilous beetle assemblage patterns. This
 research was designed in a spatially hierarchical fashion (fine scale to
 broad scale) and compared microhabitats (cranial versus caudal regions of
 a rat carcass) and macrohabitats (woodland and grassland) at three study
 sites within the Kansas Flint Hills physiographic region. These data unite
 ecological patterns and processes with forensic entomology and crime scene
 investigation.
description: For methods and data collection, refer to the supplemental
 document entitled, “Experimental design for repeatable carrion ecology
 study with true replication (not pseudoreplication)” (Engasser et al.
 2021).
description: For each dataset, refer to the accompanying ReadMe text file for
 usage information and metadata. Additional by-catch
 specimens and quadrat photos are available upon request.
 Related works are: Engasser, E.L., R.L. Stone,
 and M.L. Jameson. 2021. Habitat Associations of Carrion Beetles
 (Coleoptera: Silphidae) Across a Full Annual Cycle. Environmental
 Entomology 50(2). DOI: 10.1093/ee/nvab011 Stone, R. L,
 Engasser, E.L., and M.L. Jameson. 2021. Heads or Tails? Dung Beetle
 (Coleoptera: Scarabaeidae: Scarabaeinae & Aphodiinae) Attraction
 to Carrion. Environmental Entomology 50(2). DOI:
 10.1093/ee/nvab012
DOI: 10.5061/dryad.612jm642h
title: Preference, performance, and chemical defense in an endangered butterfly using novel and ancestral host plants

description: Adoption of novel host plants by herbivorous insects can require new
 adaptations and may entail loss of adaptation to ancestral hosts. We
 examined relationships between an endangered subspecies of the butterfly
 Euphydryas editha (Taylor’s checkerspot) and three host plant species. Two
 of the hosts (Castilleja hispida, Castilleja levisecta) were used
 ancestrally while the other, Plantago lanceolata, is exotic and was
 adopted more recently. We measured oviposition preference, neonate
 preference, larval growth, and secondary chemical uptake on all three
 hosts. Adult females readily laid eggs on all hosts but favored Plantago
 and tended to avoid C. levisecta. Oviposition preference changed over
 time. Neonates had no preference among host species, but consistently
 chose bracts over leaves within both Castilleja species. Larvae developed
 successfully on all species and grew to similar size on all of them unless
 they ate only Castilleja leaves (rather than bracts) which limited their
 growth. Diet strongly influenced secondary chemical uptake by larvae.
 Larvae that ate Plantago or C. hispida leaves contained the highest
 concentrations of iridoid glycosides, and iridoid glycoside composition
 varied with host species and tissue type. Despite having largely switched
 to a novel exotic host and generally performing better on it, this
 population has retained breadth in preference and ability to use other
 hosts.
DOI: 10.5061/dryad.x69p8czh5
title: Sequencing data and normalized counts for tripartite RNAseq of Drosophila, Wolbachia, and SINV virus

description: Wolbachia is a maternally transmitted bacterium that manipulates arthropod
 and nematode biology in myriad ways. The Wolbachia strain colonizing
 Drosophila melanogaster creates sperm-egg incompatibilities and protects
 its host against RNA viruses, making it a promising tool for vector
 control. Despite successful trials using Wolbachia-transfected mosquitoes
 for Dengue control, knowledge of how Wolbachia and viruses jointly affect
 insect biology remains limited. Using the Drosophila melanogaster model,
 transcriptomics and gene expression network analyses revealed pathways
 with altered expression and splicing due to Wolbachia colonization and
 virus infection. Included are metabolic pathways previously unknown to be
 important for Wolbachia-host interactions. Additionally,
 Wolbachia-colonized flies exhibit a dampened transcriptomic response to
 virus infection, consistent with early blocking of virus replication.
 Finally, using Drosophila genetics, we show Wolbachia and expression of
 nucleotide metabolism genes have interactive effects on virus replication.
 Understanding the mechanisms of pathogen blocking will contribute to the
 effective development of Wolbachia-mediated vector control programs.
description: Whole RNA, extracted from flies with or without Wolbachia
 infection, with or without SINV infection, was sequenced on an Illumina
 NextSeq. Resultant reads were mapped to existing genome assembiles for
 each entity and, using the RSEM workflow, quantified. Differential gene
 expression and splicing was assessed with EdegR.
description: <b>Supplemental Table
 S1. </b>Sequencing library metadata, statistics, and accession
 numbers. <b>Supplemental Table S2.
 </b>Transcriptomic response to <i>Wolbachia</i>. DEGs
 are those with corrected P values &lt; 0.05. <b>Supplemental Table S3.
 </b>Transcriptomic response to SINV. DEGs are those with corrected P
 values &lt; 0.05. <b>Supplemental Table S4.
 </b>Transcriptomic response to SINV*TIME. DEGs are those with
 corrected P values &lt; 0.05. <b>Supplemental Table S5.
 </b>All normalized counts for all genes across all
 samples. <b>Supplemental Table S6.
 </b>Genes with significant differences in isoform usage according to
 explanatory variable coefficients. <b>Supplemental Table
 S7.</b> Genes with significant differences in isoform usage due to
 <i>Wolbachia</i>*SINV and/or
 <i>Wolbachia</i>*SINV*TIME along with functional annotations
 and notes to references in previously published literature.
 <b>Supplemental Table
 S8. </b>Enriched terms in the joint STRING network.
DOI: 10.5061/dryad.rv15dv475
title: Data from: Glucocorticoid levels predict subsequent social tactic in females of a facultatively social mammal

description: Facultatively social species, in which individuals can switch between
 group- and solitary-living tactics, offer an opportunity to shed light on
 proximate mechanisms underlying alternative life histories. Promising
 hormonal mediators of social tactic include glucocorticoids, which control
 energy allocation and are negatively related to body condition, and
 testosterone which regulates numerous social behaviours. Here, we
 investigated hormonal profiles associated with social tactic in eight
 generations of free-living female striped mice (Rhabdomys pumilio).
 Females are group living during the non-breeding season but live
 solitarily or with female kin in communally-breeding groups during the
 breeding season. We tested whether females’ baseline levels of
 corticosterone (a glucocorticoid) and testosterone measured during the
 breeding season differed before and after females left the group (i.e.
 when they switched from a group-living to solitary social tactic), and
 whether the hormone levels of females that remained group living differed
 before and after their nestmates became solitary. We also asked whether
 seasonal variation in hormone levels was associated with social tactic.
 During the breeding season, corticosterone levels were lower in solitary
 than group-living females both before and after solitary females left the
 group, and did not differ in solitary females before and after leaving. In
 group-living females, corticosterone was higher after their nestmates
 became solitary than before they left. Testosterone levels did not differ
 before and after females became solitary and were not associated with
 social tactic. Corticosterone was higher during the breeding than the
 non-breeding season in group-living females but did not differ between the
 seasons in solitary females. Testosterone levels were higher in both
 social tactics during the non-breeding season. We conclude that baseline
 corticosterone but not testosterone levels are associated with female
 social tactic, and that corticosterone levels at the start of the breeding
 season, when all females are group living, may be an indicator of
 subsequent tactic: solitary females’ corticosterone levels were lower than
 those of females that remained group living even before the solitary
 phenotype was expressed. Glucocorticoids might therefore play a modulatory
 role in social organisation in facultatively social species. 
description: Please refer to the Materials and Methods section of our paper in
 Functional Ecology for details of how these data were collected.
description: Please refer to the README files for general information and
 column descriptors: 
 README_Hill_Hormones&SocialTactics
 README_Hill_Hormones&PairedSocialTactics
DOI: 10.5061/dryad.j9kd51cb7
title: Active modification of cavity nest-entrances is a common strategy in arboreal ants

description: The majority of tropical arboreal ant species nest in tree cavities. These
 cavities, often produced initially by wood-boring beetles, can be in live
 or dead wood and represent long-lasting and highly defensible nesting
 resources. Yet the size of cavity entrances can constrain their use.
 Active entrance modification may be an effective way to overcome this
 constraint. Here, we conduct the first systematic study of nest-entrance
 modification in an arboreal ant community. Using field experiments
 deployed across a number of tree species, we show that 14% of 2631
 experimental cavities were modified by either enlargement, or reducing
 entrance size by construction. Entrance modifications, which were made by
 a majority (18/29 species) of the species that occupied experimental
 nests, used a variety of construction techniques and materials. Combined,
 these modifications were context-dependent with respect to available
 entrance sizes: enlargement was more common when the diversity of
 available entrance sizes was limited, whereas reduction was more prevalent
 when the diversity of entrance sizes was higher. Nevertheless, the context
 of tree species identity did not significantly influence the number of
 modified cavities or the construction materials. Overall, we show that
 nest-entrance modification is a widespread, active, and context-dependent
 strategy in the nesting ecology of arboreal ants.