cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.02v6wwq50
title: Stress induced TDP-43 mobility loss independent of stress granules

description: TAR DNA binding protein 43 (TDP-43) is closely related to the pathogenesis
 of amyotrophic lateral sclerosis (ALS) and translocates to stress granules
 (SGs). The role of SGs as aggregation-promoting “bioreactors” for TDP-43,
 however, is still under debate. We analyzed TDP-43 mobility and
 localization under different stress and recovery conditions using live
 cell single-molecule tracking and super-resolution microscopy. Besides
 reduced mobility within SGs, a stress induced decrease of TDP-43 mobility
 in the cytoplasm and the nucleus was observed. Stress removal led to a
 recovery of TDP-43 mobility, which strongly depended on the stress
 duration. ‘Stimulated-emission depletion microscopy’ (STED) and ‘tracking
 and localization microscopy’ (TALM) revealed not only TDP-43 substructures
 within stress granules but also numerous patches of slow TDP-43 species
 throughout the cytoplasm. The data provide new insights into the
 aggregation of TDP-43 in living cells and provide evidence suggesting that
 TDP-43 oligomerization takes place in the cytoplasm separate from SGs.
DOI: 10.5061/dryad.q573n5tkh
title: Evisceration residues from hunted roe deer as a resource for necrophagous insect fauna in the Black Forest, Germany: a preliminary study

description: This dataset is used to investigate if evisceration residues of roe deer
 are used as a resource by necrophagous insects. Pit fall traps
 baited with eviceration residues, entire carcasses or unbaited were used
 to sample invertebrates. 
description: Two
 pitfall traps were placed at all nine experimental sites (9 cm opening
 diameter) in the northwest and southeast corner of metal cages. Overall
 experimental set-up was adapted following von Hoermann et al. 2018. From
 the start of the experiment pitfall-traps were emptied in two-day (48
 hour) intervals for a total of 18 intervals (I01-I18). Distilled water
 with odourless detergent were used as trapping liquid. Carcass and residue
 samples were placed inside the metal cage right before the first trapping
 interval. All invertebrates sampled by pit-fall traps were transferred to
 70% ethanol solution and later determined in the laboratory. Most
 non-beetle groups were sorted to order level, while most beetles were
 sorted to family level. Burying and dung-beetles were identified to
 species.
description: Three samples at carcasses sites were made unusable by vertebrate
 scavengers.
DOI: 10.15468/dl.qf8s4z
title: Occurrence Download

description: A dataset listing the 31037 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is Herbario Nacional Colombiano (COL)"
 ]
}

 The dataset's 31037 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003052-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.h70rxwdkw
title: Territorial response predictability in radio-tagged great tits Parus major

description: Territorial animals often use signals to advertise territorial occupancy
 within their larger home ranges. Songbirds are among
 the best-studied territorial signaling taxa, and when competitors
 start singing during a territorial intrusion, residents usually show
 elevated spatial and vocal responses. These responses could be used by
 intruders and distant eavesdroppers to predict future responses or to
 compare responses across competitors. Yet, the extent to which responses
 of a resident to a territorial intrusion predict its future responses and
 its overall spatial behavior (home range) within a neighborhood is less
 well understood. We used wild great tits (Parus major) as a model species
 in repeated song playback trials, simulating territorial intrusions
 combined with radio-tracking before and during playback trials. The time
 spent close to the loudspeaker in response to an initial simulated
 intrusion predicted the same response variable during a second simulated
 intrusion on the next day, whereas singing activity during the first
 simulated intrusion did not predict singing during the second simulated
 intrusion. We also show that more explorative males (as determined by a
 novel environment test) and males with smaller home ranges sang more and
 spent more time near the loudspeaker in response to both simulated
 intrusions. Thus, by probing residents, intruders can obtain reliable
 information about subsequent response probabilities, while eavesdroppers
 from a distance, who can use auditory information only, would not receive
 sufficient predictive information. Our findings also suggest that males
 with larger home ranges are more tolerant towards intruders, which could
 reflect a trade-off between tendencies to respond strongly and to range
 widely. The lack of predictability of singing activity with regard to
 responses to future intrusions might explain why territorial animals
 continuously exchange vocal signals and regularly foray into neighboring
 territories, as a way to obtain regular information updates.
description: See manuscript for details.
DOI: 10.5061/dryad.5tb2rbp5r
title: To disperse or compete? Coevolution of traits leads to a limited number of reproductive strategies

description: Reproductive strategies are defined by a combination of behavioural,
 morphological, and life-history traits. Reproductive investment and
 offspring propagule size are two key traits defining reproductive
 strategies. While a substantial amount of work has been devoted to
 understanding the independent fitness effects of each of these traits, it
 remains unclear how coevolution between them ultimately affects the
 evolution of reproductive strategies, and how this might influence the
 relationship between dispersal and environmental factors. In this study,
 we explore how the evolution of reproductive strategies defined by these
 two coevolving traits is influenced by resource availability and spatial
 structuring of the environment using a simulation model. We find three
 possible equilibrium strategies across all scenarios: a competitor
 strategy with high reproductive investment (producing large propagules
 which disperse short distances), and two coloniser strategies differing in
 reproductive investment (both producing small propagules which disperse
 long distances). The possible equilibrium strategies for each scenario
 depended on starting conditions, spatial structure and resource
 availability. Evolutionary transitions between these equilibrium
 strategies were more likely in heterogeneous than homogeneous landscapes
 and at higher resource levels. Transition from coloniser strategy to
 competitor strategy was usually a two-step process, with changes in
 propagule size following initial evolution in investment. This highlights
 how the interaction between the two trait axes affects the evolution of
 reproductive strategies, particularly where fitness valleys preclude the
 simultaneous evolution of traits. Our results highlight the need to
 incorporate trait coevolution into evolutionary models to help develop a
 more integrative understanding of the structure of natural populations and
 how the interaction between traits constrains or hinders evolutionary
 processes.
DOI: 10.5061/dryad.gqnk98spv
title: Agropyron_cristatum_scaffolds

description: Agropyron cristatum is a wild crop relative what makes this species
 attractive as a possible donor of genes for crop improvement. This species
 is well known for its resistance and tolerance genes. We sequenced
 individual chromosomes of Agropyron cristatum cv. Parkway and its
 wheat-Agropyron addition lines to find simple sequence repeat markers that
 could help breeders in their breeding programs.  Firstly, we used
 flow cytometry sorting of studied plant material, which is the
 well-established approach in our laboratory. We sorted individual
 chromosomes (1P - 7P) of Agropyron followed by amplification of their DNA
 using two different amplification methods. Libraries for sequencing were
 prepared and sequencing was done on HiSeq and MiSeq Illumina
 instruments.  Secondly, we used the datasets for de novo
 assembly, SSR markers development and their verification via PCR method
 with appropriate primers. Other usage of the sequences was to study
 orthologous relationship between Agropyron and wheat subgenomes and we
 also looked at representation of genic and non-genic sequences in
 Agropyron itself. Stored datasets are assembled scaffolds of each
 Agropyron chromosomes, that could be of a high value in breeding studies
 for the characterization of a progeny or a breeding material
 itself.
DOI: 10.5061/dryad.v41ns1rz5
title: Data from: Plant life history traits rather than soil legacies determine colonisation of soil patches in a multi-species grassland

description: Interactions between plants and soil biota are increasingly shown to play
 critical roles in plant species co-existence processes. Plant species
 co-existence is thought to be promoted via biotic legacies that plant
 species leave behind in the soil after a plant disappears. These soil
 legacies are hypothesised to supress colonisation success when the
 preceding plant is of the same species, that is, when a plant species
 encounters its own, species-specific soil antagonists. However,
 colonisation of vacant spots in plant communities is in the first place
 determined by the ability of plants to reach such vacant locations. We
 currently lack an understanding of the explicit role of soil legacy
 effects and their relative contribution to colonisation processes in plant
 communities consisting of plant species inherently differing in
 colonisation ability. In experimental, outdoor plant communities
 consisting of eight grassland species, we tested the effect of five
 differently conditioned soil patches on plant species colonisation success
 over three consecutive growing seasons. We found that colonisation success
 was largely determined by the species’ reproductive strategy, lateral
 spread and growth rate, and not by the plant species that conditioned the
 soil patch. Fast spreading, clonal plant species reached the soil patches
 first and initially attained the highest biomass inside the patch. One
 year later, slower spreading plant species colonised the patch via
 seedlings. Species with intrinsically high growth rates attained the
 highest biomass, decreasing biomass of the initial colonisers. While
 subtle differences between conditioned soil patches did occur, these were
 not strong enough to overcome the inherent differences in colonisation
 ability between the various plant species. Synthesis: Our results reject
 the hypothesis that colonisation of vacant soil patches in plant
 communities is strongly affected by the legacy that is left behind by the
 preceding plant species. Instead, plant species life history strategy
 plays a prominent role, driving sequential plant species replacements.
 Based on our results and recent accounts in literature we present a
 conceptual model for local cyclic dynamics in grassland communities, where
 soil legacy plays a role in affecting the performance of established plant
 species rather than colonisation of vacant patches.
DOI: 10.5061/dryad.qfttdz0jr
title: Stress axis programming generates long-term effects on cognitive abilities in a cooperative breeder

description: The ability to flexibly adjust behaviour to social and non-social
 challenges is important for successfully navigating variable environments.
 Social competence, i.e., adaptive behavioural flexibility in the social
 domain, allows individuals to optimize their expression of social
 behaviour. Behavioural flexibility outside the social domain aids in
 coping with ecological challenges. However, it is unknown if social and
 non-social behavioural flexibility share common underlying cognitive
 mechanisms. Support for such shared mechanism would be provided if the
 same neural mechanisms in the brain affected social and non-social
 behavioural flexibility similarly. We used individuals of the
 cooperatively-breeding fish Neolamprologus pulcher that
 had undergone early-life programming of the
 hypothalamic-pituitary-interrenal (HPI) axis by exposure to (i) cortisol,
 (ii) the glucocorticoid-receptor antagonist mifepristone or (iii) control
 treatments, and where effects of stress-axis programming on social
 flexibility occurred. One year after the treatments, adults learned a
 colour-discrimination task, and subsequently, a reversal-learning task
 testing for behavioural flexibility. Early-life mifepristone treatment
 only marginally affected learning performance, whereas cortisol treatment
 significantly reduced behavioural flexibility. Thus, early-life cortisol
 treatment reduced both social and non-social behavioural flexibility,
 suggesting a shared cognitive basis of behavioural flexibility. Further
 our findings imply that early-life stress programming affects the ability
 of organisms to flexibly cope with environmental stressors.
DOI: 10.15468/dl.sxavhd
title: Occurrence Download

description: A dataset containing 13880 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is IAS pilot - Observations of alien plant species using a vehicle-mounted camera system in Flanders (Belgium)",
 "Country is Belgium"
 ]
}

 The dataset includes 13880 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003037-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25338/b8tk96
title: Experimental disruption of social structure reveals totipotency in the orchid bee, Euglossa dilemma

description: Eusociality has evolved multiple times across the insect phylogeny. Social
 insects with greater levels of social complexity tend to exhibit
 specialized castes with low levels of individual phenotypic plasticity. In
 contrast, species with simple social groups may consist of totipotent
 individuals that transition among behavioral and reproductive states.
 However, recent work has shown that in simple social groups, there can
 still be constraint on individual plasticity, caused by differences in
 maternal nourishment or  social interaction. It is not well
 understood how these constraints arise, ultimately leading to the
 evolution of nonreproductive workers. Some species of orchid bees form
 social groups of a dominant and 1-2 subordinate helpers where all
 individuals are reproductive. Females can also disperse to start their own
 nest as a solitary foundress, which includes a nonreproductive phase,
 characterized by ovary inactivation, not typically expressed by
 subordinates. Little is known about individual flexibility across these
 trajectories. Here, using the orchid bee Euglossa dilemma, we assess the
 plasticity of subordinate helpers, finding that they are capable of the
 same behavioral, physiological, transcriptomic, and chemical changes seen
 in foundresses. Our results suggest that the lack of nonreproductive
 workers in E. dilemma is not due to a lack of subordinate plasticity.
description: Data consist of ovary size measurements, gene expression data,
 and cuticular hydrocarbon data from the orchid bee <em>Euglossa
 dilemma</em>. In addition, the accompanying R Code will guide
 analysis based on the .csv files.
description: For general analysis, see the README_START_HERE.txt file for
 additional details about the .csv files.
DOI: 10.5061/dryad.xsj3tx9h3
title: Nuclear phylogeography reveals strong impacts of gene flow in big brown bats

description: Aim: Understanding speciation mechanisms requires disentangling processes
 that promote and erode population-level divergence. Three hypotheses are
 raised that contemporary population structure is mainly shaped by refugial
 divergence, post-glacial gene flow, or combined effects of both. Testing
 these hypotheses requires range-wide phylogeography and integrative
 analyses across scales. Here we aim to 1) re-estimate the previously
 unresolved nuclear phylogeography of a widespread bat; 2) test the above
 three phylogeographic hypotheses; and 3) inform conservation management
 under climate change. Location: North America including Caribbean. Taxon:
 The big brown bat (Eptesicus fuscus). Methods: We collected range-wide
 samples and genome-wide markers using restriction site-associated DNA
 sequencing. Population structure was analyzed by clustering methods and
 spatial estimations. Nuclear phylogeography was estimated using tree
 methods (concatenation and coalescent) and network analyses (TreeMix).
 Phylogeographic hypotheses were tested by comparing alternative
 evolutionary scenarios using demographic modeling. Species distribution
 modeling was used to help identify Pleistocene refugia and predict future
 range shifts under climate change. Results: We identified three
 populations in the Caribbean, Eastern, and Western North America. The west
 population further split into three phylogeographic clades in Pacific,
 Southwestern North America, and Mexico. Discordances among mitochondrial
 and nuclear topologies reflected strong impacts of gene flow without sex
 biases. Demographic modeling supported scenarios of historical isolation
 followed by secondary gene flow and estimated Holocene divergence time.
 Species distribution was overall continuous during glaciation with
 possible regional isolation, and northward range shifts were predicted
 under future climate change. Main Conclusions: Our results supported the
 hypothesis that combined effects of historical isolation and secondary
 gene flow shaped the contemporary population divergence. We showed that
 climate change probably triggered the initial divergence and that gene
 flow has strong impacts on the observed nuclear phylogeography. Our
 empirical study demonstrates dynamic within-species processes generating
 the population divergence that predates speciation.
description: Please refer to the README file.
DOI: 10.15468/dl.hy9tg6
title: Occurrence Download

description: A dataset containing 349531 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Herbario Nacional Colombiano (COL)"
 ]
}

 The dataset includes 349531 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003053-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.63xsj3v3w
title: Rapid increase in China’s industrial ammonia emissions: evidence from unit-based mapping

description: Ammonia (NH3) is an important precursor of secondary inorganic aerosols
 and greatly impacts nitrogen deposition and acid rain. Previous studies
 have mainly focused on the agricultural NH3 emissions, while recent
 research has noted that industrial sources could be significant in China.
 However, detailed estimates of NH3 emitted from industrial sectors in
 China are lacking. Here we established an unprecedented
 high-spatial-resolution dataset of China’s industrial NH3 emissions using
 up-to-date measurements of NH3 and point source-level information covering
 eight major industries and 27 subdivided process categories. We found that
 China emitted 798 (90% confidence interval: 668–933) gigagrams of
 industrial NH3 to the atmosphere in 2019, equivalent to 44±20% of the
 industrial emissions worldwide; this flux is three-fold larger than that
 in 1998 and has fluctuated since 2014. Furthermore, although fertilizer
 production is responsible for approximately half of the emissions in
 China, the emissions from cement production and coal-fired power plants
 increased dramatically from near zero to 164 and 41 gigagrams,
 respectively, in the past two decades, primarily due to the NH3 escape
 caused by the large-scale application of the denitration process. Our
 results reveal that, unlike other major air pollutants, China’s industrial
 NH3 emission control is still in a critical period, and stricter NH3
 emission standards and innovation in pollution control technologies are
 highly desirable.
description: Please refer to the article for a detailed description of the
 methods.
description: The dataset includes unit-based geographical locations
 (longitudes and latitudes) and ammonia emissions covering nitrogen
 fertilizer production, catalytic cracking, coke, iron and steel
 production, wastewater treatment, and soda ash production for years 2013,
 2008, 2003, and 1998. Data of cement production, solid waste treatment
 (incineration), and coal-fired power plants are also included for the year
 2013.
DOI: 10.5061/dryad.b5mkkwhfb
title: Whole genome resequencing reveals signatures of rapid selection in a virus affected commercial fishery

description: Infectious diseases are recognised as one of the greatest global threats
 to biodiversity and ecosystem functioning. Consequently, there is a
 growing urgency to understand the speed at which adaptive phenotypes can
 evolve and spread in natural populations to inform future management. Here
 we provide evidence of rapid genomic changes in wild Australian blacklip
 abalone (Haliotis rubra) following a major population crash associated
 with an infectious disease. Genome scans on H. rubra were performed using
 pooled whole genome re-sequencing data from commercial fishing stocks
 varying in historical exposure to haliotid herpesvirus-1 (HaHV-1).
 Approximately 25,000 SNP loci associated with virus exposure were
 identified, many of which mapped to genes known to contribute to HaHV-1
 immunity in the New Zealand pāua (H. iris) and herpesvirus response
 pathways in haliotids and other animal systems. These findings indicate
 genetic changes across a single generation in H. rubra fishing stocks
 decimated by HaHV-1, with stock recovery potentially determined by rapid
 evolutionary changes leading to virus resistance. This is a novel example
 of rapid adaptation in natural populations of a non-model marine organism,
 highlighting the pace at which selection can potentially act to counter
 disease in wildlife communities.
description: For information on datasets, please refer to README.txt. For
 access to raw resequencing data, please contact the corresponding
 author.
DOI: 10.48804/jifft3
title: Replication Data for: Ketogenic Nutrition in Combination with PPARα Activation Induced Metabolic Failure and Exacerbated Muscle Weakness in Septic Mice

description: Suppression of the peroxisome proliferator-activated receptor alpha (PPARα) has been related to poor outcome in sepsis and may compromise ketogenesis during critical illness. Infusion of 3-hydroxybutyrate (3HB) was shown to attenuate muscle weakness in septic mice. We hypothesize that endogenous ketogenesis induced by pharmacological PPARα activation, either alone or combined with ketogenic nutrition, is safe and can also mitigate muscle weakness in septic mice.
In a fluid-resuscitated, antibiotic-treated mouse model of prolonged sepsis, we first (Study 1) assessed the safety and effectiveness (impact on ketosis and muscle weakness,) of the PPARα agonist pemafibrate (1mg/kg/d, n=16), versus placebo (n=15) combined with standard balanced parenteral nutrition (PN), composed of glucose, amino acids and long-chain triglycerides (LCT) (balanced-TPN). We subsequently (Study 2) evaluated the impact of pemafibrate combined with four types of PN on ketosis and muscle weakness: balanced-TPN (n=18), TPN with extra LCTs (TPN+LCT, n=18), low-dose pure LCT emulsion (Low-LCT, n=16) and high-dose pure LCT emulsion (High-LCT n=18). Carbohydrates and amino acids were omitted in the pure LCT groups. Healthy control mice (HC, n=19) served as reference. Ex vivo muscle force was measured as the primary outcome. Metabolic, inflammatory and microstructural parameters were assessed on plasma and in muscle and liver tissue by targeted metabolomics, gene expression analysis, biochemical and metabolite assays and histological assessment.