cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1c59zw3vx
title: Geophysical and geochemical evidence for a new mafic magmatic province within the Northwest Shelf of Australia: Supplementary material

description: Buried magmatic provinces are rarely identified and difficult to classify.
 The Northwest Shelf of Australia contains large volumes of potentially
 interconnected mafic igneous material across several sedimentary basins.
 However, limited study and a lack of surface exposure have prevented
 detailed description and classification of these rocks. In this study, the
 distribution and composition of these mafic igneous rocks is described
 using an integrated geophysical and geochemical approach, which included
 over 10,000 km of 2D historical seismic data, well log data and chemical
 analysis of samples from 14 wells across the Browse, Roebuck, Canning and
 North Carnarvon basins. Using this combined dataset, we demonstrate
 interconnectivity of buried mafic igneous rocks across the Northwest Shelf
 and calculate for these mafic rocks a total surface area exceeding 280,000
 km2 and a cumulative minimum volume of ~140,000 km3. Petrology
 and geochemistry of samples indicate they are basaltic and doleritic with
 alkaline and sub-alkaline compositions and formed in a continental rift
 setting. Collectively, the igneous rocks meet the criteria for
 classification as a mafic magmatic province (MMP) and closely match the
 criteria required for classification as a large igneous province (LIP).
 The interconnected mafic igneous rocks found across the Northwest Shelf of
 Australia are here formally defined as an MMP. Emplacement of the
 Northwest Shelf MMP may represent hotspot magmatism that could have
 initiated rifting of the Cimmerian Block from NW Australia near the end
 Permian, and may have broad implications for petroleum prospectivity, CO2
 sequestration and new resource opportunities in the Northwest Shelf.
DOI: 10.5061/dryad.rr4xgxd8m
title: Macrophage-derived IL-6 trans-signaling as a novel target in the pathogenesis of bronchopulmonary dysplasia (RNA-seq-P14-HYXvsNOX)

description: Rationale: Premature infants exposed to oxygen are
 at risk for bronchopulmonary dysplasia (BPD), which is characterized by lung growth arrest. Inflammation is important, but the mechanisms remain elusive. Here, we investigated inflammatory pathways and therapeutic targets in severe clinical and experimental BPD. Methods and Results: First, transcriptomic analysis with in-silico cellular deconvolution identified a lung-intrinsic M1-like-driven cytokine pattern in newborn mice after hyperoxia. These findings were confirmed by gene expression of macrophage-regulating chemokines (Ccl2, Ccl7, Cxcl5) and markers (Il6, Il17A, Mmp12). Second, hyperoxia-activated IL-6/STAT3 signaling was measured in vivo and related to loss of alveolar epithelial type II cells (ATII) as well as increased mesenchymal marker. Il6 null mice exhibited preserved ATII survival, reduced myofibroblasts and improved elastic fiber assembly, thus enabling lung growth and protecting lung function. Pharmacological inhibition of global IL-6 signaling and IL-6 trans-signaling promoted alveolarization and ATII survival after hyperoxia. Third, hyperoxia triggered M1-like polarization, possibly via Klf4; hyperoxia-conditioned medium of macrophages and IL-6 impaired ATII proliferation. Finally, clinical data demonstrate elevated macrophage-related plasma cytokines as potential biomarkers that identify infants receiving oxygen at increased risk of developing BPD. Moreover, macrophage-derived IL6 and active STAT3 were related to loss of epithelial cells in BPD lungs. Conclusion: We present a novel IL-6-mediated mechanism by which hyperoxia activates macrophages in immature lungs, impairs ATII homeostasis, and disrupts elastic fiber formation, thereby inhibiting lung growth. The data provide evidence that IL-6 trans-signaling could offer an innovative pharmacological target to enable lung growth in severe neonatal chronic lung disease.
DOI: 10.5061/dryad.jdfn2z3bn
title: Drought has negative consequences on aphid fitness and plant vigour: insights from a meta-analysis

description: 1. Aphids are abundant in natural and managed vegetation, supporting a
 diverse community of organisms and causing damage to agricultural crops.
 Due to a changing climate, periods of drought are anticipated to increase,
 and the potential consequences of this for aphid-plant interactions are
 unclear. 2. Using a meta-analysis and synthesis approach, we aimed to
 advance understanding of how increased drought incidence will affect this
 ecologically and economically important insect group, and to characterise
 any potential underlying mechanisms. We used qualitative and quantitative
 synthesis techniques to determine whether drought stress has a negative,
 positive, or null effect on aphid fitness and examined these effects in
 relation to 1) aphid biology, 2) geographical region, 3) host plant
 biology. 3. Across all studies, aphid fitness is typically reduced under
 drought. Subgroup analysis detected no difference in relation to aphid
 biology, geographical region, or the aphid-plant combination, indicating
 the negative effect of drought on aphids is potentially universal.
 Furthermore, drought stress had a negative impact on plant vigour and
 increased plant concentrations of defensive chemicals, suggesting the
 observed response of aphids is associated with reduced plant vigour and
 increased chemical defence in drought-stressed plants. 4. We propose a
 conceptual model to predict drought effects on aphid fitness in relation
 to plant vigour and defence to stimulate further research.
description: Data was collected and curated using standard systematic
 literature synthesis approaches. The effect size (Hedges' g) reported
 in the dataset was calculated from extracted means and standard
 deviations.
description: Please check the ReadMe for an explanation of the values included
 in the dataset. Please note that n/a values are included in the
 Global_Dataset tab for plant meta-analysis data (_Plant_Vigour,
 _Plant_Defence, and _Plant_Nutrition), these indicate studies that did not
 report these parameters.
DOI: 10.5061/dryad.zkh1893b3
title: The mitochondrial genome datasets of phylogenetic analysis from the subfamily Coelidiinae

description: 58 leafhopper and 5 treehoppers species were selected to participate in
 the phylogenetic tree construction after the removal of unverified, lacks
 the accurate scientiﬁc name, and repeated species sequences. Phylogenetic
 analysis was performed using alignments of the 13 PCGs of leafhopper with
 the other complete or near
 complete genomes of the treehopper
  species.  The two species of Cosmoscarta bispecularis
 (KP064511)  and  Tettigades auropilosa (KM000129) (Yan
 & Zu, 2019) were used as the outgroup.
description: The two complete
 mitogenomes of C. biungulata and C. robusta were sequenced by Berry
 Genomics on the HiSeq 2,500 platform (Illumina) with 150-bp paire end
 reads. The average insert length was 350 bp and 6 GB of clean data were
 obtained. Each mitogenome was assembled usingGeneious Prime 2019.2.1
 software and based on a mitochondrial reference sequence of Olidiana
 ritcheriina (MK738125) (Wang et al., 2019b). The assembled mitochondrial
 gene sequences were compared with the homologous sequences of O.
 ritcheriina (MK738125) and Taharana fasciana (KY886913) , which were
 retrieved from GenBank and identified via BLAST searches in NCBI to
 confirm sequence accuracy. We used the MITOS web server  and BLAST
 searches in NCBI  to annotate the assembled sequences using invertebrate
 genetic codes.
description: (13PCG12, 1st and 2nd codons of 13 PCGs [6,676 bp]; the amino acid [AA] sequences of 13 PCGs [3,338 bp])
DOI: 10.5061/dryad.pg4f4qrq2
title: Ant predation towards termite and treehopper baits in the Ecuadorian Amazon

description: Animals may develop mutualistic associations with other species, whereby
 prey offer resources or services in exchange for protection from
 predators. Alternatively, prey may offer resources or services directly to
 their would-be predators in exchange for their lives. The latter may be
 the case of hemipterans that engage in mutualistic interactions with ants
 by offering a honeydew reward. We test the extent to which a honeydew
 offering vs. partner recognition may play a role as proximate mechanisms
 deterring ants from predating upon their hemipteran partners. We show
 that, when presented with a choice between a hemipteran partner and an
 alternative prey type, mutualist ants were less likely to attack and more
 likely to remain probing their hemipteran partners. This occurred even in
 the absence of an immediate sugary reward, suggesting either an evolved or
 learned partner recognition response. To a similar extent, however, ants
 were also less likely to attack the alternative prey type when laced with
 honey, even after the honey had been depleted, suggesting an ability of
 ants to recognize new potential sources of honey. Either possibility
 suggests a degree of innate or learned partner recognition.
DOI: 10.5061/dryad.d2547d839
title: Bayesian morphological clock versus parsimony: An insight into the relationships and dispersal events of postvacuum Cricetidae (Rodentia, Mammalia)

description: Establishing an evolutionary timescale is fundamental for tackling a great
 variety of topics in evolutionary biology, including the reconstruction of
 patterns of historical biogeography, coevolution and diversification.
 However, the tree of life is pruned by extinction and very generally
 molecular data cannot be gathered for extinct lineages. Methodological
 challenges have prevented until recently the application of tip-dating
 Bayesian approaches in morphology-based fossil-only datasets. Herein we
 present a morphological dataset for a group of cricetid rodents to which
 we apply a battery of methods fairly new in palaeontology that can be used
 by palaeontologists for the analysis of entirely extinct clades. We
 compare the tree topologies obtained by traditional parsimony, Bayesian
 dated and undated phylogenetic approaches and calculate stratigraphic
 congruence indices for each. Bayesian tip-dated clock methods seem to
 outperform parsimony in the case of our dataset, which includes highly
 homoplastic morphological characters. Regardless, all three topologies
 support the monophyly of Megacricetodontinae, Democricetodontinae and
 Cricetodontinae. Dispersal and speciation events inferred through Bayesian
 Binary Markov chain Monte Carlo and biodiversity analyses provide evidence
 for a correlation between biogeographic events, climatic changes and
 diversification in cricetids.
description: The material and methods
 section of the article contains all details concerning the methods used in
 this study.
description: The readme file contains an
 explanation of each file uploaded in supplementary files.
DOI: 10.5061/dryad.1vhhmgqt8
title: Body size and circulating levels of different molecules from tree swallows (Tachycineta bicolor) exposed to different doses of lipopolysaccharide (LPS)

description: The purpose of mounting an immune response is to destroy pathogens, but
 this response comes at a physiological cost, including the generation of
 oxidative damage. However, many studies on the effects of immune
 challenges employ a single high dose, meaning that the consequences of
 more mild immune challenges are poorly resolved. We tested whether the
 degree of immunological challenge in tree swallows (Tachycineta bicolor)
 affects oxidative physiology and body mass, and whether these metrics
 correlate with parasitic nest mite load. We injected 14-day-old nestlings
 with either 0, 0.01, 0.1, or 1 mg lipopolysaccharide (LPS) per kg body
 mass, then collected a blood sample 24-h later to quantify multiple
 physiological metrics, including oxidative damage (i.e., d-ROMs),
 circulating amounts of triglyceride and glycerol, and levels of the acute
 phase protein haptoglobin. After fledging, we identified and counted
 parasitic nest mites (Dermanyssus spp. and Ornithonyssus spp.). We found
 that only nestlings injected with 1 mg LPS/kg body mass, which is a common
 dosage in ecoimmunological studies, lost more body mass than individuals
 from other treatment groups. However, every dose of LPS resulted in a
 commensurate increase in oxidative damage. Parasitic mite abundance had no
 effect on oxidative damage across treatments. Amount of oxidative damage
 correlated with haptoglobin levels, suggesting compensatory mechanisms to
 limit self-damage during an immune response. We conclude that while only
 the highest-intensity immune challenges resulted in costs related to body
 mass, even low-intensity immune challenges result in detectable increases
 of oxidative damage.
description: Field- and lab-based data. Stored in Excel. Analyzed in SAS.
DOI: 10.5061/dryad.n8pk0p2vx
title: Effects of heat hardening on life parameters and thermostability of Bradysia odoriphaga larva and adults

description: High temperature in summer is a key barrier for Bradysia odoriphaga
 (Diptera: Sciaridae), a serious pest of vegetables in China. Because mild
 heat hardening can enhance the thermotolerance of many insects, we
 determined if heat hardening was beneficial for B. odoriphaga adaptation
 to high summer temperatures. We studied the biological performance,
 antioxidant responses and hsp70 and hsp90 expression of B. odoriphaga 4th
 instar larvae and adults after pre-exposure to mild heat hardening
 temperatures (30-36°C). The tolerance of larvae to severe heat stress was
 enhanced after mild heat hardening (32-36°C). However, life parameters
 were significantly inhibited, development was delayed, longevity was
 shortened and fecundity was decreased. Mild heat hardening (30-34°C)
 caused serious adverse effects on life parameters and less enhancement of
 heat resistance for 4th larvae. Mild heat hardening at 36°C weakened the
 heat tolerance of adults. The activity of four antioxidant enzymes in B.
 odoriphaga changed dramatically after heat hardening at 32-36°C. CAT and
 GST maintained successive higher activities, and POD also had higher
 activities in larvae after 48 h recovery at 25°C, pupae, and adults.
 Simultaneously, the expression levels of hsp70 and hsp90 increased
 significantly upon thermal hardening. Higher expression levels were also
 detected in larvae after 48 h recovery at 25°C, pupae, and adults. Mild
 heat hardening played an important role in heat tolerance plasticity of B.
 odoriphaga larvae. The antioxidant system and hsp70 and hsp90 genes were
 relevant to this adaptation process.
DOI: 10.5061/dryad.47d7wm3d9
title: South African Tursiops aduncus ddRAD genepop file

description: Many marine species exhibit fine-scale population structure despite high
 mobility and a lack of physical barriers to dispersal, but the
 evolutionary drivers of differentiation in these systems are generally
 poorly understood. Here we investigate the potential role of habitat
 transitions and seasonal prey distributions on the evolution of population
 structure in the Indo-Pacific bottlenose dolphin, Tursiops aduncus, off
 South Africa’s coast, using double-digest Restriction-site Associated DNA
 sequencing (ddRADseq). Population structure was identified between the
 eastern and southern coasts and correlated with the habitat transition
 between the temperate Agulhas (southern) and subtropical Natal (eastern)
 Bioregions, suggesting differentiation driven by resource specialisations.
 Differentiation along the Natal coast was comparatively weak, but evident
 in some analyses and varied depending on whether the samples were
 collected during or outside the seasonal sardine (Sardinops sagax) run.
 This local abundance of prey could influence the ranging patterns and
 apparent genetic structure of T. aduncus. These findings have significant
 and transferable management implications, most importantly in terms of
 differentiating populations inhabiting distinct Bioregions and seasonal
 structural patterns within a region associated with the movement of prey
 resources.
description: Data were generated using the ddRADseq method (Peterson et al.
 2012), sequenced on an Illumina HighSeq 2500 platform.  Genotype data
 were generated in the program STACKS (Catchen et al.,
 2011).  Single-nucleotide polymorphisms (SNPs) were detected using
 ref_map (to the turTRU reference sequence). During short-read alignment
 the minimum depth of coverage to create a stack was 3, and the maximum
 distance (in bp) between stacks was 2. The number of mismatches allowed
 when building a catalogue was 2. Loci were filtered using Populations,
 removing those that had a stack depth below eight, or were not present in
 at least 70% of individuals or in all five groups according to sampling
 areas.
DOI: 10.5061/dryad.4b8gthtcx
title: A novel index to aid in prioritizing habitats for site-based conservation

description: Funding biodiversity conservation strategies are usually minimal, thus
 prioritizing habitats at high risk should be conducted.  We
 developed and tested a conservation priority index (CPI) that ranks
 habitats to aid in prioritizing them for conservation. We tested the index
 using 1897 fish species from 273 African inland lakes and 34 countries. In
 the index, lake surface area, rarity, and their International Union for
 Conservation of Nature (IUCN) Red List status were incorporated. 
 We retrieved data from the Global Biodiversity Information Facility
 (GBIF), and IUCN data repositories. Lake Nyasa had the highest species
 richness (424), Tanganyika (391), Nokoué (246), Victoria (216), and Ahémé
 (216). However, lakes Otjikoto and Giunas had the highest CPI of 137.2 and
 52.1, respectively. Lakes were grouped into high priority (CPI &gt;
 0.5; n=56) and low priority (CPI &lt;0.5; n=217). The median surface
 area between priority classes was significantly different (W = 11768,
 p&lt;0.05, effect size = 0.65). Prediction accuracy of Random Forest
 (RF) and eXtreme Gradient Boosting (XGBoost) for priority classes were
 0.912 and 0.954 respectively. Both models exhibited lake surface area as
 the variable with the highest importance. CPI generally increased with a
 decrease in lake surface area. This was attributed to less ecological
 substitutability and higher exposure levels of anthropogenic stressors
 such as pollution to a species in smaller lakes. Also, the highest species
 richness per unit area was recorded for high-priority lakes. Thus, smaller
 habitats or lakes may be prioritized for conservation although larger
 water bodies or habitats should not be ignored. The index can be
 customized to local, regional, and international scales as well as marine
 and terrestrial habitats.
description: We considered fish species records from all the lakes in Africa
 found in the Global Biodiversity Information Facility (GBIF, 2020). We
 retrieved the records with the <em>occ_download_get</em>
 function in <em>rgbif </em>package (Chamberlain et al. 2020),
 and genera names were changed in conformity with FishBase nomenclature
 (Froese & Pauly 2021), which is based on Oijen (1996).
description: Only species data used was retained in the analysis dataset
DOI: 10.5061/dryad.fttdz08t5
title: CarniFOSS: A database of the body mass of fossil carnivores

description: Motivation: Body mass is one of the most important determinants of animal
 ecology. Unlike other important traits it is also readily inferable from
 fossils and it is therefore one of the only traits that can be directly
 analyzed and compared between fossil and contemporary communities. Despite
 this, no comprehensive database of the body mass of larger clades of
 extinct species exists. Analysis of fossils has therefore been restricted
 to small clades or to smaller, potentially biased, subsets of species. We
 here describe CarniFoss, an open-access database of body masses of all
 1322 extinct species of non-pinniped Carnivoramorpha and two related
 extinct groups of carnivorous mammals, Hyaenodonta, and Oxyaenida. Main
 types of variables contained: We gathered lengths of teeth of fossil and
 extant species and body mass for extant species and a few of the
 best-known fossil species. Following this we estimated body mass for all
 species through phylogenetic imputation. Spatial location and grain:
 Global, terrestrial Time period and grain: We collected data on all known
 species within the focal groups. The known species all lived in the
 Paleogene, Neogene or Quaternary (i.e. the last 66 Mya). Major taxa and
 level of measurement: We searched for data on reported tooth size of all
 described species of Carnivoramorpha (excluding pinnipeds) and selected
 extinct related groups (Hyaenodonta and Oxyaenidae). We combined this with
 measured body mass for all extant species and inferred body mass based on
 long-bones for selected extinct species, as well as a species-level
 phylogeny including all extant and extinct species in the group, and
 inferred the body mass for all species using phylogenetic imputation.
 Software format: Data is provided as a series of .csv files, with all
 metadata in a separate PDF file.
description: All holes in the data are filled by imputation. Imputation is
 clearly marked in the dataset but we urge all users to consider when this
 imputation influences their downstream analyses.
description: The dataset may be updated in the future and we urge all users to
 check the page on GitHub to see if there is any newer version available
 (https://github.com/sorenfaurby/CarniFOSS)
DOI: 10.5061/dryad.gb5mkkwqb
title: Genome-wide molecular phylogenetic analyses and mating experiments which reveal the evolutionary history and an intermediate stage of speciation of a giant water bug

description: The intermediate stages of speciation are important for
 understanding the processes involved in the creation of
 biodiversity, and also comprise a number of interesting
 phenomena. However, difficulties are associated
 with dividing clear speciation stages because speciation is a
 continuous process. Therefore, the elucidation
 of speciation is an interesting and important task in evolutionary
 biology. We herein present an
 example of a species in an intermediate stage of speciation using
 the giant water bug Appasus japonicus (Heteroptera,
 Belostomatidae) that was investigated using mating
 experiments and phylogenetic analyses of
 the mtDNA COI (658 bp) and 16S rRNA (435 bp)
 regions, and nDNA SSR (13 loci) and its genome-wide SNPs (11,241 SNPs).
 The results of our phylogenetic analyses based on their mtDNA dataset and
 the genome-wide SNPs dataset strongly supported the paraphyly of the
 Japanese populations. Therefore, it is suggested that their ancestral
 lineage which being distributed in the Japanese Archipelago subsequently
 migrated to the Eurasian Continent (i.e., “back-dispersal” occurred).
 Furthermore, the results of the mating experiments suggested that
 among A. japonicus, even between closely related lineages,
 pre-mating reproductive isolation has been established by the
 differentiation of copulatory organ morphologies. In
 contrast, pre-mating reproductive isolation is not
 established in the absence of the differentiation of copulatory
 organ morphologies, even if genetic differentiation is prominent. These
 results suggested that their phylogenetic distance does not predict
 pre-mating reproductive isolation. Furthermore, in the present study,
 we present a clear example of pre-mating reproductive
 isolation driving speciation between closely related lineages.