cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1pr59gf
title: Data from: Moderate grazing promotes the root biomass in Kobresia meadow on the northern Qinghai-Tibet Plateau

description: Grazing is an important modulator of both plant productivity and
 biodiversity in grassland community, yet how to determine a suitable
 grazing intensity in alpine grassland is still controversy. Here, we
 explore the effects of different grazing intensities on plant biomass and
 species composition, both at community level and functional group level,
 and examines the productivity–species richness relationship under four
 grazing patterns: no grazing (CK), light grazing (LG), moderate grazing
 (MG) and heavy grazing (HG), attempt to determine a suitable grazing
 intensity in alpine grassland. The results were as follows. The total
 aboveground biomass (AGB) reduced with increasing grazing intensity, and
 the response of plant functional groups was different. AGB of both sedges
 and legumes increased from MG to HG, while the AGB of forbs reduced
 sharply and the grass AGB remained steady. There was a significant
 positive relationship between productivity and species richness both at
 community level and functional group level. In contrast, the belowground
 biomass (BGB) showed a unimodal relationship from CK to HG, peaking in MG
 (8297.72±621.29 g m-2). Interestingly, the grassland community tends to
 allocate more root biomass to the upper soil layer under increasing
 grazing intensities. Our results suggesting that moderate levels of
 disturbance may be the optimal grassland management strategy for alpine
 meadow in terms of root production.
description: dataBiomass, mattic epipedon
 thickness, infiltration rate and species richness data
DOI: 10.5061/dryad.t4k343g
title: Data from: Disentangling ecologically equivalent from neutral species: the mechanisms of population regulation matter

description: 1. The Neutral Theory of Biodiversity explored the structure of a
 community of ecologically equivalent species. Such species are expected to
 display community drift dynamics analogous to neutral alleles undergoing
 genetic drift. While entire communities of species are not ecologically
 equivalent, recent field experiments have documented the existence of
 guilds of such neutral species embedded in real food webs. 2. What
 demographic outcomes of the interactions within and between species in
 these guilds are expected to produce ecological drift versus coexistence
 remains unclear. To address this issue, and guide empirical testing, we
 consider models of a guild of ecologically equivalent competitors feeding
 on a single resource to explore when community drift should manifest. 3.
 We show that community drift dynamics only emerge when the
 density-dependent effects of each species on itself are identical to its
 density-dependent effects on every other guild member. In contrast, if
 each guild member directly limits itself more than it limits the abundance
 of other guild members, all species in the guild are coexisting, even
 though they all are ecologically equivalent with respect to their
 interactions with species outside the guild (i.e., resources, predators,
 mutualists). Hence, considering only interspecific ecological differences
 generating density-dependence, and not fully accounting for the
 preponderance of mechanisms causing intraspecific density-dependence, will
 provide an incomplete picture for segregating between neutrality and
 coexistence. We also identify critical experiments necessary to
 disentangle guilds of ecologically equivalent species from those
 experiencing ecological drift, as well as provide an overview of ways of
 incorporating a mechanistic basis into studies of species coexistence and
 neutrality. 4. Identifying these characteristics, and the mechanistic
 basis underlying community structure, is not merely an exercise in
 clarifying the semantics of coexistence and neutral theories, but rather
 reflects key differences that must exist among community members in order
 to determine how and why communities are structured.
description: TwoPreds_OnePrey_V2Matlab code used to run simulations.
DOI: 10.5061/dryad.f2kh311
title: Data from: Conservation of the genome-wide recombination rate in white-footed mice

description: Despite being linked to the fundamental processes of chromosome
 segregation and offspring diversification, meiotic recombination rates
 vary within and between species. Recent years have seen progress in
 quantifying recombination rate evolution across multiple temporal and
 genomic scales. Nevertheless, the level of variation in recombination rate
 within wild populations – a key determinant of evolution in this trait –
 remains poorly documented on the genomic scale. To address this notable
 gap, we used immunofluorescent cytology to quantify genome-wide
 recombination rates in a wild population of male white-footed mouse,
 Peromyscus leucopus. For comparison, we measured recombination rates in a
 second population of male P. leucopus raised in the laboratory and in a
 lab strain of deer mouse, Peromyscus maniculatus bairdii. Although we
 found differences between individuals in the genome-wide recombination
 rate, levels of variation were low – within populations, between
 populations, and between species. Quantification of synaptonemal complex
 length and crossover positions along chromosome 1 using a novel automated
 approach also revealed conservation in broad-scale crossover patterning,
 including strong crossover interference. We propose stabilizing selection
 targeting recombination or correlated processes as the explanation for
 these patterns.
description: Precuration.csvMeasures from a sub-set of cell images for validating results from DNACrossOver. Each row corresponds to a type of bivalent measure with a manual and automated measure.PreCuration.csvPostCurationSimilar dataset as the Precuration dataset after a manual validation removed bad segmentation objects.Chrm1_DataDataset of validated chromosome 1 measures. Each row corresponds to a chromosome 1 bivalent. ‘boxNumber’ records the assigned index from DNACrossOver or if the bivalent was measured by hand. All values are in pixels, except SC.length.um. IFD stands for ‘Interfocal distance’ and reports the distance between the first and second (IFD1) or second and third MLH1 focus (IFD2).MLH1_DataFull dataset for MLH1 quantification from spermatocyte spreads. Each row corresponds to a cell image. ‘Batch’ refers to the quantification set which used a randomly assigned name. Quality is a manually assigned score, 1 given to highest quality cells to 5 low quality cells.Bivalent DataOutput of all images run through DNACrossOver. Each row corresponds to a bivalent-object measure. Each foci identified within the bivalent-object has an absolute and percent position and intensity value. These measures have not been validated.BivData.csvPermutationsScript for running permutations for analyses.CommonFuncCommon functions called within the analysis scripts.DataSetupSetting up the data for analysis and display.IsolateChrm1Script used to make a list of putative chromosome 1 measures for manual curation.AnalysisAll analyses of results reported in the published paper.
DOI: 10.5061/dryad.79q74n7
title: Data from: Plant uptake offsets silica release from a large Arctic tundra wildfire

description: Rapid climate change at high latitudes is projected to increase wildfire
 extent in tundra ecosystems by up to five-fold by the end of the century.
 Tundra wildfire could alter terrestrial silica (SiO2) cycling by
 restructuring surface vegetation and by deepening the seasonally-thawed
 active layer. These changes could influence the availability of silica in
 terrestrial permafrost ecosystems and alter lateral exports to downstream
 marine waters, where silica is often a limiting nutrient. In this context,
 we investigated the long-term effects of the largest Arctic tundra fire in
 recent times on plant and peat amorphous silica content and dissolved
 silica concentration in streams. Ten-years after the fire, vegetation in
 burned areas had 73% more silica in aboveground biomass compared to
 adjacent, unburned areas. This increase in plant silica was attributable
 to significantly higher plant silica concentration in bryophytes and
 increased prevalence of silica-rich gramminoids in burned areas. Tundra
 fire redistributed peat silica, with burned areas containing significantly
 higher amorphous silica concentrations in the O-layer, but 29% less silica
 in peat overall due to shallower peat depth post burn. Despite these
 dramatic differences in terrestrial silica dynamics, dissolved silica
 concentration in tributaries draining burned catchments did not differ
 from unburned catchments, potentially due to the increased uptake by
 terrestrial vegetation. Together, these results suggest that tundra
 wildfire enhances terrestrial availability of silica via permafrost
 degradation and associated weathering, but that changes in lateral silica
 export may depend on vegetation uptake during the first decade of
 post-wildfire succession.
description: Thaw
 depthThis file contains
 annual thaw depths at moderate and severe and unburned plots, along with
 standard deviations and standard errors for each year2008-2017ARF_ThawDepths_7.9.19.csvPlant_BSi_ConcentrationsThis file contains plant BSi concentrations (as SiO2 by dry weight) for each individual plant sample collected. Treatment data and plant functional type for each sample also indicated.Anaktuvuk_PlantSiData_7.9.19.csvTributary_DSiConcentrations_1.15.19This file contains DSi concentrations in burned and unburned tributaries from the summer (June, July, August) of 2017.Peat_ASiConcentrationData_7.9.19This datafile contains soil (peat) ASi concentration data for all burn types for the O and A soil horizonsSoil_ASiData_7.9.19.csv
DOI: 10.5061/dryad.t7r7899
title: Data from: Urbanization and elevated cholesterol in American crows

description: Although urban areas can be sources of abundant food for wildlife,
 anthropogenic foods may be lower in quality than natural food sources.
 Overall, the consequences of anthropogenic food consumption for wildlife
 are poorly understood. Here, we examined how urbanization and
 anthropogenic food were linked to cholesterol, condition, and survival of
 American crows (Corvus brachyrhynchos). We collected cholesterol and
 landscape data from 140 crow nestlings along an urban to rural gradient in
 Davis, CA, USA, and we ran a supplementation experiment with
 high-cholesterol fast food (McDonald’s cheeseburgers) on 86 nestlings in a
 rural population in Clinton, NY, USA. We used these data to evaluate links
 between cholesterol level, urbanization, condition, and crow survival. We
 found that plasma cholesterol increased with percentage of impervious
 surface along the urban to rural gradient. Cholesterol levels were
 sensitive to anthropogenic foods: crows supplemented with fastfood
 cheeseburgers had higher cholesterol levels than unsupplemented crows.
 Elevated cholesterol levels had no detectable effects on survival and were
 associated with higher indices of body condition, although urbanization
 itself was linked to lower survival. Elevated cholesterol levels could
 indicate access to high-calorie, high-fat anthropogenic foods, which
 might, in some contexts, improve body condition, potentially offsetting
 other negative effects of urbanization. Observations over a longer
 time-scale, assessing additional indices of health and fitness, are needed
 to evaluate long-term costs or benefits of elevated cholesterol for urban
 crows.
description: Townsend et al_Condor
 2019_crow cholesterol dataContains cholesterol,
 percentage of impervious surface, age, and condition data from California
 and New York populations; fledging success from California
 populationTownsend et al_Condor
 2019_mark-recap dataEncounter history in
 Mark-Recapture format for Davis, California population. Individual
 covariates: cholesterol and % impervious surface in 10ha buffers around
 nests.
DOI: 10.5061/dryad.sj7fc13
title: Data from: Nest predation predicts infanticide in a cooperatively breeding bird

description: In cooperatively breeding species, social conflict is typically assumed to
 underlie destructive behaviours like infanticide. However, an untested
 alternative hypothesis in birds is that infanticide in the form of egg
 tossing may simply be a parental response to partial nest predation
 representing a life history tradeoff. We examined egg tossing behaviour in
 the colonial and cooperatively breeding grey-capped social weaver
 (Pseudonigrita arnaudi), a plural breeder in which pairs nest separately,
 often in the same tree. Using infrared nest cameras, we found that 78% of
 the tossing events from 2012 to 2017 were committed by parents, suggesting
 that social conflict is unlikely to be the main reason underlying egg
 tossing in this species. Instead, reductions in clutch size due to both
 natural and experimentally-simulated predation induced parental egg
 tossing. Our study suggests that destructive behaviour in cooperatively
 breeding birds can be shaped by a variety of mechanisms beyond social
 conflict and that alternative hypotheses must be considered when studying
 the adaptive significance of infanticide in group-living species.
description: weaver egg tossing
 eventsThis contains data for
 analysis of the egg tossing events.weaver egg
 survivalThis contains data for
 analysis of egg survival in relation to predation during the laying stage
 (Fig.1b).
DOI: 10.3886/icpsr300452
title: Control Group Participant Exposure to Social Issue, Election, and Political Ads, Excluding Official Presidential Campaign Ads
title: Archival Version

description: <p><b><strong>These data are restricted and require an application. To apply, see SOMAR’s </strong></b><a href="https://icpsr.atlassian.net/servicedesk/customer/portal/53"><u><b><strong>Application Portal</strong></b></u></a><b><strong> and </strong></b><a href="https://somar.atlassian.net/wiki/x/M4DdDg"><u><b><strong>Application Guide</strong></b></u></a><b><strong>.</strong></b></p><p><span>This dataset contains aggregated metrics summarizing U.S. adult active users' exposure to social issues, elections, and political ads (excluding official presidential campaign ads) on Facebook and Instagram during the study period.</span></p>
DOI: 10.3886/icpsr300452.v1
title: Control Group Participant Exposure to Social Issue, Election, and Political Ads, Excluding Official Presidential Campaign Ads
title: Version 1

description: <p><b><strong>These data are restricted and require an application. To apply, see SOMAR’s </strong></b><a href="https://icpsr.atlassian.net/servicedesk/customer/portal/53"><u><b><strong>Application Portal</strong></b></u></a><b><strong> and </strong></b><a href="https://somar.atlassian.net/wiki/x/M4DdDg"><u><b><strong>Application Guide</strong></b></u></a><b><strong>.</strong></b></p><p><span>This dataset contains aggregated metrics summarizing U.S. adult active users' exposure to social issues, elections, and political ads (excluding official presidential campaign ads) on Facebook and Instagram during the study period.</span></p>
DOI: 10.5061/dryad.d17bg6h
title: Data from: Repeated jumps from Northwest Africa to the European continent: the case of peripheral populations of an annual plant

description: Peripheral populations (i.e., those occurring on the edge of a species’
 distribution range) can have different origins and genetic
 characteristics, and they may be critical for conservation of genetic
 diversity. We investigated European peripheral populations of Scrophularia
 arguta, a widespread, annual plant distributed from Arabia to Northwest
 Africa and Macaronesia. Only two small disjunct population groups of this
 species occur in Europe, specifically in West‐Central and Southeast
 Iberia. To disclose the origin of these populations and determine their
 importance for conservation of S. arguta genetic diversity, we analysed
 DNA sequences from two nuclear and two plastid regions and AFLP markers in
 populations sampled mainly across the western distribution range of the
 species, and modelled the species distribution under present and late
 Quaternary conditions. The analyses revealed the presence of three
 distinct lineages of S. arguta in Europe, as a result of multiple
 colonisation waves at different times in the Quaternary. Two of these
 lineages, occurring in Southeast Iberia, are the result of more or less
 recent dispersal from Northwest Africa. In contrast, West‐Central Iberian
 populations are strongly differentiated from the remaining range of S.
 arguta, and can be considered as peripheral relict populations. Our study
 is the first to demonstrate the occurrence of at least three colonisations
 of the European continent from Africa by a native plant species. The
 diverse histories and genetic makeup of resulting populations confirm the
 importance of peripheral populations, and particularly of ancient relict
 populations, for conservation of global genetic diversity in widespread
 species.
description: Sarguta_AFLPsMatrix of AFLP fragments from Scrophularia argutaDPA_DatasetInput XML files and resulting maximum clade credibility trees from the discrete phylogeographic analyses based on ptDNA and ITS/ETS sequences of Scrophularia argutaSDM_DatasetFiltered ocurrences of Scrophularia arguta and result from species distribution modelling in Maxent
DOI: 10.5061/dryad.3jf80g4
title: Data from: Herring gulls respond to human gaze direction

description: Human-wildlife conflict is one of the greatest threats to species
 populations worldwide. One species facing national declines in the UK is
 the herring gull (Larus argentatus), despite an increase in numbers in
 urban areas. Gulls in urban areas are often considered a nuisance due to
 behaviours such as food-snatching. Whether urban gull feeding behaviour is
 influenced by human behavioural cues, such as gaze direction, remains
 unknown. We therefore measured the approach times of herring gulls to a
 food source placed in close proximity to an experimenter who either looked
 directly at the gull or looked away. We found that only 26% of targeted
 gulls would touch the food, suggesting that food-snatching is likely to be
 conducted by a minority of individuals. When gulls did touch the food,
 they took significantly longer to approach when the experimenter’s gaze
 was directed towards them compared to directed away. However,
 inter-individual behaviour varied greatly, with some gulls approaching
 similarly quickly in both treatments while others approached much more
 slowly when the experimenter was looking at them. These results indicate
 that reducing human-herring gull conflict may be possible through small
 changes in human behaviour, but will require consideration of behavioural
 differences between individual gulls.
description: Goumas et al. main
 datasetThe repeated measures
 data from fieldwork on gaze aversion in herring gulls that was used in the
 linear mixed-effects model.gulldata.txtGoumas et al. R codeThe R code used for the statistical analyses (linear mixed-effects model, model comparisons, and correlations) in Goumas et al. "Herring gulls respond to human gaze direction".Herring gull code.RGoumas et al. supplementary dataThe data used in correlation analyses of within-individual approach times.pairs.txtGoumas et al. full dataThe complete data (including GPS coordinates of experimental locations to 3 decimal places) collected during fieldwork for "Herring gulls respond to human gaze direction".
DOI: 10.5061/dryad.s786348
title: Data from: Behavior influences range limits and patterns of coexistence across an elevational gradient in tropical birds

description: Does competition influence patterns of coexistence between closely related
 taxa? Here we address this question by analyzing patterns of range overlap
 between related species of birds (“sister pairs”) co-occurring on a
 tropical elevational gradient. We explicitly contrast the behavioral
 dimension of interspecific competition (interference competition) with
 similarity in resource acquisition traits (exploitative competition).
 Specifically, we ask whether elevational range overlap in 118 sister pairs
 that live along the Manu Transect in southeastern Peru is predicted by
 proxies for competition (intraspecific territorial behavior) or niche
 divergence (beak divergence and divergence times, an estimate of
 evolutionary age). We find that close relatives that defend year-round
 territories tend to live in non-overlapping elevational distributions,
 while close relatives that do not defend territories tend to broadly
 overlap in elevational distribution. In contrast, neither beak divergence
 nor evolutionary age was associated with patterns of range limitation. We
 interpret these findings as evidence that behavioral
 interactions⎯particularly direct territorial aggression⎯can be important
 in setting elevational range limits and preventing coexistence of closely
 related species, though this depends upon the extent to which
 intraspecific territorial behavior can be extended to territorial
 interactions between species. Our results suggest that interference
 competition can be an important driver of species range limits in diverse
 assemblages, and thus highlight the importance of considering behavioral
 dimensions of the niche in macroecological studies.
description: DatasetADataset A: Species list for the Manu region from Walker et al. (2006), with notes on the species included in this analysis and the source of the molecular phylogeny used to define sister pairs for different groups.DatasetBDataset B: Dataset used in analysis, including information on elevational overlap, genetic distance, beak divergence and territoriality for each sister pair.
DOI: 10.5061/dryad.g9j13fm
title: Data from: Maple phylogeny and biogeography inferred from phylogenomic data

description: Acer (the maple genus) is one of the diverse tree genera in the Northern
 Hemisphere with about152 species, most of which are in eastern Asia. There
 are roughly a dozen of species in Europe/western Asia and a dozen in North
 America. Several phylogenetic studies of Acer have been conducted since
 1998, but none have provided a satisfactory resolution for basal
 relationships among sections of Acer. Here we report the first
 well-resolved phylogeny of Acer based on DNA sequences of over 500 nuclear
 loci generated using the anchored hybrid enrichment method and explore the
 implications of the robust phylogeny for Acer systematics and
 biogeography. Our phylogenetic results support the most recent taxonomic
 treatment of Acer by de Jong with some modifications; section Pentaphylla
 may be expanded to include section Trifoliata, and A. yangbiense may be
 included in section Lithocarpa. Sections Spicata, Negundo, Arguta, and
 Palmata form a clade sister to the rest of the genus where sections Glabra
 and Parviflora comprise the first clade followed by section Macrantha,
 sections Ginnala, Lithocarpa, Indivisa, sections Platanoidea and
 Macrophylla, section Rubra, section Acer, and section Pentaphylla.
 Monotypic sections Glabra and Macrophylla in North America are sister to
 the Japanese section Parviflora and Eurasian section Platanoidea,
 respectively. Ancestral area inferences using S-DIVA (statistical
 dispersal and vicariance analysis) and DEC (dispersal and extinction
 cladogenesis) methods suggest that Asia might be the most likely ancestral
 area of Acer as proposed by Wolfe and Tanai and molecular dating using
 BEAST (Bayesian evolutionary analysis by sampling trees) indicate that
 section diversifications of Acer might have completed largely in the late
 Eocene and the intercontinental disjunctions of Acer between eastern Asia
 and eastern North America formed mostly in the Miocene.
description: Li et
 al.Acer116.AHEdatasetNuclear DNA sequences of
 over 500 loci generated using the Anchored Hybrid Enrichment probes
 designed by Buddenhagen et al. (2016) from 69 plant samples representing
 Aesculus and Dipteronia as outgorups and species of Acer. There are
 421,723 aligned sites.