cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3rf15cg
title: Data from: The theory of island biogeography and soundscapes: species diversity and the organization of acoustic communities

description: Aim: On islands, species richness is reduced and interspecific competition
 relaxed in relation to the mainland, allowing species to use broader
 ecological niches. These factors are known to affect diet and morphology,
 but can also affect communication and acoustic signaling in particular.
 However, no study has ever compared insular and continental soundscapes to
 determine to which extent islands present reduced acoustic richness
 (number of co-vocalizing species) and fewer constraints for vocalizing
 species. Location: São Tomé Island, Mount Cameroon, Madeira Island,
 Southern France Taxon: Birds Methods: We compared two pairs of insular and
 continental soundscapes: one in a temperate zone, the other in the
 tropics. We recorded sounds produced in similar types of primary forests
 and measured acoustic richness and ambient noise profiles. We then
 assessed acoustic niche organization by computing, for each community,
 species turnover, temporal and frequency overlaps, and acoustic avoidance.
 Results: We found fewer species co-vocalizing on islands compared to
 mainland and in temperate compared to tropical region. Ambient noise was
 louder in the tropics and occupied a wider frequency range, especially on
 the mainland, thereby revealing a reduction in available acoustic space
 for tropical mainland birds. In this more crowded and noisy soundscape,
 species presented a higher acoustic turnover, overlapped less in time and
 in frequency with each other and acoustically avoided each other more when
 compared to the three other communities. Main conclusions: Soundscapes
 differed and imposed fewer constraints on vocalizing species along the
 species diversity gradient from tropical mainland to temperate island.
 Acoustic niche partitioning increased with species richness and was
 associated with increased levels of acoustic interference. Results set a
 scene for an effect of relaxed competition on song evolution on islands,
 especially in the tropics.
description: Freq_and_temp_overlap_weightspectral and temporal overlap for focal species (Fig 3)Jaccard_indice_3min_periodNumber_bird_species_detected_3min_periodPercentage_undisturbed_signalpropagation experimentRelative_background_noiseTotal background noise for each 3 min period of each morningRelative_non_avian_noisedata_power_spectra_Fig2_non_avian_noisedata_power_spectra_Fig2_Totalnoise
DOI: 10.5061/dryad.5gk37t8
title: Data from: ddRAD‐seq data reveal significant genome‐wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America

description: Recently evolved species typically share genetic variation across their
 genomes due to incomplete lineage sorting and/or ongoing gene flow. Given
 only subtle allele frequency differences at most loci and the expectation
 that divergent selection may affect only a tiny fraction of the genome,
 distinguishing closely related species based on multi‐locus data requires
 substantial genomic coverage. In this study, we used ddRAD‐seq to sample
 the genomes of five recently diverged, New World “mallards” (Anas spp.), a
 group of dabbling duck species characterized by diagnosable phenotypic
 differences but minimal genetic differentiation. With increased genomic
 sampling, we aimed to characterize population structure within this group
 and identify genomic regions that may have experienced divergent selection
 during speciation. We analyzed 3,017 autosomal ddRAD‐seq loci and 177 loci
 from the Z‐chromosome. In contrast to previous studies, the ddRAD‐seq data
 were sufficient to assign individuals to their respective species or
 subspecies and to generate estimates of gene flow in a phylogenetic
 framework. We find limited evidence of contemporary gene flow between the
 dichromatic mallard and several monochromatic taxa, but find evidence for
 historical gene flow between some monochromatic species pairs. We conclude
 that the overall genetic similarity of these taxa likely reflects retained
 ancestral polymorphism rather than recent and extensive gene flow. Thus,
 despite recurring cases of hybridization in this group, our results
 challenge the current dogma predicting the genetic extinction of the New
 World monochromatic dabbling ducks via introgressive hybridization with
 mallards. Moreover, ddRAD‐seq data were sufficient to identify previously
 unknown outlier regions across the Z‐chromosome and several autosomal
 chromosomes, regions that may have been involved in the diversification of
 species in this recent radiation.
description: Input files for PCA,
 ADMIXTURE, fineRADstructure, BayeScan, TreeMix, as well as individual
 & concatenated FASTA files(1) Run-ready input
 files for (a) ADMIXTURE (i.e, ped/map input files), (b) BAYESCAN, (c)
 fineRADstructure, (d) PCA, (e) TreeMix for 3,017 Autosomal and 177 Z
 linked markers identified using ddRAD-seq protocols for 176 Mallards,
 American black ducks, Mexican ducks, West-gulf Coast Mottled ducks, and
 Florida Mottled ducks. (2) Individual and concatenated fasta files for
 3,017 Autosomal and 177 Z linked markers identified using ddRAD-seq
 protocols for 176 Mallards, American black ducks, Mexican ducks, West-gulf
 Coast Mottled ducks, and Florida Mottled ducks.Lavretsky.etal_DRYAD.UPLOAD.zip
DOI: 10.5061/dryad.rb8hr57
title: Data from: Intrinsic traits of woodland caribou Rangifer tarandus caribou calves depredated by black bears Ursus americanus and coyotes Canis latrans

description: Individuals in substandard physical condition are predicted to be more
 vulnerable to predation. Support for this prediction is inconsistent
 partly as a result of differences across systems in the life histories of
 predator and prey species. Our objective was to examine the physical
 condition of woodland caribou (Rangifer tarandus caribou) calves
 depredated by two predators with different life histories in Newfoundland,
 Canada. Black bears (Ursus americanus) are capable of chasing calves at
 high speeds over short distances and primarily prey on calves &lt;1
 month of age. Coyotes (Canis latrans) are cursorial predators that pursue
 prey over longer distances, which is expected to result in the selection
 of substandard individuals. We hypothesized that (i) black bears will kill
 calves in substandard physical condition, while (ii) coyotes will kill
 calves from across the distribution of individual conditions. We used
 mitochondrial DNA species identification tests to assign predator species
 to calf mortalities. We then used molecular identifications and field
 observations to build a predictive model using generalized boosted trees
 to predict the predator species where a molecular identification was
 unavailable. We tested our hypotheses using Cox proportional hazards
 models under a competing risks framework. Bears killed younger calves and
 lighter calves, while coyotes killed heavier calves. Coyotes also killed
 more late-born calves, which might suggest prey switching as calves become
 more abundant later in the season. Our findings suggest that the physical
 constraints of predators play a greater role than predator hunting
 strategies in this system, but other processes are likely influential. The
 tendency for coyotes to kill heavier calves might result from sustained
 coyote predation over time, following the removal by black bears of
 lighter calves during their first month of age. This research illuminates
 the complexity of predator-prey interactions in Newfoundland and
 highlights an important source of variability for predator-prey systems.
description: Predictive Model
 DataObservation data
 collected from caribou calf mortality locations used in a generalized
 boosted tree model to predict the predator species.PredictiveModelData.csvCox Regression Model DataData from collared caribou calves used in a Cox proportional hazards model to identify differences in the intrinsic traits of calves killed by black bears versus coyotes.CoxModelData.csv
DOI: 10.5061/dryad.6505nf4
title: Data from: Does trait variation within broadly distributed species mirror patterns across species? A case study in Puerto Rico

description: Although populations are phenotypically diverse, the majority of
 trait-based studies have focused on examining differences among species.
 The justification for this broadly applied approach is based on the
 assumption that differences among species are always greater than within
 species. This is likely true for local communities, but species are often
 broadly distributed across a wide range of environments and patterns of
 intraspecific variation might surpass differences among species.
 Therefore, an appropriate interpretation of the functional diversity
 requires an assessment of patterns of trait variation across different
 ecological scales. In this study, we examine and characterize patterns of
 leaf trait variation for species that are broadly distributed along an
 elevational gradient. We focus on seven leaf traits that represent a main
 axis of functional differentiation in plants reflecting the balance
 between photosynthetic efficiency, display, and stomatal conductance. We
 evaluated patterns of trait variance across ecological scales (elevation,
 species, populations, and individuals) and examined trait covariance at
 both within species and across species levels, along the elevation
 gradient. Our results show three key patterns: (1) intraspecific leaf
 trait variation for broadly distributed species is comparable to the
 inter-specific trait variation, (2) the trait variance structure is highly
 variable across species and (3) trait coordination between pairs of leaf
 traits is evident across-species along the gradient, but not always within
 species. Combined, our results show that trait coordination and covariance
 are highly idiosyncratic across broadly distributed and co-occurring
 species, indicating that species may achieve similar functional roles even
 when exhibiting different phenotypes. This result challenges the
 traditional paradigm of functional ecology that assumes single trait
 values as optimal solutions for environments. In conclusion, patterns of
 trait variation both across and within species should be considered in
 future studies that assess trade-offs among traits over environmental
 gradients.
description: TraitsDryad-EcologyTrait data for 6 tree species distributed across an altitudinal gradient in, El Yunque, Puerto Rico.
DOI: 10.5061/dryad.kh2gv5f
title: Data from: StomataCounter: a neural network for automatic stomata identification and counting

description: Stomata regulate important physiological processes in plants and are often
 phenotyped by researchers in diverse fields of plant biology. Currently,
 there are no user friendly, fully-automated methods to perform the task of
 identifying and counting stomata, and stomata density is generally
 estimated by manually counting stomata. We introduce StomataCounter, an
 automated stomata counting system using a deep convolutional neural
 network to identify stomata in a variety of different microscopic images.
 We use a human-in-the-loop approach to train and refine a neural network
 on a taxonomically diverse collection of microscopic images. Our network
 achieves 98.1% identification accuracy on Ginkgo SEM micrographs, and
 94.2% transfer accuracy when tested on untrained species. To facilitate
 adoption of the method, we provide the method in a publicly available
 website at http://www.stomata.science/.
description: Test
 setMicrographs used for
 testing neural networktest_set.zipTraining setMicrographs used for the training data set for neural networks.train_set.zipCaffe model weights and model structureZip file contains the caffe model weights (sc_feb2019.caffemodel) and caffe model structure definition file (sc_feb2019.prototxt)sc_feb2019.zip
DOI: 10.5061/dryad.k9f1p42
title: Data from: Habitat type influences Danaus plexippus (Lepidoptera: Nymphalidae) oviposition and egg survival on Asclepias syriaca (Gentianales: Apocynaceae)

description: As agricultural practices intensify, species once common in agricultural
 landscapes are declining in abundance. One such species is the monarch
 butterfly (Danaus plexippus L.), whose eastern North American population
 has decreased approximately 80% during the past 20 years. One hypothesis
 explaining the monarch’s decline is reduced breeding habitat via loss of
 common milkweed (Asclepias syriaca L.) from agricultural landscapes in the
 north central United States due to adoption of herbicide tolerant row
 crops. Current efforts to enhance monarch breeding habitat primarily
 involve restoring milkweed in perennial grasslands. However, prior surveys
 found fewer monarch eggs on common milkweed in grassland versus crop
 habitats, indicating potential preference for oviposition in row crop
 habitats, or alternately, greater egg loss to predation in grasslands. We
 tested these alternative mechanisms by measuring oviposition and egg
 predation on potted A. syriaca host plants. Our study revealed that
 habitat context influences both monarch oviposition preference and egg
 predation rates, and that these patterns vary by year. We found higher
 monarch egg predation rates during the first 24 h after exposure and that
 much of the predation occurs at night. Overall we documented up to 90% egg
 mortality over 72 h in perennial grasslands, while predation rates in corn
 were lower (10–30% mortality) and more consistent between years. These
 findings demonstrate that weekly monarch egg surveys are too infrequent to
 distinguish oviposition habitat preferences from losses due to egg
 predation and suggest that monarch restoration efforts need to provide
 both attractive and safe habitats for monarch reproduction.
description: Monarch Survival
 Experiment August 2016Aug_2016_survival_manuscript_csv.csvMonarch Survival Experiment July 2017July_2017_survival_manuscript_csv.csvMonarch Survival Experiment August 2017Aug_2017_survival_manuscript_csv.csvMonarch Oviposition Experiment 2016oviposition2016.csvMonarch Oviposition Experiment 2017oviposition2017.csvMonarch Survival Experiment Predator Surveys August 2016predator_surveys_Aug_2016.csvMonarch Survival Experiment Predator Surveys July & August 2017predator_surveys_July_&_August_2017.csvMonarch Oviposition Experiment Adult Observations 2016 & 2017oviposition_adult_observations_2016_&_2017.csvR script for analysis of monarch butterfly oviposition data for 2016 and 2017monarch_manuscript_oviposition_analysis.RR script for analysis of monarch butterfly survival data and predator community data for August 2016, July 2017, and August 2017monarch_manuscript_survival_analysis.R
DOI: 10.5061/dryad.m171n70
title: Data from: Invertebrate community response to fire and rodent activity in the Mojave and Great Basin Deserts

description: Recent increases in the frequency and size of desert wildfires bring into
 question the impacts of fire on desert invertebrate communities.
 Furthermore, consumer communities can strongly impact invertebrates
 through predation and top‐down effects on plant community assembly. We
 experimentally applied burn and rodent exclusion treatments in a full
 factorial design at sites in both the Mojave and Great Basin deserts to
 examine the impact that fire and rodent consumers have on invertebrate
 communities. Pitfall traps were used to survey invertebrates from April
 through September 2016 to determine changes in abundance, richness, and
 diversity of invertebrate communities in response to fire and rodent
 treatments. Generally speaking, rodent exclusion had very little effect on
 invertebrate abundance or ant abundance, richness or diversity. The one
 exception was ant abundance, which was higher in rodent access plots than
 in rodent exclusion plots in June 2016, but only at the Great Basin site.
 Fire had little effect on the abundances of invertebrate groups at either
 desert site, with the exception of a negative effect on flying‐forager
 abundance at our Great Basin site. However, fire reduced ant species
 richness and Shannon's diversity at both desert sites. Fire did
 appear to indirectly affect ant community composition by altering plant
 community composition. Structural equation models suggest that fire
 increased invasive plant cover, which negatively impacted ant species
 richness and Shannon's diversity, a pattern that was consistent at
 both desert sites. These results suggest that invertebrate communities
 demonstrate some resilience to fire and invasions but increasing fire and
 spread of invasive due to invasive grass fire cycles may put increasing
 pressure on the stability of invertebrate communities.
description: Data for
 DRYADInvertebrate samples
 from Mojave and Great Basin research sites
DOI: 10.5061/dryad.56bk548
title: Data from: Expanding the toolbox of nutrient limitation studies: novel method of soil microbial in-growth bags to evaluate nutrient demands in tropical forests

description: 1.Ecosystem processes and the organisms involved are generally limited by
 the availability of one or more element in soil, an important phenomenon
 to consider for our understanding of ecosystem functioning and future
 changes. Especially in tropical forests, typically growing on nutrient
 depleted soils, nitrogen (N), phosphorus (P) or other limitations are
 assumed. However, large‐scale nutrient manipulation experiments revealed
 complex site‐specific patterns and several authors raised the need for
 novel approaches to reveal deeper mechanistic insights on limitation
 patterns, especially concerning soil microbial activity. 2.In order to
 gain such deeper knowledge, based on a short review of previous
 small‐scale studies focusing on soil microorganisms, we developed an
 experimental approach which controls for common biases, including indirect
 treatment effects, addition of co‐elements or nutrient pulses. Using this
 technique, we tested the hypotheses that fungi growing in tropical forest
 soils are mainly limited by P, and that N versus P limitations shift along
 an altitudinal gradient. 3.Mesh bags of 38 μm filled with sand were
 amended with weak ion exchange resins loaded with N, P or potassium (K)
 and buried underneath the litter layer at three altitudinal sites in
 Southern Ecuador. After a period of four months, the in‐growth of fungal
 hyphae was quantified, phospholipid fatty acids were analyzed for a subset
 of samples and chemical properties were determined. 4.In line with the
 first hypothesis, hyphal abundance was increased in P amended mesh bags,
 indicating P limitation. However, this pattern was not significantly
 shifted along the altitudinal gradient. By contrast, N addition increased
 hyphal abundance at the lowest site, compared to significant reductions at
 2000 and 3000 m – not only in fungi but also in bacterial abundance as
 indicated by PLFA analyses, contradicting common soil‐age hypotheses.
 Decreased nutrient immobilization and fungal in‐growth at higher
 elevations suggest slow microbial activity, including nitrification, which
 may have caused toxic ammonium accumulation. 5.The experimental design
 offers a promising tool to provide more mechanistic and soil focused
 analyses specifically targeting microbes, which in this system strongly
 supported the hypothesis of primary fungal P limitation in tropical forest
 soils.
description: Data_Camenzind
 2019These data include all
 hyphal length counts presented in this manuscript, as well as PLFA data
 and "AM-like" hyphal length. Furthermore, cation, nitrogen and
 phosphorus content measured before and after the experiment in nutrient
 loaded mesh bags are reported.
DOI: 10.34740/kaggle/dsv/11885268
title: LLM RAG Chatbot Training Dataset
DOI: 10.15468/dl.jdu2q2
title: Occurrence Download

description: A dataset containing 177 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "DatasetKey is iNaturalist Research-grade Observations",
 "OccurrenceStatus is Present",
 "PublishingOrg is 28eb1a3f-1c15-4a95-931a-4af90ecb574d",
 "TaxonKey is Saxifraga adscendens L."
 ]
}

 The dataset includes 177 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009761-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.38a8p8
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Occurrence evidence",
 "TaxonKey is Podophyllum hexandrum Royle",
 "Year 1990-2025"
 ]
}

 The dataset includes 19 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009763-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/e231322
title: NCVAS State Summary Mississippi FY2019

description: Map and tables with data describing Mississippi's veteran population. Data tables cover: Veterans Affairs (VA) facilities and expenditures; veteran population including age distribution, period of service, household income, and educational attainment; veterans' use of VA healthcare and benefits; and projected veteran population changes as well as projections by age, age distribution over time, gender, period of service, and race/ethnicity.
DOI: 10.3886/e231322v1
title: NCVAS State Summary Mississippi FY2019

description: Map and tables with data describing Mississippi's veteran population. Data tables cover: Veterans Affairs (VA) facilities and expenditures; veteran population including age distribution, period of service, household income, and educational attainment; veterans' use of VA healthcare and benefits; and projected veteran population changes as well as projections by age, age distribution over time, gender, period of service, and race/ethnicity.
DOI: 10.15468/dl.hm8h9w
title: Occurrence Download

description: A dataset containing 196 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Daboia mauritanica"
 ]
}

 The dataset includes 196 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007544-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3ubn2c
title: Occurrence Download

description: A dataset containing 5871122 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Royal Botanic Gardens, Kew - Herbarium Specimens"
 ]
}

 The dataset includes 5871122 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007538-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.