cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.x0k6djhjw
title: Species co-occurrence shapes spatial variability in plant diversity–biomass relationships in natural rangelands under different grazing intensities

description: Grazing can alter plant species interactions in natural rangelands, which
 in turn might influence the productivity of the ecosystem but we do not
 fully understand how spatial variability in plant diversity-biomass
 relationships are modulated by grazing intensity. Here, we hypothesized
 that plant species co-occurrence in rangelands is mainly driven by niche
 segregation due to grazing and heterogeneity in local resources, and that
 grazing therefore modulates diversity–biomass relationships. We tested our
 hypothesis across 35 rangeland sites in Iran, using a species
 co-occurrence index to assess plant spatial aggregation within each site.
 At each site, we measured aboveground biomass, plant diversity,
 topography, soil nutrients and three levels of grazing intensity. High
 spatial segregation of plant communities (low species co-occurrence) was
 found at heavily grazed sites, whereas greater spatial aggregation (high
 species co-occurrence) was found on low and moderate grazed sites, showing
 varied associational patterns of species with grazing intensity. Soil
 nutrients increased with grazing intensity and spatial segregation of
 plant communities was greater at sites with high soil nutrient
 concentrations, indicating that grazing intensity influences the spatial
 heterogeneity of plant communities via nutrients deposited in urine and
 faeces. Declining plant biomass with grazing intensity was related to a
 strong decline in graminoid species diversity, which suggests that the
 diversity-biomass relationship is influenced by selective grazing of
 palatable species. The relationships between species co-occurrence and
 biomass or plant diversity suggest non-random patterns in species
 co-occurrences with grazing intensity, which could be the result of
 competition driven by high livestock grazing intensity. We therefore
 suggest that rangeland stocking rates should be managed properly to
 maintain rangeland production while promoting plant diversity.
DOI: 10.5061/dryad.mpg4f4r0s
title: Forecasting NDVI in the Galapagos

description: Forecasting ecosystem response to climate change is critical for guiding
 policy-making but challenging due to: complicated relationships between
 microclimates and regional climates; species’ responses that are driven by
 extremes rather than averages; the multifaceted nature of species’
 interactions; and the lack of historical analogs to future
 climates. Given these challenges, even model systems such as the
 Galapagos Islands, a world-famous biodiversity hotspot and World Heritage
 Site, lack clear forecasts for future environmental change. Here,
 we developed a novel non-parametric method for simulating the ecosystem
 futures based on observed vegetation productivity (NDVI) during analogous
 weather observed historically. Using satellite images taken from
 the past to piece together a simulated future, we projected that
 productivity of terrestrial vegetation of the Galapagos will increase over
 the next century by approximately one standard deviation archipelago-wide,
 with increases largest during the wet season (January to June), and in the
 arid zones. This greening may impact a variety of ecological and
 evolutionary processes, species of conservation concern, and agricultural
 practices. Our straightforward approach can be applied to many
 other regions, particularly those with rapid ecosystem responses to
 stochastic inter-annual climatic fluctuations that provide appropriate
 climate analogs for forecasting.
DOI: 10.5061/dryad.w9ghx3fq7
title: Plastic mulch film residues in agriculture: impact on soil suppressiveness, plant growth, and microbial communities

description: Plastic mulch film residues have been accumulating in agricultural soils
 for decades, but so far, little is known about its consequences on soil
 microbial communities and functions. Here, we tested the effects of
 plastic residues of low-density polyethylene and biodegradable mulch films
 on soil suppressiveness and microbial community composition. We
 investigated how plastic residues in a Fusarium culmorum suppressive soil
 affect the level of disease suppressiveness, plant biomass, nutrient
 status, and microbial communities in rhizosphere using a controlled pot
 experiment. The addition of 1% plastic residues to the suppressive soil
 did not affect the level of suppression and the disease symptoms index.
 However, we did find that plant biomasses decreased, and that plant
 nutrient status changed in the presence of plastic residues. No
 significant changes in bacterial and fungal rhizosphere communities were
 observed. Nonetheless, bacterial and fungal communities closely attached
 to the plastisphere were very different from the rhizosphere communities
 with overrepresentation of potential plant pathogens. The plastisphere
 revealed a high abundance of specific bacterial phyla (Actinobacteria,
 Bacteroidetes, and Proteobacteria) and fungal genera (Rhizoctonia and
 Arthrobotrys). Our work revealed new insights and raises emerging
 questions for further studies on the impact of microplastics on the
 agroecosystems.
description: The
 amplicon library preparation and sequencing was carried out at the McGill
 University and Genome Québec Innovation Centre (Montréal, Canada). The
 PCRs of the bacterial 16S rRNA gene V3-V4 region were performed with the
 primer set 515F (5’-GTGCCAGCMGCCGCGGTAA-3’) and 806R
 (5’-GGACTACHVGGGTWTCTAAT-3’). The PCRs of the fungal rDNA gene ITS region
 was performed with the primer set ITS1F (5’-CTTGGTCATTTAGAGGAAGTAA-3’) and
 58A2R (5’-CTGCGTTCTTCATCGAT-3’). Sequencing was carried out on an Illumina
 MiSeq platform with 4 biological replicates per
 treatment.
DOI: 10.5061/dryad.sj3tx965c
title: The role of neutral and adaptive genomic variation in population diversification and speciation in two ground squirrel species of conservation concern

description: Understanding the neutral (demographic) and adaptive processes leading to
 the differentiation of species and populations is a critical component of
 evolutionary and conservation biology. In this context, recently diverged
 taxa represent a unique opportunity to study the process of genetic
 differentiation. Northern and southern Idaho ground squirrels (Urocitellus
 brunneus – NIDGS, and U. endemicus - SIDGS, respectively) are a recently
 diverged pair of sister species that have undergone dramatic declines in
 the last 50 years and are currently found in metapopulations across
 restricted spatial areas with distinct environmental pressures. Here we
 genotyped single-nucleotide polymorphisms (SNPs) from buccal swabs with
 restriction site-associated DNA sequencing (RADseq). With these data we
 evaluated neutral genetic structure at both the inter- and intraspecific
 level, and identified putatively adaptive SNPs using population structure
 outlier detection and genotype-environment association (GEA) analyses. At
 the interspecific level, we detected a clear separation between NIDGS and
 SIDGS, and evidence for adaptive differentiation putatively linked to
 torpor patterns. At the intraspecific level, we found evidence of both
 neutral and adaptive differentiation. For NIDGS, elevation appears to be
 the main driver of adaptive differentiation, while neutral variation
 patterns match and expand information on the low connectivity between some
 populations identified in previous studies using microsatellite markers.
 For SIDGS, neutral substructure generally reflected natural geographic
 barriers, while adaptive variation reflected differences in land cover and
 temperature, as well as elevation. These results clearly highlight the
 roles of neutral and adaptive processes for understanding the complexity
 of the processes leading to species and population differentiation, which
 can have important conservation implications in susceptible and threatened
 species.
description: This dataset contains custom scripts required to perform all
 analyses based on the thirteen-lined ground squirrel VCFs (available raw
 data and bam files from NCBI's BioProject PRJNA747996). The provided
 VCF files should be used with the three custom scripts (0-1-2) with a .csv
 file with metadata relating to individuals location, and environmental
 variable values for their geographic positions. Custom scripts
 "commands_0_filtering" refer to quality filtering steps, with
 one for each dataset (IDGS, NIDGS and SIDGS); "commands_1_GEA"
 refer to the genotype-environment association analysis steps; and
 "commands_2_diversity_differentiation" refer to the genetic
 diversity and differentiation analysis. The scripts should be used in this
 order.
DOI: 10.5061/dryad.xwdbrv1dr
title: Capabilities and limitations of using DNA metabarcoding to study plant-pollinator interactions

description: Many pollinator populations are experiencing declines, emphasizing the
 need for a better understanding of the complex relationship between bees
 and flowering plants. Using DNA metabarcoding to describe plant-pollinator
 interactions eliminates many challenges associated with traditional
 methods and has the potential to reveal a more comprehensive
 understanding of foraging behavior and pollinator life history. Here we
 use DNA metabarcoding of ITS2 and rbcL gene regions to identify plant
 species present in pollen loads of 404 bees from three habitats in eastern
 Oregon. Our specific objectives were to 1) determine whether plant species
 identified using DNA metabarcoding are consistent with plant species
 identified using observations, 2) compare characterizations of diet
 breadth derived from foraging observations to those based on plant species
 assignments obtained using DNA metabarcoding, and 3) compare plant species
 assignments produced by DNA metabarcoding using a “regional” reference
 database to those produced using a “local” database. At the three
 locations, 31-86% of foraging observations were consistent with DNA
 metabarcoding data, 8-50% of diet breadth characterizations based on
 observations differed from those based on DNA metabarcoding data, and
 22-25% of plant species detected using the regional database were not
 known to occur in the study area in question. Plant-pollinator networks
 produced from DNA metabarcoding data had higher sampling completeness and
 significantly lower specialization than networks based on observations.
 Here, we examine some strengths and limitations of using DNA metabarcoding
 to identify plant species present in bee pollen loads, make ecological
 inferences about foraging behavior, and provide guidance for future
 research.
description: Native bees were sampled by handnetting, pollen loads were
 isolated individually from each bee, DNA was extracted from pollen loads,
 PCR was using to amplify the rbcL gene and ITS2 gene region, and a
 bioinformatics pipeline was used to determine which plant species were
 present in each pollen load. We compared plant species assignments
 obtained using regional and local reference databases. 
description: This file contains plant species assignments obtained using DNA
 metabarcoding with both local and regional reference databases for 404
 native bee pollen loads. Bees were collected by handnetting in 2018 from 8
 sites at Threemile Canyon Farms, 10 sites at USFS Starkey Experimental
 Forest and Range, and 7 sites at TNC's Zumwalt Prairie Preserve. This
 dataset includes sampling location, month captured, and a foraging
 observation for each individual bee.
DOI: 10.5061/dryad.t1g1jwt2t
title: Single molecule images for: An empirical energy landscape reveals mechanism of proteasome in polypeptide translocation

description: The ring-like ATPase complexes in the AAA+ family perform diverse cellular
 functions that require coordination between the conformational transitions
 of their individual ATPase subunits.  How the energy from ATP
 hydrolysis is captured to perform mechanical work by these coordinated
 movements is not known.  In this study, we developed a novel
 approach for delineating the nucleotide-dependent free-energy landscape
 (FEL) of the proteasome's heterohexameric ATPase complex based on
 complementary structural and kinetic measurements.  We used the
 FEL to simulate the dynamics of the proteasome and quantitatively
 evaluated the predicted structural and kinetic properties. The FEL model
 predictions were widely consistent with experimental observations in this
 and previous studies and suggested novel features of the mechanism of
 proteasomal ATPase. We find that the cooperative movements of the ATPase
 subunits result from the design of the ATPase hexamer entailing a unique
 free-energy minimum for each nucleotide-binding state.  ATP
 hydrolysis dictates the direction of substrate translocation by triggering
 an energy-dissipating conformational transition of the ATPase complex.
DOI: 10.5061/dryad.76hdr7sx3
title: Data from: Large-scale evolution of body temperatures in land vertebrates

description: Body temperature is a crucial variable in animals that affects nearly
 every aspect of their lives. Here we analyze for the first time
 large-scale patterns in the evolution of body temperatures across
 terrestrial vertebrates (tetrapods, including amphibians, mammals, birds
 and other reptiles). Despite the traditional view that endotherms (birds
 and mammals) have higher body temperatures than ectotherms, we find they
 are not significantly different. However, rates of body-temperature
 evolution are significantly different, with lower rates in endotherms than
 ectotherms, and the highest rates in amphibians. We find that body
 temperatures show strong phylogenetic signal over 350 million years of
 evolutionary history in tetrapods, and some lineages appear to have
 retained similar body temperatures over time for hundreds of millions of
 years. Although body temperatures are often unrelated to climate in
 tetrapods, we find that body temperatures are significantly related to
 day-night activity patterns. Specifically, body temperatures are generally
 higher in diurnal species than nocturnal species, both across ectotherms
 and, surprisingly, across endotherms also. Overall, our results suggest
 that body temperatures are significantly linked to phylogeny and
 diel-activity patterns within and among tetrapod groups, rather than just
 climate and the endotherm-ectotherm divide.
DOI: 10.5061/dryad.z8w9ghxcr
title: The bearing capacity of limestone strata roof containing a shallow buried spherical Karst cave

description: The chief objective of the article is to study the bearing capacity of
 limestone strata roof containing a shallow buried spherical Karst cave.
 Firstly, taking into account the effect of external load, stress
 field in the Earths crust, internal filling and the characteristics of
 Karst landform in China, a
 spatial axial-symmetrical model was established.
 Concurrently, Love displacement method was introduced, the expressions of
 stress components were gained. Subsequently, combining failure mechanism
 of ground collapse and the expressions of stress components, the bearing
 capacity calculation formula of limestone strata roof was determined.
 Finally, a comparison of calculation result was carried out, using the
 general solution and P-S method respectively. The result indicates the
 error is less than 5%, which meets the proposal standard necessity in
 practice. As a result, the research result would provide scientific basis
 for construction and operation of infrastructure in mantled Karst region
 in China.
DOI: 10.5061/dryad.vdncjsxvg
title: Valenzuela phylogenomic dataset from: Illumina whole genome sequencing indicates ploidy level differences within the Valenzuela flavidus (Psocodea: Psocomorpha: Caeciliusidae) species complex

description: This contains data for the manuscript: "Illumina Whole
 Genome Sequencing indicates Ploidy Level Differences within the Valenzuela
 flavidus (Psocodea: Psocomorpha: Caeciliusidae) Species Complex".
 Valenzuela flavidus is a species of bark louse which is known to
 have asexual parthenogenetic populations in Europe but is believed to have
 sexual and asexual populations in North America as well.
 Historically, Valenzuela aurantiacus was the species
 epithet recognized for North American members until reports of asexual
 reproduction surfaced in certain North American populations. Cytogenetic
 studies have demonstrated European all-female populations are triploid.
 However, males are often reported in North America suggesting diploidy for
 sexual populations. With the use of Illumina whole genome sequencing,
 genetic diversity among North American and European populations was
 explored with phylogenomic methods. Ploidy level was estimated by
 examining allele frequencies of read-mapped homologous gene regions.
 Results indicate divergent populations between Europe and North America.
 North American populations containing males are estimated to be diploid
 suggesting a different mechanism of genomic reproduction. These results
 suggest divergent population structure among European asexual and North
 American sexual members of V. flavidus providing insight
 for future studies to understand patterns of asexuality reported within
 the complex. The following file contains all gene
 alignments, concatenated supermatrix, and mitochondrial alignment for this
 manuscript. In addition, the BAM files used to estimate allele
 frequencies. Also, gene trees for coalescent analysis, resultant
 treefiles from IQ-tree searches, and MCMCtree result.
DOI: 10.5061/dryad.vx0k6djs0
title: Choice of nest attributes as a frontline defense against brood parasitism

description: Breeding- and nest-site choice is a behavioral strategy often used to
 counter negative interactions. Site choices prior to breeding prevents
 costs of predation and competition but has been neglected in the context
 of brood parasitism. For hosts of brood parasites, the earlier brood
 parasitism is prevented in the breeding cycle the lower the future costs.
 Suitable nest-sites for cavity-nesting common redstarts (Phoenicurus
 phoenicurus), a host of the common cuckoo (Cuculus canorus), are a limited
 resource, but their cavity-nesting strategy could potentially deter
 predators and brood parasites. We altered the entrance size of breeding
 cavities and investigated redstart nest site choice and its consequences
 to nest predation and brood parasitism risk, while accounting for
 potential interspecific competition for nest sites. We set-up paired
 nest-boxes and let redstarts choose between 7 cm and 5 cm entrance sizes.
 Additionally, we monitored occupancy rates in nest-boxes with 3 cm, 5 cm
 and 7 cm entrance sizes and recorded brood parasitism and predation
 events. We found that redstarts preferred to breed in 5 cm entrance size
 cavities, where brood parasitism was eliminated but nest predation rates
 were comparable to 7 cm entrance size cavities. Only in 3 cm cavities were
 both brood parasitism and predation rates reduced. In contrast to the
 other cavity-nesting species, redstart settlement was lowest in 3 cm
 entrance size cavities, potentially suggesting interspecific competition
 for small entrance size cavities. Nest site choice based on entrance size
 could be a front-line defense strategy that redstarts use to reduce brood
 parasitism.
description: Each set-up has its own cvs file. For
 2012-2013 the data from the general population and the choice experiment
 was compiled. Note that the column cavity size corresponds to the choice
 between the pair of nest-boxes (i.e. one 5 cm and one 7 cm nest box) used
 in the choice experiment. Given that one of the nest-boxes was never
 occupied, it was not included in the dataset to avoid confusion, as both
 nest-boxes had the same box ID. Also, note that the
 2019 data has more than one row per nest box as the entrance size is a
 time-dependent variable because additional covers were placed onto a
 subset of the nest-boxes at different times along the season. Moreover,
 the 2019 data has two columns for species: SpeciesCox and Species.
 SpeciesCox is the one used for the cox model, and all nest-boxes occupied
 by great tits were scored as empty. While for the Species column one can
 see which boxes were occupied by great tits.
DOI: 10.5061/dryad.sn02v6x4c
title: Data from: Can conflicting selection from pollinators and nectar-robbing antagonists drive adaptive pollen limitation? A conceptual model and empirical test

description: Pollen limitation is widespread, despite predictions that it shouldn’t be.
 We propose a novel mechanism generating pollen limitation: conflicting
 selection by pollinators and antagonists on pollinator attraction traits.
 We introduce a heuristic model demonstrating antagonist-induced adaptive
 pollen limitation, and present a field study illustrating its occurrence
 in a wild population.  For antagonist-induced adaptive pollen
 limitation to occur, four criteria must be met: 1) correlated attraction
 of pollinators and antagonists, 2) greater response by antagonists than
 pollinators to altered investment in attraction traits, 3) reduced
 investment in pollinator attraction leading to pollen limitation, and 4)
 higher fitness for plants with reduced investment in pollinator
 attraction. We surveyed nectar robbery and reproductive output for
 109 Odontonema cuspidatum (Acanthaceae) plants in a
 pollen-limited population over two years and used experimental
 floral arrays to evaluate how flower number affects pollination and nectar
 robbery. Both pollinators and nectar robbers preferred larger floral
 displays, and nectar robbery reduced reproductive output, suggesting
 conflicting selection. Survey and experimental data agreed closely on the
 optimum flower number under antagonist-induced pollen limitation; this
 number was substantially overrepresented in the population. While criteria
 for antagonist-induced adaptive pollen limitation are restrictive, the
 necessary conditions may often be realized. Considering interactions
 beyond the plant-pollinator dyad illuminates previously overlooked
 mechanisms generating pollen limitation.