cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.z08kprr9p
title: Data from: Modification of reproductive schedule in response to pathogen exposure in a wild insect: support for the terminal investment hypothesis

description: Trade-offs in the time and energy allocated to different functions, such
 as reproductive activities, can be driven by alterations in condition
 which reduce resources, often in response to extrinsic factors such as
 pathogens or parasites. When individuals are challenged by a pathogen they
 may either reduce reproduction as a cost of increasing defence mechanisms,
 or alternatively, modify reproductive activities so as to increase
 fecundity thereby minimizing the fitness costs of earlier death, a
 behaviour consistent with the terminal investment hypothesis (TIH). The
 TIH predicts that individuals with decreased likelihood of future
 reproduction will maximize current reproductive effort, which may include
 shifts in reproductive timing. We examined how wild, adult female click
 beetles (Agriotes obscurus) responded after exposure to
 the fungal pathogenMetarhizium brunneum. Field-collected beetles exposed
 to a high concentration of M. brunneum died earlier and
 in greater numbers than those exposed to a low concentration. Using a
 multi-variate approach we examined the impact of pathogen challenge on
 lifespan and a suite of reproductive traits. Stepdown regression analysis
 showed that only female lifespan differed among the fungal treatments.
 Fungal-induced reductions in lifespan drove changes in the reproductive
 schedule, characterized by a decrease in preoviposition period. Moving the
 start of egg laying forward allowed the females to offset the costs of a
 shortened lifespan. These changes suggest that there is a threshold for
 terminal investment which is dependent on strength of the survival threat.
 From an applied perspective, our findings imply that exposing adult click
 beetles to M. brunneum to reduce their population
 densitymight not succeed and is an approach that needs further
 investigation.
description: Exposure of field-collected beetles to a fungal pathogen in a
 controlled laboratory experiment with frequent monitoring until
 death.  Transformed where necessary and analysed using
 generalized linear models, MANOVA amd step down analysis.
description: All values used in the data analsys in the manuscript are
 provided and the headings should be self-explanatory. 
 Met=fungal treatment/death; U = Not killed by fungus. Time are in
 days. Lengths are in microns.
DOI: 10.5061/dryad.44j0zpcbx
title: Data from: Accelerating homogenization of the global plant–frugivore meta-network

description: Introductions of species by humans are causing the homogenization of
 species composition across biogeographic barriers. The ecological and
 evolutionary consequences of introduced species derive from their
 effects on networks of species interactions, but we lack a
 quantitative understanding of the impacts of introduced species on
 ecological networks and their biogeographic patterns globally. Here we
 address this data gap by analysing mutualistic seed-dispersal interactions
 from 410 local networks, encompassing 24,455 unique pairwise interactions
 between 1,631 animal and 3,208 plant species. We show that species
 introductions reduce biogeographic compartmentalization of the global
 meta-network, in which nodes are species and links are interactions
 observed within any local network. This homogenizing effect extends across
 spatial scales, decreasing beta diversity among local networks and
 modularity within networks. The prevalence of introduced interactions is
 directly related to human environmental modification and is accelerating,
 having increased sevenfold over the past 75 years. These dynamics alter
 the coevolutionary environments that mutualists experience, and we find
 that introduced species disproportionately interact with other introduced
 species. These processes are likely to amplify biotic homogenization in
 future ecosystems and may reduce the resilience of
 ecosystems by allowing perturbations to propagate more quickly
 and exposing disparate ecosystems to similar drivers. Our results
 highlight the importance of managing the increasing homogenization of
 ecological complexity. 
description: Open the .Rproj file and run 'network homogenization
 analysis.R' within the analysis folder to reproduce analyses and
 figures.
DOI: 10.5061/dryad.73n5tb2v2
title: Latitudinal variation in climate-associated genes imperils range-edge populations

description: The ecological impacts of increasing global temperatures are evident in
 most ecosystems on Earth, but our understanding of how climatic variation
 influences natural selection and adaptive resilience across latitudes is
 still largely unknown. Latitudinal gradients allow testing general
 ecosystem-level theories relevant to climatic adaptation. We assessed
 differences in adaptive diversity of populations along a latitudinal
 region spanning highly variable temperate to subtropical climates. We
 generated and integrated large-scale information from environmental
 mapping, phenotypic variation and genome-wide data for 21 populations of
 rainbowfish (Melanotaenia duboulayi), an emerging aquatic system for
 studies of climate change. We detected, after controlling for spatial
 population structure, strong interactions between genotypes and
 environment associated to variation in stream flow and temperature. Some
 of these hydroclimate-associated genes were found to interact within
 functional protein networks that contain genes of adaptive significance
 for projected future climates in rainbowfish. Hydroclimatic selection was
 also associated with variation in phenotypic traits, including traits
 known to affect fitness of rainbowfish exposed to different flow
 environments. Consistent with predictions from the ‘climatic variability
 hypothesis’, populations exposed to extremes of important environmental
 variables showed stronger adaptive divergence and less variation in
 climate-associated genes compared to populations at the center of the
 environmental gradient. This suggests that populations that evolved at
 environmental range margins may be more vulnerable to changing climates, a
 finding with implications for predicting adaptive resilience and managing
 biodiversity under climate change.
DOI: 10.5061/dryad.3n5tb2rf8
title: Hidden introductions of freshwater red algae via the aquarium trade exposed by DNA barcodes

description: The global aquarium trade can introduce alien freshwater invaders,
 potentially impacting local aquatic ecosystems and their biodiversity. The
 role of the aquarium trade in spreading freshwater red macroalgae that
 hitchhike on ornamental aquatic plants and animals is unassessed. We
 investigated this human-mediated phenomenon via a broad biodiversity
 survey and genetic analysis of freshwater red algae in the field and
 aquarium shops in East Asia. Results We found 26 molecular operational
 taxonomic units (mOTUs) in Taiwan, some of which are cryptic.
 Phylogeographical analysis revealed three potential introduced mOTUs in
 Taiwan, which exhibit no local genetic variation in Taiwan and are
 distributed across continents. Also, we posit that some presumably
 endangered freshwater red algae may be preserved in aquaria, an
 unintentional ex situ conservation site for these organisms that are
 vulnerable to water pollution from anthropogenic disturbances. Main
 Conclusions Collectively, these data suggest that freshwater red algae
 have been hitchhiking and dispersed via the aquarium trade, an important
 and overlooked mechanism of introduction of these organisms across the
 globe.
description: <b>Location</b><br> Field sites and aquaria across Taiwan and in Hong Kong, Japan (Okinawa), the Philippines, and Thailand. Forty additional countries with GenBank sequences. <b>Methods</b><br> Using <i>rbc</i>L-based DNA barcoding, we surveyed 125 samples from 46 field sites and 88 samples from 53 aquarium shops (213 samples in total) mostly across Taiwan—a key hub in the global aquarium trade—as well as in Hong Kong, Okinawa (Japan), the Philippines, and Thailand. We augmented our <i>rbc</i>L sequences with GenBank <i>rbc</i>L sequences that represent 40 additional countries globally.
DOI: 10.5061/dryad.fqz612jqw
title: Dataset marmoset Snowdrift

description: Social primates constantly face situations in which their preferences
 collide and they need to engineer strategies to overcome conflicts of
 interest. Studies with chimpanzees have found that they use competitive
 strategies to overcome social dilemmas, maximizing their own benefits
 while minimizing the loss of rewards. However, little is known about how
 other primates that rely more on cooperation would overcome similar
 dilemmas. We therefore presented male-female pairs of common marmosets
 (cooperative breeders) with two experiments of an action-based paradigm
 that creates a conflict of interest over access to an unequal reward
 distribution. Rather than engaging in mutual defection, marmosets were
 able to overcome this social dilemma over time, by developing a mix of
 strategic behaviors (predominantly by females) and tolerance to
 disadvantageous reward distributions (predominantly by males). This mix of
 behavioral strategies yielded more and better rewards for the females.
 Importantly, such a net outcome is consistent with the natural history of
 this species where females, who carry a high energetic burden of
 reproduction, tend to be less prosocial and are receivers, rather than
 donors, in food sharing events among adults.
DOI: 10.5061/dryad.ncjsxkss3
title: Divergence in coding sequence and expression of different functional categories of immune genes between two wild rodent species

description: Differences in immune function between species could be a result of
 interspecific divergence in coding sequence and/or expression of immune
 genes. Here, we investigate how the degree of divergence in coding
 sequence and expression differs between functional categories of immune
 genes, and if differences between categories occur independently of other
 factors (e.g. expression level, pleiotropy). To this end, we compared
 spleen transcriptomes of wild-caught yellow-necked mice and bank voles.
 Immune genes expressed in the spleen were divided into four categories
 depending on the function of the encoded protein: Pattern Recognition
 Receptors (PRR); signal transduction proteins; transcription factors; and
 cyto- and chemokines and their receptors. Genes encoding PRR and cytokines
 etc had higher sequence divergence than genes encoding signal transduction
 proteins and transcription factors, even when controlling for potentially
 confounding factors. Genes encoding PRR also had higher expression
 divergence than genes encoding signal transduction proteins and
 transcription factors. There was a positive correlation between expression
 divergence and coding sequence divergence, in particular for PRR genes. We
 propose that this is a result of that divergence in PRR coding sequence
 leads to divergence in PRR expression. When controlling for sequence
 divergence, expression divergence of PRR genes did not differ from other
 categories. Taken together, the results indicate that coding sequence
 divergence of PRR genes is a major cause of differences in immune function
 between species.
description: RNA-sequencing of spleen transcriptomes from bank voles and
 yellow-necked mice.
description: Alignmnets with "(modified)" in file name have been
 edited manually.
DOI: 10.5061/dryad.wstqjq2j3
title: A comprehensive sampling of species sheds light on the molecular phylogenetics of Calothecinae (Poaceae, Pooideae): evidence for a new subtribe and multiple genera within the Chascolytrum clade

description: The circumscription of subtribe Calothecinae has undergone several changes
 since its description. Currently, three genera are considered in the
 subtribe: Chascolytrum, Laegaardia and Paramochloa, although no
 phylogenetic evidence for the placement of the two last genera was
 published so far. In this study we aim to evaluate the circumscription of
 Calothecinae and the infrageneric classification recently proposed for
 Chascolytrum using a more comprehensive sampling of taxa and molecular
 markers. We included species of all genera of Calothecinae, plus two South
 American species of Trisetum s.l. that have been suggested to be related
 to Chascolytrum, and representatives from subtribes Agrostidinae,
 Echinopogoninae, Brizinae, Torreyochloinae, Phalaridinae and Koeleriinae.
 We performed Bayesian and Maximum Likelihood analyses using a total of six
 molecular markers, including four plastid DNA regions (atpF-atpH, matK,
 rps16 intron, and trnL-trnF) and two ribosomal nuclear regions (ITS and
 ETS). Our results revealed that neither Calothecinae nor Chascolytrum are
 monophyletic considering their last circumscription. Trisetum brasiliense
 and T. bulbosum appeared nested to Chascolytrum, and are formally included
 in Calothecinae as incertae sedis. More studies are needed to confirm
 their taxonomic position. Based on morphological characters, Laegaardia
 and Paramochloa are transferred to the new subtribe Paramochloinae, and
 Chascolytrum is splitted in nine different genera, of which two are newly
 described: Boldrinia (gen. nov.), Calotheca, Chascolytrum, Erianthecium,
 Lombardochloa, Microbriza, Poidium, Rhombolytrum, and Rosengurttia (gen.
 nov.).
description: DNA data matrix from the concatenated Bayesian and Maximum
 Likelihood analyses.
DOI: 10.5061/dryad.t4b8gtj0b
title: Code for Individual Based Model to assess impact of KHV release on carp population

description: 1: Common carp (Cyprinus carpio) is one of the top global invasive
 vertebrates and can cause significant ecological damage. The Australian
 Government’s National Carp Control Program (NCCP) proposes to release Koi
 Herpesvirus (KHV) to eradicate feral carp in one of the largest ecological
 interventions ever attempted. Ecological and human health risks have been
 highlighted regarding the release of a highly pathogenic viral biocontrol
 for an aquatic species. The efficacy of KHV has also been questioned, and
 it has not been demonstrated to produce lasting population reductions.
   2. We developed an individual-based model (IBM) to examine the
 ecological and evolutionary response of a carp population after KHV
 release. This simulated the interaction between fish life history, viral
 epidemiology, host genetic resistance and population demography to
 critically evaluate the impact of KHV release under optimal conditions and
 a “best case scenario” for disease transmission.   3. KHV will
 rarely result in prolonged reductions or population extinctions.
 Crucially, realistic scenarios result in a rapidly rebounding population
 of resistant individuals. Additional measures aimed to reduce carp
 population recovery rate (e.g. with genetic engineering) require rapid
 efficacy to significantly reduce carp numbers alongside KHV.   4.
 Fish fecundity has an overwhelming influence on viral efficacy as a
 biocontrol agent when combined with genetic resistance within a
 population. A high probability of population extinction is only met when
 carp fecundity is reduced to 1% of biological observations.   5.
 Synthesis and applications. We use an individual-based model to
  evaluate the efficacy of Koi Herpesvirus biocontrol in Common
 Carp, and find that high host fecundity combined with genetic resistance
 results in rapid population rebound after initial large fish-kills.
 Biocontrol approaches relying on natural selection lose efficacy over
 successive generations as resistance genes increases in frequency. Given
 the intense logistical effort and risks to ecosystems and human health
 associated with large fish kills after viral release, we suggest that
 sustained manual removal, alongside ecological restoration to favour
 recovery of native species, provides a risk-free approach to reducing
 populations.  
description: computer code
description: Annotations in file
DOI: 10.15468/dl.edy8yt
title: Occurrence Download

description: A dataset containing 1908 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lepidosaphes beckii)"
 ]
}

 The dataset includes 1908 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002510-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.sf7m0cg40
title: Insights into the genetic basis of predator-induced response in Daphnia galeata

description: Phenotypic plastic responses allow organisms to rapidly adjust when facing
 environmental challenges - these responses comprise morphological,
 behavioral but also life-history changes. Alteration of life-history
 traits when exposed to predation risk have been reported often in the
 ecological and genomic model organism Daphnia. However, the molecular
 basis of this response is not well understood, especially in the context
 of fish predation. Here, we characterized the transcriptional profiles of
 two Daphnia galeata clonal lines with opposed life histories when exposed
 to fish kairomones. First, we conducted a differential gene expression,
 identifying a total of 125 candidate transcripts involved in the
 predator-induced response, uncovering substantial intra-specific
 variation. Second, we applied a gene co-expression network analysis to
 find clusters of tightly linked transcripts revealing the functional
 relations of transcripts underlying the predator-induced response. Our
 results showed that transcripts involved in remodeling of the cuticle,
 growth and digestion correlated with the response to environmental change
 in D. galeata. Furthermore, we used an orthology-based approach to gain
 functional information for transcripts lacking gene ontology (GO)
 information, as well as insights into the evolutionary conservation of
 transcripts. We could show that our candidate transcripts have orthologs
 in other Daphnia species but almost none in other arthropods. The unique
 combination of methods allowed us to identify candidate transcripts, their
 putative functions and evolutionary history associated with
 predator-induced responses in Daphnia. Our study opens up to the question
 as to whether the same molecular signature is associated with fish
 kairomones-mediated life-history changes in other Daphnia species.
description: RNA seq, Illumina short read sequencing
 Weighted Gene Co-expression Network Analysis (WGCNA)
 Differential expression, DESeq2 Gene Ontology
 analysis, Orthology based approach
description: Detailed information on the uploaded files can be found in the
 document "Readme_Tams2020EcolEvol.txt"
DOI: 10.15468/dl.sv93yd
title: Occurrence Download

description: A dataset containing 658771 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Polystichum"
 ]
}

 The dataset includes 658771 records from 2099 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002460-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25326/c4w8-6e84
title: alpha-pinene+OH + O3 - Aerosol study - hygroscopicity - 2007-08-31

description: Publication of the dataset
DOI: 10.5281/zenodo.15474049
title: Database publications about drilling monitoring technology in mining

description: A comprehensive literature review about the application of drilling monitoring systems in geological engineering was conducted through comprehensive meta-analysis of 110 scientific documents. The research repository comprised papers, conference proceedings, thesis, and book chapters strategically curated to investigate emerging trends in MWD technological applications and data processing methodologies. Document selection criteria prioritized studies demonstrating substantive scientific contribution in mining, quarrying, geotechnical engineering, tunnelling, and geological characterization domains, with selective integration of petrochemical industry research featuring advanced rock characterization techniques. Scientific publications constituted the predominant document type (93%), systematically evaluated through bibliometric indicators including journal impact factor and quartile classification. The most relevant journals (Q1) with higher number of publications listed in the repository are the International Journal of Mining Science and Technology, International Journal of Rock Mechanics and Mining Sciences, Journal of Rock Mechanics and Geotechnical Engineering, Rock Mechanics and Rock Engineering, and Tunnelling and Underground Space Technology. The rest of the works different from the paper type were usually linked with the same authors in derived participations.
DOI: 10.5281/zenodo.15474050
title: Database publications about drilling monitoring technology in mining

description: A comprehensive literature review about the application of drilling monitoring systems in geological engineering was conducted through comprehensive meta-analysis of 110 scientific documents. The research repository comprised papers, conference proceedings, thesis, and book chapters strategically curated to investigate emerging trends in MWD technological applications and data processing methodologies. Document selection criteria prioritized studies demonstrating substantive scientific contribution in mining, quarrying, geotechnical engineering, tunnelling, and geological characterization domains, with selective integration of petrochemical industry research featuring advanced rock characterization techniques. Scientific publications constituted the predominant document type (93%), systematically evaluated through bibliometric indicators including journal impact factor and quartile classification. The most relevant journals (Q1) with higher number of publications listed in the repository are the International Journal of Mining Science and Technology, International Journal of Rock Mechanics and Mining Sciences, Journal of Rock Mechanics and Geotechnical Engineering, Rock Mechanics and Rock Engineering, and Tunnelling and Underground Space Technology. The rest of the works different from the paper type were usually linked with the same authors in derived participations.
DOI: 10.25326/yhej-3628
title: alpha-pinene+OH + O3 - Aerosol study - hygroscopicity - 2007-08-17

description: Publication of the dataset
DOI: 10.25326/vfzs-0q67
title: alpha-pinene+OH + O3 - Aerosol study - hygroscopicity - 2007-08-29

description: Publication of the dataset
DOI: 10.25326/12qw-kj37
title: alpha-pinene+OH + O3 - Aerosol study - hygroscopicity - 2007-08-20

description: Publication of the dataset
DOI: 10.25326/v64g-4r36
title: alpha-pinene+OH + O3 - Aerosol study - hygroscopicity - 2007-09-03

description: Publication of the dataset
DOI: 10.15468/dl.mp4j69
title: Occurrence Download

description: A dataset containing 1066 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lonicera pileata",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1066 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049540-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.