cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d18mc
title: Data from: De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease

description: Geosmithia morbida is a filamentous ascomycete that causes thousand
 cankers disease in the eastern black walnut tree. This pathogen is
 commonly found in the western U.S.; however, recently the disease was also
 detected in several eastern states where the black walnut lumber industry
 is concentrated. G. morbida is one of two known phytopathogens within the
 genus Geosmithia, and it is vectored into the host tree via the walnut
 twig beetle. We present the first de novo draft genome of G. morbida. It
 is 26.5 Mbp in length and contains less than 1% repetitive elements. The
 genome possesses an estimated 6,273 genes, 277 of which are predicted to
 encode proteins with unknown functions. Approximately 31.5% of the
 proteins in G. morbida are homologous to proteins involved in
 pathogenicity, and 5.6% of the proteins contain signal peptides that
 indicate these proteins are secreted. Several studies have investigated
 the evolution of pathogenicity in pathogens of agricultural crops; forest
 fungal pathogens are often neglected because research efforts are focused
 on food crops. G. morbida is one of the few tree phytopathogens to be
 sequenced, assembled and annotated. The first draft genome of G. morbida
 serves as a valuable tool for comprehending the underlying molecular and
 evolutionary mechanisms behind pathogenesis within the Geosmithia genus.
description: geosmithia.morbida.transcriptsThe file contains in silico generated transcripts for Geosmithia morbida.geosmithia.morbida.proteinsThis file contains in silico generated protein sequences for Geosmithia morbida.
DOI: 10.5061/dryad.j4d25
title: Data from: Egg rejection and clutch phenotype variation in the plain prinia (Prinia inornata)

description: Avian hosts of brood parasites can evolve anti-parasitic defenses to
 recognize and reject foreign eggs from their nests. Theory predicts that
 higher inter-clutch and lower intra-clutch variation in egg appearance
 facilitates hosts to detect parasitic eggs as egg-rejection mainly depends
 on the appearance of the egg. Therefore, we predict that egg patterns and
 rejection rates will differ when hosts face different intensity of cuckoo
 parasitism. We tested this prediction in two populations of the plain
 prinia (Prinia inornata): Guangxi in mainland China with high diversity
 and density of cuckoo species, and Taiwan where there is only one breeding
 cuckoo species, the Oriental cuckoo (Cuculus optatus). As expected, egg
 patterns were similar within clutches but different among clutches
 (polymorphic eggs) in the mainland population, while the island population
 produced more uniform egg morphs. Furthermore, the mainland population
 showed a high rate of egg rejection, while the island population exhibited
 dramatically reduced egg grasp-rejection ability in the absence of
 parasitism by the common cuckoo (Cuculus canorus). Our study suggests that
 prinias show lower intra-clutch consistency in egg colour and lose
 egg-rejecting ability under relaxed selection pressure from brood
 parasitism.
description: uploaded data for
 JAV-00786.R3data package for
 JAV-00786.R3uploaded
 data_JAV-00786.R3.zip
DOI: 10.15468/dl.2kcatv
title: Occurrence Download

description: A dataset containing 8999 species occurrences available in GBIF matching the query:
{
 "DatasetId" : [
 "is eu4health_cp-g-22-04.01"
 ]
}

 The dataset includes 8999 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001454-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.39d23
title: Data from: Geographic differentiation of domesticated einkorn wheat and possible Neolithic migration routes

description: To analyse the spread of domesticated einkorn into Europe, 136 landraces,
 9 wild einkorns and 3 Triticum urartu were fingerprinted by the diversity
 array technology sequence (DArT-seq) marker technology. The obtained 3455
 single-nucleotide polymorphism (SNP) markers confirmed earlier results
 about the separation of wild and domesticated einkorn from T. urartu and
 about the pinpointing of the domesticated forms to the Karacadağ Mountains
 (Turkey). Further analyses identified two major domesticated landrace
 einkorn groups, one relating to the Prealpine region and the other to the
 Maghreb/Iberian region. The previously published four geographical
 provenance groups were mostly identified in our results. The earlier
 reported unique position of the Maghreb/Iberia einkorns cannot be
 confirmed, as the three landrace clusters we identified with STRUCTURE
 also occur in the remaining einkorn, although at different frequencies.
 The results are discussed with respect to the spreading of domesticated
 einkorn into Western Europe and two possible Neolithic migration routes
 are indicated.
description: Brandolini - dataset -
 Einkorn EuropeSNP DaRT data of 148
 diploid wheat accessions (136 T. monococcum, 9 T. boeoticum and 3 T.
 urartu)Brandolini - List of
 accessions - Einkorn EuropeList of the accessions
 tested and their geographical origin
DOI: 10.5061/dryad.qb74m
title: Data from: Local adaptation is associated with zinc tolerance in Pseudomonas endophytes of the metal-hyperaccumulator plant Noccaea caerulescens

description: Metal hyperaccumulating plants, which are hypothesised to use metals for
 defence against pests and pathogens, provide a unique context in which to
 study plant–pathogen co-evolution. Previously, we demonstrated that the
 high concentrations of zinc found in leaves of the hyperaccumulator
 Noccaea caerulescens provide protection against bacterial pathogens, with
 a potential trade-off between metal-based and pathogen-induced defences.
 We speculated that an evolutionary arms race between zinc-based defences
 in N. caerulescens and zinc tolerance in pathogens might have driven the
 development of the hyperaccumulation phenotype. Here, we investigate the
 possibility of local adaptation by bacteria to the zinc-rich environment
 of N. caerulescens leaves and show that leaves sampled from the
 contaminated surroundings of a former mine site harboured endophytes with
 greater zinc tolerance than those within plants of an artificially created
 hyperaccumulating population. Experimental manipulation of zinc
 concentrations in plants of this artificial population influenced the zinc
 tolerance of recovered endophytes. In laboratory experiments, only
 endophytic bacteria isolated from plants of the natural population were
 able to grow to high population densities in any N. caerulescens plants.
 These findings suggest that long-term co-existence with zinc
 hyperaccumulating plants leads to local adaptation by endophytic bacteria
 to the environment within their leaves.
description: Bacterial
 archiveData concerning all
 endophytic bacteria isolated in this work; descriptions, LOPAT and GAtta
 assay results, BLAST hits, plant from which isolated,
 site.Field
 HMILD50 data for all
 enophytic bactera isolated in this workkruskall wallis env
 microKruskall Wallis
 testingSnowdonia high zn
 trialPlate reader output and
 graphs for zinc tolerance testsWytham strains high zinc
 testsPlate reader output and
 graphs for zinc tolerance assaysMetal Contents
 dataMetal concentrations in
 plants leavesall_rpoD_alignment.fasPhylogeny - alignmentall rpoD consensusConsensus tree
DOI: 10.5061/dryad.qc264
title: Data from: A before-and-after assessment of patch-burn grazing and riparian fencing along headwater streams

description: Fire and grazing are common in grasslands world-wide to maintain grass
 cover and cattle production. The effects of fire, cattle grazing and
 riparian fencing efficacy on prairie stream ecology are not well
 characterized at catchment scales. We examined alterations to stream water
 quality and biology from patch-burn grazing (PBG) in tallgrass prairie
 during a five-year, replicated, catchment scale experiment that used a
 Before-After/Control-Impact (BACI) design and was analysed by
 mixed-effects models. Treatments included two patch-burned control
 catchments (fire but no grazers) and PBG in two riparian-fenced and two
 unfenced catchments. We assessed the effectiveness of riparian fencing for
 mitigating potential water quality impacts by monitoring water quality and
 riparian usage by cattle via Global Positioning System. Riparian fences
 effectively excluded cattle; however, in unfenced pastures, cattle
 aggregated along streams 10–20% of the grazing season. After initiation of
 PBG, we detected large increases in some nutrients, Escherichia coli,
 algal biomass, primary productivity and community respiration in all
 catchments with PBG. Some water quality variables, such as E. coli
 concentrations, recovered quickly after cattle were removed from pasture,
 which indicated resiliency. Riparian fencing moderately reduced the
 impacts to stream variables, indicating either overland flow and/or
 subsurface flow allowed nutrients and bacteria to enter the streams.
 Synthesis and applications. Patch-burn grazing is a measurable disturbance
 that can alter the ecological condition of streams. Riparian fencing
 lessened the degree of impact, yet some water quality variables still
 exceeded regional reference conditions. Managers will need to assess the
 costs of riparian fencing compared to the moderate benefits that fencing
 provides to water quality.
description: Areas of watersheds,
 burn areas, and riparian zonesSummary data table of
 watershed areas, riparian zone areas, and burn areas for each of the study
 years.Water
 and Burn Areas.csvWater Chemistry
 DataData for years 2009-2013
 at Osage Prairie, Missouri. Variables include: ammonium, nitrate, total
 nitrogen, total phosphorus, soluble reactive phosphorus, total suspended
 solids, organic suspended solids, inorganic suspended solids and
 metabolism (gross primary production, community respiration, and net
 ecosystem production).Water
 Chemistry.zipCattle Positions in
 ArcGISRaw data files for
 ArcGIS analysis of cattle location position in 4 watersheds at Osage
 Prairie.
DOI: 10.5061/dryad.601fd
title: Data from: Ecosystem interactions underlie the spread of avian influenza A viruses with pandemic potential

description: Despite evidence for avian influenza A virus (AIV) transmission between
 wild and domestic ecosystems, the roles of bird migration and poultry
 trade in the spread of viruses remain enigmatic. In this study we
 integrate ecosystem interactions into a phylogeographic model to assess
 the contribution of wild and domestic hosts to AIV distribution and
 persistence. Analysis of globally sampled AIV datasets shows frequent
 two-way transmission between wild and domestic ecosystems. In general,
 viral flow from domestic to wild bird populations was restricted to within
 a geographic region. In contrast, spillover from wild to domestic
 populations occurred both within and between regions. Wild birds mediated
 long-distance dispersal at intercontinental scales whereas viral spread
 among poultry populations was a major driver of regional spread. Viral
 spread between poultry flocks frequently originated from persistent
 lineages circulating in regions of intensive poultry production. Our
 analysis of long-term surveillance data demonstrates that meaningful
 insights can be inferred from integrating ecosystem into phylogeographic
 reconstructions that may be consequential for pandemic preparedness and
 livestock protection.
description: Bahl et al H9
 DatasetBahl et al H3
 DatasetBahl et al H6
 DatasetSuppDataFile2 - Sequence
 MetadataThis file contains all
 the associated metadata used in the ancestral reconstruction of discrete
 geographic states.SuppDataFile2
 v2.xlsx
DOI: 10.5061/dryad.cc03n
title: Data from: Evolutionary potential in the Alpine: trait heritabilities and performance variation of the dwarf willow Salix herbacea from different elevations and microhabitats

description: Alpine ecosystems are seriously threatened by climate change. One of the
 key mechanisms by which plants can adapt to changing environmental
 conditions is through evolutionary change. However, we still know little
 about the evolutionary potential in wild populations of long-lived alpine
 plants. Here, we investigated heritabilities of phenological traits, leaf
 size, and performance traits in natural populations of the long-lived
 alpine dwarf shrub Salix herbacea using relatedness estimates inferred
 from SSR (Simple Sequence Repeat) markers. Salix herbacea occurs in early-
 and late-snowmelt microhabitats (ridges and snowbeds), and we assessed how
 performance consequences of phenological traits and leaf size differ
 between these microhabitats in order to infer potential for evolutionary
 responses. Salix herbacea showed low, but significant, heritabilities of
 leaf size, clonal and sexual reproduction, and moderate heritabilities of
 phenological traits. In both microhabitats, we found that larger leaves,
 longer intervals between snowmelt and leaf expansion, and longer GDD
 (growing-degree days) until leaf expansion resulted in a stronger increase
 in the number of stems (clonal reproduction). In snowbeds, clonal
 reproduction increased with a shorter GDD until flowering, while the
 opposite was found on ridges. Furthermore, the proportion of flowering
 stems increased with GDD until flowering in both microhabitats. Our
 results suggest that the presence of significant heritable variation in
 morphology and phenology might help S. herbacea to adapt to changing
 environmental conditions. However, it remains to be seen if the rate of
 such an evolutionary response can keep pace with the rapid rate of climate
 change.
description: Sedlacek_etal_MarkerDataThis data file provides the data on the SSR markers. An explanation of the variables is provided in the ReadMe file.Sedlacek_etal_PhenotypicDataThis data file provides all raw phenotypic data collected on the Salix herbacea plants in the field. Note that some of these variables were not used for the publication. An explanation of the variables is given in the ReadMe file.
DOI: 10.5061/dryad.7tb57
title: Data from: A powerful test of independent assortment that determines genome-wide significance quickly and accurately

description: In the analysis of DNA sequences on related individuals, most methods
 strive to incorporate as much information as possible, with little or no
 attention paid to the issue of statistical significance. For example, a
 modern workstation can easily handle the computations needed to perform a
 large-scale genome-wide inheritance-by-descent (IBD) scan, but accurate
 assessment of the significance of that scan is often hindered by
 inaccurate approximations and computationally intensive simulation. To
 address these issues, we developed gLOD-a test of co-segregation that, for
 large samples, models chromosome-specific IBD statistics as a collection
 of stationary Gaussian processes. With this simple model, the parametric
 bootstrap yields an accurate and rapid assessment of significance-the
 genome-wide corrected P-value. Furthermore, we show that (i) under the
 null hypothesis, the limiting distribution of the gLOD is the standard
 Gumbel distribution; (ii) our parametric bootstrap simulator is
 approximately 40 000 times faster than gene-dropping methods, and it is
 more powerful than methods that approximate the adjusted P-value; and,
 (iii) the gLOD has the same statistical power as the widely used maximum
 Kong and Cox LOD. Thus, our approach gives researchers the ability to
 determine quickly and accurately the significance of most large-scale IBD
 scans, which may contain multiple traits, thousands of families and tens
 of thousands of DNA sequences.
description: T1D
 pedigreeThis is a simple text
 file containing the biological relationships of individuals across 422
 affected families. Each affected family was ascertained through a single
 proband with type 1 diabetes (T1D). This file is in the standard MERLIN
 pedigree format, with the first 6 columns specifying relationships, and
 the remaining columns specifying genotypes.wg.scan.pedT1D mapFor each marker, this simple text file gives the name, the chromosome, and the chromosome-specific location. The order of the markers in this file, corresponds to the order of the columns in 'T1D pedigree'. In particular, there are 3697 markers in 'T1D map', which means that there are (6 + 2 * 3697) = 7400 columns in 'T1D pedigree'.wg.scan.map
DOI: 10.5061/dryad.809v4
title: Data from: Parallel and non-parallel behavioural evolution in response to parasitism and predation in Trinidadian guppies

description: Natural enemies such as predators and parasites are known to shape
 intra-specific variability of behaviour and personality in natural
 populations, yet several key questions remain: (1) What is the relative
 importance of predation versus parasitism in shaping intra-specific
 variation of behaviour across generations? (2) What are the contributions
 of genetic and plastic effects to this behavioural divergence? And (3) to
 what extent are responses to predation and parasitism repeatable across
 independent evolutionary lineages? We addressed these questions using
 Trinidadian guppies (Poecilia reticulata) (1) varying in their exposure to
 dangerous fish predators and Gyrodactylus ectoparasites, for (2) both
 wild-caught F0 and laboratory-reared F2 individuals and coming from (3)
 multiple independent evolutionary lineages (i.e. independent drainages).
 Several key findings emerged. First, a population's history of
 predation and parasitism influenced behavioural profiles, but to different
 extent depending on the behaviour considered (activity, shoaling or
 boldness). Second, we had evidence for some genetic effects of predation
 regime on behaviour, with differences in activity of F2 laboratory-reared
 individuals, but not for parasitism, which had only plastic effects on the
 boldness of wild-caught F0 individuals. Third, the two lineages showed a
 mixture of parallel and non-parallel responses to predation/parasitism,
 with parallel responses being stronger for predation than for parasitism
 and for activity and boldness than for shoaling. These findings suggest
 that different sets of behaviours provide different pay-offs in
 alternative predation/parasitism environments, and that parasitism have
 more transient effects in shaping intra-specific variation of behaviour
 than does predation.
description: Behavioural data for
 F0F2 guppiesdata guppies
 F0F2.txt
DOI: 10.5061/dryad.c289v
title: Data from: Capturing neutral and adaptive genetic diversity for conservation in a highly structured tree species

description: Preserving intraspecific genetic diversity is essential for long-term
 forest sustainability in a climate change scenario. Despite that, genetic
 information is largely neglected in conservation planning, and how
 conservation units should be defined is still heatedly debated. Here, we
 use maritime pine (Pinus pinaster Ait.), an outcrossing long lived tree
 with a highly fragmented distribution in the Mediterranean biodiversity
 hotspot, to prove the importance of accounting for genetic variation - at
 both neutral molecular markers and quantitative traits - to define useful
 conservation units. Six gene pools associated to distinct evolutionary
 histories were identified within the species using 12 microsatellites and
 266 Single Nucleotide Polymorphisms (SNPs). In addition, height and
 survival standing variation, their genetic control and plasticity were
 assessed in a multisite clonal common garden experiment (16,544 trees). We
 found high levels of quantitative genetic differentiation within
 previously defined neutral gene pools. Subsequent cluster analysis and
 post-hoc trait distribution comparisons allowed us to define ten
 genetically homogeneous population groups with high evolutionary
 potential. They constitute the minimum number of units to be represented
 in a maritime pine dynamic conservation program. Our results uphold that
 the identification of conservation units below the species level should
 account for key neutral and adaptive components of genetic diversity,
 especially in species with strong population structure and complex
 evolutionary histories. The environmental zonation approach currently used
 by the pan-European genetic conservation strategy for forest trees would
 be largely improved by gradually integrating molecular and quantitative
 trait information, as data become available.
description: Molecular marker
 dataMolecular marker data
 (genotyping results) for 266 Single Nucleotide Polimorphisms and 12
 nuclear microsatellites for 517 maritime pine trees from 35 populations
 sampled across the species natural range.MolMarker_Data_SNPs_nuSSRs.xlsxPhenotypic DataSurvival and total height (cm) field measurements in four maritime pine common garden trials. The four trials (Asturias, Portugal, Madrid and Cáceres) have the same number of clones, with eight replicates per genotype, in a randomized complete block design. The four trial sites provided contrasting environmental conditions.Phenotypic_Data.xlsxClimatic dataClimatic data (temperatures and rainfall) for each of the 35 maritime pine provenances included in the study. Populations were sorted by neutral gene pool.Climatic_Data.xlsx
DOI: 10.5281/zenodo.18386898
title: SP-based coding dataset for sustainability in SE

description: This dataset contains the coded extraction of a Systematic Mapping Study among the Software Engineering and Sustainability fields.

The dataset includes:- Bibliographic data of 59 primary studies- SP1–SP8 coding in FSSD- Alignment quality (Alignment/Mixed/Misalignment)- Domain, SDLC phase, AI involvement, and contribution types

The dataset supports transparency, reproducibility, and future reuse of the research.
DOI: 10.5281/zenodo.18386899
title: SP-based coding dataset for sustainability in SE

description: This dataset contains the coded extraction of a Systematic Mapping Study among the Software Engineering and Sustainability fields.

The dataset includes:- Bibliographic data of 59 primary studies- SP1–SP8 coding in FSSD- Alignment quality (Alignment/Mixed/Misalignment)- Domain, SDLC phase, AI involvement, and contribution types

The dataset supports transparency, reproducibility, and future reuse of the research.
DOI: 10.5061/dryad.7sj4h
title: Data from: Active and reactive behaviour in human mobility: the influence of attraction points on pedestrians

description: Human mobility is becoming an accessible field of study thanks to the
 progress and availability of tracking technologies as a common feature of
 smart phones. We describe an example of a scalable experiment exploiting
 these circumstances at a public, outdoor fair in Barcelona (Spain).
 Participants were tracked while wandering through an open space with
 activity stands attracting their attention. We develop a general modeling
 framework based on Langevin Dynamics, which allows us to test the
 influence of two distinct types of ingredients on mobility: reactive or
 context-dependent factors, modelled by means of a force field generated by
 attraction points in a given spatial configuration, and active or inherent
 factors, modelled from intrinsic movement patterns of the subjects. The
 additive and constructive framework model accounts for some observed
 features. Starting with the simplest model (purely random walkers) as a
 reference, we progressively introduce different ingredients such as
 persistence, memory, and perceptual landscape, aiming to untangle active
 and reactive contributions and quantify their respective relevance. The
 proposed approach may help in anticipating the spatial distribution of
 citizens in alternative scenarios and in improving the design of public
 events based on a facts-based approach.
description: BeePath2012