cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m1bm5
title: Data from: Extending RAD tag analysis to microbial ecology: a comparison between multi locus sequence typing (MLST) and 2b-RAD to investigate Listeria monocytogenes genetic structure

description: The advent of next-generation sequencing (NGS) has dramatically changed
 bacterial typing technologies, increasing our ability to differentiate
 bacterial isolates. Despite it is now possible to sequence a bacterial
 genome in a few days and at reasonable costs, most genetic analyses do not
 require whole-genome sequencing, which also remains impractical for large
 population samples due to the cost of individual library preparation and
 bioinformatics. More traditional sequencing approaches, however, such as
 MultiLocus Sequence Typing (mlst) are quite laborious and time-consuming,
 especially for large-scale analyses. In this study, a genotyping approach
 based on restriction site-associated (RAD) tag sequencing, 2b-RAD, was
 applied to characterize Listeria monocytogenes strains. To verify the
 feasibility of the method, an in silico analysis was performed on 30
 available complete genomes. For the same set of strains, in silico mlst
 analysis was conducted as well. Subsequently, 2b-RAD and mlst analyses
 were experimentally carried out on 58 isolates collected from food samples
 or food-processing sites. The obtained results demonstrate that 2b-RAD
 predicts mlst types and often provides more detailed information on
 population structure than mlst. Moreover, the majority of variants
 differentiating identical sequence type isolates mapped against accessory
 fragments, thus providing additional information to characterize strains.
 Although mlst still represents a reliable typing method, large-scale
 studies on molecular epidemiology and public health, as well as bacterial
 phylogenetics, population genetics and biosafety could benefit of a low
 cost and fast turnaround time approach such as the 2b-RAD analysis
 proposed here.
description: 2bRAD_Listeria_
 package_PaulettoIt contains a copy of
 Structure and Phyloviz input files exactly as used for this paper. In
 addition it includes Stacks and Panseq output files and provides the files
 required for performing an integrated analysis of additional L.
 monocytogenes isolates, as described in the supplemental figure
 S2.
DOI: 10.5061/dryad.t6hh8
title: Data from: Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes

description: The free-living (FL) and particle-attached (PA) marine microbial
 communities have repeatedly been proved to differ in their diversity and
 composition in the photic ocean and also recently in the bathypelagic
 ocean at a global scale. However, although high taxonomic ranks have been
 proved to exhibit preferences for a PA or FL mode of life, it remains
 poorly understood whether two clear lifestyles do exist and how these are
 distributed across the prokaryotic phylogeny. We studied the FL and PA
 prokaryotes in 30 stations distributed worldwide within the bathypelagic
 oceanic realm using high throughput sequencing of their 16S rDNA. A high
 proportion of the bathypelagic prokaryotes were mostly found either
 attached to particles or freely in the surrounding water but rarely in
 both types of environments. In particular, this trait was deeply conserved
 through their phylogeny suggesting that the deep-ocean particles and the
 surrounding water constitute two highly distinct niches and that
 transitions from one to the other have been rare at an evolutionary
 time-scale. As a consequence, PA and FL communities had clear alpha- and
 beta-diversity differences that exceeded the global-scale geographical
 variation. Our study organizes the bathypelagic prokaryotic diversity into
 a reasonable number of ecologically coherent taxa regarding their
 association to particles, a first step for understanding which are the
 microbes responsible for the processing of the dissolved and particulate
 pools of organic matter that have a very different biogeochemical role in
 the deep ocean. --
description: Abundance table for
 bathypelagic prokaryotes from Malaspina 2010 ExpeditionAbundance table
 containing the number of reads for the Operational Taxonomic Units (OTUs)
 of particle-attached (PA) and free-living (FL) prokaryotes detected in 30
 globally distributed stations from the Malaspina 2010 Expedition.
 Corresponds to 16SrDNA amplicons Illumina-based sequencing. Table is
 rarefied to 10,617 reads/sample. Columns are the samples; Rows are the
 OTUs. Taxonomy is attached after the last sample.OTUtable_Salazar_etal_2015_Molecol.txtAuxiliary data for the samplesAuxiliary data containing information on the station, size-fraction, date of sampling, ocean, depth and coordinates.Metadata_Salazar_etal_2015_Molecol.txtPhylogeny of the OTUs representative sequencesPhylogeny reconstruction of the OTUs. Newick format. Constructed with RAxML by the evolutionary placement of short sequences within an initial phylogeny of close full length sequences from SILVA database (See details in M&M).FinalTree_Salazar_etal_2015_Molecol.nwkAlignment used for phylogeny constructionAlignment used for the phylogenetic reconstruction.Alignment_Salazar_etal_2015_Molecol.phylip
DOI: 10.5061/dryad.v6p3h
title: Data from: Evolution and biogeography of the endemic Roucela complex (Campanulaceae: Campanula) in the eastern Mediterranean

description: At the intersection of geological activity, climatic fluctuations, and
 human pressure, the Mediterranean Basin – a hotspot of biodiversity –
 provides an ideal setting for studying endemism, evolution, and
 biogeography. Here, we focus on the Roucela complex (Campanula subgenus
 Roucela), a group of 13 bellflower species found primarily in the eastern
 Mediterranean Basin. Plastid and low-copy nuclear markers were employed to
 reconstruct evolutionary relationships and estimate divergence times
 within the Roucela complex using both concatenation and species tree
 analyses. Niche modeling, ancestral range estimation, and diversification
 analyses were conducted to provide further insights into patterns of
 endemism and diversification through time. Diversification of the Roucela
 clade appears to have been primarily the result of vicariance driven by
 the breakup of an ancient landmass. We found geologic events such as the
 formation of the mid-Aegean trench and the Messinian Salinity Crisis to be
 historically important in the evolutionary history of this group. Contrary
 to numerous past studies, the onset of the Mediterranean climate has not
 promoted diversification in the Roucela complex and, in fact, may be
 negatively affecting these species. This study highlights the diversity
 and complexity of historical processes driving plant evolution in the
 Mediterranean Basin.
description: Campanuloideae_Roucela_atpB_matK_petD_rbcL_Spacer_AT11_AT70FASTA alignment file of all Campanuloideae taxa (including Roucela species) included in the study. Alignment contains atpB, matK, petD, rbcL, atpB-rbcL spacer region, AT11, and AT70 sequences.Camp_Roucela_atpB_matK_petD_rbcL_Spacer_AT1_AT3_TotEvid_MoreThanOneMarkerIngroup.nex.fasta
DOI: 10.5281/zenodo.18390989
title: Test data set for napariTFM

description: Related to https://github.com/ArturRuppel/napariTFM

To use the dataset, install napariTFM according to the instructions on the github. Then, use the batch analysis widget to load the config.yaml, select one or more of the examples and hit run!
DOI: 10.5281/zenodo.18390988
title: Test data set for napariTFM

description: Related to https://github.com/ArturRuppel/napariTFM

To use the dataset, install napariTFM according to the instructions on the github. Then, use the batch analysis widget to load the config.yaml, select one or more of the examples and hit run!
DOI: 10.5061/dryad.b1g80
title: Data from: Persistence of distinctive morphotypes in the native range of the CITES-listed Aldabra giant tortoise

description: Understanding the extent of morphological variation in the wild population
 of Aldabra giant tortoises is important for conservation, as morphological
 variation in captive populations has been interpreted as evidence for
 lingering genes from extinct tortoise lineages. If true, this could impact
 reintroduction programmes in the region. The population of giant tortoises
 on Aldabra Atoll is subdivided and distributed around several islands.
 Although pronounced morphological variation was recorded in the late
 1960s, it was thought to be a temporary phenomenon. Early researchers also
 raised concerns over the future of the population, which was perceived to
 have exceeded its carrying capacity. We analyzed monthly monitoring data
 from 12 transects spanning a recent 15-year period (1998–2012) during
 which animals from four subpopulations were counted, measured, and sexed.
 In addition, we analyzed survival data from individuals first tagged
 during the early 1970s. The population is stable with no sign of
 significant decline. Subpopulations differ in density, but these
 differences are mostly due to differences in the prevailing vegetation
 type. However, subpopulations differ greatly in both the size of animals
 and the degree of sexual dimorphism. Comparisons with historical data
 reveal that phenotypic differences among the subpopulations of tortoises
 on Aldabra have been apparent for the last 50 years with no sign of
 diminishing. We conclude that the giant tortoise population on Aldabra is
 subject to varying ecological selection pressures, giving rise to stable
 morphotypes in discrete subpopulations. We suggest therefore that (1) the
 presence of morphological differences among captive Aldabra tortoises does
 not alone provide convincing evidence of genes from other extinct species;
 and (2) Aldabra serves as an important example of how conservation and
 management in situ can add to the scientific value of populations and
 perhaps enable them to better adapt to future ecological pressures.
description: Aldabra_Giant_Tortoise_Transect_Data_1998_2012Aldabra Giant Tortoise Data from 12 Monitored Transects (1998-2012) across Aldabra Atoll, Seychelles. Please refer to Readme File for abbreviations used in the dataset.
DOI: 10.5061/dryad.8h9b1
title: Data from: Spatial analysis of anthropogenic landscape disturbance and Buruli ulcer disease in Benin

description: Background: Land use and land cover (LULC) change is one anthropogenic
 disturbance linked to infectious disease emergence. Current research has
 focused largely on wildlife and vector-borne zoonotic diseases, neglecting
 to investigate landscape disturbance and environmental bacterial
 infections. One example is Buruli ulcer (BU) disease, a necrotizing skin
 disease caused by the environmental pathogen Mycobacterium ulcerans (MU).
 Empirical and anecdotal observations have linked BU incidence to landscape
 disturbance, but potential relationships have not been quantified as they
 relate to land cover configurations. Methodology/Principal Findings: A
 landscape ecological approach utilizing Bayesian hierarchical models with
 spatial random effects was used to test study hypotheses that land cover
 configurations indicative of anthropogenic disturbance were related to
 Buruli ulcer (BU) disease in southern Benin, and that a spatial structure
 existed for drivers of BU case distribution in the region. A final
 objective was to generate a continuous, risk map across the study region.
 Results suggested that villages surrounded by naturally shaped, or
 undisturbed rather than disturbed, wetland patches at a distance within
 1200m were at a higher risk for BU, and study outcomes supported the
 hypothesis that a spatial structure exists for the drivers behind BU risk
 in the region. The risk surface corresponded to known BU endemicity in
 Benin and identified moderate risk areas within the boundary of Togo.
 Conclusions/Significance: This study was a first attempt to link land
 cover configurations representative of anthropogenic disturbances to BU
 prevalence. Study results identified several significant variables,
 including the presence of natural wetland areas, warranting future
 investigations into these factors at additional spatial and temporal
 scales. A major contribution of this study included the incorporation of a
 spatial modeling component that predicted BU rates to new locations
 without strong knowledge of environmental factors contributing to disease
 distribution.
description: BU_dataGeographic coordinates, numbers of cases, and community population used in this analysis. Land use land cover classification at 30 m resolution in .img format. Values corresponding to land cover classes available in the ReadMe file.manuscript_data.zip
DOI: 10.5061/dryad.62247
title: Data from: Processes driving the adaptive radiation of a tropical tree (Diospyros, Ebenaceae) in New Caledonia, a biodiversity hotspot

description: Due to its special geological history, the New Caledonian Archipelago is a
 mosaic of soil types, and in combination with climatic conditions this
 results in a heterogeneous environment across relatively small distances.
 A group of over 20 endemic species of Diospyros (Ebenaceae) has rapidly
 and recently radiated on the archipelago after a single long-distance
 dispersal event. Most of the Diospyros species in the radiating group are
 morphologically and ecologically well differentiated, but they exhibit low
 levels of DNA variability. To investigate the processes that shaped the
 diversification of this group we employed restriction site associated DNA
 sequencing (RADseq). Over 8,400 filtered SNPs generally confirm species
 delimitations and produce a well-supported phylogenetic tree. Our analyses
 document local introgression, but only a limited potential for gene flow
 over longer distances. The phylogenetic relationships point to an early
 regional clustering among populations and species, indicating that
 allopatric speciation with respect to macrohabitat (i.e., climatic
 conditions) may have had a role in the initial differentiation within the
 group. A later, more rapid radiation involved divergence with respect to
 microhabitat (i.e., soil preference). Several sister species in the group
 show a parallel divergence in edaphic preference. Searches for genomic
 regions that are systematically differentiated in this replicated
 phenotypic divergence pointed to loci potentially involved in ion binding
 and cellular transport. These loci appear meaningful in the context of
 adaptations to soil types that differ in heavy-metal and mineral content.
 Identical nucleotide changes affected only two of these loci, indicating
 that introgression may have played a limited role in their evolution. Our
 results suggest that both allopatric diversification and (parapatric)
 ecological divergence shaped successive rounds of speciation in the
 Diospyros radiation on New Caledonia.
description: Dataset1Dataset D1Dataset2Dataset D2DatasetD2.xmlDataset3Dataset D3DatasetD3.txtSupplFig1Supplementary Figure 1SupplFig2Supplementary Figure 2SupplFig3Supplementary Figure 3SupplFig4Supplementary Figure 4SupplFig5Supplementary Figure 5SupplFig6Supplementary Figure 6SupplTable1Supplementary Table 1
DOI: 10.5061/dryad.2rd32
title: Data from: Death by sex in an Australian icon: a continent-wide survey reveals extensive hybridization between dingoes and domestic dogs

description: Hybridization between domesticated animals and their wild counterparts can
 disrupt adaptive gene combinations, reduce genetic diversity, extinguish
 wild populations and change ecosystem function. The dingo is a
 free-ranging dog that is an iconic apex predator and distributed
 throughout most of mainland Australia. Dingoes readily hybridize with
 domestic dogs, and in many Australian jurisdictions, distinct management
 strategies are dictated by hybrid status. Yet, the magnitude and spatial
 extent of domestic dog–dingo hybridization is poorly characterized. To
 address this, we performed a continent-wide analysis of hybridization
 throughout Australia based on 24 locus microsatellite DNA genotypes from
 3637 free-ranging dogs. Although 46% of all free-ranging dogs were
 classified as pure dingoes, all regions exhibited some hybridization, and
 the magnitude varied substantially. The southeast of Australia was highly
 admixed, with 99% of animals being hybrids or feral domestic dogs, whereas
 only 13% of the animals from remote central Australia were hybrids. Almost
 all free-ranging dogs had some dingo ancestry, indicating that domestic
 dogs could have poor survivorship in nonurban Australian environments.
 Overall, wild pure dingoes remain the dominant predator over most of
 Australia, but the speed and extent to which hybridization has occurred in
 the approximately 220 years since the first introduction of domestic dogs
 indicate that the process may soon threaten the persistence of pure
 dingoes.
description: Microsatellite genotypes
 formatted for the program STRUCTUREInput file for
 STRUCTURE. One line format. Accompanying data for each individual listed
 in file Genotypes and ResultsStructure
 input.csvPCoA Input
 fileDistance matrix used as
 input for PCOA. Data associated with each individual is available in the
 file Genotypes and Results.Dryad_PCoA.csvGenotypes and ResultsGenotypes, results of 3Q and Structure analysis, location data for all individualsGenotypes and results.csv
DOI: 10.5061/dryad.5d23f
title: Data from: Climate, demography, and lek stability in an Amazonian bird

description: Lekking is a rare, but iconic mating system where polygynous males
 aggregate and perform group displays to attract females. Existing theory
 postulates that demographic and environmental stability are required for
 lekking to be an evolutionarily viable reproductive strategy. However, we
 lack empirical tests for the hypotheses that lek stability is facilitated
 by age-specific variation in demographic rates, and by predictable,
 abundant resources. To address this knowledge gap, we use multistate
 models to examine how two demographic elements of lek stability—male
 survival and recruitment—vary with age, social status and phase of the El
 Niño Southern Oscillation (ENSO) in a Neotropical frugivorous bird, the
 wire-tailed manakin (Pipra filicauda). Our results show that demographic
 and environmental conditions were related to lek stability in the
 Ecuadorean Amazon. Apparent annual survival probability of territorial
 males was higher than that of non-territorial floaters, and recruitment
 probability increased as males progressed in an age-graded queue.
 Moreover, annual survival of territorial males and body condition of both
 floaters and territory holders were higher following years with El Niño
 conditions, associated with reduced rainfall and probably higher fruit
 production in the northern Neotropics, and lower after years with wet, La
 Niña conditions that predominated our study. Recruitment probabilities
 varied annually, independent of ENSO phase, and increased over our study
 period, but the annual mean number of territorial males per lek declined.
 Our results provide empirical support for hypothesized demographic and
 environmental drivers of lek dynamics. This study also suggests that
 climate-mediated changes in resource availability can affect demography
 and subsequent lek stability in a relatively buffered, lowland rainforest.
description: PIPFIL_MALES for
 MULTIMultistate Capture
 HistoriesMorphological Data for
 BCIMorphological variables
 used for condition indicesPIPFIL_M_BCI.csvPIPFIL_Mark_ModelsMark Model DBF files
DOI: 10.5281/zenodo.18386716
title: SuperDARN data in netCDF format (2005-Dec)

description: 2005-Dec SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'
DOI: 10.5281/zenodo.6633541
title: SuperDARN data in netCDF format (2005-Dec)

description: 2005-Dec SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'