cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1r7j2r7
title: Data from: The evolution of climate tolerance in conifer-feeding aphids in relation to their host’s climatic niche

description: Climate adaptation has major consequences in the evolution and ecology of
 all living organisms. Though phytophagous insects are an important
 component of Earth’s biodiversity, there are few studies investigating the
 evolution of their climatic preferences. This lack of research is probably
 because their evolutionary ecology is thought to be primarily driven by
 their interactions with their host plants. Here, we use a robust
 phylogenetic framework and species-level distribution data for the
 conifer-feeding aphid genus Cinara to investigate the role of climatic
 adaptation in the diversity and distribution patterns of these
 host-specialised insects. Insect climate niches were reconstructed at a
 macroevolutionary scale, highlighting that climate niche tolerance is
 evolutionarily labile, with closely related species exhibiting strong
 climatic disparities. This result may suggest repeated climate niche
 differentiation during the evolutionary diversification of Cinara.
 Alternatively, it may merely reflect the use of host plants that occur in
 disparate climatic zones, and thus, in reality the aphid species’
 fundamental climate niches may actually be similar but broad. Comparisons
 of the aphids’ current climate niches with those of their hosts show that
 most Cinara species occupy the full range of the climatic tolerance
 exhibited by their set of host plants, corroborating the hypothesis that
 the observed disparity in Cinara species’ climate niches can simply mirror
 that of their hosts. However, 29 % of the studied species only occupy a
 subset of their hosts’ climatic zone, suggesting that some aphid species
 do indeed have their own climatic limitations. Our results suggest that in
 host-specialized phytophagous insects, host associations cannot always
 adequately describe insect niches and abiotic factors must be taken into
 account.
description: Appendix 7 -
 Cinara_occurrencesAppendix 8 -
 Pinus_occurrencesAppendix 9 - Cinara host
 plant matrixCinara/Pinus association
 matrix. 1 means presence. 0 means abscence.Appendix 10 - Accession
 numbercinara_full_ladCinara dated tree with outgroup and 95% intervals.anotated.tre
DOI: 10.5061/dryad.2dt2d96
title: Data from: The inverted U-shaped effect of urban hotspots spatial compactness on urban economic growth

description: The compact city, as a sustainable concept, is intended to augment the
 efficiency of urban function. However, previous studies have concentrated
 more on morphology than on structure. The present study focuses on urban
 structural elements, i.e., urban hotspots consisting of high-density and
 high-intensity socioeconomic zones, and explores the economic performance
 associated with their spatial structure. We use nighttime luminosity (NTL)
 data and the Loubar method to identify and extract the hotspot and
 ultimately draw two conclusions. First, with population increasing, the
 hotspot number scales sublinearly with an exponent of approximately
 0.50~0.55, regardless of the location in China, the EU or the US, while
 the intersect values are totally different, which is mainly due to
 different economic developmental level. Secondly, we demonstrate that the
 compactness of hotspots imposes an inverted U-shaped influence on economic
 growth, which implies that an optimal compactness coefficient does exist.
 These findings are helpful for urban planning.
description: hotspot2019
 Data for
 analyzing the hotspot.
DOI: 10.5061/dryad.v6460s3
title: Data from: Prolonged exposure to manure from livestock administered antibiotics decreases ecosystem carbon-use efficiency and alters nitrogen cycling

description: Microbial communities drive soil ecosystem function but are also
 susceptible to environmental disturbances. We investigated whether
 exposure to manure sourced from cattle either administered or not
 administered antibiotics affected microbially-mediated terrestrial
 ecosystem function. We quantified changes in microbial community
 composition via amplicon sequencing, and terrestrial elemental cycling via
 a stable isotope pulse-chase. Exposure to manure from antibiotic-treated
 cattle caused: i) changes in microbial community structure; and ii)
 alterations in elemental cycling throughout the terrestrial system. This
 exposure caused changes in fungal:bacterial, as well as changes in
 bacterial community structure. Additionally, exposure to manure from
 cattle treated with pirlimycin resulted in an approximate two-fold
 increase in ecosystem respiration of recently fixed-carbon, and a greater
 proportion of recently-added nitrogen in plant and soil pools compared to
 the control manure. Manure from antibiotic-treated cattle therefore
 affects terrestrial ecosystem function via the soil microbiome, causing
 decreased ecosystem carbon use efficiency, and altered nitrogen cycling.
description: Wepking_et_al_2019_fastq_files16S and ITS sequencing dataWepking_fastq_files.zipWepking_et_al_2019_DataNon-sequencing dataData_Wepking.xlsx
DOI: 10.5061/dryad.741vs1j
title: Data from: Eudicot pollen-feeding in a Cretaceous stinging wasp (Angiospermae; Hymenoptera: Aculeata)

description: Angiosperms and their insect pollinators form a foundational symbiosis,
 evidence for which from the Cretaceous is mostly indirect, based on
 fossils of insect taxa that today are anthophilous, and of fossil insects
 and flowers that have apparent anthophilous and entomophilous
 specializations, respectively. We present exceptional direct evidence
 preserved in mid-Cretaceous Burmese amber, 100 mya, for feeding on pollen
 in the eudicot genus Tricolporoidites by a basal new
 aculeate wasp, Prosphex anthophilos, gen. et sp. nov., in the
 lineage that contains the ants, bees, and other stinging wasps. Plume of
 hundreds of pollen grains wafts from its mouth and an apparent pollen mass
 was detected by micro-CT in the buccal cavity: clear evidence that the
 wasp was foraging on the pollen. Eudicots today comprise nearly
 three-quarters of all angiosperm
 species. Prosphex feeding
 on Tricolporoidites supports the hypothesis that
 relatively small, generalized insect anthophiles were important
 pollinators of early angiosperms.
description: Grimaldi et al - Amber
 pollen wasp NRRD image
 (http://teem.sourceforge.net/nrrd/)
DOI: 10.5061/dryad.98th04m
title: Metabolic rate in common shrews is unaffected by temperature, leading to lower energetic costs through seasonal size reduction

description: Small endothermic mammals have high metabolisms, particularly at cold
 temperatures. In light of this, some species have evolved a seemingly
 illogical strategy: they reduce the size of the brain and several organs
 to become even smaller in winter. To test how this morphological strategy
 affects energy consumption across seasonally shifting ambient
 temperatures, we measured oxygen consumption and behaviour in the three
 seasonal phenotypes of the common shrew (Sorex araneus), which differ in
 size by about 20%. Body mass was the main driver of oxygen consumption,
 not the reduction of metabolically expensive brain mass. Against our
 expectations, we found no change in relative oxygen consumption with low
 ambient temperature. Thus, smaller body size in winter resulted in
 significant absolute energy savings. This could only partly be explained
 by a change in activity budgets. Our findings highlight that these shrews
 manage to avoid one of the most fundamental and intuitive rules of ecology
 allowing them to subsist with lower resource availability and successfully
 survive the harsh conditions of winter.
description: Data2 - Aggregated
 Oxygen consumption valuesAggregated absolute and
 mass specific oxygen consumption rates for Sorex araneus. Raw values were
 collected at 1 Hz and a mean and standard deviation calculated over
 non-overlapping 180 s windows. Scaled values used in the glmm analyses are
 included.Data2 - Aggregated Metabolic
 Rates.csvData1 - Activity
 BudgetActivity of video
 recorded Sorex araneus during respirometry trials.
DOI: 10.5061/dryad.bm8r6pr
title: Data from: Exploring rainforest diversification using demographic model testing in the African foam-nest treefrog (Chiromantis rufescens)

description: Aim: Species with wide distributions spanning the African Guinean and
 Congolian rainforests are often composed of genetically distinct
 populations or cryptic species with geographic distributions that mirror
 the locations of the remaining forest habitats. We used phylogeographic
 inference and demographic model testing to evaluate diversification models
 in a widespread rainforest species, the African Foam-nest Treefrog
 (Chiromantis rufescens). Location: Guinean and Congolian rainforests, West
 and Central Africa. Taxon: Chiromantis rufescens. Methods: We collected
 mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) data
 for 130 samples of Chiromantis rufescens. After estimating population
 structure and inferring species trees using coalescent methods, we tested
 demographic models to evaluate alternative population divergence histories
 that varied with respect to gene flow, population size change, and periods
 of isolation and secondary contact. Species distribution models were used
 to identify regions of climatic stability that could have served as forest
 refugia since the Last Interglacial. Results: Population structure within
 Chiromantis rufescens resembles the major biogeographic regions of the
 Guinean and Congolian forests. Coalescent-based phylogenetic analyses
 provide strong support for an early divergence between the western Upper
 Guinean forest and the remaining populations. Demographic inferences
 support diversification models with gene flow and population size changes
 even in cases where contemporary populations are currently allopatric,
 which provides support for forest refugia and barrier models. Species
 distribution models suggest that forest refugia were available for each of
 the populations throughout the Pleistocene. Main conclusions: Considering
 historical demography is essential for understanding population
 diversification, especially in complex landscapes such as those found in
 the Guineo-Congolian forest. Population demographic inferences help
 connect patterns of genetic variation to diversification model
 predictions. The diversification history of Chiromantis rufescens was
 shaped by a variety of processes, including vicariance from river
 barriers, forest fragmentation, and adaptive evolution along environmental
 gradients.
description: Mitochondrial DNA (16S)
 sequence data alignment Mitochondrial DNA (16S)
 sequence alignment in nexus format. Includes 130 taxa and 563 aligned
 characters. 16s.nex
 
 16s STARBEAST2
 input file Mitochondrial DNA (16S)
 input file for species tree inference using STARBEAST2.
 rufi.xml
 
 SNPs in Structure
 format SNP data in Structure
 format chiro121_7326.str
 
 SNP data for
 SNAPP SNP data formatted for
 species tree analysis with SNAPP. chiro.xml
 
 geographicSFS
 2D SFS files for
 populations that are geographically adjacent.   
 phylogenetic
 SFS 2D SFS files for
 populations that are sister taxa on the phylogenetic tree.
 phylogeneticSFS.zip
DOI: 10.5061/dryad.03c7292
title: Data from: A high-density exome capture genotype-by-sequencing panel for forestry breeding in Pinus radiata

description: Development of genome-wide resources for application in genomic selection
 or genome-wide association studies, in the absences of full reference
 genomes, present a challenge to the forestry industry, where longer
 breeding cycles could benefit from the accelerated selection possible
 through marker-based breeding value predictions. In particular, large
 conifer megagenomes require a strategy to reduce complexity, whilst
 ensuring genome-wide coverage is achieved. Using a transcriptome-based
 reference template, we have successfully developed a high density exome
 capture genotype-by-sequencing panel for radiata pine (Pinus radiata
 D.Don), capable of capturing in excess of 80,000 single nucleotide
 polymorphism (SNP) markers with a minor allele frequency above 0.03 in the
 population tested. This represents approximately 29,000 gene models from a
 core set of 48,914 probes. A set of 704 SMP markers capable of pedigree
 reconstruction and differentiating individual genotypes were tested within
 two full-sib mapping populations. While as few as 70 markers could
 reconstruct parentage in almost all cases, the impact of missing genotypes
 was noticeable in several offspring. Therefore, sets of 60 sets of 110
 randomly selected SNP markers were compared for both parentage
 reconstruction and clone differentiation. The performance in parentage
 reconstruction showed little variation over 60 iterations. However, there
 was notable variation in discriminatory power between closely related
 individuals, indicating a higher density SNP marker panel may be required
 to elucidate hidden relationships in complex pedigrees.
description: Genotypic
 dataGenotypes generated by
 using combination of exome capture and genotyping-by-sequening
 platformSupplements.zip
DOI: 10.5061/dryad.sq067ng
title: Data from: A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean

description: The fish clade Pelagiaria, which includes tunas as its most famous
 members, evolved remarkable morphological and ecological variety in a
 setting not generally considered conducive to diversification: the open
 ocean. Relationships within Pelagiaria have proven elusive due to short
 internodes subtending major lineages suggestive of rapid early
 divergences. Using a novel sequence dataset of over 1000 ultraconserved
 DNA elements (UCEs) for 94 of the 286 species of Pelagiaria (more than 70%
 of genera), we provide a time-calibrated phylogeny for this widely
 distributed clade. Some inferred relationships have clear precedents (e.g.
 the monophyly of ‘core’ Stromateoidei, and a clade comprising ‘Gempylidae’
 and Trichiuridae), but others are unexpected despite strong support (e.g.
 Chiasmodontidae + Tetragonurus). Relaxed molecular clock analysis using
 node-based fossil calibrations estimates a latest Cretaceous origin for
 Pelagiaria, with crown-group families restricted to the Cenozoic.
 Estimated mean speciation rates decline from the origin of the group in
 the latest Cretaceous, although credible intervals for root and tip rates
 are broad and overlap in most cases, and there is higher-than-expected
 partitioning of body shape diversity (measured as fineness ratio) between
 clades concentrated during the Palaeocene-Eocene. By contrast, more direct
 measures of ecology show either no substantial deviation from a null model
 of diversification (diet) or patterns consistent with evolutionary
 constraint or high rates of recent change (depth habitat). Collectively,
 these results indicate a mosaic model of diversification. Pelagiarians
 show high morphological disparity and modest species richness compared to
 better-studied fish radiations in contrasting environments. However, this
 pattern is also apparent in other clades in open-ocean or deep-sea
 habitats, and suggests that comparative study of such groups might provide
 a more inclusive model of the evolution of diversity in fishes.
description: Supporting data and
 analytical scriptsData and analytical
 scripts for phylogenetic and comparative analyses in Friedman et al.
 (2019): A phylogenomic framework for pelagiarian fishes (Acanthomorpha:
 Percomorpha) highlights mosaic radiation in the open
 oceanFriedman et al. 2019
 PRSB.zip
DOI: 10.5061/dryad.4qh3sf5
title: Data from: Changes in potential nitrous oxide efflux during grassland restoration

description: Nitrous oxide efflux from soil is an important ecological process in terms
 of global climate impacts, stratospheric chemistry, and soil fertility.
 The effects of grassland restoration on nitrous oxide (N2O) efflux in
 formerly cultivated agricultural soils are not well known. Restoration
 changes the storage and availability of soil C and N, with potential
 consequences for N2O efflux. We examined changes in potential N2O efflux
 across a 35-year chronosequence of grassland restorations, using lab
 incubations at moisture levels that maximized N2O emissions, to quantify
 the relationship between N2O efflux and soil properties known to change
 predictably during grassland restoration. We found that restoring
 cultivated agricultural land to grassland rapidly decreased N2O efflux
 from soils, though native prairie had a potential N2O efflux higher than
 the agricultural land. The oldest restoration had N2O efflux 50 times
 lower than native prairie. Changes in N2O efflux were more strongly
 correlated with N mineralization than C mineralization, according to
 multiple regression analysis. These results suggest that grassland
 restoration could mitigate nitrous oxide emissions for decades.
description: Aug 2013 spp comp
 SRC_JEQVascular plant species
 composition from restored prairies and native prairie. Values are visual
 estimations of percent cover in August 2013.Restored sites
 dataNitrous oxide efflux and
 associated soil variables from restored prairies.Reference sites
 dataNitrous oxide efflux and
 associated soil variables from a native prairie and cultivated
 field.
DOI: 10.5061/dryad.s45jd1v
title: Data from: Interaction of serum vitamin B12 and folate with MTHFR genotypes on risk of ischemic stroke

description: Abstract Objective We evaluated the interaction of serum folate and
 vitamin B12 (B12) with methylenetetrahydrofolate reductase (MTHFR) C677T
 genotypes, on the risk of first ischemic stroke, and on the efficacy of
 folic acid (FA) treatment in prevention of first ischemic stroke. Methods
 A total of 20,702 hypertensive adults were randomized to a double-blind
 treatment of daily enalapril 10mg and FA 0.8mg or enalapril 10mg alone.
 Participants were followed-up every three months. Results Median values of
 folate and B12 concentrations at baseline were 8.1 ng/mL and 280.2 pmol/L,
 respectively. Over a median of 4.5 years, among those not receiving FA,
 participants with baseline serum B12 and/or serum folate above the median
 had a significantly lower risk of first ischemic stroke (HR, 0.74; 95%CI:
 0.57-0.96), especially in those with MTHFR 677 CC genotype (wild type)
 (HR, 0.49; 95%CI: 0.31-0.78). FA treatment significantly reduced the risk
 of first ischemic stroke in participants with both folate and B12 below
 the median (2.3% in enalapril-folic acid group vs. 3.6% in enalapril-only
 group; HR, 0.62; 95%CI: 0.46-0.86), particularly in MTHFR 677 CC carriers
 (1.6% vs. 4.9%; HR, 0.24; 95%CI: 0.11-0.55). However, carriers of TT
 responded better with both folate and B12 levels above the median (HR,
 0.28; 95%CI: 0.10-0.75). Conclusions The risk of first ischemic stroke was
 significantly higher in hypertensive patients with low levels of both
 folate and B12. Effect of FA treatment was greatest in patients with low
 folate and B12 with the CC genotype, and with high folate and B12 with the
 TT genotype.
description: Supplemental
 dataTable e1-13; Figuer
 e1-3Supplemental
 dataSuppelemental figures
 and tables
DOI: 10.5061/dryad.1718r30
title: Data from: Impact of the modality of mechanical ventilation on bleeding during pituitary surgery: A single blinded randomized trial

description: [No abstract provided]
description: anonymized
 dataLe-Guen-Data-anonymized-EN.xls
DOI: 10.5061/dryad.s5v553b
title: Data from: Evolutionary relationship of fat body endoreduplication and queen fecundity in termites

description: Endoreduplication or nuclear genome replication without cell division is
 widely observed in the metabolically active tissues of plants and animals.
 The fat body cells of adult female insects produce abundant yolk proteins
 and become polyploid, which is assumed to accelerate egg production.
 Recently, it was reported that in termites, endopolyploidy in the fat body
 occurs only in queens but not in the other females; however, the
 relationship between the fecundity and ploidy level in the fat body
 remains unclear. Termite queens exhibit a huge variation in their egg
 producing capacity among different species; queens in the species with a
 foraging lifestyle, in which workers leave the nest to forage outside, are
 much more fecund than those in the species living in a single piece of
 wood. In this study, we conducted ploidy analyses on three foraging and
 three wood-dwelling termites via flow cytometry. In all the species, the
 fat body of queens contained significantly more polyploid cells than that
 of other nonreproductive females, considering their body size effect.
 However, the male fat body, which is not involved in yolk production, did
 not show consistency in polyploid cell numbers among the species studied.
 Moreover, highly fecund queens in foraging termites exhibit higher levels
 of endopolyploidy in their fat body than those with less fecundity in
 wood-dwelling termites. These results suggest that endopolyploidy in the
 fat body of termite queens can boost their egg production, and the level
 of endopolyploidy in their fat body is linked to their fecundity. Our
 study provides a novel insight into the evolutionary relationship between
 endoreduplication and caste specialization in social insects.
description: Data from Nozaki &
 Matsuura 2019The data was collected
 from field sampled insects by flow cytometry and published in Nozaki &
 Matsuura 2019.
DOI: 10.5061/dryad.65492qt
title: Data from: Old World and New World Phasmatodea: phylogenomics resolve the evolutionary history of stick and leaf insects

description: Phasmatodea comprises over 3,000 extant species and stands out as one of
 the last remaining insect orders for which a robust, higher-level
 phylogenetic hypothesis is lacking. New research suggests that the extant
 diversity is the result of a surprisingly recent and rapid radiation that
 has been difficult to resolve with standard Sanger sequence data. In order
 to resolve the early branching events of stick and leaf insects, we
 analyzed transcriptomes from 61 species, including 38 Phasmatodea species
 comprising all major clades and 23 outgroup taxa, including all other
 Polyneoptera orders. Using a custom-made ortholog set based on reference
 genomes from four species, we identified on average 2,274 orthologous
 genes in the sequenced transcriptomes. We generated various sub-alignments
 and performed maximum-likelihood analyses on several representative
 datasets to evaluate the effect of missing data and matrix composition on
 our phylogenetic estimates. Based on our new data, we are able to reliably
 resolve the deeper nodes between the principal lineages of extant
 Phasmatodea. Among Euphasmatodea, we provide strong evidence for a basal
 dichotomy of Aschiphasmatodea and all remaining euphasmatodeans, the
 Neophasmatodea. Within the latter clade, we recovered a previously
 unrecognized major New World and Old World lineage, for which we introduce
 the new names Oriophasmata tax. nov. (“Eastern phasmids”) and
 Occidophasmata tax. nov. (“Western phasmids”). Occidophasmata comprise
 Diapheromerinae, Pseudophasmatinae, and Agathemera, whereas all remaining
 lineages form the Oriophasmata, including Heteropterygidae, Phylliinae,
 Bacillus, Lonchodidae (Necrosciinae + Lonchodinae), Clitumninae,
 Cladomorphinae, and Lanceocercata. We furthermore performed a divergence
 time analysis and reconstructed the historical biogeography for stick and
 leaf insects. Phasmatodea either originated in Southeast Asia or in the
 New World. Our results suggest that the extant distribution of Phasmatodea
 is largely the result of dispersal events in a recently and rapidly
 diversified insect lineage rather than the result of vicariant processes.
description: Molecular datasets to
 estimate relationships of stick and leaf insects
 (Phasmatodea).Supplementary_Archive_1.zipMolecular datasets to estimate divergence times of stick and leaf insects (Phasmatodea).Supplementary_Archive_2.zip