cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1qc3q
title: Data from: Mitochondrial–nuclear epistasis affects fitness within species but does not contribute to fixed incompatibilities between species of Drosophila

description: Efficient mitochondrial function requires physical interactions between
 the proteins encoded by the mitochondrial and nuclear genomes. Coevolution
 between these genomes may result in the accumulation of incompatibilities
 between divergent lineages. We test whether mitochondrial–nuclear
 incompatibilities have accumulated within the Drosophila melanogaster
 species subgroup by combining divergent mitochondrial and nuclear lineages
 and quantifying the effects on relative fitness. Precise placement of nine
 mtDNAs from D. melanogaster, D. simulans, and D. mauritiana into two D.
 melanogaster nuclear genetic backgrounds reveals significant
 mitochondrial–nuclear epistasis affecting fitness in females. Combining
 the mitochondrial genomes with three different D. melanogaster X
 chromosomes reveals significant epistasis for male fitness between
 X-linked and mitochondrial variation. However, we find no evidence that
 the more than 500 fixed differences between the mitochondrial genomes of
 D. melanogaster and the D. simulans species complex are incompatible with
 the D. melanogaster nuclear genome. Rather, the interactions of largest
 effect occur between mitochondrial and nuclear polymorphisms that
 segregate within species of the D. melanogaster species subgroup. We
 propose that a low mitochondrial substitution rate, resulting from a low
 mutation rate and/or efficient purifying selection, precludes the
 accumulation of mitochondrial–nuclear incompatibilities among these
 Drosophila species.
description: mitofitnessFinalCDMExcel file with fitness scores from mitonuclear genotypes
DOI: 10.5061/dryad.7kn53
title: Data from: Conditional vulnerability of plant diversity to atmospheric nitrogen deposition across the United States

description: Atmospheric nitrogen (N) deposition has been shown to decrease plant
 species richness along regional deposition gradients in Europe and in
 experimental manipulations. However, the general response of species
 richness to N deposition across different vegetation types, soil
 conditions, and climates remains largely unknown even though responses may
 be contingent on these environmental factors. We assessed the effect of N
 deposition on herbaceous richness for 15,136 forest, woodland, shrubland,
 and grassland sites across the continental United States, to address how
 edaphic and climatic conditions altered vulnerability to this stressor. In
 our dataset, with N deposition ranging from 1 to 19 kg N⋅ha−1⋅y−1, we
 found a unimodal relationship; richness increased at low deposition levels
 and decreased above 8.7 and 13.4 kg N⋅ha−1⋅y−1 in open and closed-canopy
 vegetation, respectively. N deposition exceeded critical loads for loss of
 plant species richness in 24% of 15,136 sites examined nationwide. There
 were negative relationships between species richness and N deposition in
 36% of 44 community gradients. Vulnerability to N deposition was
 consistently higher in more acidic soils whereas the moderating roles of
 temperature and precipitation varied across scales. We demonstrate here
 that negative relationships between N deposition and species richness are
 common, albeit not universal, and that fine-scale processes can moderate
 vegetation responses to N deposition. Our results highlight the importance
 of contingent factors when estimating ecosystem vulnerability to N
 deposition and suggest that N deposition is affecting species richness in
 forested and nonforested systems across much of the continental United
 States.
description: Simkin_et_al_2016_data_from_PNAS_Diversity_and_N_depositionEach row in the "Simkin_et_al_2016_data_from_PNAS_Div_and_N_dep.csv" dataset represents one of 15,136 sites, and each of the 16 columns is a separate variable. The "README.csv" file contains descriptions corresponding to the 16 column header names, including the site coordinates (latitude and longitude), the response variable (species richness), the environmental variables (niitrogen deposition, precipitation, temperature, and pH), the output variables (critical loads of nitrogen with 95% confidence interval, as well as corresponding exceedance values), and assorted vegetation classification and data source variables. The "README.csv" also has further details about the multiple vegetation data sources corresponding to the abbreviated values in the "proj_orig" variable. The description of vegetation data sources is a text file adaptation of Table S1 in the Supplemental Material of Simkin et al. 2016 in the PNAS paper.Simkin_et_al_2016_data_from_PNAS_Div_and_N_dep.csv
DOI: 10.5061/dryad.fc324
title: Data from: Counting cats: spatially explicit population estimates of cheetah (Acinonyx jubatus) using unstructured sampling data

description: Many ecological theories and species conservation programmes rely on
 accurate estimates of population density. Accurate density estimation,
 especially for species facing rapid declines, requires the application of
 rigorous field and analytical methods. However, obtaining accurate density
 estimates of carnivores can be challenging as carnivores naturally exist
 at relatively low densities and are often elusive and wide-ranging. In
 this study, we employ an unstructured spatial sampling field design along
 with a Bayesian sex-specific spatially explicit capture-recapture (SECR)
 analysis, to provide the first rigorous population density estimates of
 cheetahs (Acinonyx jubatus) in the Maasai Mara, Kenya. We estimate adult
 cheetah density to be between 1.22 ± 0.301 and 1.28 ± 0.322
 individuals/100km2 across four candidate models specified in our analysis.
 Our spatially explicit approach revealed 'hotspots' of cheetah
 density, highlighting that cheetah are distributed heterogeneously across
 the landscape. The SECR models incorporated a movement range parameter
 which indicated that male cheetah moved four times as much as females,
 possibly because female movement was restricted by their reproductive
 status and/or the spatial distribution of prey. We show that SECR can be
 used for spatially unstructured data to successfully characterise the
 spatial distribution of a low density species and also estimate population
 density when sample size is small. Our sampling and modelling framework
 will help determine spatial and temporal variation in cheetah densities,
 providing a foundation for their conservation and management. Based on our
 results we encourage other researchers to adopt a similar approach in
 estimating densities of individually recognisable species.
description: maracheetahCHFile with the location and sampling occasion for each cheetah that was sighted during the sampling periodmaracheetahEffortThe amount of effort (in log(kilometers)) per grid cell (rows) for each sampling occasion (days in columns)maracheetahHabitatSuitable (1) and unsuitable (0) habitat within the study areamaracheetahSexThe ID and sex (1 = male and 0 = female) of each cheetah sighted during the sampling periodmaracheetahTrapsGrid cells (incl coordinates in UTM) where a cheetah was sighted during a particular sampling occasion
DOI: 10.15468/dl.saxpvf
title: Occurrence Download

description: A dataset containing 2377 records in GBIF matching the query:
SELECT
 '413' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 37.42857426825602
 AND decimalLatitude &lt;= 41.89415215079384
 AND decimalLongitude &gt;= 57.564121794054664
 AND decimalLongitude &lt;= 65.93482227598784
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 2377 records were derived from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001416-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.58tswd
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Himalrandia lichiangensis"
 ]
}

 The dataset includes 49 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001443-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7f368
title: Data from: Behavioural response to combined insecticide and temperature stress in natural populations of Drosophila melanogaster

description: Insecticide resistance evolves extremely rapidly, providing an
 illuminating model for the study of adaptation. With climate change
 reshaping species distribution, pest and disease vector control needs
 rethinking to include the effects of environmental variation and insect
 stress physiology. Here we assessed how both long term adaptation of
 populations to temperature and immediate temperature variation affects the
 genetic architecture of DDT insecticide response in Drosophila
 melanogaster. Mortality assays and behavioral assays based on continuous
 activity monitoring were used to assess the interaction between DDT and
 temperature on three field-derived populations from climate extremes
 (Raleigh for warm temperate, Tasmania for cold oceanic and Queensland for
 hot tropical). The Raleigh population showed the highest mortality to DDT
 whereas the Queensland population, epicentre for derived alleles of the
 resistance gene Cyp6g1, showed the lowest. Interaction between insecticide
 and temperature strongly affected mortality, particularly for the
 Tasmanian population. Activity profiles analyzed using self-organizing
 maps show the insecticide promoted an early response while elevated
 temperature promoted a later response. These distinctive early or later
 activity phases revealed similar responses to temperature and DDT dose
 alone but with more or less genetic variance depending on the population.
 This change in genetic variance among populations suggests that selection
 particularly depleted genetic variance for DDT response in the Queensland
 population. Finally, despite similar (co)variation between traits in
 benign conditions, the genetic responses across population differed under
 stressful conditions. This showed how stress-responsive genetic variation
 only reveals itself in specific conditions and thereby escapes potential
 trade-offs in benign environments.
description: Fournier-Leveletal2016_JEB_DataArchiveData archive and analysis script in the R programming language
DOI: 10.5061/dryad.t402g
title: Data from: Posterior parietal cortex drives inferotemporal activations during three-dimensional object vision

description: The primate visual system consists of a ventral stream, specialized for
 object recognition, and a dorsal visual stream, which is crucial for
 spatial vision and actions. However, little is known about the
 interactions and information flow between these two streams. We
 investigated these interactions within the network processing
 three-dimensional (3D) object information, comprising both the dorsal and
 ventral stream. Reversible inactivation of the macaque caudal
 intraparietal area (CIP) during functional magnetic resonance imaging
 (fMRI) reduced fMRI activations in posterior parietal cortex in the dorsal
 stream and, surprisingly, also in the inferotemporal cortex (ITC) in the
 ventral visual stream. Moreover, CIP inactivation caused a perceptual
 deficit in a depth-structure categorization task. CIP-microstimulation
 during fMRI further suggests that CIP projects via posterior parietal
 areas to the ITC in the ventral stream. To our knowledge, these results
 provide the first causal evidence for the flow of visual 3D information
 from the dorsal stream to the ventral stream, and identify CIP as a key
 area for depth-structure processing. Thus, combining reversible
 inactivation and electrical microstimulation during fMRI provides a
 detailed view of the functional interactions between the two visual
 processing streams.
description: openData_newxls files contain percent signal change per run.img/hdr files show tvalues for contrasts see readme.txt for more information
DOI: 10.5061/dryad.5145k
title: Data from: How many broadleaved trees are enough in conifer plantations? The economy of land sharing, land sparing, and quantitative targets

description: 1. For biodiversity conservation to be an effective and significant social
 investment, non-marketed values of biodiversity conservation and its
 associated opportunity costs should be evaluated in monetary terms. 2. In
 this study, we measured the willingness to pay (WTP) for bird abundance
 using a choice experiment (CE) based on the random utility model. We
 performed a cost–benefit analysis to identify the optimal proportion of
 broad-leaved trees in conifer plantations on a volume basis to maximize
 the social benefits of bird conservation and wood production. 3. The
 results suggested that respondents to the CE were not satisfied with their
 current situation and preferred an increase in bird abundance. However,
 the estimated WTP indicated diminishing returns of bird conservation. More
 specifically, WTP first greatly increased before gradually experiencing
 decreasing marginal values, reaching its peak, and finally decreasing
 slightly with increasing bird abundance. 4. Optimization analyses
 indicated that when the relation between bird abundance and broad-leaved
 tree proportion was convex, semi-natural plantations with non-zero
 broad-leaved tree proportion (0.02–0.22) were always optimal options. When
 the relation was linear, optimal broad-leaved tree proportion ranged from
 0 to 0.78 and was greatly affected by wood values. When the relation was
 concave, there were only two optimal broad-leaved tree proportions: a very
 high proportion (approximately 0.90) and the lowest possible proportion
 (0). When the convex and concave relations approached the linear form,
 comparable benefits could be attained across broad ranges of broad-leaved
 tree proportion both within and across the relations. In such cases, it
 would be useful to increase the likelihood of a feasible land-use strategy
 of either land sparing or land sharing in order to be successful. 5.
 Synthesis and applications. It can be difficult to set quantitative
 targets in biodiversity conservation solely on an ecological basis, and
 social benefits of biodiversity conservation can create diminishing
 returns in many situations. The framework we proposed shows how to
 reconcile resource production and biodiversity conservation in the real
 world.
description: Original data obtained
 from the choice experimentBird_2014_CE.xlsxTransformed data for the analysis of STATABird_2014_CE_STATA.dtaCommand used in the analysis of STATASTATA_Command.txt
DOI: 10.15468/dl.6v3rvt
title: Occurrence Download

description: A dataset containing 369 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "TaxonKey is Chazara prieuri"
 ]
}

 The dataset includes 369 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001442-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k83b3
title: Data from: Genome-wide screening of candidate genes for improving fertility in Egyptian native Rahmani sheep

description: [No description entered]
description: raw SNP data_Rahmani
 sheep
DOI: 10.15468/dl.2tm678
title: Occurrence Download

description: A dataset containing 248 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is List of herbs, grasses, and sedges collected in Guindy National Park, Chennai in 1992"
 ]
}

 The dataset includes 248 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001446-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.61jq1
title: Data from: Spatial and temporal variability in propagule limitation of California native grasses

description: Community composition and diversity arise from limitations in propagule
 supply (i.e. propagule or seed limitation) and propagule establishment
 after arriving at a site (i.e. establishment or microsite limitation).
 Recent meta-analyses suggest that the degree of propagule limitation
 depends on local abiotic and biotic conditions, which in turn are likely
 to vary spatially and temporally. Nevertheless, seed addition studies
 testing propagule limitation are rarely replicated in multiple locations
 and years and often lack experimental manipulations of critical
 determinants of propagule limitation, such as the density and species
 richness of the propagule pool and disturbance and resource supply of
 recipient site. The invasion of California (USA) grasslands by exotic
 annual species from the Mediterranean region is unique in its scope (over
 9 million ha) and persistence (more than 150 years). This invasion
 provides an exciting context in which to test the role of spatial and
 temporal variability in mediating propagule limitation and ultimately the
 potential for restoration. Here I present the results of native-grass,
 seed-addition trials conducted along a 500 km gradient in California in
 three consecutive years spanning a wide range of environmental conditions
 and initial conditions (e.g. rainfall, seeding density and disturbance).
 While native grasses were able to establish at many locations, per capita
 seed survival was low suggesting that the fate of these species is
 governed by interplay between propagule and establishment limitation.
 Establishment primarily varied spatially, with the most successful
 establishment occurring at fertile locations with low resident species
 richness. While recruitment was highly variable among years initially,
 there was no difference among seedling trials after three years.
description: seed-add-data-output-file-descriptionsDescription of remaining data files. Additional publication associated with these data : Brandt, Angela J., and Eric W. Seabloom. "Regional and decadal patterns of native and exotic plant coexistence in California grasslands." Ecological Applications 21.3 (2011): 704-714.seed-add-data-output-biomassseed-add-data-output-block-soilsContains data on soil chemistry of each blockseed-add-data-output-full-plant-biomass-noseedseed-add-data-output-full-plant-coverseed-add-data-output-full-plant-cover-noseedseed-add-data-output-plot-utmsseed-add-data-output-taxa-table-biomassContains data on each individual taxa in the biomass data setseed-add-data-output-taxa-table-coverContains data on each individual taxa in the cover data set
DOI: 10.5061/dryad.540q6
title: Data from: Fossilization of melanosomes via sulfurization

description: Fossil melanin granules (melanosomes) are an important resource for
 inferring the evolutionary history of colour and its functions in animals.
 The taphonomy of melanin and melanosomes, however, is incompletely
 understood. In particular, the chemical processes responsible for
 melanosome preservation have not been investigated. As a result, the
 origins of sulfur-bearing compounds in fossil melanosomes are difficult to
 resolve. This has implications for interpretations of original colour in
 fossils based on potential sulfur-rich phaeomelanosomes. Here we use
 pyrolysis gas chromatography mass spectrometry (Py-GCMS), fourier
 transform infrared spectroscopy (FTIR) and time of flight secondary ion
 mass spectrometry (ToF-SIMS) to assess the mode of preservation of fossil
 microstructures, confirmed as melanosomes based on the presence of
 melanin, preserved in frogs from the Late Miocene Libros biota (NE Spain).
 Our results reveal a high abundance of organosulfur compounds and
 non-sulfurized fatty acid methyl esters in both the fossil tissues and
 host sediment; chemical signatures in the fossil tissues are inconsistent
 with preservation of phaeomelanin. Our results reflect preservation via
 the diagenetic incorporation of sulfur, i.e. sulfurization (natural
 vulcanization), and other polymerization processes. Organosulfur compounds
 and/or elevated concentrations of sulfur have been reported from
 melanosomes preserved in various invertebrate and vertebrate fossils and
 depositional settings, suggesting that preservation through sulfurization
 is likely to be widespread. Future studies of sulfur-rich fossil
 melanosomes require that the geochemistry of the host sediment is tested
 for evidence of sulfurization in order to constrain interpretations of
 potential phaeomelanosomes and thus of original integumentary colour in
 fossils.
description: SEM image of fossil
 melanosomesfossil_001.tifSEM image of fossil melanosomesfossil_006.tifSEM image of fossil melanosomesfossil_007.tifTEM image of fossil melanosomes (stained section)gen4.tifTEM image of fossil melanosomes (stained section)cu1.tifTEM image of fossil melanosomes (unstained section)NN1b.tifTEM image of unstained fossil melanosomes (unstained section)LL2B.tifSEM image of fossil melanosomesD4d_q00.jpg