cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r4g853s
title: Lack of spatial and temporal genetic structure of Japanese eel (Anguilla japonica) populations

description: Japanese eel (Anguilla japonica) is an important food source in East Asia
 whose population has dramatically declined since the 1970s. Despite past
 analysis with DNA sequencing, microsatellite and isozyme methods,
 management decisions remain hampered by contradictory findings. For
 example, it remains unresolved whether Japanese eels are a single
 panmictic population or whether they harbor significant substructure.
 Accurate assessment of population genetic substructure, both spatial and
 temporal, is essential for determining the relevant number of distinct
 management units appropriate for this species. In the present study, we
 assayed genetic variation genome-wide using Restriction Site Associated
 DNA Sequencing (RAD-seq) technology to analyze the population genetic
 structure of Japanese eels. For analysis of temporal isolation, five
 “cohort” samples were collected yearly from 2005 to 2009 in the Yangtze
 River Estuary. For analysis of spatial structure, five “arrival wave”
 samples were collected in China in 2009, and two arrival wave samples were
 collected in Japan in 2001. In each cohort of each arrival wave, five
 individuals were collected for a total of 55 eels sampled. In total,
 214,210 loci were identified from these individuals, 106,652 of which
 satisfied quality checks and were retained for further analysis. There was
 relatively little population differentiation between arrival waves and
 cohorts collected either at different locations during the same year
 (Fst = 0.077) or at the same location collected over subsequent years
 (Fst = 0.082), and locations displayed no consistent
 isolation-by-distance.
description: All analysis scripts can be found here:
 https://github.com/erdavenport/japaneseEel
DOI: 10.5061/dryad.1g30729
title: Data from: Increased diversity and concordant shifts in community structure of coral-associated Symbiodiniaceae and bacteria subjected to chronic human disturbance

description: Coral-associated bacteria and endosymbiotic algae (Symbiodiniaceae spp.)
 are both vitally important for the biological function of corals. Yet
 little is known about their co-occurrence within corals, how their
 diversity varies across coral species, or how they are impacted by
 anthropogenic disturbances. Here, we sampled coral colonies (n =
 472) from seven species, encompassing a range of life history traits,
 across a gradient of chronic human disturbance (n = 11 sites on Kiritimati
 (Christmas) atoll) in the central equatorial Pacific, and quantified the
 sequence assemblages and community structure of their associated
 Symbiodiniaceae and bacterial communities. Although Symbiodiniaceae alpha
 diversity did not vary with chronic human disturbance, disturbance was
 consistently associated with higher bacterial Shannon diversity and
 richness, with bacterial richness by sample almost doubling from sites
 with low to very high disturbance. Chronic disturbance was also associated
 with altered microbial beta diversity for Symbiodiniaceae and bacteria,
 including changes in community structure for both and increased variation
 (dispersion) of the Symbiodiniaceae communities. We also found concordance
 between Symbiodiniaceae and bacterial community structure, when all corals
 were considered together, and individually for two massive species,
 Hydnophora microconos and Porites lobata, implying that symbionts and
 bacteria respond similarly to human disturbance in these species. Finally,
 we found that the dominant Symbiodiniaceae ancestral lineage in a coral
 colony was associated with differential abundances of several distinct
 bacterial taxa. These results suggest that increased beta diversity of
 Symbiodiniaceae and bacterial communities may be a reliable indicator of
 stress in the coral microbiome, and that there may be concordant responses
 to chronic disturbance between these communities at the whole-ecosystem
 scale.
description: Claar_etal_2020_16S_data 16S bacterial sequencing data for Claar et al. 2020   Claar_etal_2020_ITS2_data ITS2 Symbiodiniaceae sequencing data for Claar et al. 2020
DOI: 10.5061/dryad.84sm048
title: Data from: The evolution of polymorphism in the warning coloration of the Amazonian poison frog Adelphobates galactonotus

description: While intraspecific variation in aposematic signals can be selected for by
 different predatory responses, their evolution is also contingent
 on other processes shaping genetic variation. We evaluate the relative
 contributions of selection, geographic isolation and random genetic drift
 to the evolution of aposematic color polymorphism in the poison
 frog Adelphobates galactonotus, distributed throughout
 eastern Brazilian Amazonia. Dorsal coloration was measured for 111
 individuals and genetic data were obtained from 220 individuals at two
 mitochondrial genes (mtDNA) and 7963 Single Nucleotide
 Polymorphisms (SNPs). Four color categories were described (brown, blue,
 yellow, orange) and our models of frog and bird visual systems indicated
 that each color was distinguishable for these taxa. Using outlier
 and correlative analyses we found no compelling genetic evidence for color
 being under divergent selection. A time-calibrated mtDNA tree
 suggests that the present distribution of dorsal coloration resulted from
 processes occurring during the Pleistocene. Separate phylogenies based on
 SNPs and mtDNA resolved the same well supported clades, each
 containing different colored populations. Ancestral character
 state analysis provided some evidence for evolutionary transitions in
 color type. Genetic structure was more strongly associated with geographic
 features, than color category, suggesting that the distribution of color
 is explained by localized processes. Evidence for geographic isolation
 together with estimates of low effective population size implicates drift
 as playing a key role in color diversification. Our results
 highlight the relevance of  considering the neutral processes
 involved with the evolution of traits with important fitness
 consequences.
description: Genomic DNA extracted from 186 tissue samples was sent to
 Diversity Array Tecnologies where SNP discovery and genotyping was
 performed using the standart DartSeq<sup>TM</sup> protocol.
 The provided dataset was further using the following criteria: We only
 included SNPs with a call rate of &gt;98 % (i.e. less than 2 % missing
 data), where the average read depth for both alleles was &gt;5 and the
 Minor Allele Frequency (MAF) &gt; 0.05. We retained only a single SNP
 per fragment to avoid creating a dataset containing closely linked loci.
 For analyses were populations with five or more samples.
description: Dataset containing: 1) Geographic coordinates of sampling
 locations. 2) <em>Adelphobates galactonotus</em> filtered
 SNPs.
DOI: 10.5061/dryad.1t918kf
title: Data from: Rearing temperature and fatty acid supplementation jointly affect lipid fluorescence polarization and heat tolerance in Daphnia

description: The homeoviscous adaptation hypothesis states that the relative abundance
 of polyunsaturated fatty acids (PUFAs) in membrane phospholipids of
 ectothermic organisms decreases with increasing temperatures to maintain
 vital membrane properties. We reared Daphnia magna at
 15°, 20°, and 25°C and increasing dietary concentrations of the long-chain
 PUFA eicosapentaenoic acid (EPA) to test the hypothesis that the
 well-documented increase in heat tolerance of
 high-temperature-reared Daphnia is due to a reduction in
 body PUFA concentrations. Heat tolerance was assessed by measuring the
 time to immobility at a lethally high temperature
 (T imm at 37°C), and whole body lipid fluorescence
 polarization (FP) was used as an estimate of membrane fluidity. At all
 rearing temperatures, EPA supplementation resulted in an increase in the
 relative abundance of EPA in body tissues, but only at 15° and 25°C did
 this result in a decrease in heat tolerance, and only at 20°C was this
 associated with an increase in membrane fluidity (i.e., decrease in FP).
 Overall, however, the degree of tissue fatty acid unsaturation correlated
 well with heat tolerance and FP. Our results support the homeoviscous
 adaptation hypothesis by showing that
 cold-reared Daphnia accumulate PUFAs within their body
 tissues and thus are more susceptible to heat than
 hot-reared Daphnia accumulating fewer PUFAs. However,
 our data also point out that further studies are required that elucidate
 the complex relationships between PUFA supply, membrane fluidity, and heat
 tolerance in ectotherms.
description: Column headings defined in a separate tab in each
 spreadsheet.
DOI: 10.5061/dryad.pj77fc4
title: Data from: Determinants of tree cover in tropical floodplains

description: In uplands, water availability and fire limit tree cover, differentiating
 between tropical forest, savanna, and grassland biomes. In contrast, we
 know less about tropical floodplain tree cover determinants, although
 these habitats similarly include near-treeless grasslands, moderately
 treed savannas, and forests. Using GIS and remotely sensed data from 13
 large tropical and sub-tropical floodplain ecosystems on five continents,
 we show that floodplain tree cover increases with climatic water balance
 (= rainfall - potential evapotranspiration) and decreases with frequent
 fire, as in uplands. Additionally, in floodplains, higher elevations and
 steeper slopes have higher tree cover, likely because these areas escape
 the worst inundation. Moreover, the effects of fire and topography are
 stronger in wetter regions. More prolonged and frequent flooding also
 reduce tree cover in climatically wetter floodplains but increase it in
 drier ones, although the effects are surprisingly weak compared to those
 of water balance, fire, and topography. Opposite to uplands, sandier soils
 have lower tree cover, likely because the benefits presented by deep tree
 roots in uplands are less important in floodplains with abundant water.
 While outright wetland conversion proceeds globally, floodplain tree cover
 faces other anthropogenic threats, like changing fire frequency and dam
 construction, especially in wet climates.
description: Global random forest
 model code for running the
 global random forest model in R. Will require a high-performance computing
 cluster. RandomForest_Global.R RandomForest_Regional Example random forest code for a single region's model. A high-performance computing cluster will be required to run the model.   Metadata Description of the datasets and R scripts provided, including explanation of variable names.   RegionalDatasets .csv files with the full set of tree cover and predictor values for each floodplain region. Variable names and explanations are given in the Metadata.docx file.
DOI: 10.5061/dryad.05qfttdz1
title: Data from: Dynamic pore structure evolution of the ion adsorbed rare earth ore during the ion exchange process

description: During the leaching process of the ion adsorbed rare earth ore, the pore
 structure evolution of the ore body plays a vital role in the seepage of
 the leaching solution. To investigate the evolution of the pore structure
 during the leaching process, experiments have been carried out with
 remodeled rare earth ore samples based on physical characteristics of
 in-situ ores. The seepage rate difference between deionized water leaching
 solution and 2% NH4Cl leaching solution during the active leaching period
 are analyzed. The porosity and the dynamic pore size evolution of pore
 structures in the ore body are discussed. Results indicate that along with
 ion exchange between the rare earth ore and the leaching solution, the
 porosity of the sample remains constant and the pore structure shows a
 decreasing trend in the first part and an increasing trend in the second
 part. Specifically, during the ion exchange process, the number of minimal
 pores (0~5μm), small pores (5~10μm), and medium pores (10~25μm) increases
 significantly and the number of medium-large pores (25~60μm), large pores
 (60~120μm), and mega pores (&gt;120μm) decreases dramatically. Along
 with the completion of the ion exchange process, the evolution of porous
 structure shows an opposite trend. The mechanism study reveals that the
 evolution of pore structure is induced by the difference of ionic strength
 in the leaching solution during the ion exchange process, where the rare
 earth ore microparticles will be absorbed or desorbed on to the solid
 phase.
DOI: 10.5061/dryad.0zpc866t5
title: Variation at an adhesin locus suggests sociality in natural populations of the yeast Saccharomyces cerevisiae

description: Microbes engage in numerous social behaviors that are critical for
 survival and reproduction, and that require individuals to act as a
 collective. Various mechanisms ensure that collectives are composed of
 related, cooperating cells, thus allowing for the evolution and stability
 of these traits, and for selection to favor traits beneficial to the
 collective. Since microbes are difficult to observe directly, sociality in
 natural populations can instead be investigated using evolutionary genetic
 signatures, as social loci can be evolutionary hotspots. The budding yeast
 has been studied for over a century, yet little is known about its social
 behavior in nature. Flo11 is a highly regulated cell adhesin required for
 most lab social phenotypes; studies suggest it may function in cell
 recognition and its heterogenous expression may be adaptive for
 collectives such as biofilms. We investigated this locus and found
 positive selection in the areas implicated in cell-cell interaction,
 suggesting selection for kin discrimination. We also found balancing
 selection at an upstream activation site, suggesting selection on the
 level of variegated gene expression. Our results suggest this model yeast
 is surprisingly social in natural environments and is likely engaging in
 various forms of sociality. By utilizing genomic data, this research
 provides a glimpse of otherwise unobservable interactions.
description: FLO11 Sequence Data, Length Variation, and Social Scores for
 Saccharomyces cerevisiae: These files contain curated
 sequence data for the FLO11 locus from the 78 environmental isolates of
 the budding yeast, <em>Saccharomyces cerevisiae</em>. The
 locus was sequenced using next gen sequencing technology and processed to
 create <em>de novo</em> assemblies. The fasta files contain
 the infered alleles and separate the data in the following way: (1) the
 upstream regulatory region, (2) the downstream regulatory region, (3) the
 A-domain alone, (4) the C-domain alone, and (5) the A-part of B-C domains
 concatenated. The csv file contains the length of the B domain (as
 determined by fragment analysis), the allele identity of the regulatory
 region, and raw social/biofilm scores.
DOI: 10.5061/dryad.k3j9kd53g
title: Data from: Non-crop features and heterogeneity mediate overwintering bird diversity in agricultural landscapes of Southwest China

description: Farmland birds are of conservation concerns around the world. In China,
 conservation management has focused primarily on natural habitats, whereas
 little attention has been given to agricultural landscapes. Although
 agricultural land use is intensive in China, environmental heterogeneity
 can be highly variable in some regions due to variations in crop and
 non-crop elements within a landscape. We examined how non-crop
 heterogeneity, crop heterogeneity and non-crop features (non-crop
 vegetation and water body such as open water) influenced species richness
 and abundance of all birds as well as three functional groups (woodland
 species, agricultural land species and agricultural wetland species) in
 the paddy-dominated landscapes of Erhai water basin situated in Northwest
 Yunnan, China. Birds, crop, and non-crop vegetation surveys in twenty 1 km
 × 1 km landscape plots were conducted during the winter season (from 2014
 to 2015). The results revealed that bird community compositions were best
 explained by amounts of non-crop vegetation and compositional
 heterogeneity of non-crop habitat (Shannon-Wiener index). Both variables
 also had a positive effect on richness and abundance of woodland species.
 Richness of agricultural wetland species increased with increasing areas
 of water bodies within the landscape plot. Richness of total species was
 also greater in the landscapes characterized by larger areas of water
 bodies, high proportion of non-crop vegetation, high compositional
 heterogeneity of non-crop habitat or small field patches (high crop
 configurational heterogeneity). Crop compositional heterogeneity did not
 show significant effects neither on the whole community (all birds) nor on
 any of the three functional groups considered. These findings suggest that
 total bird diversity and some functional groups, especially woodland
 species would benefit from increases in the proportion of non-crop
 features such as woody vegetation and water bodies as well as
 compositional heterogeneity of non-crop features within landscape.
DOI: 10.5061/dryad.hhmgqnkc6
title: Data from: Effects of condition and sperm competition risk on sperm allocation and storage in neriid flies

description: Ejaculate traits can be sexually selected and often exhibit heightened
 condition-dependence. However, the influence of sperm competition risk in
 tandem with condition-dependent ejaculate allocation strategies is
 relatively unstudied. Because ejaculates are costly to produce,
 high-condition males may be expected to invest more in ejaculates when
 sperm competition risk is greater. We examined the condition-dependence of
 ejaculate size by manipulating nutrient concentration in the juvenile
 (larval) diet of the neriid fly Telostylinus angusticollis. Using a fully
 factorial design we also examined the effects of perceived sperm
 competition risk (manipulated by allowing males to mate first or second)
 on the quantity of ejaculate transferred and stored in the three
 spermathecae of the female reproductive tract. To differentiate male
 ejaculates, we fed males non-toxic rhodamine fluorophores (which bind to
 proteins in the body) prior to mating, labelling their sperm red or green.
 We found that high-condition males initiated mating more quickly and, when
 mating second, transferred more ejaculate to both of the female’s
 posterior spermathecae. This suggests that males allocate ejaculates
 strategically, with high-condition males elevating their ejaculate
 investment only when facing sperm competition. More broadly, our findings
 suggest that ejaculate allocation strategies can incorporate variation in
 both condition and perceived risk of sperm competition.
description: This data set was collected in two blocks and represents a fully
 factorial experimental design. The main response variable is ejaculate
 amount from each spermatheca which was collected using confocal
 fluorescence microscopy (units arbitrary). 'Post1',
 'Post2' and 'Ant' represent measures taken from the
 posterior (1 and 2) and anterior spermathecae. 'Post1std' etc
 have been standardized as per the methods within the paper.
DOI: 10.15468/dl.uez3w4
title: Occurrence Download

description: A dataset containing 1750 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Gentianopsis thermalis"
 ]
}

 The dataset includes 1750 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001915-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0cfxpnvx2
title: Rheological and thermal degradation properties of hyperbranched polyisoprene prepared by anionic polymerisation

description: Hyperbranched polyisoprene was prepared by anionic copolymerisation under
 high vacuum condition. Size exclusion chromatography (SEC) was used to
 characterise the molecular weight and branching nature of these polymers.
 The characterisation by differential scanning calorimetry (DSC) and melt
 rheology indicated lower Tg and complex viscosity in the branched polymers
 as compared to the linear polymer. Degradation kinetics of these polymers
 was explored using thermogravimetric analysis (TGA) via non-isothermal
 techniques. The polymers were heated under nitrogen from ambient
 temperature to 600 °C using heating rates from 2, to 15 °C min-1. Three
 kinetics methods namely Friedman, Flynn–Wall–Ozawa (FWO) and
 Kissinger–Akahira–Sunose (KAS) were used to evaluate the dependence of
 activation energy (Ea) on conversion (α). The hyperbranched polyisoprene
 decomposed via multistep mechanism as manifested by the nonlinear
 relationship between α and Ea while the linear polymer exhibited a decline
 in Ea at higher conversions. The average Ea values range from 258 to 330
 kJmol-1 for the linear, and 260 to 320 kJmol-1 for the branched polymers.
 The thermal degradation of the polymers studied involved one-dimensional
 diffusion mechanism as determined by Coats–Redfern method.  This
 study may help in understanding the effect of branching on the rheological
 and decomposition kinetics of polyisoprene.
DOI: 10.15468/dl.yquk5d
title: Occurrence Download

description: A dataset containing 5222 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is one of (Elapidae, Viperidae)"
 ]
}

 The dataset includes 5222 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001914-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zj2zmm
title: Occurrence Download

description: A dataset containing 379 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Switzerland",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Emys orbicularis"
 ]
}

 The dataset includes 379 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001912-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.57b7jw
title: Occurrence Download

description: A dataset containing 9409 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Switzerland",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lacerta agilis"
 ]
}

 The dataset includes 9409 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001913-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.