cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4h6v0
title: Data from: Microbial consortia controlling biogenic gas formation in the Qaidam Basin of western China

description: Knowledge of what controls the activity of subsurface microbial
 communities is critical for assessing and managing biogenic methane
 resources. In this study, 19 formation waters and five gas samples were
 collected at depths of 800 to 1900 m from Quaternary biogenic gas fields
 of the Qaidam Basin, China. The formation waters were brines with chloride
 (Cl) concentrations from 1200 to 2700 mM. Bacterial 16S rRNA gene copies
 ranged from 3.75 × 104 to 2.23 × 106 copies mL−1 of water, and those of
 archaea ranged from 2.44 × 103 to 4.66 × 107 copies mL−1 of water. Both
 bacterial and archaea 16 s rRNA gene copies were negatively correlated
 with Cl concentration. The microbial community structure differed
 significantly depending on Cl concentrations. At high Cl waters
 (&gt;1800 mM), the microbial community showed a halophilic signature
 made up of several abundant taxonomic groups within Firmicules,
 γ-Proteobacteria, and methylotrophic Methanosarcinales. At low Cl,
 Firmicules and hydrogenotrophic methanogens were dominant members. The
 proportion of inferred hydrogenotrophic methanogens decreased from 89% to
 14% of total archaeal reads with increasing Cl concentration; in contrast,
 methylotrophic species increased from 11% to 85%. Given that the
 proportion of hydrogenotrophic species was positively correlated with the
 archaeal gene abundances, we suggest that Cl concentrations primarily
 constrain the activity of archaea catalyzing H2 reduction of CO2. Our
 results show that dilution of formation waters is critical in the process
 of biogenic gas formation, suggesting that an engineered decrease in Cl
 concentrations may induce methanogenesis as a potential method to increase
 gas reserves in such areas in the future.
description: shuai2014
DOI: 10.5061/dryad.136q467
title: Data from: Modelling bat distributions and diversity in a mountain landscape using focal predictors in ensemble of small models

description: Aim: Bats are important components of mammalian biodiversity and strong
 bioindicators, but their fine scale distributions often remain less known
 than other taxa (e.g. plants, birds). Yet as highly mobile species with
 multiple needs in the landscape, bats impose serious modelling challenges,
 such as advanced use of neighbourhood analyses. The aims of this study
 were to test the use of a designed sampling of bats for biodiversity and
 conservation assessments, and to find appropriate modelling solutions for
 providing nature practitioners with reliable potential bat distribution
 maps in a mountain area of high conservation interest . Location: The
 western Swiss Alps of Vaud Methods: We conducted a one-year field survey
 combining passive acoustic recordings supplemented by mist net catching to
 collect data on bats. These data were then used to create univariate
 models with focal land use/cover variables using different focal window
 sizes to detect the optimal species specific scale of influence for each
 variable. The large number of selected variables was then used to create
 ensembles of small models at a 100mx100m resolution, and the resulting
 habitat suitability maps were transformed into species distribution maps
 for practitioners. Results: We were able to collect data to model 14
 different bat species representing 66% of the Swiss bat diversity,
 including 4 red list species. In general, the most important variables
 were Euclidean distance to road or water, temperature and slope, but there
 was large variation among species both for the variable importance and the
 optimal focal window size. Main Conclusion: Our study greatly increased
 the knowledge of bats in this region and showed that many of the red list
 species are nowadays disappearing from the intensively used lowland plains
 and restricted to the remaining forests along the slopes . Additionally,
 we highlighted the importance of selecting the variable scale on a species
 specific basis accounting for their mobility and range sizes.
description: Data used for
 modellingThis archive contains
 the processed data used for modelling.Raw occurence
 dataThis file contains the
 data from both the acoustic sampling and capture of bats with additional
 information about locations, field experts and bio-metric data of the
 bats.
DOI: 10.5061/dryad.kv472
title: Data from: Genetic differences between willow warbler migratory phenotypes are few and cluster in large haplotype blocks

description: It is well established that differences in migratory behavior between
 populations of songbirds have a genetic basis but the actual genes
 underlying these traits remains largely unknown. In an attempt to identify
 such candidate genes we de novo assembled the genome of the willow warbler
 Phylloscopus trochilus, and used whole-genome resequencing and a SNP array
 to associate genomic variation with migratory phenotypes across two
 migratory divides around the Baltic Sea that separate SW migrating P. t.
 trochilus wintering in western Africa and SSE migrating P. t. acredula
 wintering in eastern and southern Africa. We found that the genomes of the
 two migratory phenotypes lack clear differences except for three highly
 differentiated regions located on chromosomes 1, 3, and 5 (containing 146,
 135, and 53 genes, respectively). Within each migratory phenotype we found
 virtually no differences in allele frequencies for thousands of SNPs, even
 when comparing geographically distant populations breeding in Scandinavia
 and Far East Russia (&gt;6000 km). In each of the three differentiated
 regions, multidimensional scaling-based clustering of SNP genotypes from
 more than 1100 individuals demonstrates the presence of distinct haplotype
 clusters that are associated with each migratory phenotype. In turn, this
 suggests that recombination is absent or rare between haplotypes, which
 could be explained by inversion polymorphisms. Whereas SNP alleles on
 chromosome 3 correlate with breeding altitude and latitude, the allele
 distribution within the regions on chromosomes 1 and 5 perfectly matches
 the geographical distribution of the migratory phenotypes. The most
 differentiated 10 kb windows and missense mutations within these
 differentiated regions are associated with genes involved in fatty acid
 synthesis, possibly representing physiological adaptations to the
 different migratory strategies. The ∼200 genes in these regions, of which
 several lack described function, will direct future experimental and
 comparative studies in the search for genes that underlie important
 migratory traits.
description: Supplementary
 dataZipped folder containing
 genome assembly, genome annotation file, repeats file, SNP array data set
 and associated scriptsSupplementary_data_dryad_ww.zip
DOI: 10.5061/dryad.mp935
title: Data from: The effect of demographic correlations on the stochastic population dynamics of perennial plants

description: Understanding the influence of environmental variability on population
 dynamics is a fundamental goal of ecology. Theory suggests that, for
 populations in variable environments, temporal correlations between
 demographic vital rates (e.g., growth, survival, reproduction) can
 increase (if positive) or decrease (if negative) the variability of
 year-to-year population growth. Because this variability generally
 decreases long-term population viability, vital rate correlations may
 importantly affect population dynamics in stochastic environments. Despite
 long-standing theoretical interest, it is unclear whether vital rate
 correlations are common in nature, whether their directions are
 predominantly negative or positive, and whether they are of sufficient
 magnitude to warrant broad consideration in studies of stochastic
 population dynamics. We used long-term demographic data for three
 perennial plant species, hierarchical Bayesian parameterization of
 population projection models, and stochastic simulations to address the
 following questions: (1) What are the sign, magnitude, and uncertainty of
 temporal correlations between vital rates? (2) How do specific pairwise
 correlations affect the year-to-year variability of population growth? (3)
 Does the net effect of all vital rate correlations increase or decrease
 year-to-year variability? (4) What is the net effect of vital rate
 correlations on the long-term stochastic population growth rate (λS)? We
 found only four moderate to strong correlations, both positive and
 negative in sign, across all species and vital rate pairs; otherwise,
 correlations were generally weak in magnitude and variable in sign. The
 net effect of vital rate correlations ranged from a slight decrease to an
 increase in the year-to-year variability of population growth, with
 average changes in variance ranging from -1% to +22%. However, vital rate
 correlations caused virtually no change in the estimates of λS (mean
 effects ranging from -0.01% to +0.17%). Therefore, the proportional
 changes in the variance of population growth caused by demographic
 correlations were too small on an absolute scale to importantly affect
 population growth and viability. We conclude that in our three focal
 populations and perhaps more generally, vital rate correlations have
 little effect on stochastic population dynamics. This may be good news for
 population ecologists, because estimating vital rate correlations and
 incorporating them into population models can be data-intensive and
 technically challenging.
description: DataScriptsResultsThis file contains the data and R scripts to: 1. fit vital rate models, 2. build population projection models, and 3. run stochastic simulations. The 'Results' directory also reports the results of vital rate models and simulations. Readme and metadata files are provided within the main, and 'Data' folders, respectively.
DOI: 10.5061/dryad.g3466
title: Data from: Underwater hyperspectral classification of deep sea corals exposed to 2-methylnaphthalene

description: Tropical corals are routinely monitored from satellite and aeroplane using
 remote sensing techniques, revealing the health of coral reefs. Notably,
 coral bleaching is continuously monitored using multi- or hyperspectral
 imagery from satellites and aeroplanes. For deep-water corals, however, no
 established remote sensing technique exists, and for this reason, much
 less is known about the status of their habitats over time. The purpose of
 the present work was to evaluate the use of underwater hyperspectral
 imaging to detect changes in health status of both orange and white color
 morphs of the coral species L. pertusa. In this study, we examine the
 feasibility of similar ecosystem health monitoring by the use of
 underwater hyperspectral imagery. A total of 66 coral samples were exposed
 to 2-methylnaphthalene concentrations from 0 mg L-1 to 3.5 mg L-1,
 resulting in corals of varying health condition. By use of a machine
 learning model for classification of reflectance spectra, we were able to
 classify exposed corals according to lethal concentration (LC) levels LC5
 (5% mortality) and LC25 (25% mortality). This is a first step in
 developing a remote sensing technique able to assess environmental impact
 on deep-water coral habitats over larger areas underwater.
description: spectral and
 healthExcel datasheet with all
 data for paper.df_spectral_and_health_plosone.xlsxspectral and healthAll data for the paper contained in a pandas dataframe saved as h5file.df_spectral_and_health_plosone.h5
DOI: 10.5061/dryad.fj0f8
title: Data from: MicroRNA stability in FFPE tissue samples: dependence on GC content

description: MicroRNAs (miRNAs) are small non-coding RNAs responsible for fine-tuning
 of gene expression at post-transcriptional level. The alterations in miRNA
 expression levels profoundly affect human health and often lead to the
 development of severe diseases. Currently, high throughput analyses, such
 as microarray and deep sequencing, are performed in order to identify
 miRNA biomarkers, using archival patient tissue samples. MiRNAs are more
 robust than longer RNAs, and resistant to extreme temperatures, pH, and
 formalin-fixed paraffin-embedding (FFPE) process. Here, we have compared
 the stability of miRNAs in FFPE cardiac tissues using next-generation
 sequencing. The mode read length in FFPE samples was 11 nucleotides (nt),
 while that in the matched frozen samples was 22 nt. Although the read
 counts were increased 1.7-fold in FFPE samples, compared with those in the
 frozen samples, the average miRNA mapping rate decreased from 32.0% to
 9.4%. These results indicate that, in addition to the fragmentation of
 longer RNAs, miRNAs are to some extent degraded in FFPE tissues as well.
 The expression profiles of total miRNAs in two groups were highly
 correlated (0.88
description: Human cardiac miRNA
 sequencing of paired frozen and FFPE samplesMicroRNA deep sequencing
 of human cardiac tissues. 3 pairs of fresh and formalin-fixed
 paraffin-embedded (FFPE) samples are analyzed by Ion PGM
 system.MiRNA
 Seq.zip
DOI: 10.5061/dryad.v0c77
title: Data from: Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes

description: The spatial structure of the environment (e.g., the configuration of
 habitat patches) may play an important role in determining the strength of
 local adaptation. However, previous studies of habitat heterogeneity and
 local adaptation have largely been limited to simple landscapes, which
 poorly represent the multi-scale habitat structure common in nature. Here,
 we use simulations to pursue two goals: (1) we explore how landscape
 heterogeneity, dispersal ability, and selection affect the strength of
 local adaptation, and (2) we evaluate the performance of several
 genotype-environment association (GEA) methods for detecting loci involved
 in local adaptation. We found that the strength of local adaptation
 increased in spatially aggregated selection regimes, but remained strong
 in patchy landscapes when selection was moderate to strong. Weak selection
 resulted in weak local adaptation that was relatively unaffected by
 landscape heterogeneity. In general, the power of detection methods
 closely reflected levels of local adaptation. False positive rates (FPRs),
 however, showed distinct differences across GEA methods based on levels of
 population structure. The univariate GEA approach had high FPRs (up to
 55%) under limited dispersal scenarios, due to strong isolation by
 distance. By contrast, multivariate, ordination-based methods had
 uniformly low FPRs (0-2%), suggesting these approaches can effectively
 control for population structure. Specifically, constrained ordinations
 had the best balance of high detection and low FPRs, and will be a useful
 addition to the GEA toolkit. Our results provide both theoretical and
 practical insights into the conditions that shape local adaptation and how
 these conditions impact our ability to detect selection.
description: Simulation
 dataThe final generation
 (generation 1250) of each simulation run and replicate. Simulations are
 divided into no selection simulations ("Nsims"), gradient
 selection simulations ("Gsims"), and discrete selection
 simulations ("H1/H5/H9sims").Simulations.zipSelection surfaces and sampling fileOne of the gradient selection files ("gradient1024x1024_N0_S1.txt") and a full set of habitat configuration rasters (H1/H5/H9 with 10 replicates each). The 500 randomly sampled individuals are provided in "sample500.csv".Surfaces_Sample.zip
DOI: 10.5061/dryad.771gr
title: Data from: Four rodent and vole biodiversity models for Europe

description: The mechanisms underlying associations between rodent diversity and the
 spread of rodent borne diseases are still unclear. The number of potential
 host species may influence a disease by either spreading the pathogen (or
 vectors) more rapidly or conversely by reducing contact with other hosts
 through the effects of dilution. In either case the number of potential
 hosts may impact on the distribution of a disease or its vectors. Four
 spatially modelled indices of rodent species richness have been generated
 to support distribution modelling of rodent borne diseases specifically
 initially focussing on Hantaviruses and tick borne diseases.
description: Vole Biodiversity
 LayersFour rodent and vole
 biodiversity index predicted distribution maps have been generated to
 support investigations on how species richness can affect the spread of
 Hantavirus and Tick Borne Virus (TBV).volebiodivv2.zip
DOI: 10.15468/dl.rb237u
title: Occurrence Download

description: A dataset containing 348 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ambystoma rivulare"
 ]
}

 The dataset includes 348 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000371-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pf4b7
title: Data from: Conserved genetic architecture underlying recombination rate variation in a wild population of Soay sheep (Ovis aries)

description: Meiotic recombination breaks down linkage disequilibrium and forms new
 haplotypes, meaning that it is an important driver of diversity in
 eukaryotic genomes. Understanding the causes of variation in recombination
 rate is important in interpreting and predicting evolutionary phenomena
 and for understanding the potential of a population to respond to
 selection. However, despite attention in model systems, there remains
 little data on how recombination rate varies at the individual level in
 natural populations. Here, we used extensive pedigree and high-density SNP
 information in a wild population of Soay sheep (Ovis aries) to investigate
 the genetic architecture of individual autosomal recombination rate.
 Individual rates were high relative to other mammal systems, and were
 higher in males than in females (autosomal map lengths of 3748 cM and 2860
 cM, respectively). The heritability of autosomal recombination rate was
 low but significant in both sexes (h2 = 0.16 & 0.12 in females and
 males, respectively). In females, 46.7% of the heritable variation was
 explained by a sub-telomeric region on chromosome 6; a genome-wide
 association study showed the strongest associations at the locus RNF212,
 with further associations observed at a nearby ~374kb region of complete
 linkage disequilibrium containing three additional candidate loci, CPLX1,
 GAK and PCGF3. A second region on chromosome 7 containing REC8 and RNF212B
 explained 26.2% of the heritable variation in recombination rate in both
 sexes. Comparative analyses with 40 other sheep breeds showed that
 haplotypes associated with recombination rates are both old and globally
 distributed. Both regions have been implicated in rate variation in mice,
 cattle and humans, suggesting a common genetic architecture of
 recombination rate variation in mammals.
description: GENETICS_2015_185553_dataConserved genetic architecture underlying recombination rate variation in a wild population of Soay sheep (Ovis aries).
DOI: 10.15468/dl.hzsbzn
title: Occurrence Download

description: A dataset containing 1254 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhynchopsitta pachyrhyncha"
 ]
}

 The dataset includes 1254 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000370-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.69t48k87
title: Data from: Comparative transcriptomics and gene expression in larval tiger salamander (Ambystoma tigrinum) gill and lung tissues as revealed by pyrosequencing

description: Biologists are beginning to unravel the complexities of gene expression in
 model organisms by studying the transcriptome, the complement of genes
 that are transcribed in a given tissue. It is unclear, however, if
 findings from model systems apply to non-model organisms because of
 environmental effects on gene expression. Furthermore, there have been few
 efforts to quantify how transcriptome or gene expression varies across
 individuals and across tissues in natural environments. Herein, we
 describe transcriptomic profiling of gene expression in lung and gill
 tissue of three larval tiger salamanders. We do so with a hierarchical
 experimental design that captures variation in expression among genes,
 among tissues, and among individuals. Using 454 pyrosequencing, we
 produced high-quality sequence data of 59 megabases and assembled ~200,000
 reads into 19,501 contigs. These contigs BLASTed to 3,599 transcripts, of
 which 721 were expressed in both tissues, 1,668 were unique to gill, and
 1,210 unique to lung. Our data showed tissue-specific patterns in gene
 expression level with variation among transcripts and individuals. We
 identified genes and gene ontology terms related to respiration and
 compared their relative expression levels between gill and lung tissues.
 We also found evidence of exogenous genes associated with larval
 salamanders, and we identified ~1400 potential molecular markers
 (microsatellites and single nucleotide polymorphisms) that are associated
 with expressed genes. Given the tissue-specific differences we observed in
 transcriptomes, these data reinforce the idea that changes in gene
 expression serve as a primary mechanism underlying phenotypic plasticity.
description: TigerSalamanderLarvae_RawFilesFrom454TigerSalamanderLarvae_ContigFromPCAPThis is a .zip-compressed file, containing contig sequences (fasta format) produced by PCAP analysis (.fasta files).TigerSalamanderLarvae_TopBlastThis is a .zip-compressed file, containing information on top blast (Blastx and tBlastx) analysis for each contig (.txt files).