cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wpzgmsbjd
title: Data from: The enemy within: how does a bacterium inhibit the foraging aptitude and risk management behavior of Allenby’s gerbils?

description: Microbes inhabiting multi-cellular organisms have complex, often subtle
 effects on their hosts. Gerbillus andersoni allenbyi are
 commonly infected with the Mycoplasma haemomuris-like bacteria,
 which may cause mild nutrient (choline, arginine) deficiencies. However,
 are there more serious ecological consequences of infection such
 as effects on foraging aptitudes and risk management? We tested
 alternatives: 1) nutrient compensation hypothesis, does nutrient
 deficiency induce infected gerbils to make up for the shortfall by
 foraging more and taking greater risks? or 2) lethargy
 hypothesis, do sick gerbils forage less, and are they compromised in their
 ability to detect predators or risky microhabitats? We compared the
 foraging and risk management behavior of infected and non-infected
 gerbils. We experimentally infected gerbils with the bacteria, which
 allowed us to compare between non-infected, acutely infected (peak
 infection loads), and chronically infected (low infection loads)
 individuals. Our findings supported the lethargy
 hypothesis over the nutrient compensation
 hypothesis. Infected individuals incurred dramatically
 elevated foraging costs, including less efficient foraging, diminished
 “quality” of time spent vigilant, and increased owl predation.
 Interestingly, gerbils that were chronically infected (lower bacteria
 load) experienced larger ecological costs than acutely infected
 individuals (i.e. peak infection loads). This suggests that the
 debilitating effects of infection occur gradually, with a progressive
 decline in the quality of time gerbils allocated to foraging and
 managing risk. These increased long-term costs of infection
 demonstrate how small direct physiological costs of infection can
 lead to large indirect ecological costs. The indirect ecological costs of
 this parasite appear much greater than the direct physiological costs.
DOI: 10.5061/dryad.q573n5tgj
title: Impact of Helicoverpa zea salivary GOX on stomatal conductance and volatile emission of host plants

description: This data set contain raw data associated with the
 manuscript titled "Silencing the alarm: An insect salivary
 enzyme closes plant stomata and inhibits volatile release". 
 Herbivore-induced plant volatiles (HIPVs) are widely recognized as
 ecologically important to plant. While the majority of studies focused on
 the induction of this “cry for help”, little is known about whether insect
 herbivores have evolved mechanisms to reduce the release of HIPVs. Here we
 show that a caterpillar (Helicoverpa zea) salivary enzyme, glucose oxidase
 (GOX), commonly secreted on plant leaves causes stomatal closure and
 reductions in emissions of several HIPVs involved in plant defenses. We
 found that application of GOX to wounded regions of leaves led to
 reductions in stomatal conductance on tomato (Solanum lycopersicum) and
 soybean (Glycine max) for at least two days. The role of GOX in reducing
 stomatal aperture was confirmed using GOX knockout lines of H. zea
 (CRISPR-Cas9 mutagenesis), and microscopic observations of stomata. In
 addition, GOX reduced the emission of several HIPVs during feeding by H.
 zea, including (Z)-3-hexenol, (Z)-jasmone, and (Z)-3-hexenyl acetate,
 which are important air borne signals in plant defenses. Our findings
 highlight a novel mechanism where insect herbivore reduces the release of
 HIPVs during feeding by targeting fundamental plant structure (i.e.
 stomata), and the link between of stomatal dynamics and releases of HIPVs.
 We demonstrate the existence of HIPVs-interfering mechanisms as a
 potential evolutionary strategy for insect herbivores to interfere with
 plant air borne signals.
description: For detailed methodology please refer to the paper. 
description: Data are in ".csv" files. The R codes that are used to
 analyze the data are also included in thte data set. Plant volatile data
 are named based on the plant species and treatments of the experiments.
 All other data are named according to its corresponding figure panel in
 the paper.
DOI: 10.5061/dryad.mkkwh70x0
title: Data from: Interactions between seed-dispersing ant species affect plant community composition in field mesocosms

description: 1. In generalized mutualisms, species vary in the quality of services they
 provide to their partners directly via traits that affect partner fitness
 and indirectly via traits that influence interactions with mutualist
 species that play similar functional roles. Myrmecochory, or seed
 dispersal by ants, is a generalized mutualism with ant species varying in
 the quality of dispersal services they provide to their plant partners.
 Variation in ant species identity can directly impact seed dispersal
 patterns and plant community composition; however, we know less about how
 interactions among seed-dispersing ant species indirectly influence plant
 partners. 2. The invasive ant, Myrmica rubra, is a high-quality
 seed-disperser in its native range and interacts with myrmecochores
 (ant-dispersed plants) and the high-quality seed disperser Aphaenogaster
 sp. in its invaded range. We use this system to examine how interactions
 between two functionally similar mutualist ant species influence the
 recruitment and community composition of ant-dispersed plants. 3. We
 performed a field mesocosm experiment and a lab behavioral experiment to
 compare discovery and dominance behaviors between ant species, and seed
 dispersal and seedling recruitment of four myrmecochore species among
 intraspecific interaction treatments of each ant species and an
 interspecific interaction treatment. 4. We found that M. rubra was better
 at discovering and dispersing seeds, but that Aphaenogaster sp. was
 dominantly aggressive over M. rubra. Interspecific interactions dampened
 seed dispersal relative to dispersal by the better disperser. Despite this
 dampening, we found no effect of interspecific interaction on seedling
 recruitment. However, community composition of seedlings in the
 interspecific interaction treatment was more similar to composition in the
 aggressively dominant ant (Aphaenogaster sp.) treatment than in the better
 discoverer ant (M. rubra) treatment. 5. We show that interspecific
 interaction between mutualist species in the same functional guild affects
 the outcome of mutualistic interactions with partner species. Despite the
 native ant dispersing fewer seeds, its dominance over the subordinate
 (invasive) ant has the potential to allow for some level of biotic
 resistance against the effects of M. rubra on plant communities when these
 species co-exist.
description: See details in Manuscript.
description: See acronym definitions in Dryad file.
DOI: 10.5061/dryad.4tmpg4f76
title: The influence of a priori grouping on inference of genetic clusters: simulation study and literature review of the DAPC method

description: Inference of genetic clusters is a key aim of population genetics,
 sparking development of numerous analytical methods. Within these, there
 is a conceptual divide between finding de novo structure versus assessment
 of a priori groups. Recently developed, Discriminant Analysis of Principal
 Components (DAPC), combines discriminant analysis (DA) with principal
 component (PC) analysis. When applying DAPC, the groups used in the DA
 (specified a priori or described de novo) need to be carefully assessed.
 While DAPC has rapidly become a core technique, the sensitivity of the
 method to misspecification of groups and how it is being empirically
 applied, are unknown. To address this, we conducted a simulation study
 examining the influence of a priori versus de novo group designations, and
 a literature review of how DAPC is being applied. We found that with a
 priori groupings, distance between genetic clusters reflected underlying
 FST. However, when migration rates were high and groups were described de
 novo there was considerable inaccuracy, both in terms of the number of
 genetic clusters suggested and placement of individuals into those
 clusters. Nearly all (90.1%) of 224 studies surveyed used DAPC to find de
 novo clusters, and for the majority (62.5%) the stated goal matched the
 results. However, most studies (52.3%) omit key run parameters, preventing
 repeatability and transparency. Therefore, we present recommendations for
 standard reporting of parameters used in DAPC analyses. The influence of
 groupings in genetic clustering is not unique to DAPC, and researchers
 should consider their goal and which methods will be most appropriate.
description: The R script used to conduct DAPC analyses, measure
 F<sub>ST</sub>, and conduct regression analyses in the
 simulation study along with the database of papers used in the literature
 review.
description: Detailed description of files are given
 in Miller_et_al_Dryad_Read_Me.txt.
DOI: 10.5061/dryad.z8w9ghx91
title: Data from: Australian rodents reveal conserved craniofacial evolutionary allometry across 10 million years of murid evolution

description: Among vertebrates, placental mammals are particularly variable in the
 covariance between cranial shape and body size (allometry), with rodents a
 major exception. Australian murid rodents allow an assessment of the cause
 of this anomaly because they radiated on an ecologically diverse continent
 notably lacking other terrestrial placentals. Here we use 3D geometric
 morphometrics to quantify species-level and evolutionary allometries in 38
 species (317 crania) from all Australian murid genera. We ask if
 ecological opportunity resulted in greater allometric diversity compared
 to other rodents, or if conserved allometry suggests intrinsic constraints
 and/or stabilizing selection. We also assess whether cranial shape
 variation follows the proposed “rule of craniofacial evolutionary
 allometry” (CREA), whereby larger species have relatively longer snouts
 and smaller braincases. To ensure we could differentiate parallel versus
 non-parallel species-level allometric slopes, we compared the slopes of
 rarefied samples across all clades. We found exceedingly conserved
 allometry and CREA-like patterns across the 10 million year split between
 Mus and Australian murids. This could support both intrinsic constraints
 and stabilizing selection hypotheses for conserved allometry. Large-bodied
 frugivores evolved faster than other species along the allometric
 trajectory, which could suggest stabilizing selection on the shape of the
 masticatory apparatus as body size changes.
description: 3D skulls (stored in Morphosource - see associated link) from
 four Australian museums were landmarked in Viewbox 4.0. The 3D coordinates
 are stored here along with the molecular phylogeny modified from Smissen
 and Rowe 2018 and ecological trait information from Breed and Ford 2007.
 These are the raw data used for all analyses. Full methods for data
 collection provided in the associated American Naturalist article (or the
 preprint DOI provided below). Instructions for reproducing all analyses,
 figures, and tables are provided in the readme file as well as in the
 RMarkdown files provided in the zip file. Alternatively, the same data
 and code can be viewed at the GitHub link below. 
description: All scripts are in RMarkdown format (.Rmd) and can be opened in
 RStudio. There, you can edit and run code chunks as normal or use the Knit
 button to create HTML versions with both code and output. Remember to
 either set your working directory to the allometry-rodents folder on your
 computer or open an RStudio project from that folder.
DOI: 10.5061/dryad.k98sf7m46
title: Signatures of selection in a recent invasion reveals adaptive divergence in a highly vagile invasive species

description: A detailed understanding of population genetics in invasive populations
 helps us to identify drivers of successful alien introductions. Here, we
 investigate putative signals of selection in Australian populations of
 invasive common starlings, Sturnus vulgaris, and seek to understand how
 these have been influenced by introduction history. We used reduced
 representation sequencing to determine population structure, and identify
 Single Nucleotide Polymorphisms (SNPs) that are putatively under
 selection. We found that since their introduction into Australia, starling
 populations have become genetically differentiated despite the potential
 for high levels of dispersal, and that starlings have responded to
 selective pressures imposed by a wide range of environmental conditions
 across their geographic range. Isolation-by-distance appears to have
 played a strong role in determining genetic substructure across the
 starling’s Australian range. Analyses of candidate SNPs that are
 putatively under selection indicated that aridity, precipitation, and
 temperature may be important factors driving adaptive variation across the
 starling’s invasive range in Australia. However, we also noted that the
 historic introduction regime may leave footprints on sites flagged as
 being under adaptive selection, and encourage critical interpretation of
 selection analyses in non-native populations.
description: We collected
 a total of 568 starling samples from 24 localities across the invasive
 range in Australia. We recorded Global Position System (GPS) coordinates
 upon collection, which was used to obtain climate variables for the sample
 metadata.  The Cornell
 University Institute of Biotechnology Genomics Facility conducted library
 construction and Genotyping-by-Sequencing (GBS), using the restriction
 enzyme <i>PstI</i>. Each individual received a unique barcode
 before multiplexing 96 individuals per lane (Illumina HiSeq 2000; 6 lanes,
 100 bp single-end reads). We processed raw sequence data using TASSEL 3.0 and
 called SNPs for all individuals using the UNEAK
 pipeline. Full details in
 the associated manuscript.
DOI: 10.17632/77rgscfm4c
title: Data from the research interviews on Novelties Production and Contextual Knowledge

description: The Reca Project was defined as the research locus, which demonstrates a successful case, given its visibility at a national level, for investigating the production of novelties. Considering this case, data collection was defined through recorded semi-structured interviews.The interviews were conducted in November 2020 and lasted an average of 1 hour. A total of 11 interviews were conducted. The interviews were conducted in person, with the purpose of understanding the development process of producing new products, where they were able to explain the entire process in detail.
DOI: 10.5061/dryad.rr4xgxd6j
title: Video of nest predation of an African Paradise Flycatcher (Terpsiphone viridis) by an Olive Sunbird (Cyanomitra olivacea)

description: Nest predation is the dominant cause of nest failure in the tropics.
 However, our knowledge about tropical nest predator identity and community
 structure is still quite limited. On 9 January 2019, we video-recorded an
 Olive Sunbird (Cyanomitra olivacea) removing and flying off with an egg
 from an African Paradise Flycatcher (Terpsiphone viridis) nest in the East
 Usambara Mountains, Tanzania. This observation is surprising because the
 Olive Sunbird is a specialized nectarivore. Nectar, however, is a poor
 source of nitrogen and cannot meet the protein requirements for
 nectarivores. We hypothesize that bird eggs are a potential source of
 protein for selected long-billed sunbird species–species that can grasp
 and handle small bird eggs. Our observation of nest predation by an Olive
 Sunbird adds a heretofore unknown behavior to nectarivores in general and
 to sunbirds specifically.
DOI: 10.17632/77rgscfm4c.1
title: Data from the research interviews on Novelties Production and Contextual Knowledge

description: The Reca Project was defined as the research locus, which demonstrates a successful case, given its visibility at a national level, for investigating the production of novelties. Considering this case, data collection was defined through recorded semi-structured interviews.The interviews were conducted in November 2020 and lasted an average of 1 hour. A total of 11 interviews were conducted. The interviews were conducted in person, with the purpose of understanding the development process of producing new products, where they were able to explain the entire process in detail.
DOI: 10.17632/nhhk42wvxd
title: A systems analysis of performance monitoring and evaluation

description: Perfomance monitoring and evaluation data: DSD KZN
DOI: 10.17632/64ry35r64t
title: ITAGV, a specific biomarker associated with the pathogenesis of idiopathic pulmonary fibrosis

description: DATA contains the data generated during the experiment.
data2 contains the data generated during the bioinformatics analysis.
DOI: 10.17632/nhhk42wvxd.1
title: A systems analysis of performance monitoring and evaluation

description: Perfomance monitoring and evaluation data: DSD KZN
DOI: 10.25345/c5zg6gm81
title: MassIVE MSV000100608 - GNPS - timsMetabo demo on fecal, plasma, DOM, wastewater samples
title: timsMetabo 4D MoRE demo on one fecal, one plasma, one DOM, and one wastewater samples.
DOI: 10.17632/64ry35r64t.1
title: ITAGV, a specific biomarker associated with the pathogenesis of idiopathic pulmonary fibrosis

description: DATA contains the data generated during the experiment.
data2 contains the data generated during the bioinformatics analysis.
DOI: 10.17632/jw3zk4cr32
title: Supplementary material of the publication "Gaining Ground On Pterosaur Biomechanics: A General Overview"

description: Supplementary material of the publication "Gaining Ground On Pterosaur Biomechanics: A General Overview". This publication aims to review on the literature encompassing pterosaur locomotion and general biomechanics.
DOI: 10.17632/jw3zk4cr32.1
title: Supplementary material of the publication "Gaining Ground On Pterosaur Biomechanics: A General Overview"

description: Supplementary material of the publication "Gaining Ground On Pterosaur Biomechanics: A General Overview". This publication aims to review on the literature encompassing pterosaur locomotion and general biomechanics.
DOI: 10.17632/9g3db22n8t
title: Rapid plasticity of default-mode local network architectures following adult-onset blindness

description: Data for Mesik et al. paper.
DOI: 10.17632/9g3db22n8t.1
title: Rapid plasticity of default-mode local network architectures following adult-onset blindness

description: Data for Mesik et al. paper.
DOI: 10.5281/zenodo.15157518
title: TABLE 1 in A catalog of Nemestrinidae (Diptera: Brachycera: Nemestrinoidea) from Chile

description: TABLE 1. Nemestrinidae subfamilies, genera, subgenus, and species recorded from Chile.
SubfamilyGenusSubgenusSpeciesAuthorFalleniinaeNeorhynchocephalus Lichtwardtmendozanus(Lichtwardt, 1910)HirmoneurinaeHirmoneuropsis Bequaertbrevirostrata(Bigot, 1857)luctuosa(Philippi, 1865)orellanai(Stuardo, 1936)punctipennis(Philippi, 1865)silvai(Stuardo, 1936)strobelii(Rondani, 1868)Hyrmophlaeba RondanianthophilaBernardi, 1977anthracoides(Philippi, 1865)articulata(Philippi, 1865)bellula(Philippi, 1865)carbonifera(Angulo, 1971)cuprofulgida(Angulo, 1971)lurida(Rondani, 1868)maculipennis(Macquart, 1850)paraluctuosa(Angulo, 1971)pipistrella(Angulo, 1971).rubronigraBernardi, 1977ruizi(Stuardo, 1936)NemestrininaeTrichophthalma WestwoodEurygastromyia LichtwardtamaenaBigot, 1881andina(Philippi, 1862)barbarossa(Bigot, 1857)commutata(Philippi, 1865)eximia(Philippi, 1865)herbsti(Lichtwardt, 1910)jaffueliStuardo, 1936landbecki(Philippi, 1865)murina(Lichtwardt, 1910)niveibarbis(Bigot, 1857)nubipennisRondani, 1863philippiiRondani, 1863porteriStuardo, 1934scalarisBigot, 1881sexmaculataEdwards, 1930subaurata(Westwood, 1835)tigrinaAngulo, 1971ursula(Philippi, 1865)
...... continued on the next page
description: Published as part of González, Christian R., Elgueta, Mario, Carvacho, Camila, Pañinao-Monsálvez, Laura & Barahona-Segovia, Rodrigo M., 2023, A catalog of Nemestrinidae (Diptera: Brachycera: Nemestrinoidea) from Chile, pp. 153-154 in Zootaxa 5360 (2) on page 153, DOI: 10.11646/zootaxa.5360.2.1, http://zenodo.org/record/10150116
DOI: 10.5281/zenodo.15157519
title: TABLE 1 in A catalog of Nemestrinidae (Diptera: Brachycera: Nemestrinoidea) from Chile

description: TABLE 1. Nemestrinidae subfamilies, genera, subgenus, and species recorded from Chile.
SubfamilyGenusSubgenusSpeciesAuthorFalleniinaeNeorhynchocephalus Lichtwardtmendozanus(Lichtwardt, 1910)HirmoneurinaeHirmoneuropsis Bequaertbrevirostrata(Bigot, 1857)luctuosa(Philippi, 1865)orellanai(Stuardo, 1936)punctipennis(Philippi, 1865)silvai(Stuardo, 1936)strobelii(Rondani, 1868)Hyrmophlaeba RondanianthophilaBernardi, 1977anthracoides(Philippi, 1865)articulata(Philippi, 1865)bellula(Philippi, 1865)carbonifera(Angulo, 1971)cuprofulgida(Angulo, 1971)lurida(Rondani, 1868)maculipennis(Macquart, 1850)paraluctuosa(Angulo, 1971)pipistrella(Angulo, 1971).rubronigraBernardi, 1977ruizi(Stuardo, 1936)NemestrininaeTrichophthalma WestwoodEurygastromyia LichtwardtamaenaBigot, 1881andina(Philippi, 1862)barbarossa(Bigot, 1857)commutata(Philippi, 1865)eximia(Philippi, 1865)herbsti(Lichtwardt, 1910)jaffueliStuardo, 1936landbecki(Philippi, 1865)murina(Lichtwardt, 1910)niveibarbis(Bigot, 1857)nubipennisRondani, 1863philippiiRondani, 1863porteriStuardo, 1934scalarisBigot, 1881sexmaculataEdwards, 1930subaurata(Westwood, 1835)tigrinaAngulo, 1971ursula(Philippi, 1865)
...... continued on the next page
description: Published as part of González, Christian R., Elgueta, Mario, Carvacho, Camila, Pañinao-Monsálvez, Laura & Barahona-Segovia, Rodrigo M., 2023, A catalog of Nemestrinidae (Diptera: Brachycera: Nemestrinoidea) from Chile, pp. 153-154 in Zootaxa 5360 (2) on page 153, DOI: 10.11646/zootaxa.5360.2.1, http://zenodo.org/record/10150116
DOI: 10.5061/dryad.f7m0cfxt3
title: Oxidative costs of cooperation in cooperatively breeding Damaraland mole-rats

description: Within cooperatively breeding societies, individuals adjust cooperative
 contributions to maximise indirect fitness and minimize direct fitness
 costs. Yet, little is known about the physiological costs of cooperation,
 which may be detrimental to direct fitness. Oxidative stress, the
 imbalance between reactive oxygen species (by-products of energy
 production) and antioxidant protection, may represent such a cost when
 cooperative behaviours are energetically demanding. Oxidative stress can
 lead to the accumulation of cellular damage, compromising survival and
 reproduction, thus mediating the trade-off between these competing life
 history traits. Here we experimentally increased energetically demanding
 cooperative contributions in captive Damaraland mole-rats (Fukomys
 damarensis). We quantified oxidative stress related effects of increased
 cooperation on somatic and germline tissues, and the trade-off between
 them. Increased cooperative contributions induced oxidative stress in
 females and males, without increasing somatic damage. Males accumulated
 oxidative damage in their germline despite an increase in antioxidant
 defences. Finally, oxidative damage accumulation became biased towards the
 germline, while antioxidant protection remained biased towards the soma,
 suggesting that males favour the maintenance of somatic tissues, i.e.
 survival over reproduction. Our results show that, heightened cooperative
 contributions can ultimately affect direct fitness through oxidative
 stress costs, which may represent a key selective pressure for the
 evolution of cooperation.