cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.31168015
title: Dataset: Native rhizobia from arid and semi arid regions of Algeria exhibit drought tolerance

description: Dataset of the article: Native rhizobia from arid and semi arid regions of Algeria exhibit drought tolerance
DOI: 10.6084/m9.figshare.31168015.v1
title: Dataset: Native rhizobia from arid and semi arid regions of Algeria exhibit drought tolerance

description: Dataset of the article: Native rhizobia from arid and semi arid regions of Algeria exhibit drought tolerance
DOI: 10.5061/dryad.69p8cz93w
title: The effect of methodological considerations on the construction of gene-based plant pan-genomes

description: Pan-genomics is an emerging approach for studying the genetic diversity
 within plant populations. In contrast to common resequencing studies that
 compare whole genome sequencing data to a single reference genome, the
 construction of a pan-genome involves the direct comparison of multiple
 genomes to one another, thereby enabling the detection of genomic
 sequences and genes not present in the reference, as well as the analysis
 of gene content diversity. While multiple studies describing pan-genomes
 of various plant species have been published in recent years, our
 understanding regarding the effect of the computational procedures used
 for pan-genome construction is still limited. Here we examine the effect
 of several key methodological factors on the obtained gene pool and on
 gene presence-absence detections by constructing and comparing multiple
 pan-genomes of Arabidopsis thaliana and cultivated soybean, as well as
 conducting a meta-analysis on published pan-genomes. These factors include
 the construction method, the sequencing depth, and the extent of input
 data used for gene annotation. We observe substantial differences between
 pan-genomes constructed using three common procedures (De novo assembly
 and annotation, Map-to-pan, and Iterative assembly), and that results are
 dependent on the extent of the input data. Specifically, we report low
 agreement between the gene content inferred using different procedures and
 input data. Our results should increase the awareness of the
 community to the consequences of methodological decisions made during the
 process of pan-genome construction and emphasize the need for
 further investigation of commonly applied methodologies.
description: Please see the DRYAD_README.txt file for details.
DOI: 10.15468/dl.7jrdyq
title: Occurrence Download

description: A dataset containing 549 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Nepal",
 "DatasetKey is EOD – eBird Observation Dataset",
 "TaxonKey is Grus antigone"
 ]
}

 The dataset includes 549 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003065-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.prr4xgxp2
title: Investigating gas-exchange performance between wheat landraces and commercial varieties

description: Improvement of photosynthetic traits in crops to increase yield potential
 and crop resilience has recently become a major breeding target. Synthetic
 biology and genetic technologies offer unparalleled opportunities to
 create new genetics for photosynthetic traits driven by existing
 fundamental knowledge. However, large “gene bank” collections of germplasm
 comprising of historical collections of crop species and their relatives
 offer a wealth of opportunities to find novel allelic variation in the key
 steps of photosynthesis, to identify new mechanisms and to accelerate
 genetic progress in crop breeding programs. Here we explore the available
 genetic resources in food and fibre crops, strategies to selectively
 target allelic variation in genes underpinning key photosynthetic
 processes and deployment of this variation via gene editing in modern
 elite material.
description: Gas-exchange data presented:<br>A subset of Vavilov wheat
 landraces from a single seed descent and four commercial checks (Mace,
 Baxter, Banks and Pastor) were grown in 2 x 3m plots in the field (Yanco,
 NSW - 2018). Commercial checks represent current elite and older released
 commercial varieties. A-Ci curves were measured on the youngest fully
 expanded leaf for n=2-3 plants between 10 - 4pm at an irradiance of 1500
 PAR. <br>Analysis of data to determine Vcmax and J:<br>Using
 PlantEcoWrap (Stinziano et al., 2020) and the wheat kinetic parameters
 determined by Kane et al. (1994) and Prins et al. (2016) with the wheat
 gmes and gamma star from Silva-Perez et al. (2017). The data was
 normalised to 25oC using the Ea for Kcair and gmes from tobacco (Bernacchi
 et al., 2002).
DOI: 10.5061/dryad.gf1vhhmrv
title: Dataset: Resource limitation has a limited impact on the outcome of virus-fungus co-infection in an insect host

description: Infection by pathogens is strongly affected by the diet or condition of
 the prospective host. Studies that examine the impact of diet have mainly
 focussed on single pathogens; however, co-infections within a single host
 are thought to be common. Different pathogen groups might respond
 differently to resource availability and diverse infections could increase
 the costs of host defence, meaning the outcome of mixed infections under
 varying dietary regimes is likely to be hard to predict. We used the
 generalist cabbage looper, Trichoplusia ni and two of its pathogens, the
 DNA virus T. ni nucleopolyhedrovirus (TniSNPV) and the entomopathogenic
 fungus, Beauveria bassiana to examine how nutrient reduction affected the
 outcome of mixed pathogen infection. We challenged insects with a low or
 high effective dose of virus, alone or combined with a single dose of
 fungus. We manipulated food availability after pathogen challenge by
 diluting artificial diet with cellulose, a non-nutritious bulking agent,
 and examined its impact on host and pathogen fitness. Reducing diet
 quantity did not alter overall or pathogen-specific mortality. In all
 cases, TniSNPV-induced mortality was negatively affected by fungus
 challenge. Similarly, B. bassiana-induced mortality was negatively
 affected by TniSNPV challenge, but only at the higher virus dose. Dietary
 dilution mainly affected B. bassiana speed of kill when mixed with a high
 dose of TniSNPV, with an increase in the duration of fungal infection when
 cellulose was low (high quantity). One pathogen dominated the production
 of transmission stages in the cadavers and co-infection did not affect the
 yield of either pathogen. There was no evidence that co-infections were
 more costly to the survivors of pathogen challenge. In conclusion, dietary
 dilution did not determine the outcome of mixed pathogen infection, but it
 had more subtle effects, that differed between the two pathogens and could
 potentially alter pathogen recycling and host-pathogen dynamics.
DOI: 10.5061/dryad.73n5tb2zw
title: Pseudocongruent phylogeography reflects unique responses to environmental perturbations in a biodiversity hotspot

description: Aim: Comparative phylogeographic studies provide important insights into
 the biogeographical processes shaping regional patterns of diversity. Yet,
 comparative studies are lacking for southern African herpetofauna, despite
 their high diversity. We statistically compare phylogeographic structure
 and divergence-time estimates among five co-distributed forest-living
 herpetofaunal taxa to assess rivers, climatic refugia, and climatic
 gradients as congruent drivers of phylogeographic diversity. Location:
 Maputoland-Pondoland-Albany biodiversity hotspot, Southern Africa. Taxon:
 herpetofauna (reptiles and amphibians). Methods: Phylogeographic structure
 and divergence-times within species were estimated from mitochondrial and
 nuclear DNA sequence data. Phylogeographic concordance factors were used
 to estimate the degree of phylogeographic congruence among sympatric
 localities. Full-likelihood Bayesian comparisons were used to estimate
 synchronous divergence between phylogeographic regions and across a
 putative river barrier. Paleoclimatic niche models were compared among
 taxa to identify congruent climatic refugia. Non-parametric statistics
 were used to identify climatic differences between regions and among
 populations within each species. Finally, redundancy analyses were used to
 assess geographic distance, climate, and the putative river barrier as
 explanatory variables to genetic diversity. Results: There is
 comprehensive phylogeographic structuring within each species, comprising
 distinct northerly and southerly clades. Phylogeographic concordance
 factors generally support co-diversification in a north/south axis. Yet,
 analyses of the divergence-time estimates through the Mio/Plio/Pleistocene
 indicate asynchronous phylogeographic histories. Climatic niche models
 identified idiosyncratic responses to paleoclimatic change. Climatic
 variables are significantly different among populations in all species and
 correlated with latitude. A combined model of distance, climate, and
 rivers explained the greatest proportion of genetic diversity in most
 taxa, of which climate explained the highest variance. Main Conclusions:
 Ancient and recent species-specific responses to climatic and geological
 processes resulted in pseudo-congruent phylogeographic histories among the
 five co-distributed species. The presence of a congruent north/south
 pattern in multiple taxonomic groups occupying different forested
 microhabitats, from fossorial to arboreal, supports latitudinal gradients
 as global drivers of phylogeographic diversity along the east coast of
 South Africa.
description: Occurrence data used to generate Maxent models for each of the
 five co-distributed forest herpetofaunal species.  All
 datasets were spatially filtered by ~5km.
DOI: 10.5061/dryad.tht76hf1c
title: Pollinator richness, pollination networks and diet adjustment along local and landscape gradients of resource diversity

description: Loss of habitats and native species, introduction of invasive species, and
 changing climate regimes lead to the homogenization of landscapes and
 communities, affecting the availability of habitats and resources for
 economically important guilds, such as pollinators. Understanding how
 pollinators and their interactions vary along resource diversity gradients
 at different scales may help to determine their adaptability to current
 diversity loss related to global change. We used data on 20
 plant-pollinator communities along gradients of flower richness (local
 diversity) and landscape heterogeneity (landscape diversity) to understand
 how the diversity of resources at local and landscape scales affected: (1)
 wild pollinator abundance and richness (accounting also for honeybee
 abundance); (2) the structure of plant-pollinator networks; (3) the
 proportion of actively selected interactions (those not occurring by
 neutral processes) and (4) pollinator diet breadth and species’
 specialization in networks. Wild pollinator abundance was higher overall
 in flower-rich and heterogeneous habitats, while wild pollinator richness
 increased with flower richness (more strongly for beetles and wild bees)
 and decreased with honeybee abundance. Network specialization (H2’),
 modularity, and functional complementarity were all positively related to
 floral richness and landscape heterogeneity, indicating niche segregation
 as the diversity of resources increases at both scales. Flower richness
 also increased the proportion of actively selected interactions
 (especially for wild bees and flies), whereas landscape heterogeneity had
 a weak negative effect on this variable. Overall, network-level metrics
 responded to larger landscape scales than pollinator-level metrics did.
 Higher floral richness resulted in a wider taxonomic and functional diet
 for all the study guilds, while functional diet increased mainly for
 beetles. Despite this, specialization in networks (d’) increased with
 flower richness for all the study guilds, because pollinator species fed
 on a narrower subset of plants as communities became richer in species.
 Our study indicates that pollinators are able to adapt their diet to
 resource changes at local and landscape scales. However, resource
 homogenization might lead to poor and generalist pollinator communities,
 where functionally specialized interactions are lost. This study
 highlights the importance of including different scales to understand the
 effects of global change on pollination service through changes in
 resource diversity.
DOI: 10.5061/dryad.3j9kd51m1
title: Data from: Cretaceous lophocoronids with short proboscis and retractable female genitalia provide the earliest evidence for their feeding and oviposition habits

description: We describe two new species of Lophocoronidae:
 Acanthocorona hedida Zhang, Shih and Engel sp. n. and
 Acanthocorona venulosa Zhang, Shih and Engel sp. n., and
 an undetermined specimen from mid-Cretaceous
 Kachin amber. Phylogenetic analysis of basal lepidopteran
 lineages, including three extinct families, was undertaken. The
 analysis supported monophyly of Glossata although
 internal relationships remain controversial.
 Acanthocorona and Lophocorona form a
 monophyletic group. It is likely that short and simply
 structured proboscides of Acanthocorona were used to sip
 water droplets, pollination drops from gymnosperms, nectar from early
 flowers, or sap from injured leaves. Both retracted and extended
 ovipositors are preserved in the material reported here,
 revealing their morphology and indicating that these Cretaceous
 lophocoronids inserted eggs into the tissues of their host plants.
DOI: 10.5061/dryad.31zcrjdnk
title: Morphology and paleobiology of the Late Cretaceous large-sized shark Cretodus crassidens (Dixon, 1850) (Neoselachii; Lamniformes)

description: The definition of the Cretaceous shark genus Cretodus Sokolov, 1965, was
 primarily based on isolated teeth. This genus includes five species. Among
 these, C. houghtonorum is the only species based on a partially preserved
 skeleton. Here, the taxonomic attribution of a virtually complete skeleton
 of Cretodus from the Turonian of northeastern Italy is discussed, together
 with a few specimens from the Turonian of England. One of these latter is
 investigated through micropaleontological analysis to determine its
 stratigraphic position. The material is referred to Cretodus crassidens
 (Dixon, 1850), whose diagnosis is emended herein. The dentition is
 tentatively reconstructed, exhibiting strong similarities with the
 congeneric species, though it differs in having strong vertical folds on
 the main cusp labial face, mesiodistally broad tooth aspect, weak and
 well-spaced ‘costulae’ at crown baseand different dental formula in the
 number of parasymphyseal and lateral rows. Some tooth malformations are
 interpreted as feeding-related or senile characters. The Italian specimen
 suggests that Cretodus crassidens had a wide and laterally expanded mouth
 and head, a stout body and attained a gigantic size. Cretodus crassidens
 was a moderate speed swimming shark ecologically similar to the extant
 tiger shark Galeocerdo cuvier. The age estimate from vertebral bands
 counting suggests that the Italian individual was at least 23 years old
 and the growth model indicates a longevity of 64 years and a maximum
 attainable total length of 9-11 m. Cretodus crassidens occurs both in
 Boreal and Tethyan domains, implying a broad paleobiogeographic
 distribution and a preference towards the offshore settings.
DOI: 10.5061/dryad.rbnzs7hcw
title: Data from: Does egg carotenoid improve larval quality in Arctic charr (Salvelinus alpinus)?

description: Females in mutually ornamented species are often less conspicuously
 ornamented than their male conspecifics. It has been hypothesized that
 offspring quality may decrease if females invest more resources into
 ornaments at the expense of resources in eggs. An experiment was carried
 out to test whether natural variation in carotenoid in the eggs from a
 wild population of Arctic charr (Salvelinus alpinus) was associated with
 survival and growth of their offspring until hatching. Wild Arctic charr
 were caught at a spawning ground during the spawning period. Eggs from two
 different females, one female with yellowish carotenoid-rich eggs and one
 with paler eggs, were fertilized by sperm from the same male. This was
 repeated until gametes were collected from 42 females and 21 males, giving
 a total of 21 groups. After fertilization, the zygotes from each of the
 two females were reared in four replicated groups. These 168 groups were
 reared separately until hatching when the surviving larvae were counted
 and their body length measured. For the two response variables survival
 and body length at hatching, no effect was demonstrated of any of the
 predictors (i) amount of carotenoid in the unfertilized eggs, (ii) the
 mothers’ body condition or (iii) ornament intensity of their red
 carotenoid-based abdominal ornament. Thus, this study gives no support for
 the hypothesis that females investing less carotenoid into their eggs
 suffer from decreased offspring quality until hatching. This lack of
 association between female ornament intensity and their fitness is not as
 expected if female ornaments evolved due to direct sexual selection from
 males on the more ornamented females (“direct selection hypothesis”).
description: See the article for a describtion of the methods.
DOI: 10.5061/dryad.44j0zpcgc
title: Data from: Biomass partitioning of plants under soil pollution stress

description: Polluted sites are ubiquitous worldwide but how plant partition their
 biomass between different organs in this context is unclear. Here, we
 identified three possible drivers of biomass partitioning in our
 controlled study along pollution gradients: plant size reduction
 (pollution effect) combined with allometric scaling between organs; early
 deficit in root surfaces (pollution effect) inducing a decreased water
 uptake; increased biomass allocation to roots to compensate for lower soil
 resource acquisition consistent with the optimal partitioning theory
 (plant response). A complementary meta-analysis showed variation in
 biomass partitioning across published studies, with grass and woody
 species having distinct modifications of their root: shoot ratio. However,
 the modelling of biomass partitioning drivers showed that single harvest
 experiments performed in previous studies prevent identifying the main
 drivers at stake. The proposed distinction between pollution effects and
 plant response will help to improve our knowledge of plant allocation
 strategies in the context of pollution.
description: Refer to the methods provided in the manuscript
DOI: 10.5061/dryad.ns1rn8pvr
title: Neural effects of continuous theta-burst stimulation in macaque parietal neurons

description: Theta-burst transcranial magnetic stimulation (TBS) has become a standard
 non-invasive technique to induce offline changes in cortical excitability
 in human volunteers. Yet, TBS suffers from a high variability across
 subjects. A better knowledge about how TBS affects neural activity in vivo
 could uncover its mechanisms of action and ultimately allow its mainstream
 use in basic science and clinical applications. To address this issue, we
 applied continuous TBS (cTBS, 300 pulses) in awake behaving rhesus monkeys
 and quantified its after-effects on neuronal activity. Overall, we
 observed a pronounced, long-lasting and highly reproducible reduction in
 neuronal excitability after cTBS in individual parietal neurons, with some
 neurons also exhibiting periods of hyperexcitability during the recovery
 phase. These results provide the first experimental evidence of the
 effects of cTBS on single neurons in awake behaving monkeys, shedding new
 light on the reasons underlying cTBS variability.
description: We recorded single-unit activity
 in PFG using tungsten microelectrodes (impedance: 1 MΩ at 1 kHz; FHC)
 inserted through the dura by means of a 23-gauge stainless steel guide
 tube and a hydraulic microdrive (FHC, USA). We combined these recordings
 with Transcranial Magnetic Stimulation (TMS) using two different
 protocols: single-pulse TMS (sTMS) and continuous Theta-Burst Stimulation
 (cTBS). We performed extracellular recordings before and after cTBS to
 investigate the changes in neuronal excitability, assessed with sTMS
 during passive fixation.
description: All original data files used for building the final graphs are
 uploaded. However, due to size limitations, these files do not include the
 filtered, raw signal acquired in a separate channel and containing the
 continuous recording acquired across the entire experimental session.
 These files can be shared on demand.
DOI: 10.5061/dryad.pnvx0k6pq
title: Effect of thermal variation on the cardiac thermal limits of a eurythermal marine teleost (Girella nigricans)

description: Although most animals live in complex, thermally variable environments,
 the impact of this variability on specific physiological systems is still
 unresolved. The ectotherm heart is known to change in both structure and
 function to ensure appropriate oxygen delivery under different thermal
 regimes, but the plasticity of the upper thermal limits of the heart under
 stable or variable thermal acclimation conditions remains unknown. To
 investigate the role of thermal variability on cardiac acclimation
 potential, we acclimated a eurythermal fish, opaleye (Girella nigricans),
 to three static temperature treatments (13, 16, and 19 °C) as well as two
 oscillating treatments which cycled between maximum and minimum
 temperatures every 12 h (13–19 °C and 16–22 °C). These temperatures and
 daily thermal ranges were chosen to mimic the conditions observed in the
 rocky intertidal environments in Santa Barbara, CA, USA where the fish
 were collected. We hypothesized that increasing temperature would increase
 upper thermal limits of the heart, and that variable acclimations would
 result in broader acute thermal performance curves (TPCs) compared to
 static acclimations. We measured maximum heart rate during acute warming
 to determine cardiac thermal performance (i.e., the temperature
 corresponding to the onset of cardiac arrythmia, the temperature at
 maximum heart rate, absolute maximum heart rate, and the Arrhenius
 breakpoint temperature) and construct acute TPCs. Rising static
 acclimation temperatures increased upper thermal limits but had no impact
 on peak maximum heart rate. The warmest static temperature did, however,
 cause a narrowing of the acute TPC. Fish acclimated to variable conditions
 had the same upper thermal limits compared to fish acclimated to static
 conditions with the same mean temperature in all metrics of thermal
 performance. Further, there was no significant broadening of the acute
 TPC. This study suggests that cardiac plasticity is robust to thermal
 variation in this eurythermal fish.
description: Please see main manuscript for detailed information
 regarding the methods used to collect/analyze this data.
description: There is a readme file
 describing this dataset.