cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kd4jq6h
title: Data from: Insights into the genetic basis of blueberry fruit-related traits using diploid and polyploid models in a GWAS context

description: Polyploidization is an ancient and recurrent process in plant evolution,
 impacting the diversification of natural populations and plant breeding
 strategies. Polyploidization occurs in many important crops; however, its
 effects on inheritance of many agronomic traits are still poorly
 understood compared with diploid species. Higher levels of allelic dosage
 or more complex interactions between alleles could affect the phenotype
 expression. Hence, the present study aimed to dissect the genetic basis of
 fruit-related traits in autotetraploid blueberries and identify candidate
 genes affecting phenotypic variation. We performed a genome-wide
 association study (GWAS) assuming diploid and tetraploid inheritance,
 encompassing distinct models of gene action (additive, general, different
 orders of allelic interaction and the corresponding diploidized models). A
 total of 1,575 southern highbush blueberry individuals from a breeding
 population of 117 full-sib families were genotyped using sequence capture
 and next-generation sequencing, and evaluated for eight fruit-related
 traits. For the diploid allele calling, 77,496 SNPs were detected; while
 80,591 SNPs were obtained in tetraploid, with a high degree of overlap
 (95%) between them. A linear mixed model that accounted for population and
 family structure was used for the GWAS analyses. By modeling tetraploid
 genotypes, we detected 15 SNPs significantly associated with five
 fruit-related traits. Alternatively, seven significant SNPs were detected
 for only two traits using diploid genotypes, with two SNPs overlapping
 with the tetraploid scenario. Our results showed that the importance of
 tetraploid models varied by trait and that the use of diploid models has
 hindered the detection of SNP-trait associations and, consequently, the
 genetic architecture of some commercially important traits in
 autotetraploid species. Furthermore, 14 SNPs co-localized with candidate
 genes, five of which lead to non-synonymous amino acid changes. The
 potential functional significance of these SNPs is discussed.
description: Diploid and Tetraploid
 data used for GWAS analysis in blueberryThis dataset contains
 the genotypic and phenotypic information used in the manuscript
 "Insights into the genetic basis of blueberry fruit-related traits
 using diploid and polyploid models in a GWAS context". In the
 original manuscript, a blueberry breeding population was genotyped and
 phenotyped for eight traits - weight, size, firmness, stem scar diameter,
 pH, soluble solids content, flower bud density, and yield. Genotypic data
 (SNPs) are stored in two .csv files (tetraploid and diploid
 parameterizations, called using the FreeBayes software). Phenotype data
 for both parameterizations are also stored in two .csv files. For more
 details, see Ferrão et al., 2018.data_set.zip
DOI: 10.5061/dryad.0hm4r
title: Data from: Detecting epistasis from an ensemble of adapting populations

description: The role that epistasis plays during adaptation remains an outstanding
 problem, which has received considerable attention in recent years. Most
 of the recent empirical studies are based on ensembles of replicate
 populations that adapt in a fixed, laboratory controlled condition.
 Researchers often seek to infer the presence and form of epistasis in the
 fitness landscape from the time-evolution of various statistics averaged
 across the ensemble of populations. Here we provide a rigorous analysis of
 what quantities, drawn from time-series of such ensembles, can be used to
 infer epistasis for populations evolving under weak mutation on
 finite-site fitness landscapes. First we analyze the mean fitness
 trajectory—that is, the time course of the ensemble average fitness. We
 show that for any epistatic fitness landscape and starting genotype, there
 always exists a non-epistatic fitness landscape that produces the exact
 same mean fitness trajectory. Thus, the presence of epistasis is not
 identifiable from the mean fitness trajectory. By contrast, we show that
 two other ensemble statistics—the time evolution of the fitness variance
 across populations, and the time evolution of the mean number of
 substitutions—can detect certain forms of epistasis in the underlying
 fitness landscape.
description: Mathematica notebook
 used to make NK landscapesThis is a Mathematica
 notebook containing code to construct NK landscapes and the corresponding
 mean fitness trajectories.McCandlishEtAl_MakeNK.nbNK landscapes with N=10 and K=11000 NK landscapes with N=10 and K=1. Comma separated values. First line gives genotypes as binary strings; each subsequent line corresponds to one fitness landscape and gives the fitness values for each genotype. Mean fitness trajectories were calculated starting from the genotype with all sites equal to zero.N_10_K_1.csvNK landscapes with N=10 and K=21000 NK landscapes with N=10 and K=2. Comma separated values. First line gives genotypes as binary strings; each subsequent line corresponds to one fitness landscape and gives the fitness values for each genotype. Mean fitness trajectories were calculated starting from the genotype with all sites equal to zero.N_10_K_2.csvNK landscapes with N=10 and K=91000 NK landscapes with N=10 and K=9. Comma separated values. First line gives genotypes as binary strings; each subsequent line corresponds to one fitness landscape and gives the fitness values for each genotype. Mean fitness trajectories were calculated starting from the genotype with all sites equal to zero.N_10_K_9.csv
DOI: 10.5061/dryad.8t5d4
title: Data from: Prioritizing sites for ecological restoration based on ecosystem services

description: 1. Restoration ecology is moving towards designing restoration actions to
 maximize ecosystem services (ES). Such restoration actions require
 planning at large spatial scales, as these are often more meaningful for
 ecosystem functioning and ES supply. As economic resources to undertake
 ecological restoration at large scales are scarce, prioritizing sites to
 enhance multiple ES supply is critical. 2. Our study presents an index,
 the Relative Aggregated Value of ES (RAVES), to prioritize sites for
 ecological restoration based on the assessment of multiple ES. We tested
 the spatial heterogeneity of ES to identify the relevant scale to managing
 ES and to applying the RAVES index using a local case study. We also used
 the RAVES index to compare three alternative restoration scenarios to
 enhance ES based on the availability of socio-economic resources. 3. The
 highest RAVES values were found in areas with natural vegetation and in
 gorges with riparian forests. The lowest RAVES values were found in crop
 fields, steep slopes, and river stretches without riparian forest. 4. The
 multi-scale spatial analysis indicated that most ES showed significant
 heterogeneity at multiple spatial scales, especially at broad (20–30 km)
 and very broad (40–50 km) scales. However, at spatial scales smaller than
 2 km, only biological control showed significant heterogeneity. 5. The
 optimal socio-economic conditions to enhance ES supply were met in a
 scenario where both private and public land and economic funds were
 available to implement ecological restoration. As most areas with low
 RAVES were in private lands, even with scarce economic funds restoration
 of private lands would result in a large increase of RAVES. 6. Synthesis
 and applications. The RAVES index is a practical tool to hierarchically
 prioritize sites for ecological restoration across large spatial scales.
 When linked to scenario analysis, the RAVES index can also be used to
 identify optimal management scenarios. By linking ES assessments to the
 identification of the spatial scales at which ES show largest
 heterogeneity, our analyses can help decision-makers identifying the
 spatial scale at which ES are more likely to respond to management and
 highlight the need to integrate local and regional management
 plans.09-Nov-2017
description: Table S4. Average ES
 values for each LULC type.Average ES values for
 each LULC type. (See Table S1 for the description of the LULC types and
 Table S2 for units).Table
 S4.docxTable S1. Description of
 Land Use Land Cover (LULC) types identified at the River Piedra
 watershed.Description of Land Use
 Land Cover (LULC) types identified at the River Piedra
 watershed.Table
 S1.docxTable S2.Ecosystem
 services assessed, indicators and source of information.Ecosystem services
 assessed, indicators and source of information.Table
 S2_ok.docx
DOI: 10.5061/dryad.760r5b6
title: Data from: Deep neural networks for accurate predictions of crystal stability

description: Predicting the stability of crystals is one of the central problems in
 materials science. Today, density functional theory (DFT) calculations
 remain comparatively expensive and scale poorly with system size. Here we
 show that deep neural networks utilizing just two descriptors—the Pauling
 electronegativity and ionic radii—can predict the DFT formation energies
 of C3A2D3O12 garnets and ABO3 perovskites with low mean absolute errors
 (MAEs) of 7–10 meV atom−1 and 20–34 meV atom−1, respectively, well within
 the limits of DFT accuracy. Further extension to mixed garnets and
 perovskites with little loss in accuracy can be achieved using a binary
 encoding scheme, addressing a critical gap in the extension of
 machine-learning models from fixed stoichiometry crystals to infinite
 universe of mixed-species crystals. Finally, we demonstrate the potential
 of these models to rapidly transverse vast chemical spaces to accurately
 identify stable compositions, accelerating the discovery of novel
 materials with potentially superior properties.
description: CrystalDNNPython scripts, models and data used to predict the formation energies(Ef) and to calculate the energies above hull(Ehull) of garnet and perovskite crystals accompanying the above publication.
DOI: 10.5061/dryad.bp23483h
title: Data from: Modeling effects of environmental change on wolf population dynamics, trait evolution, and life history

description: Environmental change has been observed to generate simultaneous responses
 in population dynamics, life history, gene frequencies, and morphology in
 a number of species. But how common are such eco-evolutionary responses to
 environmental change likely to be? Are they inevitable, or do they require
 a specific type of change? Can we accurately predict eco-evolutionary
 responses? We address these questions using theory and data from the study
 of Yellowstone wolves. We show that environmental change is expected to
 generate eco-evolutionary change, that changes in the average environment
 will affect wolves to a greater extent than changes in how variable it is,
 and that accurate prediction of the consequences of environmental change
 will probably prove elusive.
description: wolf
 RDataReadme file explains the
 structure of the RData workspace filewolf.RDATAsimulate and perturbR code to run simulations
DOI: 10.34740/kaggle/dsv/14631163
title: Berita UNPAM
DOI: 10.5061/dryad.d21j6
title: Data from: Feedbacks between shallow groundwater dynamics and surface topography on runoff generation in flat fields

description: In winter, saturation excess (SE) ponding is observed regularly in
 temperate lowland regions. Surface runoff dynamics are controlled by small
 topographical features that are unaccounted for in hydrological models. To
 better understand storage and routing effects of small scale topography
 and their interaction with shallow groundwater under SE conditions, we
 developed a model of reduced complexity to investigate SE runoff
 generation, emphasizing feedbacks between shallow groundwater dynamics and
 mesotopography. The dynamic specific yield affected unsaturated zone water
 storage, causing rapid switches between negative and positive head and a
 flatter groundwater mound than predicted by analytical agro-hydrological
 models. Accordingly, saturated areas were larger and local groundwater
 fluxes smaller than predicted, leading to surface runoff generation.
 Mesotopographic features routed water over larger distances, providing a
 feedback mechanism that amplified changes to the shape of the groundwater
 mound. This in turn enhanced runoff generation, but whether it also
 resulted in runoff events depended on the geometry and location of the
 depressions. Whereas conditions favourable to runoff generation may abound
 during winter, these feedbacks profoundly reduce the predictability of SE
 runoff: statistically identical rainfall series may result in completely
 different runoff generation. The model results indicate that waterlogged
 areas in any given rainfall event are larger than those predicted by
 current analytical groundwater models used for drainage design. This
 change in the groundwater mound extent has implications for crop growth
 and damage assessments.
description: FASTR model validation
 dataFile contains water
 balance results generated with the FASTR hydrological model for three
 numerical validation experiments.Data_FASTR_Validation.xlsxFASTR experiment 1: role of the unsaturated zone moisture profileFile contains water balance results simulated with the FASTR hydrological model for 15,000 combinations of initial groundwater level, soil hydraulic parameters, saturated hydraulic conductivity, and precipitation structure.Data_Experiment1_UnsatZoneProfile.xlsxFASTR experiment 2: seasonal saturation excess runoff generation in fields with mesotopographyFile contains water balance results simulated with the FASTR hydrological model for 1,080 combinations of mesotopography, soil hydraulic parameters, saturated hydraulic conductivity, and precipitation structure.Data_Experiment2_Mesotopography.xlsx
DOI: 10.5061/dryad.kj4n8
title: Data from: Transcriptome sequencing of sea cucumber (Apostichopus japonicus) and the identification of gene-associated markers

description: Sea cucumber (Apostichopus japonicus) is an ecologically and economically
 important species in East and South-East Asia. This project aimed to
 identify large numbers of gene-associated markers and differentially
 expressed genes (DEGs) after lipopolysaccharides (LPS) challenge in A.
 japonicus using high-throughput transcriptome sequencing. A total of 162
 million high-quality reads of 174 million raw reads were obtained by deep
 sequencing using Illumina HiSeq™ 2000 platform. Assembly of these reads
 generated 94 704 unigenes, with read length ranging from 200 to 16 153 bp
 (average length of 810 bp). A total of 36 005 were identified as coding
 sequences (CDSs), 32 479 of which were successfully annotated. Based on
 the assembly transcriptome, we identified 142 511 high-quality single
 nucleotide polymorphisms (SNPs). Among them, 33 775, 63 120 and 45 616
 were located in sequences without predicted CDS (non-CDSs), CDSs and
 untranslated regions (UTRs), respectively. These putative SNPs included 82
 664 transitions and 59 847 transversions. Totally, 89 375 (59.1%) were
 distributed in 15 473 known genes. A total of 6417 microsatellites were
 detected in 5970 unigenes, 3216 of which were annotated and 2481 were
 successfully subjected for primer design. The numbers of simple sequence
 repeats (SSRs) identified in non-CDSs, CDSs and UTRs were 2367, 2316 and
 1734. These potential SNPs and SSRs are expected to provide abundant
 resources for genetic, evolutionary and ecological studies in sea
 cucumber. Transcriptome comparison revealed 1330, 1347 and 1291 DEGs in
 the coelomocytes of A. japonicus at 4 h, 24 h and 72 h after LPS
 challenge, respectively. Approximately 58.4% (1802) of total DEGs have
 been successfully annotated.
description: Apostichopus_SNPApostichopus_SSRApostichopus-Unigenes
DOI: 10.5061/dryad.j2v6q
title: Data from: Contribution of spatial heterogeneity in effective population sizes to the variance in pairwise measures of genetic differentiation

description: 1. Pairwise measures of neutral genetic differentiation are supposed to
 contain information about past and on-going dispersal events and are thus
 often used as dependent variables in correlative analyses to elucidate how
 neutral genetic variation is affected by landscape connectivity. However,
 spatial heterogeneity in the intensity of genetic drift, stemming from
 variations in population sizes, may inflate variance in measures of
 genetic differentiation and lead to erroneous or incomplete
 interpretations in terms of connectivity. Here, we tested the efficiency
 of two distance-based metrics designed to capture the unique influence of
 spatial heterogeneity in local drift on genetic differentiation. These
 metrics are easily computed from estimates of effective population sizes
 or from environmental proxies for local carrying capacities, and allow us
 to introduce the hypothesis of
 Spatial-Heterogeneity-in-Effective-Population-Sizes (SHNe). SHNe can be
 tested in a way similar to isolation-by-distance or
 isolation-by-resistance within the classical landscape genetics
 hypothesis-testing framework. 2. We used simulations under various models
 of population structure to investigate the reliability of these metrics to
 quantify the unique contribution of SHNe in explaining patterns of genetic
 differentiation. We then applied these metrics to an empirical genetic
 dataset obtained for a freshwater fish (Gobio occitaniae). 3. Simulations
 showed that SHNe explained up to 60% of variance in genetic
 differentiation (measured as Fst) in the absence of gene flow, and up to
 20% when migration rates were as high as 0.10. Furthermore, one of the two
 metrics was particularly robust to uncertainty in the estimation of
 effective population sizes (or proxies for carrying capacity). In the
 empirical dataset, the effect of SHNe on spatial patterns of Fst was five
 times higher than that of isolation-by-distance, uniquely contributing to
 41% of variance in pairwise Fst. Taking the influence of SHNe into account
 also allowed decreasing the signal-to-noise ratio, and improving the upper
 estimate of effective dispersal distance. 4. We conclude that the use of
 SHNe metrics in landscape genetics will substantially improve the
 understanding of evolutionary drivers of genetic variation, providing
 substantial information as to the actual drivers of patterns of genetic
 differentiation in addition to traditional measures of Euclidean distance
 or landscape resistance.
description: Simulated and Empirical
 dataSHNe_data.zip
DOI: 10.15468/dl.jvrh8w
title: Occurrence Download

description: A dataset containing 2166 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Leptophis mexicanus"
 ]
}

 The dataset includes 2166 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000487-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.tk5ts47
title: Data from: Circadian rhythmicity persists through the Polar night and midnight sun in Svalbard reindeer

description: Studies of locomotor activity in Svalbard reindeer reported the temporary
 absence of diel rhythms under Arctic photic conditions. However, using
 Lomb-Scargle periodogram analyses with high statistical power we found
 diel or circadian rhythmicity throughout the entire year in measures of
 behaviour, temperature in the rumen and heart rate in free-living Svalbard
 reindeer. Significant diel rhythmicity was only lacking during some of the
 15-day intervals analysed in the less frequently measured heart rate.
 During Polar Night these rhythms were free-running and attenuated. During
 continual daylight in summer, rhythms where entrained to 24 hours
 corresponding with the daily variation in the intensity of solar
 radiation, but attenuated when continuous daylight coincided with the
 period of growing forage. Diel rhythmicity was reduced during this short
 period of peak foraging activity, which coincided with peak heart rate and
 temperature in the rumen, most likely to facilitate fattening when food is
 abundant. For the rest of the year, heart rate and temperature showed the
 most pronounced and long-lasting suppression ever found in ungulates. The
 profound seasonal changes in foraging, metabolic activity, and power of
 diel and circadian rhythmicity of Svalbard reindeer can be viewed as
 adaptations to the extreme living conditions in the High Arctic.
description: NDVI
 DataNDVI Data for the three
 study sites 2012-2014EVI_NDVI one
 sheet.csvTelemetry data file for
 the individual recordedHB11187_ID02_Filtered.csvTelemetry data file for the individual recordedHB11229_ID01_Filtered.csvTelemetry data file for the individual recordedHB11245_ID04_Filtered.csvTelemetry data file for the individual recordedHB11373_ID03_Filtered.csv
DOI: 10.15468/dl.s2v68m
title: Occurrence Download

description: A dataset containing 3503 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Caracara cheriway"
 ]
}

 The dataset includes 3503 records from 261 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000486-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.83kd9
title: Data from: Multilocus phylogeography of a widespread savanna-woodland adapted rodent reveals the influence of Pleistocene geomorphology and climate change in Africa’s Zambezi region

description: Understanding historical influences of climate and physiographic barriers
 in shaping patterns of biodiversity remains limited for many regions of
 the world. For mammals of continental Africa, phylogeographic studies,
 particularly for West African lineages, implicate both geographic barriers
 and climate oscillations in shaping small mammal diversity. In contrast,
 studies for southern African species have revealed conflicting
 phylogenetic patterns for how mammalian lineages respond to both climate
 change and geologic events such as river formation, especially during the
 Pleistocene. However, these studies were often biased by limited
 geographic sampling or exclusively focused on large-bodied taxa. We
 exploited the broad southern African distribution of a
 savanna–woodland-adapted African rodent, Gerbilliscus leucogaster
 (bushveld gerbil) and generated mitochondrial, autosomal and sex
 chromosome data to quantify regional signatures of climatic and vicariant
 biogeographic phenomena. Results indicate the most recent common ancestor
 for all G. leucogaster lineages occurred during the early Pleistocene. We
 documented six divergent mitochondrial lineages that diverged ~0.270–0.100
 mya, each of which was geographically isolated during periods
 characterized by alterations to the course of the Zambezi River and its
 tributaries as well as regional ‘megadroughts’. Results demonstrate the
 presence of a widespread lineage exhibiting demographic expansion
 ~0.065–0.035 mya, a time that coincides with savanna–woodland expansion
 across southern Africa. A multilocus autosomal perspective revealed the
 influence of the Kafue River as a current barrier to gene flow and regions
 of secondary contact among divergent mitochondrial lineages. Our results
 demonstrate the importance of both climatic fluctuations and physiographic
 vicariance in shaping the distribution of southern African biodiversity.
description: G_leucogaster_phylogeography_dryadThe compressed folder includes the following: a) sequence alignments for all individuals and loci, b) .xml files used for BEAST analyses (divergence time estimates and extended Bayesian skyline plot), c) MAXENT parameter files, d) spatial diffusion analysis parameter files, and D) STUCTURE parameter file.