cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3df2q0k
title: Data from: Agriculturally dominated landscapes reduce bee phylogenetic diversity and pollination services

description: Land-use change threatens global biodiversity and may reshape the tree of
 life by favoring some lineages over others. Whether phylogenetic diversity
 loss compromises ecosystem service delivery remains unknown. We address
 this knowledge gap using extensive genomic, community, and crop datasets
 to examine relationships among land use, pollinator phylogenetic
 structure, and crop production. Pollinator communities in highly
 agricultural landscapes contain 230 million fewer years of evolutionary
 history; this loss was strongly associated with reduced crop yield and
 quality. Our study links landscape–mediated changes in the phylogenetic
 structure of natural communities to the disruption of ecosystem services.
 Measuring conservation success by species counts alone may fail to protect
 ecosystem functions and the full diversity of life from which they are
 derived.
description: bamm-scriptR script for running BAMM analysis to detect rate shiftscontrolBAMM configuration file for speciation/extinction analysisevent_dataBAMM event data file for speciation/extinction analysismcmc_outmcmc output file from BAMM speciation/extinction analysismy_treerooted time calibrated tree for BAMM speciation/extinction analysismyPriorsPrior Block for BAMM speciation/extinction analysissample_probsBAMM speciation/extinction sample probabilitiescomm_data_bySiteandYearcommunity data formatted for path analysisExaBayes_topologies.renamed.run-0Nexus file containing trees from ExaBayes run-1ExaBayes_topologies.renamed.run-1Nexus file containing trees from ExaBayes run 2comm_datawild bee community data for phylodiversity analysiscomm_data_wHBcommunity data including both wild bees and honey beescomm_phylosigcommunity data for phylogenetic signal analysesfruit_datameasures of apple fruits including shape, size, and number of seedsNestednessTurnover_comm_datacommunity data formatted for analysis of nestedness and turnovertrait_dataspecies' traits including body size (ITD), average visit duration, proportion of top-working vs. side-working, pollen load purity, and species' response to agricultural gradient.transect_datametadata for each sample in the community datasetPhyDiv_analysis_codeR script for calculating phylogenetic diversity metricsNestednessTurnover_codeR script for assessing nestedness and turnover in community compositionPhyloSig_analysis_codeR script to calculate phylogenetic signal for traits in trait_data filepath_analysis_codeR script for path analysis of direct and indirect effects of landscape and community on fruit datachronos.treeNexus file containing a rooted time-calibrated phylogeny of the apple pollinator community
DOI: 10.5061/dryad.8301107
title: Data from: Examining the microclimate hypothesis in Amazonian birds: indirect tests of the ‘visual constraints’ mechanism

description: Proposed mechanisms for the decline of terrestrial and understory
 insectivorous birds in the tropics include a related subset that together
 has been termed the “microclimate hypothesis.” One prediction from this
 hypothesis is that sensitivity to bright light environments discourages
 birds of the dimly lit rainforest interior from using edges, gaps, or
 disturbed forest. Using a hierarchical Bayesian framework and capture data
 across time and space, we tested this by first determining vulnerability
 based on differences in within-species capture rates between disturbed and
 undisturbed forest for 64 bird species at the Biological Dynamics of
 Forest Fragments Project in central Amazonian Brazil. We found that 35
 species (55%) were vulnerable to anthropogenic habitat degradation,
 whereas only four (6%) were more commonly captured in degraded forest. To
 infer visual sensitivity, we then examined two different characters: eye
 size (maximum pupil diameter) relative to body mass and the initiation
 time of dawn song, which presumably reflects a species’ visual capacity
 under low light intensities. We predicted that species with large relative
 eye sizes and birds with earlier dawn songs would exhibit increased
 vulnerability in degraded habitats with bright light. Contrary to our
 predictions, however, vulnerability was positively correlated with the
 mean start time of dawn song. This indicates that species that wait to
 initiate dawn song are also more vulnerable to habitat degradation. After
 correcting for body size, there was no effect of eye size on
 vulnerability. Together, our results do not provide quantitative support
 for the light sensitivity mechanism of the microclimate hypothesis. More
 sensitive, experimental tests, such as behavioral assays with controlled
 light environments, especially in a comparative framework, are needed to
 rigorously evaluate the role of light sensitivity as an aspect of the
 microclimate hypothesis among Neotropical birds.
description: 2007-2016_BDFFP_capture_rates_for_zero-inflated_Poisson_CLRuttetal
DOI: 10.5061/dryad.pr4t978
title: Data from: High-throughput synapse-resolving two-photon fluorescence microendoscopy for deep-brain volumetric imaging in vivo

description: Optical imaging has become a powerful tool for studying brains in vivo.
 The opacity of adult brains makes microendoscopy, with an optical probe
 such as a gradient index (GRIN) lens embedded into brain tissue to provide
 optical relay, the method of choice for imaging neurons and neural
 activity in deeply buried brain structures. Incorporating a Bessel focus
 scanning module into two-photon fluorescence microendoscopy, we extended
 the excitation focus axially and improved its lateral resolution. Scanning
 the Bessel focus in 2D, we imaged volumes of neurons at high-throughput
 while resolving fine structures such as synaptic terminals. We applied
 this approach to the volumetric anatomical imaging of dendritic spines and
 axonal boutons in the mouse hippocampus, and functional imaging of
 GABAergic neurons in the mouse lateral hypothalamus in vivo.
description: Figure
 2-9Raw data for figure 2
 through figure 9.Figure 10 mouse
 1Raw
 data for mouse 1 in figure 10Figure 10 mouse
 2Raw
 data for mouse 2 in figure 10
DOI: 10.5061/dryad.8s75sg6
title: Data from: Long-term sound and movement recording tags to study natural behaviour and reaction to ship noise of seals

description: The impact of anthropogenic noise on marine fauna is of increasing
 conservation concern with vessel noise being one of the major
 contributors. Animals that rely on shallow coastal habitats may be
 especially vulnerable to this form of pollution. Very limited information
 is available on how much noise from ship traffic individual animals
 experience, and how they may react to it due to a lack of suitable
 methods. To address this, we developed long‐duration audio and 3D‐movement
 tags (DTAGs) and deployed them on three harbor seals and two gray seals in
 the North Sea during 2015–2016. These tags recorded sound, accelerometry,
 magnetometry, and pressure continuously for up to 21 days. GPS positions
 were also sampled for one seal continuously throughout the recording
 period. A separate tag, combining a camera and an accelerometer logger,
 was deployed on two harbor seals to visualize specific behaviors that
 helped interpret accelerometer signals in the DTAG data. Combining data
 from depth, accelerometer, and audio sensors, we found that animals spent
 6.6%–42.3% of the time hauled out (either on land or partly submerged),
 and 5.3%–12.4% of their at‐sea time resting at the sea bottom, while the
 remaining time was used for traveling, resting at surface, and foraging.
 Animals were exposed to audible vessel noise 2.2%–20.5% of their time when
 in water, and we demonstrate that interruption of functional behaviors
 (e.g., resting) in some cases coincides with high‐level vessel noise.
 Two‐thirds of the ship noise events were traceable by the AIS vessel
 tracking system, while one‐third comprised vessels without AIS. This
 preliminary study demonstrates how concomitant long‐term continuous
 broadband on‐animal sound and movement recordings may be an important tool
 in future quantification of disturbance effects of anthropogenic
 activities at sea and assessment of long‐term population impacts on
 pinnipeds.
description: gs15_139b_TOLsTOL levels for the entire recording period for grey seal gs15_139b. Data is structured per day in 30 sec averagesgs15_139b_Accel_Depth_5HzMovement data for grey seal gs15_139b for the entire recording period.hs16_265c_TOLsTOL levels for the entire recording period for harbour seal hs16_265c. Data is in a by-day structure in 30 sec averages.hs16_265c_trackTrack file for harbour seal hs16_265cResting_video_acceleration_dataAcceleration data associated with resting dive from example in manuscript and supplementary material
DOI: 10.5061/dryad.b04s6t7
title: Data from: Multilocus genetic and morphological phylogenetic analysis reveals a radiation of shiny South Asian Jumping spiders (Araneae, Salticidae)

description: This study presents a systematic revision of South Asian members of the
 Tribe Chrysillini Simon, 1901. Here we analyzed genetic and morphological
 variation of a “similar-looking” group of species that were initially
 identified as members of the jumping spider genera Chrysilla Thorell, 1887
 and Phintella Strand, in Bösenberg & Strand, 1906 to determine
 their phylogenetic relationships. Our results suggest that part of our
 morphospecies complex constitute of three evolutionary lineages, two
 previously unrecognized, which are described and diagnosed as two new
 genera: Phintelloides gen. nov. and Proszynskia gen. nov. The third
 lineage, Phintella is sister to these proposed genera. The following new
 species are described: Phintelloides alborea sp. nov., P. brunne sp. nov.,
 P. flavoviri sp. nov., P. flavumi sp. nov., P. orbisa sp. nov., Phintella
 argentea sp. nov. and P. jaleeli sp. nov. Sri Lanka is rich in
 biodiversity, but currently has one of the highest rates of deforestation.
 Lack of clarity on diversity and distribution of the islands biodiversity
 can lead to underestimations during threat assessments and thus
 downgrading of conservation needs of individual species.
description: PhintellaMesquite (version 2.72; Maddison and Maddison 2009) edited morphological data matrixNucleotide alignment combined all neww.fastaconcatenated CO1+18S+28S in Mesquite format.Nucleotide alignment combined all newwconcatenated CO1+18S+28S in FASTA format.
DOI: 10.5061/dryad.h2f3t2n
title: Data from: Partitioning the effects of regional, spatial and local variables on beta diversity of salt marsh arthropods in Chile

description: Aim: We examined the influence of regional, spatial and local variables
 (edaphic characteristics and vegetation structure) on patterns of
 arthropod variation along the Chilean coast by partitioning beta diversity
 into its turnover and nestedness components. Location: 2000 km along the
 coast of Chile Methods: We collected ground-dwelling arthropod samples
 from 9 marshes during two seasons. A clustering method was used to examine
 patterns of arthropod similarity across salt marshes. We also calculated
 multiple site beta diversity and partitioned it into its turnover and
 nestedness components. Variation partitioning was then used to identify
 the major drivers of their variation (regional, spatial and local
 variables). We compared results for the whole arthropod community and for
 the most abundant, speciose and functionally different groups, Crustacea,
 Coleoptera and Araneae. Results: Salt marsh arthropod similarities did not
 depend on the geographic proximity of sites. Arthropod beta diversity was
 mainly determined by its turnover component. A significant fraction of
 community variation was structured according to regional (i.e. climate
 differences) or local (i.e. soil salinity) differences among marshes
 depending on the studied group. However, the exclusive contribution of
 spatial variables had also a role. Main conclusions: Each salt marsh on
 the Chilean coast has the capacity to accommodate unique invertebrate
 taxa. Niche sorting along the climatic gradient together with
 dispersal-based processes seem the key structuring force of the arthropods
 and Crustacean variation in the marshes we studied, while niche sorting
 alone might be more important for Coleoptera variation.
description: Arthropod_dataSeasonal presence absence data of each studied taxon (Family level, Crustacea, Coleoptera and Araneae)Climate and local variable usedVariables.zip
DOI: 10.5061/dryad.5t165h5
title: Data from: Getting ready for the winter: timing and determinants of molt in an alpine ungulate

description: Because growth of new hairs entails energetic costs, individual condition
 and access to food should determine the timing of molt. Previous studies
 on the timing of molt in ungulates have mostly focused on the influence of
 age-class and reproductive status, but the effects of body condition and
 environmental phenology have not been evaluated. Our goal was to assess
 how intrinsic traits and environmental conditions determine the timing of
 winter coat shedding in a mountain goat population monitored for 27 years.
 The date of molt completion followed a U-shape with age, suggesting that
 senescence occurs in terms of the molting process in mountain goats.
 Juveniles of both sexes delayed molting in a similar fashion, but molt
 timing differed between sexes during adulthood. Males molted progressively
 earlier until reaching age when reproduction peaked, after which they
 started delaying molting again. Females reached earliest molt dates at age
 of first reproduction and then progressively delayed molt date. Lactating
 females molted 10 days later than barren females on average, but this only
 occurred in females in good condition. Thus, although it has been shown
 that reproduction delays molt in ungulates, our results indicate that body
 condition can override this effect. Overall, our results revealed that
 access to both extrinsic and intrinsic resources is one of the key
 mechanisms driving molting processes in a mammalian herbivore.
description: Molt ending date of
 mountain goats of Caw Ridge, AB, Canada, 1989-2016 and variables of
 interestData needed to perform
 the same analyses that are in the publication associated. This data has
 been collected during summers from 1989 to 2016. Please read the
 "read_me" file. E-mail at Steeve.Cote@bio.ulaval.ca if
 you'd like to use this data, to ensure it is correctly used or to
 have more information on study system and other data
 available.Cote_et_al_mountain_goat_molt_1989_2016.xlsx
DOI: 10.5061/dryad.4kb762c
title: Data from: Establishment of wildflower fields in poor quality landscapes enhances micro-parasite prevalence in wild bumble bees

description: The current worldwide pollinator decline is caused by the interplay of
 different drivers. Several strategies have been undertaken to counteract
 or halt this decline, one of which is the implementation of wildflower
 fields. These supplementary flowers provide extra food resources and have
 proven their success in increasing pollinator biodiversity and abundance.
 Yet such landscape alterations could also alter the host–pathogen dynamics
 of pollinators, which could affect the populations. In this study, we
 investigated the influence of sown wildflower fields on the prevalence of
 micro-parasites and viruses in the wild bumble bee Bombus pascuorum, one
 of the most abundant bumble bee species in Europe and the Netherlands. We
 found that the effect of sown wildflower fields on micro-parasite
 prevalence is affected by the composition of the surrounding landscape and
 the size of the flower field. The prevalence of micro-parasites increases
 with increasing size of sown wildflower fields in landscapes with few
 semi-natural landscape elements. This effect was not observed in
 landscapes with a high amount of semi-natural landscape elements. We
 elaborate on two mechanisms which can support these findings: (1)
 “transmission hot spots” within the altered flower-networks, which could
 negatively impact hosts experiencing an increased exposure; (2) improved
 tolerance of the hosts, withstanding higher parasite populations.
description: Prevalence_dataPrevalence data of the parasite screeningDataForDyarad.xlsx
DOI: 10.5061/dryad.9pc7458
title: Data from: Mitotic chromosome binding predicts transcription factor properties in interphase

description: Mammalian transcription factors (TFs) differ broadly in their nuclear
 mobility and sequence-specific/non-specific DNA binding. How these
 properties affect their ability to occupy specific genomic sites and
 modify the epigenetic landscape is unclear. The association of TFs with
 mitotic chromosomes observed by fluorescence microscopy is largely
 mediated by non-specific DNA interactions and differs broadly between TFs.
 Here we combine quantitative measurements of mitotic chromosome binding
 (MCB) of 501 TFs, TF mobility measurements by fluorescence recovery after
 photobleaching, single molecule imaging of DNA binding, and mapping of TF
 binding and chromatin accessibility. TFs associating to mitotic
 chromosomes are enriched in DNA-rich compartments in interphase and
 display slower mobility in interphase and mitosis. Remarkably, MCB
 correlates with relative TF on-rates and genome-wide specific site
 occupancy, but not with TF residence times. This suggests that
 non-specific DNA binding properties of TFs regulate their search
 efficiency and occupancy of specific genomic sites.
description: Single molecule tracking
 data and code of Raccaud et. alThe file contains single
 molecule tracks and Hoechst areas of nine transcription factors and the
 code to analyse lifetimes and pseudo-on-rates.Raccaud_et._al_smt_data_and_code.rar
DOI: 10.5061/dryad.84jr187
title: Data from: Interactions among morphotype, nutrition, and temperature impact fitness of an invasive fly.

description: Invasive animals depend on finding a balanced nutritional intake to
 colonize, survive, and reproduce in new environments. This can be
 especially challenging during situations of fluctuating cold temperatures
 and food scarcity, but phenotypic plasticity may offer an adaptive
 advantage during these periods. We examined how lifespan, fecundity,
 pre-oviposition periods, and body nutrient contents were affected by
 dietary protein and carbohydrate (P:C) ratios at variable low temperatures
 in two morphs (winter morphs WM and summer morphs SM) of an invasive fly,
 Drosophila suzukii. The experimental conditions simulated early spring
 after overwintering and autumn, crucial periods for survival. At lower
 temperatures, post-overwintering WM lived longer on carbohydrate-only
 diets, and had higher fecundity on low protein diets, but there was no
 difference in lifespan or fecundity among diets for SM. As temperatures
 increased, low protein diets resulted in higher fecundity without
 compromising lifespan, while high protein diets reduced lifespan and
 fecundity for both WM and SM. Both SM and WM receiving high protein diets
 had lower sugar, lipid, and glycogen (but similar protein) body contents
 compared to flies receiving low protein and carbohydrate-only diets. This
 suggests that flies spend energy excreting excess dietary protein, thereby
 affecting lifespan and fecundity. Despite having to recover from nutrient
 depletion after an overwintering period, WM exhibited longer lifespan and
 higher fecundity than SM in favorable diets and temperatures. WM exposed
 to favorable low protein diet had higher body sugar, lipid, and protein
 body contents than SM, which is possibly linked to better performance.
 Although protein is essential for oogenesis, WM and SM flies receiving low
 protein diets did not have shorter pre-oviposition periods compared to
 flies on carbohydrate-only diets. Finding adequate carbohydrate sources to
 compensate protein intake is essential for the successful persistence of
 D. suzukii WM and SM populations during suboptimal temperatures.
description: SWD diet temperature
 lifespan fecundity preovipositionSWD WM and SM
 lifespan,fecundity, and preoviposition periods in variable diets and
 temperaturesSWD SM WM lipid sugar
 glycogen protein contentSWD SM WM lipid sugar
 glycogen protein content in various P:C dietslab overwintering SWD
 females protein sugar glycogen lipidsProtein, lipid, sugar,
 and glycogen contents of SWD females over 5 weeks of
 overwintering
DOI: 10.5061/dryad.81kk648
title: Data from: Diet and macronutrient niche of Asiatic black bear (Ursus thibetanus) in two regions of Nepal during summer and autumn

description: Relatively little is known about the nutritional ecology of omnivorous
 Asiatic black bears (Ursus thibetanus) in Nepal. We characterized the diet
 of black bears in two seasons (June–July, “summer”; and October–November
 “autumn”) and two study areas (Dhorpatan Hunting Reserve [DHR]; and
 Kailash Sacred Landscape [KSL]). We then conducted nutritional analysis of
 species consumed by black bears in each study area, in combination with
 nutritional estimates from the literature, to estimate the proportions of
 macronutrients (i.e., protein [P], lipid [L], and carbohydrate [C]) in the
 seasonal bear foods and diets, as well as their macronutrient niche
 breadth. We found that bamboo (Arundinaria spp.) had the highest relative
 frequency in both study areas and seasons. Ants and termites were found in
 DHR diets, but not KSL diets. One anthropogenic crop was found in DHR
 summer diets (Zea mays) and two were found in KSL summer diets (Z. mays;
 and Kodo millet [Paspalum scrobiculatum]). Other than insects, no animal
 prey was found in either diet. The proportions of macronutrients in diets
 (i.e., realized macronutrient niches) were relatively high in carbohydrate
 for both study areas and seasons: DHRsummer 24.1P:8.7L:67.2C; KSLsummer
 16.7P:8.2L:75.1C; DHRautumn 21.1P:10.5L:68.4C; KSHautumn
 19.0P:11.0L:70.0C. Macronutrient niche breadth was 3.1 × greater in the
 DHR than KSL during summer, and 4.0 × greater in the autumn, primarily due
 to the higher proportion of lipid in ants and termites relative to plant
 foods. Within‐study area differences in niche breadth were greater during
 summer than autumn; in the KSH the macronutrient breadth was 1.4 × greater
 in summer, while in the DHR it was 1.1 × greater in summer. Similarity in
 dietary macronutrient proportions despite differences in foods consumed
 and niche breadth are suggestive of foraging to reach a preferred
 macronutrient balance.
description: Macronutrient
 proportions of food items and diets of Asiatic black bear in
 NepalThis file contains the
 calculations used to quantify the macronutrient proportions of food items
 and diets of Asiatic black bear in Nepal.Black_bear_Nepal_RMT_data_1.xlsx