cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.63xsj3v66
title: Data for: Predator co-occurrence in alpine and Arctic tundra in relation to fluctuating prey

description: Large carnivores influence ecosystem dynamics in multiple ways, e.g. by
 suppressing meso-carnivores and providing carrions for smaller scavengers.
 Loss of large carnivores is suggested to cause meso-carnivore increase and
 expansion. Moreover, competition between meso-carnivores may be modified
 by the presence of larger carnivores. In tundra ecosystems, the smallest
 meso-carnivore, the Arctic fox, has experienced regional declines, whereas
 its larger and competitively superior congener, the red fox, has
 increased, potentially due to changes in the abundance of apex predators.
 We explored if variation in occurrence of wolverine and golden eagle
 impacted the occurrence and co-occurrence of Arctic fox and red fox in
 relation to varying abundances of small rodents within the Scandinavian
 tundra. We applied multi-species occupancy models to an extensive wildlife
 camera dataset from 2011-2020 covering 98 sites. Daily
 detection/non-detection of each species per camera trap site and study
 period (late winter; March-May) was stacked across years and species
 occupancy was related to small rodent abundance while accounting for time
 of year and status of simulated carcass. Arctic fox was more likely to
 co-occur with red fox when wolverine was present, and less likely to
 co-occur with red fox when golden eagles were present and wolverine
 absent. Red foxes increased in occupancy when co-occurring with the larger
 predators. Arctic fox responded more strongly to small rodent abundance
 than red fox and co-occurred more often with the other species at
 carcasses when rodent abundance was low. Our findings suggest that the
 interspecific interactions within this tundra predator guild appear to be
 surprisingly intricate, driven by facets of fear of predation,
 interspecific mediation and facilitation, and food resource dynamics.
 These dynamics of intraguild interactions may dictate where and when
 conservation actions targeted towards the Arctic fox should be
 implemented.
description: Data was collected using a network of wildlife cameras in four
 alpine and one Arctic region of Norway in the period 2011-2020. Cameras
 were active during late winter each year (March-May) and was baited with
 scraps and trimmings from from slaughtered reindeer (15-20 kg), simulating
 a carcass. Cameras were checked and baits replaced once after
 approximately three weeks. The cameras were set to a time-lapse interval
 of 5 minutes, and the final data set was aggregated into daily
 presence/absence of each species.
description: Files include the daily aggregated detection data on the four
 focus species (Arctic fox, red fox, wolverine and golden eagle) in CSV
 format. The data is split into two regions; alpine and Arctic, which are
 modelled separately. The R script contains routines for data import and
 modelling. See README.md for further details.
DOI: 10.5061/dryad.vmcvdncxd
title: Data from: A CRISPR-based rapid DNA repositioning strategy and the early intranuclear life of HSV-1

description: The relative positions of viral DNA genomes to the host intranuclear
 environment play critical roles in determining virus fate. Recent advances
 in the application of chromosome conformation capture-based sequencing
 analysis (3C technologies) have revealed valuable aspects of the
 spatiotemporal interplay of viral genomes with host chromosomes. However,
 to elucidate the causal relationship between the subnuclear localization
 of viral genomes and the pathogenic outcome of an infection, manipulative
 tools are needed. Rapid repositioning of viral DNAs to specific subnuclear
 compartments amid infection is a powerful approach to synchronize and
 interrogate this dynamically changing process in space and time. Herein,
 we report an inducible CRISPR-based two-component platform that relocates
 extrachromosomal DNA pieces (5 kb to 170 kb) to the
 nuclear periphery in minutes (CRISPR-nuPin). Based on
 this strategy, investigations of herpes simplex virus 1 (HSV-1), a
 prototypical member of the human herpesvirus family, revealed
 unprecedently reported insights into the early intranuclear life of the
 pathogen: I) Viral genomes tethered to the nuclear periphery upon entry,
 compared with those freely infecting the nucleus, were wrapped around
 histones with increased suppressive modifications and subjected to
 stronger transcriptional silencing and prominent growth inhibition. II)
 Relocating HSV-1 genomes at 1 hour post infection significantly promoted
 the transcription of viral genes, termed an “Escaping” effect. III) Early
 accumulation of ICP0 was a sufficient but not necessary condition for
 “Escaping”. IV) Subnuclear localization was only critical during early
 infection. Importantly, the CRISPR-nuPin tactic, in principle, is
 applicable to many other DNA viruses.
description: # A CRISPR-based instant DNA repositioning strategy and the early
 intranuclear life of HSV-1 This dataset contains all the original source
 data, original uncropped blots images for figures in the manuscript
 "A CRISPR-based instant DNA repositioning strategy and the early
 intranuclear life of HSV-1". ## Description of the Data and file
 structure The dataset contains data collected and used to blot the charts
 and figures in the manuscript with proper labels and p values calculated,
 and original blot images for western blots. Sample labels, names and their
 collection methodologies were described in the manuscript in detail. ##
 Sharing/access Information Links to other publicly accessible locations of
 the data: N/A Was data derived from another source? No
DOI: 10.5061/dryad.gb5mkkwtg
title: From CREATE workshop to course implementation: Examining downstream impacts on teaching practices and student learning at 4-year institutions

description: We provide the full data set for the research study informing the efficacy
 of the CREATE strategy for positively influencing faculty and students in
 science courses at ten institutions (4-year). CREATE (consider, read,
 elucidate hypotheses, analyze, and intrepret data; think of the next
 experiment) represents a scaffolded approach for teaching students using
 the primary literature as the foundation of course instruction. In this
 project, faculty from different institutions were trained in this pedagogy
 through a week-long workshop and then followed as they adapted CREATE for
 a science course at their home institutions. We used a variety of
 assessments (cognitive, affective) to determine the effects of
 implementation on student cohorts at each institution. These assessments
 included the Experimental Design and Ability Test (EDAT), the Critical
 Thinking Test (CTT, an adaption of the Field-Tested Learning Assessment
 Guide), a concept-map test, and an adaption of the Survey of Student
 Attitudes, Abilities, and Beliefs (SAAB) survey. 
description: See published article for the full details of this study.
DOI: 10.5061/dryad.brv15dvd0
title: Data for: Simulating effects of agricultural intensification and climate change: Nitrogen fertilization and drought stress decrease insect herbivore performance

description: Biodiversity is globally under pressure, and the current decline in insect
 biomass and diversity is likely caused by human activities. Key drivers of
 biodiversity loss include agricultural intensification and anthropogenic
 climate change. Nevertheless, a thorough understanding of potential
 interactions between both factors and the mechanisms underlying insect
 declines in general is still lacking. Here, we investigate the combined
 effects of nitrogen fertilization and drought, as applied to host plants,
 on the preference and performance of the butterfly Lycaena tityrus.
 Individuals performed best on plants having received medium nitrogen
 levels, while performance was reduced by either a lack of or strong
 fertilization, the former potentially caused by nitrogen limitation and
 the latter by increased concentrations of toxic allelochemicals. Female
 oviposition preference though was positively related to nitrogen
 fertilization, resulting in a mismatch between preference and offspring
 performance at high nitrogen levels. Plant drought stress additionally
 reduced herbivore performance, and females appeared to suffer more from
 low-quality food than males. Our results indicate that increasing nitrogen
 fertilization, as applied in intensive agriculture, may substantially
 reduce host-plant quality for insect herbivores, which may be exaggerated
 in the course of climate change due to the more frequent occurrence of
 droughts. Our study thus contributes to a better understanding of the
 mechanisms underlying human-driven insect declines in agricultural
 landscapes and beyond.
DOI: 10.5061/dryad.cz8w9gj6x
title: Parasites as ecosystem modulators: Foliar pathogens suppress top-down effects of large herbivores

description: Parasites can catalyze or inhibit interactions between their hosts and
 other species, but the ecosystem-level effects of such interaction
 modifications are poorly understood. We conducted a large-scale field
 experiment in temperate grasslands of northeastern China to understand how
 foliar fungal pathogens (e.g., rusts and leaf spots) influenced top-down
 effects of large herbivores (cattle; Bos taurus) on plant diversity and
 productivity. In the absence of foliar pathogens, cattle grazing strongly
 suppressed biomass of the dominant grass, Leymus chinensis, (↓56%),
 generating competitive release that significantly increased plant species
 richness (↑75%) and evenness (↑15%). In the absence of grazing, pathogen
 attack on L. chinensis had no measurable effect on host biomass. However,
 pathogen infection greatly weakened top-down effects of herbivory by
 inhibiting cattle grazing on L. chinensis and negating grazing effects on
 plant biomass and species richness. Mechanistically, foliar pathogens were
 linked to increased alkaloid (↑45%) and reduced nitrogen levels (↓19%) in
 leaf tissue that appeared to deter cattle grazing on L. chinensis. Our
 results demonstrate that foliar pathogens can suppress top-down effects of
 large herbivores on grassland community structure and function by
 modifying the strength of its host’s interactions with the dominant
 consumer. We propose that parasites may function primarily as modulators
 of ecosystem function when their direct effects on host density (often
 dampened by evolution) are overshadowed by influences on host traits that
 modify host interactions with strong competitors, herbivores, or
 predators.
DOI: 10.5061/dryad.gf1vhhmt5
title: Reductions in home-range size and social interactions among dehorned black rhinoceroses (Diceros bicornis)

description: Poaching for horns and tusks is driving declines of megaherbivores
 worldwide, including the critically endangered African black rhinoceros
 (Diceros bicornis). By proactively dehorning entire rhinoceros
 populations, conservationists aim to deter poaching and prevent species
 loss. However, such conservation interventions may have hidden and
 underestimated effects on animals’ behavior and ecology. Here, we combine
 &gt;15 y of black rhino–monitoring data across 10 South
 African game reserves, comprising &gt;24,000 sightings of 368
 individuals, to determine the consequences of dehorning for black rhino
 space use and social interactions. While preventative dehorning at these
 reserves coincided with a nationwide decrease in black rhino mortality
 from poaching and did not infer increased natural mortality, dehorned
 black rhinos decreased their home range area by, on average,
 11.7 km2 (45.5%) and were 37% less likely to engage in social
 encounters. We conclude that dehorning black rhinos as an antipoaching
 measure alters their behavioral ecology, although the potential
 population-level effects of these changes remain to be determined.
DOI: 10.5061/dryad.zs7h44jdn
title: Data and scripts from: Experimental evidence of size-selective harvest and environmental stochasticity effects on population demography, fluctuations, and nonlinearity

description: Theory and analyses of fisheries datasets indicate that harvesting can
 alter population structure  and destabilize nonlinear processes,
 which increases population fluctuations. We conducted a factorial
 experiment on the population dynamics of Daphnia magna in relation to
 size-selective harvesting and stochasticity of food supply. Harvesting and
 stochasticity treatments both increased population fluctuations.
 Timeseries analysis indicated that fluctuations in control populations
 were nonlinear, and nonlinearity increased substantially in response to
 harvesting. Both harvesting and stochasticity induced population
 juvenescence, but harvesting did so via depletion of adults whereas
 stochasticity increased the abundance of juveniles. A fitted fisheries
 model indicated that harvesting shifted populations towards higher
 reproductive rates and larger-magnitude damped oscillations that amplify
 demographic noise. These findings provide experimental evidence that
 harvesting increases nonlinearity of population fluctuations and that both
 harvesting and stochasticity increase population variability and
 juvenescence.
DOI: 10.15468/dl.w543d4
title: Occurrence Download

description: A dataset containing 677156 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Madagascar",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 677156 records from 124 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003334-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f2ekc9
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Scymnodalatias albicauda"
 ]
}

 The dataset includes 29 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003425-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4mw6m90dv
title: Data from: Delineating seagrass species in the genera Halodule and Halophila from Tanzanian coastal waters using ITS and rbcL DNA barcoding

description: The seagrass species in Halodule and Halophila may for several reasons be
 considered as taxonomic complexes. They show close evolutionary
 relationships, morphological plasticity, and share similar features making
 misidentifications likely when morphological identification is applied. In
 Tanzanian coastal waters, there is some uncertainty about the identity of
 members of Halodule, particularly the existence of Halodule wrightii and
 the species composition of the Halophila ovalis complex. This study used
 morphology as well as internal transcribed spacer (ITS1 and ITS2) and
 ribulose-bisphosphate carboxylase (rbcL) DNA barcoding to identify species
 of Halodule and Halophila. Seagrass samples were collected during low
 spring tides, from Tanzania’s coastal waters of Tanga, Dar es Salaam,
 Mtwara, Mafia Island, and Unguja Island, from August 2020 to February
 2022. Morphological diagnosis, phylogenetic analysis, and evolutionary
 divergences inferred from the ITS gene supported the identification of
 five species, namely Halophila ovalis, H. minor, and H. stipulacea, with
 the first two forming the H. ovalis complex; as well as Halodule uninervis
 and H. pinifolia. It is the first time that H. pinifolia is reported in
 Tanzania. This is the first study reporting the delineation of seagrass
 species in East African coastal waters using DNA barcoding coupled with
 morphology.
description: ITS and rbcL genes were sequenced using a Sanger Sequencer at
 Africa’s Genomic Company and preprocessed using Sequencher ver. 5.4
 software (Gen 114 Codes).
description: Several DNA applications, including Genome Compiler
 (multiplatform), MEGA, BioEdit, Heracle BioSoft DNA Baseer, and GSL
 Biotech SnapGene (multiplatform), can be used to open and analyze these 
 FASTA files.
DOI: 10.5061/dryad.573n5tbbr
title: Data from: Specific leaf area is lower on ultramafic than on neighbouring non-ultramafic soils

description: These are datasets in csv format for ultramafic and non-ultramafic
 sampling sites where specific leaf area (SLA) was collected in five
 climatically diverse regions: Puerto Rico (tropical wet), Costa Rica
 (tropical dry), South Africa (subtropical), California and Lesbos (both
 with Mediterranean climate). The datasets include plant species level mean
 SLA values, regional coordinates, regional climate data, bioclimatic
 variables for individual sites, and a joined dataset that includes site
 level coordinates and climate variables. The R script to reproduce all
 analyses and figures is also included.
DOI: 10.5061/dryad.00000006x
title: Data from: Widespread extinctions of co-diversified gut bacterial symbionts from humans

description: Humans and other primates harbour complex gut bacterial communities that
 influence health and disease, but the evolutionary histories of these
 symbioses remain unclear due to a lack of information about the state of
 the microbiota in ancestral primates. Here we show that hundreds of gut
 bacterial lineages co-diversified with primate species over millions of
 years, but that nearly half of these ancestral symbionts have been lost
 from humans. Analyses of thousands of metagenome-assembled genomes from
 humans, chimpanzees, bonobos, and other non-human primates revealed
 significant co-diversification within ten gut bacterial phyla. Remarkably,
 44% of the co-diversifying clades detected in African apes were absent
 from available human metagenomic data. In contrast, only ~3% of the clades
 displaying the weakest evidence for co-diversification and detected in
 African apes were absent from humans. This study identifies bacterial
 symbioses that predate hominid diversification, revealing accelerated
 extinctions of ancestral, co-diversifying symbionts from human
 populations.
DOI: 10.15468/dl.neaqs8
title: Occurrence Download

description: A dataset containing 2613 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Glycyrrhiza lepidota",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 2613 records from 143 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003424-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6078/d1xq5s
title: Signatures of contextual interference in implicit sensorimotor adaptation

description: Contextual interference refers to the phenomenon whereby a blocked
 practice schedule results in faster acquisition but poorer retention of
 new motor skills compared to a random practice schedule. While contextual
 interference has been observed under a broad range of tasks, it remains
 unclear if this effect generalizes to the implicit and automatic
 recalibration of an overlearned motor skill. To address this question, we
 compared blocked and random practice schedules on a reaching task in which
 we used a feedback perturbation method that isolates implicit adaptation.
 The degree of implicit adaptation was quantified as the change in hand
 angle in the opposite direction of the perturbation, and retention was
 quantified as the percent of adaptation remaining after visual feedback
 was extinguished. In two experiments, participants tested under a random
 practice schedule exhibited slower implicit adaptation, but better
 retention compared to participants tested under a blocked practice
 schedule, the signature of contextual interference. These results indicate
 that contextual interference is not limited to the acquisition of new
 motor skills but also applies to the implicit adaptation of established
 motor skills.
description: See the manuscript for details. 
description: Please use the data and code freely.
DOI: 10.15468/dl.uk5gaf
title: Occurrence Download

description: A dataset containing 1791 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Vindula erota"
 ]
}

 The dataset includes 1791 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003423-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7291/d1v10q
title: Population-specific vulnerability to ocean change in a multi-stressor environment

description: Variation in environmental conditions across a species’ range can alter
 their responses to environmental change through local adaptation and
 acclimation. Evolutionary responses, however, may be challenged in
 ecosystems with tightly coupled environmental conditions, where changes in
 the covariance of environmental factors may make it more difficult for
 species to adapt to global change. Here, we conduct a 3-month-long
 mesocosm experiment and find evidence for local adaptation/acclimation in
 populations of red sea urchins, Mesocentrotus franciscanus, to multiple
 environmental drivers. Moreover, populations differ in their response to
 projected concurrent changes in pH, temperature, and dissolved oxygen. Our
 results highlight the potential for local adaptation/acclimation to
 multivariate environmental regimes, but suggest thresholds in responses to
 a single environmental variable, such as temperature, may be more
 important than changes to environmental covariance. Therefore, identifying
 physiological thresholds in key environmental drivers may be particularly
 useful for preserving biodiversity and ecosystem functioning.
description: Biological data were collected during Spring 2021. During the
 experiment, red sea urchins, <em>Mesocentrotus</em>
 <em>franciscanus</em>, were reared at current and future
 coupled pH, dissolved oxygen, and temperature conditions for populations
 collected from southern California and northern California in a laboratory
 mesocosm system. Within each replicate treatment aquarium, we placed sea
 urchins in individual 0.5 L cages where they were fed twice a week for the
 duration of the experiment (except during respirometry and grazing
 trials). We measured survival, wet and buoyant weight, gonad weight,
 respiration rate, and per capita grazing rate of all
 individuals.  Chemistry data were collected during the
 mesocosm experiment. These data were used to characterize the carbonate
 chemistry system in experimental treatments. Discrete samples for
 carbonate chemistry analyses were collected approximately every two weeks
 for the duration of both experiments using best practices for ocean
 CO<sub>2</sub> measurements. Associated salinity, temperature
 and dissolved oxygen measurements were made within an hour of discrete
 sample collection. In situ oceanographic pH,
 temperature, and dissolved oxygen data were collected continuously at two
 sites in southern California (Laguna Beach and Catalina Island) and two
 sites in northern California (Point Arena and Van Damme) from ~November
 2017 to August 2021.