cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s7h44j1cj
title: Assessing the evolutionary lability of insulin signaling in the regulation of nutritional plasticity across traits and species of horned dung beetles

description: Nutrition-dependent growth of sexual traits is a major contributor to
 phenotypic diversity and a large body of research documents insulin
 signaling as a major regulator of nutritional plasticity. However,
 findings across studies raise the possibility that the role of individual
 components within the insulin signaling pathway diverge in function among
 traits and taxa. Here, we use RNAi-mediated transcript depletion in the
 gazelle dung beetle to investigate the functions of forkhead box
 O (Foxo) and two paralogs of the insulin receptor (InR1 and InR2) in
 shaping nutritional plasticity in polyphenic male head horns, exaggerated
 fore legs, and weakly nutrition-responsive genitalia. Our functional
 genetic manipulations led to three main findings: FoxoRNAi reduced the
 length of exaggerated head horns in large males, while neither InR1 nor
 InR2 knock-downs resulted in measurable horn phenotypes. These results are
 similar to those documented previously for another horned dung beetle
 species (Onthophagus taurus), but in stark contrast to findings in
 rhinoceros beetles. Secondly, knockdown of Foxo, InR1, and InR2 led to an
 increase in the intercept or slope of the scaling relationship of
 genitalia size. These results are in contrast even to results documented
 previously for O. taurus. Lastly, while FoxoRNAi reduces male
 forelegs in D. gazella and O. taurus, the effects of InR1 and InR2
 knockdowns diverged across dung beetle species. Taken together, our
 results add to the growing body of literature indicating that despite
 insulin signaling’s conserved role as a regulator of nutritional
 plasticity, the functions of its components may diversify among traits and
 species. 
description: We use
 RNAinterference-mediated transcript depletion in the gazelle dung beetle
 to investigate the functions of <em>forkhead box O</em>
 (<em>Foxo</em>) and two paralogs of the insulin receptor
 (<em>InR1</em> and <em>InR2</em>) in shaping
 nutritional plasticity in polyphenic male head horns, exaggerated fore
 legs, and weakly nutrition-responsive genitalia.
DOI: 10.5061/dryad.rjdfn2zj5
title: Phylogenomics of mulberries (Morus, Moraceae) inferred from plastomes and single copy nuclear genes

description: Mulberry (genus Morus), belonging to the order Rosales, family Moraceae,
 is an important woody plant due to its economic value in sericulture as
 well as for its nutritional benefits and medicinal values. However, the
 taxonomy and phylogeny of Morus remain challenging due to its wide
 geographical distribution, morphological plasticity, and interspecific
 hybridization. To better understand the evolutionary history of Morus, we
 combined plastomes and a large-scale nuclear gene to investigate their
 phylogenetic relationships in the present study. We assembled the
 plastomes and screened 211 single-copy nuclear genes from
 14 Morus species and related taxa. The plastomes of Morus species
 were relatively conserved in terms of genome size, gene content and order,
 IR boundary and codon usage. Using nuclear data, we yielded completely
 identical topologies based on coalescent and concatenation methods, and
 multiple individuals of the same species were intraspecific monophyletic.
 The genus Morus was supported as a monophyly, and M. notabilis
 was recovered as the first diverging, and the two North American Morus
 species, M. celtidifolia and M. rubra, were sister to the other Asian
 species. However, the relationships of Morus based on plastomes were
 strongly incongruent with those from nuclear genes, and intraspecific
 non-monophyly was retrieved in the plastid phylogeny. Comparisons of
 nuclear and plastid phylogenies, and combining with the result of network
 inference, hybridization/introgression was regarded as the main cause of
 the discordance between nuclear and plastid phylogenies in the genus
 Morus. Overall, the robust phylogenetic relationships of Morus described
 here will be useful for genetic resources development of this economically
 important genus and exploitation of sericulture industry.
DOI: 10.5061/dryad.kwh70rz9g
title: Sexually-selected male weapon increases the risk of population extinction under environmental change: An experimental evidence

description: Exaggerated sexually-selected traits, occurring more commonly in males,
 help individuals to increase reproductive success, but are costly to
 produce and maintain. These costs on the one hand may improve population
 fitness by intensifying selection against maladapted males, but on the
 other hand may increase the risk of extinction under environmental
 challenge. However, the impact of sexually selected traits on extinction
 risk have not been investigated experimentally. We used replicate
 populations of a male-dimorphic mite, Rhizoglyphus robini, to test if
 prevalence of a sexually-selected weapon affected the risk of extinction
 under gradual temperature increase (20C per generation).  In two
 independent experiments that utilized either inbred lines or lines mass
 selected for or against the weapon to establish experimental replicate
 populations differing in the prevalence of the weapon, we found that
 populations with high weapon prevalence were more likely to go extinct.
 Extinctions occurred despite partial suppression of the weapon expression
 at increased temperature and were not explained by increased male
 mortality. Our results provide the first, to our knowledge, experimental
 evidence demonstrating dramatic effect of elaborated sexual traits on the
 risk of extinction under environmental challenge.
DOI: 10.5061/dryad.rr4xgxddw
title: Data from: Frog limbs in deep time: is jumping locomotion at the roots of the anuran Bauplan?

description: The unique body plan of frogs (Lissamphibia: Anura) has been largely
 conserved from at least 200 Myr and its evolution from a more generalized
 tetrapod condition is still poorly understood, in part due to the scarce
 early fossil record of Salientia, the anuran total-group. The origin of
 the anuran Bauplan has been classically explained as an adaptation to
 jumping, but recent studies incorporating new data in a phylogenetic
 context have challenged the popular jumping hypothesis. Here we revisit
 and test this hypothesis from a palaeobiological perspective by
 integrating limb data from a wide range of extant and fossil frogs. We
 first explored the evolution of limb proportions from the Jurassic to the
 Paleogene to understand when the present limb diversity originated and
 whether, and to what extent, limb proportions have been conserved over the
 last 200 Myr. We then inferred the locomotor capabilities of extinct
 species by phylogenetic flexible discriminant analysis and, from these
 inferences, we studied the locomotor diversity of frogs over geological
 time and reconstructed the ancestral state for frog-like salientians. The
 evolution of limb proportions is characterized by an early diversification
 that was underway in the Jurassic, followed by a repeated convergence over
 a limited area of the morphospace that was already explored by the Early
 Cretaceous. In agreement with this early limb diversity, the Jurassic stem
 species were also locomotory diverse and their inferred locomotor modes do
 not support the jumping hypothesis. We propose that the patterns found
 herein of repeated convergent evolution of both limb proportions and
 locomotor capabilities over geological time hamper any attempt to
 confidently infer the ancestral locomotion mode and, therefore, it might
 be time to start focusing on other hypotheses on the origin of the anuran
 Bauplan that are not related to locomotion.
DOI: 10.5061/dryad.80gb5mkw8
title: Non-contact measurement of a free flying bumblebee's (Bombus terrestris) electrical potential as it approaches and leaves a fixed electrode

description: With increasing evidence of electroreception in terrestrial arthropods,
 understanding receptor level processes is vital to appreciating the
 capabilities and limits of this sense. Here, we examine the
 spatio-temporal sensitivity of mechanoreceptive filiform hairs in
 detecting electrical fields. We first present empirical data, highlighting
 the time-varying characteristics of biological electrical signals. We then
 explore how electrically sensitive hairs may respond to such stimuli. The
 main findings are: 1) oscillatory signals (elicited by wingbeats)
 influence the spatial sensitivity of hairs, unveiling an inextricable
 spatio-temporal link; 2) wingbeat direction modulates spatial sensitivity;
 3) electrical wingbeats can be approximated by sinusoidally modulated DC
 signals; and 4) for a moving point charge, maximum sensitivity occurs at a
 faster timescale than a hair’s frequency-based tuning.  Our
 results show that electro-mechanical sensory hairs may capture different
 spatio-temporal information, depending on an object’s movement and
 wingbeat and in comparison, to aero-acoustic stimuli. Crucially, we
 suggest that electrostatic and aero-acoustic signals may provide
 distinguishable channels of information for arthropods. Given the
 pervasiveness of electric fields in nature, our results suggest further
 study to understand electrostatics in the ecology of arthropods and to
 reveal unknown ecological relationships and novel interactions between
 species.
description: We measured the local electrical potential of buff-tailed
 bumblebees (<em>Bombus terrestris</em>, Linnaeus 1758) free
 flying around a fixed electrode.
DOI: 10.5061/dryad.5mkkwh7bt
title: Multiple alignments of Ficus benghalensis var. krishnae markers

description: Ficus benghalensis var. krishnae is a rare tree species considered to be
 endemic to India. Its peculiar feature is the presence of a cup-shaped
 structure at the base of its leaves. The taxonomic status of Ficus
 benghalensis and its variant Ficus benghalensis var. krishnae is currently
 under debate. In this study, we used two chloroplast DNA barcode markers
 (matK and rbcL) to explore the taxonomical relationship of Ficus
 benghalensis var. krishnae with other Ficus species.
description: Multiple alignments were generated using the MAFFT algorithm
 version 7.123b of the GUIDANCE2 web server (http://guidance.tau.ac.il/) (Sela, Ashkenazy, Katoh, & Pupko, 2015)
DOI: 10.5061/dryad.rn8pk0php
title: Geographical trends of soil-associated biodiversity changes due to tree plantations in South America: biome and climate constraints revealed through meta-analysis

description: Aim Evaluate the interaction between climate and biome structure when
 explaining changes in species richness of soil-associated communities due
 to tree plantations developed in different biomes. Compare the response of
 plants, soil invertebrates, and soil microorganisms, and test whether they
 should be considered sensitive-coupled biotas. Location Continental South
 America. Time period 1996–2023  Major taxa studied Plants, soil
 invertebrates and soil microorganisms  Methods Through a
 meta-analysis, the change in species richness (i.e., response ratio)
 associated with tree plantations was evaluated in 127 points of study
 across South America, considering soil-associated communities of plants,
 invertebrates and microorganisms. The influence of biome structure (open
 vs. closed habitats) on the response ratio and its interaction with the
 actual evapotranspiration (AET) and temperature seasonality was evaluated.
 Differentiated responses of different taxa were tested by comparing models
 with and without an interaction term referring to the taxon studied. The
 regional agricultural cover and plantation age were considered as
 anthropogenic variables. Results Models containing the AET were better at
 explaining the trend of change in species richness than those with
 temperature seasonality. The response to the change in species richness
 was oppositely related to the AET in open and closed biomes. Plants
 presented a higher loss in species richness than soil invertebrates and
 microorganisms. The three taxa were positively associated with AET, while
 seasonality was not relevant in any case. Both anthropogenic variables
 significantly lessened the change in species richness in all
 models.  Main conclusions The structural contrast between the
 anthropogenic habitat and the biome where it is developed is a key factor
 influencing the response of soil-associated communities to tree
 plantations. Nevertheless, its influence must be assessed together with
 climatic and anthropogenic variables given that their interaction can
 explain different geographical trends in the change in species richness
 across regions.
DOI: 10.15468/dl.g7jxrv
title: Occurrence Download

description: A dataset containing 12916 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is one of (Asia, Oceania)",
 "TaxonKey is Aristolochia"
 ]
}

 The dataset includes 12916 records from 254 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003573-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.79cnp5j1p
title: Results from groundwater pumping-induced subsidence model, San Joaquin Valley

description: The San Joaquin Valley, California has experienced dramatic subsidence
 over the past 100 years, but the regions with the most subsidence have
 shifted dramatically over this time period, from west (Kettleman City/Los
 Banos) to south (Tulare/Pixley/Corcoran). To date, no study has done an
 in-depth analysis of the mechanisms driving this shift in subsidence. We
 analyze head records, utilizing a novel approach that assimilates change
 in head data from multiple overlapping time periods, to produce an 80-year
 record of change in head over both the historical and modern regions of
 greatest subsidence. We then calibrate a deformation model to fit both
 historical (measured with leveling surveys) and modern (measured with
 Interferometric Synthetic Aperture Radar, or InSAR) datasets. We find that
 the stress history of the Kettleman City/Los Banos region with
 historically high subsidence plays a large role in reducing modern
 subsidence in that region, while declining heads in both regions are
 likely to result in major subsidence over the next several decades. This
 study highlights the need for active groundwater management to mitigate
 ongoing and future subsidence. One key dataset needed in this effort is
 accurate long-term head histories to reconstruct the stress history of
 aquifers for accurate deformation modeling.
description: We refer to the manuscript for full details. This dataset
 contains modeled deformation over two regions in the San Joaquin Valley:
 the Los Banos/Kettleman City region (western region), and the
 Tulare/Pixley region (southern region). The model was calibrated using
 historical leveling surveys and recent Interferometric Synthetic Aperture
 Radar (InSAR) data.
description: This folder contains model files for Smith (2023):
 kettleman_modeled_subs.csv tulare_modeled_subs.csv Each csv contains two
 columns: 'decimal-year', which indicates the date in decimal
 years of the modeled deformation, and 'deformation, m', which
 indicates the mean modeled deformation from each area from all accepted
 models (the top 100 models),as described in section 3.
DOI: 10.15468/dl.bc3v5d
title: Occurrence Download

description: A dataset containing 399 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hippophae tibetana"
 ]
}

 The dataset includes 399 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003572-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.47d7wm3kk
title: Permafrost thaw causes large carbon loss in boreal peatlands while changes to peat quality are limited

description: Rapid, ongoing permafrost thaw of peatlands in the discontinuous
 permafrost zone is exposing a globally significant store of soil carbon
 (C) to microbial processes. Mineralisation and release of this peat C to
 the atmosphere as greenhouse gases is a potentially important feedback to
 climate change. Here we investigated the effects of permafrost thaw on
 peat C at a peatland complex in western Canada. We collected 15 complete
 peat cores (between 2.7 abd 4.5 m deep) along four chronosequences, from
 elevated permafrost plateaus to saturated thermokarst bogs that thawed up
 to 600 years ago. The peat cores were analysed for peat C storage and peat
 quality, as indicated by decomposition proxies (FTIR and C/N ratios) and
 potential decomposability using a 200-day aerobic incubation. Our results
 suggest net C loss following thaw, with average total peat C stocks
 decreasing by ~19.3 +/- 7.2 kg C m-2 over &lt;600 years (~13% loss).
 Average post-thaw accumulation of new peat at the surface over the same
 period was ~13.1 +/- 2.5 kg C m-2. We estimate ~19% (+/- 5.8%) of deep
 peat (&gt;40 cm below surface) C is lost following thaw (average 26
 +/- 7.9 kg C m-2 over &lt;600 years). Our FTIR analysis shows peat
 below the thaw transition in thermokarst bogs is slightly more decomposed
 than peat of a similar type and age in permafrost plateaus, but we found
 no significant changes to the quality or lability of deeper peat across
 the chronosequences. Our incubation results also showed no increase in C
 mineralisation of deep peat across the chronosequences. While these
 limited changes in peat quality in deeper peat following permafrost thaw
 highlight uncertainty in the exact mechanisms and processes for C loss,
 our analysis of peat C stocks shows large C losses following permafrost
 thaw in peatlands in western Canada.
DOI: 10.6078/d1zb1s
title: Data from: Delivered complementation in planta (DCIP) enables measurement of peptide-mediated protein delivery efficiency in plants

description: Using DCIP, we demonstrate cell-penetrating peptide-mediated cytosolic
 delivery of peptides and recombinant proteins in Nicotiana benthamiana. We
 show that DCIP enables measurement of delivery efficiency and enables
 functional screening of cell-penetrating peptide efficacies for in-planta
 protein delivery. Finally, we demonstrate that DCIP detects
 cell-penetrating peptide-mediated delivery of recombinantly expressed
 proteins such as mCherry and Lifeact into intact leaves. We also
 demonstrate delivery of a recombinant plant transcription factor, WUSCHEL
 (AtWUS), into N. benthamiana. RT-qPCR analysis of AtWUS delivery in
 Arabidopsis seedlings also suggests delivered WUS can recapitulate
 transcriptional changes induced by overexpression of AtWUS. Taken
 together, our findings demonstrate that DCIP offers a new and powerful
 tool for interrogating cytosolic delivery of proteins in plants and
 highlights future avenues for engineering plant physiology.
description: The methods section of our manuscript describes how these data
 were collected and processed. They are organized in the figure structure
 of the manuscript. These zipped files contain: 
 Raw images (.czi) that were analyzed in our
 manuscript. Images (.czi) used as examples in the
 figures. The source data (.xlsx) points plotted in
 our graphs and charts in the numerical source data folder to facilitate
 download. The raw qPCR amplification data (.xlsx)
 used in our manuscript in the numerical source data folder to facilitate
 download.  The source images (.jpg, .tif) for all
 gels and blots in our manuscript.
DOI: 10.6084/m9.figshare.30664859
title: Data and Code for Quantitative Research on Technological Evolution and Collaborative Division of Labor in China’s Fusion Engineering Based on Patent Big Data

description: Data and Code for Quantitative Research on Technological Evolution and Collaborative Division of Labor in China’s Fusion Engineering Based on Patent Big Data
DOI: 10.6084/m9.figshare.30664859.v1
title: Data and Code for Patent data on nuclear fusion in China

description: Data and Code for Patent data on nuclear fusion in China
DOI: 10.6084/m9.figshare.30664859.v2
title: Data and Code for Quantitative Research on Technological Evolution and Collaborative Division of Labor in China’s Fusion Engineering Based on Patent Big Data

description: Data and Code for Quantitative Research on Technological Evolution and Collaborative Division of Labor in China’s Fusion Engineering Based on Patent Big Data
DOI: 10.15468/dl.8fkrkc
title: Occurrence Download

description: A dataset listing the 113 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-4.39129 40.35332,-4.33886 40.35332,-4.33886 40.36795,-4.39129 40.36795,-4.39129 40.35332))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 113 records were derived from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003521-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.15dv41p32
title: Data from: Genetic variation at innate and adaptive immune genes - contrasting patterns of differentiation and local adaptation in a wild gull

description: Immunogenetic variation in natural vertebrate populations is expected to
 respond to spatial and temporal fluctuations in pathogen assemblages.
 While spatial heterogeneity in pathogen-driven selection enhances local
 immunogenetic adaptations and population divergence, different immune
 genes may yield contrasting responses to the environment. Here, we
 investigated population differentiation at the key pathogen recognition
 genes of the innate and adaptive immune system in a colonial bird species,
 the black headed gull Chroicocephalus ridibundus. We assessed genetic
 variation at three toll-like receptor (TLR) genes (innate immunity) and
 the major histocompatibility complex (MHC) class I and II genes (adaptive
 immunity) in gulls from seven colonies scattered across Poland. As
 expected, we found much greater polymorphism at the MHC than TLRs.
 Population differentiation at the MHC class II, but not MHC-I, was
 significantly stronger than at neutral microsatellite loci, suggesting
 local adaptation. This could reflect spatial variation in the composition
 of extra-cellular parasite communities (e.g. helminths), possibly driven
 by sharp differences in habitat structure between colonies. Despite
 contrasting patterns of population differentiation, both MHC classes
 showed similar regimes of diversifying selection. Some significant
 population differentiation was also observed at TLRs, suggesting that
 innate immune receptors may respond to fine-scale spatial variation in
 pathogen pressure, although this pattern could have been enhanced by
 drift. Our results suggested that local adaptation at the pathogen
 recognition immune genes can be maintained at relatively small or moderate
 spatial scales in species with high dispersal potential and highlighted
 the complexity of immunogenetic responses of animals to heterogeneous
 environments.