cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k3j9kd5cj
title: Sexual recombination and temporal gene flow maintain host resistance and genetic diversity

description: Infectious disease can threaten host populations. Hosts can rapidly evolve
 resistance during epidemics, with this evolution often modulated by
 fitness trade-offs (e.g., between resistance and fecundity). However, many
 organisms switch between asexual and sexual reproduction, and this shift
 in reproductive strategy can also alter how resistance in host populations
 persists through time. Recombination can shuffle alleles selected for
 during an asexual phase, uncoupling the combinations of alleles that
 facilitated resistance to parasites and altering the distribution of
 resistance phenotypes in populations. Furthermore, in host species that
 produce diapausing propagules (e.g., seeds, spores, or resting eggs) after
 sex, accumulation of propagules into and gene flow out of a germ bank
 introduce allele combinations from past populations. Thus, recombination
 and gene flow might shift populations away from the trait distribution
 reached after selection by parasites. To understand how recombination and
 gene flow alter host population resistance, we tracked the genotypic
 diversity and resistance distributions of two wild populations of cyclical
 parthenogens. In one population, resistance and genetic diversity
 increased after recombination whereas, in the other, recombination did not
 shift already high resistance and genetic diversity. In both lakes,
 resistance remained high after temporal gene flow. This observation
 surprised us: due to costs to resistance imposed by a fecundity-resistance
 trade-off, we expected that high population resistance would be a
 transient state that would be eroded through time by recombination and
 gene flow. Instead, low resistance was the transient state, while
 recombination and gene flow re-established or maintained high resistance
 to this virulent parasite. We propose this outcome may have been driven by
 the joint influence of fitness trade-offs, genetic slippage after
 recombination, and temporal gene flow via the egg bank.
DOI: 10.6078/d1rx4x
title: Data and code from: Climate change, tree demography, and thermophilization in western US forests

description: Climate change is driving widespread changes in ecological communities.
 Warming temperatures often shift community composition toward more
 heat-tolerant taxa. The factors influencing the rate of this
 “thermophilization” process remain unclear. Using 10-year census data from
 an extensive forest plot network, we show that mature tree communities of
 the western US have undergone thermophilization. The mean magnitude of
 climate warming over the 10-year study interval was 0.32°C, whereas the
 mean magnitude of thermophilization was 0.039°C. Differential tree
 mortality was the strongest demographic driver of thermophilization,
 rather than growth or recruitment. Thermophilization rates are associated
 with recent changes in temperature and hydrologic variables, as well as
 topography and disturbance, with insect damage showing the strongest
 standardized effect on thermophilization rates. On average,
 thermophilization occurred more rapidly on cool, north-facing hillslopes.
 Our results demonstrate that warming temperatures are outpacing the
 composition of western US forest tree communities, and that climate change
 may erode biodiversity patterns structured by topographic variation.
DOI: 10.5061/dryad.1zcrjdfx2
title: Animal data associated with: Pattern dynamics and stochasticity of the brain rhythms

description: Our current understanding of brain rhythms is based on quantifying their
 instantaneous or time-averaged characteristics. What remains unexplored,
 is the actual structure of the waves–their shapes and patterns over finite
 timescales. The data published here are used to study brain wave
 patterning in different physiological contexts using two independent
 approaches: the first is based on quantifying stochasticity relative to
 the underlying mean behavior, and the second assesses
 "orderliness'' of the waves' features. The
 corresponding measures capture the waves' characteristics and
 abnormal behaviors, such as atypical periodicity or excessive clustering,
 and demonstrate coupling between the patterns' dynamics and the
 animal's location, speed, and acceleration. Specifically, patterns of
 θ, γ, and ripple waves recorded in mice hippocampi and observed
 speed-modulated changes of the wave's cadence, an antiphase
 relationship between orderliness and acceleration, as well as spatial
 selectiveness of patterns, are derived from the data. The results offer a
 complementary–mesoscale–perspective on brain wave structure, dynamics, and
 functionality.
description: The data were collected by tetrode
 recording in freely moving mice. A hyperdrive containing eight tetrodes
 was implanted during a surgery onto the skull of each mouse. Tetrodes were
 targeted at CA1 pyramidal cell layer of HP. The animal was trained in a
 familiar room to run back and forth on about a ∼ 2 m long rectangular
 track for a food reward. DigitalLynx acquisition system (Neuralynx,
 Bozeman, MU) was used for recording after the animal achieved a
 performance of at least 10 laps on the track. The daily recording
 procedure consisted of two sessions on the track, lasting about 15 min
 each, followed by one to two 15-min break in the sleeping box. The
 recording was repeated for 3–10 days. Local field potential (LFPs) data
 were sampled at 2 kHz rate. Two color diodes (red, green) were mounted
 over the animal’s head to track its positions, sampled at 33 Hz with a
 resolution of approximately 0.2 cm. Spikes were manually sorted using
 xclust2.
DOI: 10.5061/dryad.3n5tb2rnf
title: Data from: An efficient virus-induced gene silencing (VIGS) system for gene functional studies in Miscanthus

description: Virus-induced gene silencing (VIGS) is a powerful tool for transient gene
 functional analysis in plants, especially for monocot species (e.g.,
 grasses) that are recalcitrant to transformation. Despite various VIGS
 systems that have been developed in different plant species, none was
 previously available for the bioenergy crop Miscanthus. Here we report the
 establishment of an efficient and robust VIGS system mediated by Tobacco
 Rattle Virus (TRV) in Miscanthus. We first investigated the impact of
 various factors that may affect gene silencing efficiency using the
 Miscanthus sinensis Phytoene Desaturase (MsPDS) gene as a visual indicator
 of photobleaching. Then, we optimized the TRV-elicited VIGS procedure
 using an orthogonal experimental design with four factors (sprout size,
 Agrobacterium concentration, vacuum infiltration time, and co-incubation
 time) each at three levels. The following led to the highest silencing
 efficiency (~76%): inoculation of germinating seedlings (1.0-2.0 mm),
 Agrobacterium tumefaciens culture grown to optical density at 600 nm
 (OD600) of 0.4, vacuum infiltration for 90 min, and co-incubation for 5 h.
 The VIGS system established was applicable for both M. sinensis and M.
 lutarioriparius, with comparable gene silencing efficiency. We verified
 the efficacy of the VIGS system via the functional characterization of the
 role of a MYB transcription factor, MsMYB112, in salt stress tolerance.
 Expression of MsMYB112 was successfully knocked down using the VIGS
 system, and this led to compromised salt tolerance in the silenced
 Miscanthus plants. The TRV-based VIGS system established may, therefore,
 substantially facilitate functional genomic studies in Miscanthus.
description: The file includes the data required to reproduce analyses
 reported in the following paper: He et al., An efficient virus-induced
 gene silencing (VIGS) system for gene functional studies in
 Miscanthus.
DOI: 10.5061/dryad.k98sf7mb6
title: Data from: Enhanced climate tolerance for trees derived from microbial communities

description: Changing climates are pushing species outside of their evolved tolerances;
 populations must acclimate or adapt to the new conditions or migrate to
 avoid extinction. However, because plants associate with diverse microbial
 communities that shape their phenotype, shifts in microbial associations
 may provide an alternative source of novel climate tolerance. Here we show
 that tree seedlings inoculated with microbial communities sourced from
 drier, warmer, or colder sites displayed higher survival when facing
 drought, heat, or cold stress, respectively. Microbially mediated drought
 tolerance was associated with increased diversity of arbuscular
 mycorrhizal fungi, while cold tolerance was related to reduced diversity
 of non-adapted taxa. Understanding microbially mediated climate tolerance
 may enhance our ability to predict and manage the adaptability of forest
 ecosystems to changing climates.
description: See related article for methodological details.
description: R statistical program
DOI: 10.5061/dryad.w3r2280w2
title: Data for: Optimal inference of molecular interaction dynamics in FRET microscopy

description: Intensity-based time-lapse fluorescence resonance energy transfer (FRET)
 microscopy has been a major tool for investigating cellular processes,
 converting otherwise unobservable molecular interactions into fluorescence
 time series. However, inferring the molecular interaction dynamics from
 the observables remains a challenging inverse problem, particularly when
 measurement noise and photobleaching are nonnegligible—a common situation
 in single-cell analysis. The conventional approach is to process the
 time-series data algebraically, but such methods inevitably accumulate the
 measurement noise and reduce the signal-to-noise ratio (SNR), limiting the
 scope of FRET microscopy. Here, we introduce an alternative probabilistic
 approach, B-FRET, generally applicable to standard 3-cube FRET-imaging
 data. Based on filtering theory, B-FRET implements a statistically optimal
 way to infer molecular interactions and thus drastically improves the SNR.
 We validate B-FRET using simulated data and then apply it to real data,
 including the notoriously noisy in vivo FRET time series from individual
 bacterial cells to reveal signaling dynamics otherwise hidden in the
 noise.
description: Synthetic data were generated using MATLAB based on the
 photophysical model described in the article. Experimental data were taken
 under fluorescence microscopes. See the article for details.  
description: MATLAB is required to open the data files.
DOI: 10.5061/dryad.pvmcvdnqw
title: Python codes for deconstructing the effects of stochasticity on transmission of hospital-acquired infections in ICUs

description: The inherent stochasticity in transmission of hospital-acquired infections
 (HAIs) has complicated our understanding of transmission pathways. It is
 particularly difficult to detect the impact of changes in the environment
 on the acquisition rate due to stochasticity. In this study, we
 investigated the impact of uncertainty (epistemic and aleatory) on
 nosocomial transmission of HAIs by evaluating the effects of stochasticity
 on the detectability of seasonality on admission. For doing so, we
 developed an agent-based model of an ICU and simulated the acquisition of
 HAIs considering the uncertainties in the behavior of the healthcare
 workers (HCWs) and transmission of pathogens between patients, HCWs, and
 the environment. Our results show that stochasticity in HAI transmission
 weakens our ability to detect the effects of a change, such as
 seasonality, on the acquisition rate, particularly when transmission is a
 low-probability event. In addition, our findings demonstrate that data
 compilation can address this issue, while the amount of required data
 depends on the size of the said change and the amount of stochasticity.
 Our methodology can be used as a framework to assess the impact of
 interventions and provide decision-makers with insight about the minimum
 required size and target of interventions in a healthcare facility.
description: No dataset was used in the paper. The Python code for the ABM is
 provided. For deatils of the code, please refer to the README document
 (README.md), and for the details of the methodology, please refer to the
 manuscript. [Manuscript currently under review by Royal Society Open
 Science]
description: Any text-editor or MS Excel for input files and python (version
 3.7 or higher) for the code files.
DOI: 10.5061/dryad.866t1g1vh
title: Data for: Quantitative analysis of autophagy reveals the role of ATG9 and ATG2 in autophagosome formation

description: Autophagy is a catabolic pathway required for the recycling of cytoplasmic
 materials. To define the mechanisms underlying autophagy it is critical to
 quantitatively characterize the dynamic behavior of autophagy factors in
 living cells. Using a panel of cell lines expressing HaloTagged autophagy
 factors from their endogenous loci, we analyzed the abundance,
 single-molecule dynamics, and autophagosome association kinetics of a wide
 variety of autophagy proteins involved in autophagosome biogenesis.
 Surprisingly, autophagosome formation is inefficient and requires
 ATG2-mediated tethering to donor membranes. Furthermore, our observations
 support the model that phagophores are initiated by the accumulation of
 autophagy factors on mobile ATG9 vesicles, and that the ULK1 complex and
 PI3-kinase form a positive feedback loop required for autophagosome
 formation. Finally, we demonstrate that the duration of autophagosome
 biogenesis is approximately 110 seconds. In total, our work provides
 quantitative insight into autophagosome biogenesis and establishes an
 experimental framework to analyze autophagy in human cells.
DOI: 10.5061/dryad.7wm37pvxz
title: Data for: Predicting berry plant habitat under climate change in Bristol Bay, AK

description: Aim: Climate change is altering suitable habitat distributions of many
 species in high latitudes. Fleshy fruit-producing plants (hereafter “berry
 plants”), important in arctic food webs and as subsistence resources for
 human communities, may be impacted, but their response to a warming and
 increasingly variable climate at a landscape scale has not yet been
 examined.  Here, we identified influential environmental
 determinants of berry plant distribution and produced predictions on how
 climate change might shift these distributions. Location: Bristol Bay and
 Togiak NRCS Survey Areas, Alaska. Methods: We built species distribution
 models using the Random Forests algorithm to identify key characteristics
 and predict the spatial distribution of habitats suitable for five berry
 plant species: Vaccinium uliginosum L., Empetrum nigrum L., Rubus
 chamaemorus L., Vaccinium vitis-idaea L., and Viburnum edule (Michx.) Raf.
 Then, we used future climate projections (2081-2100; representative
 concentration pathways 4.5, 6.0, & 8.5) to predict shifts in
 species’ suitable habitat distributions based on future climate
 conditions. Results: The predicted amount and spatial patterns of suitable
 habitat for the current time period were variable among species,
 consistent with species’ diverse life history attributes and habitat
 preferences. Future climate models predicted both positive and negative
 changes to suitable habitat probability for all species; future binary
 classification maps predicted net declines in suitable habitat area for
 all species and climate scenarios tested. Models identified elevation,
 soil characteristics, and January and July temperatures as important
 drivers of suitable habitat distributions. Main conclusions: Our work
 contributes to understanding the response of important berry plant species
 to climate change at a landscape scale. Shifting and retracting
 distributions may alter where communities have access to harvesting areas,
 suggesting that access to these resources may become restricted in the
 future. Our prediction maps may help inform climate adaptation planning as
 communities anticipate shifting access to harvesting locations.
description: We used presence and absence data for five berry plant species
 collected by the USDA Natural Resources Conservation Service (NRCS) to
 build species distribution models. The NRCS data were collected between
 the years 2006-2013 as part of routine soil surveys conducted throughout
 the state. These location data were used in tandem with geospatial
 predictor variables (topography, soils), climate data from Alaska-specific
 climate models, and the Random Forests algorithm to assess and predict
 berry plant habitat suitability across the Bristol Bay landscape under
 current (2006-2013) and future projected (2081-2100; representative
 concentration pathways 4.5, 6.0, and 8.5) climate conditions.  
description: See README file for details.
DOI: 10.17871/try.116
title: Leaf Elemental Composition of Urban Coastal Wetland Plants

description: This dataset provides leaf elemental concentration measurements for major and trace elements in urban coastal wetland plant species sampled across two soil types. Leaf material was analyzed using inductively coupled plasma mass spectrometry (ICP-MS) and microwave acid digestion.
Taxonomic coverage: Plants
Field list: Species, Plant growth form, Soil Type, Latitude, Longitude, Altitude, Exposition, Plant maturity, Leaf age, Date, Na, Mg, Al, P, K, Ca, Mn, Fe, Cu, Zn, Cd, Pb, Digestion method, Instrument,
 Comment
DOI: 10.5061/dryad.05qfttf75
title: Data for: Neotropical mixed-species bird flocks in a community context

description: Mixed-species flocks are an important component of bird
 communities, particularly in the Neotropics, where flocks reach
 their highest diversity. The extent to which mixed-species flocks
 represent unique functional or ecological roles within
 communities, and how these attributes change over environmental gradients,
 however, is not well understood. We use a trait-based approach to examine
 functional aspects of flocking assemblages as they relate to those
 observed in the larger avian community across a 3000 m elevational
 gradient. Our results reveal similar ecological strategies among flocking
 species and the communities in which they occur, at the scale of the
 regional pool and across elevations. Trait variation in flocking and
 non-flocking assemblages is structured along two major axes defined by
 size- and resource-related traits. The trait space occupied by flocking
 species, however, represents only half (51%) that of the larger community.
 Similarly, the trait space of flocks across elevations is restricted
 compared to non-flocking species. The shared trait space across flock
 types represents small-bodied invertivores foraging in lower forest
 strata, traits associated with increased vulnerability to predation. The
 concentration of flocking species in functional trait space suggests high
 niche packing and either more overlap in ecological strategies or more
 finely divided niches relative to non-flocking species.
DOI: 10.5061/dryad.vdncjsz03
title: Ungulate occurrence in forest harvest blocks is influenced by forage availability, surrounding habitat, and silviculture practices

description: Forest harvesting causes habitat loss and alteration and can change
 predator-prey dynamics. In Canada, forest harvesting has shifted the
 distribution and abundance of ungulates (deer, elk, and moose) that prefer
 early seral forest, resulting in unsustainable caribou predation by shared
 predators (bears, cougars, and wolves). Long-term solutions for caribou
 recovery require management to reduce ungulate prey species within caribou
 ranges. Silviculture practices applied after forest harvesting directly
 affect the amount of forage available in harvested areas, and therefore
 influence ungulate distribution, but few studies have completed detailed
 assessments on how specific treatments of site preparation, planting, and
 stand tending influence ungulate use of harvest blocks. We used camera
 traps, silviculture data, GIS-derived habitat and disturbance data, and
 detailed vegetation data collected at field sites to investigate ungulate
 occurrence in harvest blocks in west-central Alberta, Canada. We compared
 seasonal ungulate occurrence and investigated how site-specific
 characteristics, the surrounding habitat and disturbance density, and
 fine-scale silviculture treatments influenced ungulate occurrence in
 blocks.  Deer, elk, and moose occurrence was higher in summer
 compared to winter. Elk, moose, and white-tailed deer occurrence were
 higher in blocks with greater availability of specific forage species.
 Moose occurrence was higher in blocks with a lower road density in the
 surrounding area, and white-tailed deer occurrence was higher in blocks
 further from seismic lines and with a lower proportion of harvest blocks
 in the surrounding area. Deer, elk, and moose occurrence were higher in
 younger harvest blocks. Mule deer and white-tailed deer occurrence were
 lower in blocks with higher planting densities of lodgepole pine, and mule
 deer occurrence was also lower in blocks that had been stand-tended. Our
 study provides detailed information on ungulate response to fine-scale
 silviculture methods used in Alberta, directly linking wildlife occurrence
 to forestry practices, and providing practical scientific information to
 inform sustainable forestry. Translating this research into practical
 landscape management decisions could benefit boreal biodiversity,
 including threatened species like caribou, and culturally and economically
 important species like deer, elk, and moose. 
description: Ungulate occurrence data were collected via camera trapping.
 Forest stand and vegetation abundance data were collected by vegetation
 assessments in the field. Silviculture data were provided by forestry
 companies. The dataset has been cleaned and processed using R
 Studio.
DOI: 10.5061/dryad.02v6wwq75
title: Spatial insurance against a heatwave differs between trophic levels in experimental aquatic communities

description: Climate change-related heatwaves are major threats to biodiversity and
 ecosystem functioning. However, our current understanding of the
 mechanisms governing community resistance to and recovery from extreme
 temperature events is still rudimentary. The spatial insurance hypothesis
 postulates that diverse regional species pools can buffer ecosystem
 functioning against local disturbances through the immigration of
 better-adapted taxa. Yet, experimental evidence for such predictions from
 multi-trophic communities and pulse-type disturbances, like heatwaves, is
 largely missing. We performed an experimental mesocosm study to test
 whether species dispersal from natural lakes prior to a simulated heatwave
 could increase the resistance and recovery of plankton communities. As the
 buffering effect of dispersal may differ among trophic groups, we
 independently manipulated the dispersal of organisms from lower
 (phytoplankton) and higher (zooplankton) trophic levels. The experimental
 heatwave suppressed total community biomass by having a strong negative
 effect on zooplankton biomass, probably due to a heat-induced increase in
 metabolic costs, resulting in weaker top-down control on phytoplankton.
 While zooplankton dispersal did not alleviate the negative heatwave
 effects on zooplankton biomass, phytoplankton dispersal enhanced biomass
 recovery at the level of primary producers, providing partial evidence for
 spatial insurance. The differential responses to dispersal may be linked
 to the much larger regional species pool of phytoplankton than of
 zooplankton. Our results suggest high recovery capacity of community
 biomass independent of dispersal. However, community composition and
 trophic structure remained altered due to the heatwave, implying
 longer-lasting changes in ecosystem functioning.