cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.02v6wwq63
title: Data from: Non-native grazers affect physiological and demographic responses of Greater Sage-grouse

description: 1. Non-native ungulate grazing has negatively impacted native species
 across the globe, leading to massive loss of biodiversity and ecosystem
 services. Despite their pervasiveness, interactions between non-native
 grazers and native species are not fully understood. We often observe
 declines in demography or survival of these native species, but lack
 understanding about the mechanisms underlying these declines.
 Physiological stress represents one mechanism of (mal)adaptation but data
 are sparse. 2. We investigated glucocorticoid levels in a native avian
 herbivore exposed to different intensities of non-native grazing in the
 cold desert Great Basin ecosystem, USA. We measured corticosterone, a
 glucocorticoid in feathers for a large sample (n = 280) of female Greater
 Sage-grouse (Centrocercus urophasianus) from three study areas in Northern
 Nevada and Southern Oregon with different grazing regimes of livestock and
 feral horses. 3. We found greater feral horse density was associated with
 higher corticosterone levels, and this effect was exacerbated by drought
 conditions. Livestock grazing produced similar results; however there was
 more model uncertainty about the livestock effect. Subsequent nesting
 success was lower with increased feather corticosterone, but
 corticosterone levels were not predictive of other vital rates. 4. Our
 results indicate a physiological response by sage-grouse to grazing
 pressure from non-native grazers. We found substantial among-individual
 variation in the strength of the response. These adverse effects were
 intensified during unfavorable weather events, highlighting the need to
 reevaluate management strategies in the face of climate change.
description: Physiological data are corticosterone mesurements from
 sage-grouse feathers collected at capture. Individual bird reproduction
 data were collected through radio telemetry monitoring. Grazing data was
 provided by the Bureau of Land Management.
description: Code requires Program R to run.
DOI: 10.5061/dryad.8cz8w9gtp
title: High-resolution climate simulations using the Model for Prediction Across Scales - Atmosphere (MPAS-A; version 5.1)

description: We present multi-seasonal simulations representative of present-day and
 future environments using the global Model for Prediction Across Scales –
 Atmosphere (MPAS-A) version 5.1 with high resolution (15 km) throughout
 the Northern Hemisphere. We select 10 simulation years with varying phases
 of El Niño–Southern Oscillation (ENSO) and integrate each for 14.5 months.
 We use analyzed sea surface temperature (SST) patterns for present-day
 simulations. For the future climate simulations, we alter present-day SSTs
 by applying monthly-averaged temperature changes derived from a 20-member
 ensemble of Coupled Model Intercomparison Project phase 5 (CMIP5) general
 circulation models (GCMs) following the Representative Concentration
 Pathway (RCP) 8.5 emissions scenario. Daily sea ice fields, obtained from
 the monthly-averaged CMIP5 ensemble mean sea ice, are used for present-day
 and future simulations. Due to storage limitations, the full dataset is
 much too large to be published (~50TB). Instead, a subset consisting of
 6-hourly warm season (May-September) 2-meter temperature, precipitation,
 and 500hPa height is presented. If you wish to access the full dataset (as
 presented in Michaelis et al. 2019), please contact one of the authors.
description: See Michaelis et al. 2019 for details on the creation of this
 dataset.
description: The files included are in NetCDF4 format so the program or
 programming language used needs to be capable of processing it. Python and
 MATLAB are both good options.
DOI: 10.5061/dryad.fn2z34txk
title: Data from: Recovery of macrobenthic communities in tidal flats following the Great East Japan Earthquake

description: Extreme geo-climatic events can occur everywhere in the world. The Great
 East Japan Earthquake, with a moment magnitude scale of 9.0 M on March 11,
 2011, was one of these events and caused huge tsunamis that changed
 largely tidal communities on the Pacific coast of eastern Japan. However,
 subsequent long-term changes in the communities after such an extreme
 geo-climatic event have rarely been examined. Therefore, we performed the
 biological monitoring over a ten-year span, before and after the
 earthquake, that was supported by citizen volunteers. The results revealed
 that the most tidal communities returned to their original states in less
 than a decade, indicating that the nearshore communities were highly
 resilient to large physical disturbances like tsunamis if the surrounding
 environmental conditions were unchanged.
DOI: 10.5061/dryad.dr7sqvb1v
title: Dataset and codes for: Partitioning the apparent temperature sensitivity between autotrophic and heterotrophic protists

description: Conventional analyses suggest the metabolism of heterotrophs is thermally
 more sensitive than that of autotrophs, implying that warming leads to
 pronounced trophodynamic imbalances. However, these analyses
 inappropriately combine within- and across-taxa trends. We present a novel
 mathematic framework to separate these, revealing that the higher
 temperature sensitivity of heterotrophs is mainly caused by within-taxa
 responses which account for 92% of the difference between autotrophic and
 heterotrophic protists. This dataset contains both the datasets and R
 codes of per capita growth rates of autotrophic and heterotrophic protists
 as well as heterotrophic bacteria and insects.
description: The datasets of per capita growth rates against temperature were
 compiled from the literature. Experimental data were included if they met
 the following criteria: at least 3 data points with positive growth rate
 (µ) and at least 2 unique temperatures at which positive µ were measured.
 To calculate apparent activation energy, we also removed data points with
 nonpositive µ and those with temperatures above the optimal growth
 temperature (defined as the temperature corresponding to the maximal
 µ).
description: We use the free software R (version 4.2.0) with R packages
 (foreach, nlme, plyr, dplyr) to analyse these datasets. R codes are also
 provided.
DOI: 10.5061/dryad.k6djh9w93
title: Role of sustainable agricultural intensification in food and nutrition security of smallholder subsistence farmers: Evidence from cereal legume intercropping in Eastern Ethiopia

description: This data set is a biological data generated through field experimentation
 on cereal legume intercropping. In general, the contents of the data set
 are type of treatment (experimental materials), site of experiment,
 biomass and grain yields, etc. There is no legal and ethical issues
 related to this data set and its process of generation. The data can be
 re-used with proper acknowledgement of the authors. 
description: <strong>Experimental
 design and Treatment</strong>
 The experiment included a
 total of six treatments laid in Randomized Complete Block design with
 three replications. The treatments were two maize varieties (BH 661 and
 BHQPY 545) as a sole and intercropped with the two common bean varieties
 on farmers’ fields, with sole planting of the common bean varieties
 included at the Raare research site only. 
 <strong>Data
 collection</strong> Biomass yield
 (BMY): Determined by weighing the total air-dried above ground biomass
 yield of plants in the two middle rows. Grain yield per
 plot (GY): Grain yield in kilogram of plants from the two middle rows and
 adjusted to 10% moisture level and then it was converted to kg
 ha-1..
description: The data is original data generated from field experimentation.
 The data was generated during 2019 cropping season. Any interested body
 can partially analyze and re-use it. The data is prepared in excell spread
 sheet.
DOI: 10.5061/dryad.8sf7m0crn
title: A simulated natural heatwave perturbs bumble bee immunity and resistance to infection

description: As a consequence of ongoing climate change, heatwaves are predicted to
 increase in frequency, intensity, and duration in many regions. Such
 extreme events can shift organisms from thermal optima for physiology and
 behavior, with the thermal stress hypothesis predicting reduced
 performance at temperatures where the maintenance of biological functions
 is energetically costly. Performance includes the ability to resist biotic
 stressors, such as infectious diseases. Climate change is a proposed
 threat to native bee pollinators, directly and through indirect effects on
 floral resources, but the thermal stress hypothesis, particularly
 pertaining to disease resistance, has received limited attention. We
 exposed adult Bombus impatiens bumble bee workers to
 simulated, ecologically relevant heatwave or control thermal regimes and
 assessed longevity, immunity, and resistance to concurrent or future
 parasite infections. We demonstrate that survival and induced
 antibacterial immunity are reduced following heatwaves. Supporting that
 heatwave exposure compromised immunity, the cost of immune activation by a
 non-pathogenic elicitor was thermal regime dependent, with costs to
 long-term survival in control but not heatwave exposed bees. However, in
 the face of real infections, an inability to mount an optimal immune
 response will be detrimental, which was reflected by higher infections
 from trypanosome parasite exposure following the heatwave, relative to the
 control regime. These results demonstrate interactions between heatwave
 exposure and bumble bee performance, including immune and infection
 outcomes. Thus, the health of bumble bee pollinator populations may be
 affected through altered interactions with parasites and pathogens, in
 addition to other effects of extreme manifestations of climate change.
description: See the uploaded readme file
 (README_Tobin_heatwave_data.txt).
DOI: 10.6086/d1q38n
title: Data for: Secondary nectar robbing by Lycaenidae and Riodinidae: opportunistic but not infrequent

description: Butterflies have rarely been reported in the literature to engage in
 secondary nectar robbing (consumption of nectar via slits in the corolla
 or nectar robbing holes. Here we report on observations of 4 taxa of
 butterflies that nectar rob from scarlet bugler (Penstemon
 centranthifolius).
description: Santa Rosa Mountains (Riverside County, CA)
 we observed a patch of blooming scarlet bugler (Plantaginaceae:
 <em>Penstemon centranthifolius</em>).We quantified visitation by Lepidoptera to 
 <em style="font-family:'Times New Roman' , serif;font-size:12pt;">P. centranthifolius</em>; we considered a butterfly to nectar at
 <em style="font-family:'Times New Roman' , serif;font-size:12pt;">P. centranthifolius</em> if it extended its proboscis and fed for
 &gt; 1 sec. Visitation was classified
 as “legitimate” if the butterfly was perched at the corolla opening and
 its proboscis was extended into the corolla. Visitation was classified as
 “secondary nectar robbing” when the butterfly’s proboscis was extended
 into pre-existing nectar robbing holes (sensu Irwin et al
 2010). Four species of butterflies
 were observed: Lycaenidae (California Hairstreak (<em style="font-family:'Times New Roman' , serif;font-size:12pt;">Satyrium californica</em>), Ceraunus Blue (<em style="font-family:'Times New Roman' , serif;font-size:12pt;">Hemiargus ceraunus</em>), and Marine Blue (<em style="font-family:'Times New Roman' , serif;font-size:12pt;">Leptotes marina</em>)) and metalmarks Riodinidae
 (<em style="font-family:'Times New Roman' , serif;font-size:12pt;">Apodemia</em> sp.).
description: Descriptions of variables are provided in the first tab
 (metadata) of the Excel file.
DOI: 10.5061/dryad.1g1jwsv0c
title: Fish assemblage composition of the four basins of Wannan Mountains, China

description: Extensive distribution of widespread species and the loss of native
 species driven by anthropogenic disturbances modify community similarity,
 resulting in a decrease or increase in community distinctiveness. Data
 from four basins in the Wannan Mountains, China, were used to evaluate the
 effects of low-head dams on patterns of fish faunal homogenization and
 differentiation based on abundance data. We aimed to examine the spatial
 changes in taxonomic and functional similarities of fish assemblages
 driven by low-head dams and whether the changes in the similarity of fish
 assemblages differed between taxonomic and functional components. We found
 that low-head dams significantly decreased the mean taxonomic similarity
 but increased the mean functional similarity of fish assemblages in
 impoundments using abundance-based approaches, suggesting that taxonomic
 differentiation accompanied functional homogenization in stream fish
 assemblages. These results show the importance of population abundance in
 structuring fish faunal homogenization and differentiation at small
 scales, especially when the major differences among assemblages are in
 species abundance ranks rather than species identities. Additionally, we
 also found only a weak positive correlation between changes in mean
 taxonomic and functional similarities, and partial pairs exhibited
 considerable variation in patterns of fish faunal homogenization and
 differentiation for taxonomic and functional components. In conclusion,
 this study highlighted that the observed taxonomic differentiation of
 current fish assemblages (short-term phenomenon) is probably an early
 warning sign of further homogenization in regions where native species are
 completely predominated, and that changes in taxonomic similarity cannot
 be used to predict changes in functional similarity. Keywords: Low-head
 dam, Stream fish, Biotic homogenization and differentiation, Taxonomic and
 functional diversities
description: A total of 106 sites were
 sampled across the Wannan Mountains during the wet season (August 2015).
 Stream fish assemblages were sampled at each site using a
 backpack electrofishing unit (CWB-2000 P, China; 12V input and 250V
 output) by wading in two passes. 
description: Software: Microsoft Office
 2007
DOI: 10.5061/dryad.3j9kd51mz
title: Proximity labeling of tau interactions in primary neurons and mouse brain

description: Microtubule-associated protein tau is a central factor in Alzheimer’s
 disease and other tauopathies. However, physiological functions of tau are
 unclear. Here, we used proximity labelling proteomics to chart functional
 tau interactomes in primary neurons and mouse brain in vivo. Here, we use
 proximity labelling with the biotin ligase BioID2 to map interactomes of
 tau in neurons. Data sets relate to mass spectrometry and protein
 identification of biotinylated proteins in primary neurons and in mouse
 brain after delivery of BioID2-tau fusion protein or BioID2 control
 protein by adeno-associated virus (AAV). Mouse brain samples are either
 from P35 wild-type mice with intracranial AAV delivery at P0 or from tau
 knockout mice at P60 after hippocampal delivery of AAV. Details on BioID2
 fusion protein expression, biotin supplementation and sample extraction
 can be obtained in the associated publication.
description: <strong>Data collection:</strong>
 Peptide samples sourced from primary neurons
 and mouse brain were run (3 μg injected per run) and captured on a C18
 cartridge (Acclaim PepMap 100, 5 μm 100 Å, Thermo Scientific Dionex,
 Waltham, USA) using a Q Exactive Orbitrap (ThermoFisher) before switching
 to a capillary column (~20 cm) containing C18 reverse phase packing
 (Reprosil-Pur, 1.9 μm, 200 Å, Dr Maisch GmbH, Ammerbuch-Entringen,
 Germany), and eluted with 40 min gradient of buffer A
 (H<sub>2</sub>O:CH<sub>3</sub>CN of 98:2 with 0.1%
 formic acid) to buffer B
 (H<sub>2</sub>O:CH<sub>3</sub>CN of 20:80 with
 0.1% formic acid) at 200 nL/min. The mass spectrometer (QExactive, Thermo)
 was set to positive ion mode. Peak lists were generated using MASCOT
 Distiller (Matrix Science, London, UK).
 <strong>Data processing:</strong>
 Peak lists were searched using the MASCOT
 search engine (v2.6.2, Matrix Science). Peak lists were matched to amino
 acid sequences from the SwissProt database (downloaded 10-8-19;
 <em>Mammalia</em> taxonomy, 66946 entries) and the Peptide
 Prophet algorithm (Keller<em> et al</em>,
 2002) assigned identity to peptides with FDR = 1.6%
 and to proteins with FDR = 0.4%. Each protein was considered identified
 when assigned 1 unique peptide with a peptide score &gt;38.
description: RAW files require MASCOT search engine (v2.6.2, Matrix Science)
 or similar mass spectrometry peak list reader. .CSV
 files can be opened in Microsoft Excel or text editing software.
DOI: 10.5061/dryad.3xsj3txk1
title: Data for: Consequences of microsporidian prior exposure for virus infection outcomes and bumble bee host health

description: Host-parasite interactions do not occur in a vacuum but in connected
 multi-parasite networks. Resulting co-exposures and coinfections during an
 individual host’s lifetime can affect host health and infectious disease
 ecology, including disease outbreaks. However, many host-parasite studies
 examine pairwise interactions, meaning we still lack a general
 understanding of the influence of co-exposures and coinfections. Using the
 bumble bee Bombus impatiens, we study the effects of larval exposure to a
 microsporidian, Nosema bombi, implicated in bumble bee declines, and adult
 exposure to Israeli Acute Paralysis Virus (IAPV), an emerging
 infectious disease from honey bee parasite spillover. We hypothesize that
 infection outcomes will be modified by co-exposure or coinfection
 depending on relevant temporal interactions, due to changes in host immune
 allocation or condition. Nosema bombi is a potentially
 severe, larval-infecting parasite, and we predict that prior exposure will
 result in decreased host resistance to adult IAPV infection. We predict a
 double exposure will also reduce host tolerance, as measured by host
 survival. Although our larval Nosema exposure mostly did
 not result in viable infections, it reduced resistance to adult IAPV
 infection. Exposure to Nosema also negatively affected survival,
 potentially due to a cost of immunity in resisting the exposure. There was
 also a significant negative effect of IAPV exposure on survivorship, but
 in contrast to resistance, prior Nosema exposure did not
 alter this survival outcome. These results again demonstrate that
 infection outcomes within multi-parasite host networks can be
 non-independent, even when exposure to one parasite does not result in a
 substantial infection.
DOI: 10.5061/dryad.sqv9s4n6j
title: Emergency-line calls as an indicator to assess human-wildlife interaction in urban areas

description: Human-wildlife interactions (HWI) are increasingly common as human
 disturbance and development continue to remove wildlife habitats.
 Documenting HWIs is critical for management agencies to develop strategies
 and management decisions that meet the needs of both people and wildlife.
 However, evaluating the frequency and types of HWI at broad spatial scales
 (e.g., national or regional level) can be costly and difficult to
 implement by managers. In this study, we apply a novel method for
 evaluating the patterns of HWI in urban areas using publicly available
 data from emergency calls placed by inhabitants of Romania’s &gt;300
 urban areas. We used information from 4,601 emergency calls (Romanian
 National Emergency Call System 112), consisting of (1) wildlife species,
 (2) spatial location, (3) date and time, and (4) a short description of
 the emergency.  Out of the 318 analyzed cities, 300 cities
 documented emergency calls on HWI between 2015–20120, with roe deer and
 brown bear as the most frequent species. There was an increasing trend in
 HWI-related emergency calls in 73% of the urban areas. We mapped the
 large-scale distribution of HWI by species and type of interactions,
 capturing variations at the national level, and further, we analyze social
 and biophysical factors influencing the occurrence and frequency of HWI.
 The results showed that social factors have the same positive or negative
 effect on all species, while the effect of the biophysical factors varied
 between species. Particularly, the presence of large natural habitats,
 represented by forests, influenced the number of calls only for brown
 bears. Seminatural landscapes with agricultural land have a different
 influence in terms of effect and significance for the considered species.
 Our results suggest that publicly available data from emergency calls can
 be used for the rapid assessment of HWI and for evaluating trends and
 predictors of HWI at broad spatial scales.
DOI: 10.5061/dryad.612jm6463
title: Causes and consequences of variation in early‐life telomere length in a bird metapopulation

description: Environmental conditions during early-life development can have lasting
 effects shaping individual heterogeneity in fitness and fitness-related
 traits. The length of telomeres, the DNA sequences protecting chromosome
 ends, may be affected by early-life conditions, and telomere length (TL)
 has been associated with individual performance within some wild animal
 populations. Thus, knowledge of the mechanisms that generate variation in
 TL, and the relationship between TL and fitness, is important in
 understanding the role of telomeres in ecology and life-history evolution.
 Here, we investigate how environmental conditions and morphological traits
 are associated with early-life blood TL and if TL predicts natal dispersal
 probability or components of fitness in 2746 wild house sparrow (Passer
 domesticus) nestlings from two populations sampled across 20 years
 (1994-2013). We retrieved weather data and we monitored population
 fluctuations, individual survival, and reproductive output using field
 observations and genetic pedigrees. We found a negative effect of
 population density on TL, but only in one of the populations. There was a
 curvilinear association between TL and the maximum daily North Atlantic
 Oscillation index during incubation, suggesting that there are optimal
 weather conditions that result in the longest TL. Dispersers tended to
 have shorter telomeres than non-dispersers. TL did not predict survival,
 but we found a tendency for individuals with short telomeres to have
 higher annual reproductive success. Our study showed how early-life TL is
 shaped by effects of growth, weather conditions, and population density,
 supporting that environmental stressors negatively affect TL in wild
 populations. In addition, shorter telomeres may be associated with a
 faster pace-of-life, as individuals with higher dispersal rates and annual
 reproduction tended to have shorter early-life TL.
description: Telomere lengths were measured using qPCR as described in the
 Methods section in the article. We retrieved weather data and we monitored
 population fluctuations, individual survival, and reproductive output
 using 20 years of field observations and microsattellite pedigrees as
 described in the Methods section in the article.