cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dk6gj
title: Data from: New resources for genetic studies in Populus nigra: genome wide SNP discovery and development of a 12k Infinium array

description: Whole genome resequencing of 51 Populus nigra (L.) individuals from across
 Western Europe was performed using Illumina platforms. A total number of
 1,878,727 SNPs distributed along the P. nigra reference sequence were
 identified. The SNP calling accuracy was validated with Sanger sequencing.
 SNPs were selected within 14 previously identified QTL regions; 2916
 expressional candidate genes related to rust resistance, wood properties,
 water-use efficiency and bud phenology and 1732 genes randomly spread
 across the genome. Over 10,000 SNPs were selected for the construction of
 a 12k Infinium BeadChip array dedicated to association mapping. The SNP
 genotyping assay was performed with 888 P. nigra individuals. The
 genotyping success rate was 91%. Our high success rate was due to the
 discovery panel design and the stringent parameters applied for SNP
 calling and selection. In the same set of P. nigra genotypes, linkage
 disequilibrium throughout the genome decayed on average within 5 to 7 kb
 to half of its maximum value. As an application test, ADMIXTURE analysis
 was performed with a selection of 600 SNPs spread throughout the genome
 and 706 individuals collected along 12 river basins. The admixture pattern
 was consistent with genetic diversity revealed by neutral markers and the
 geographical distribution of the populations. These newly developed SNP
 resources and genotyping array provide a valuable tool for population
 genetic studies and identification of QTLs through natural-population
 based genetic association studies in P. nigra.
description: List of SNPs extracted
 from HT-sequencing dataThe SNPs are denoted by
 SNP_IGA followed by the chromosome or scaffold number (V2.0) and the base
 position within the scaffold.List of SNPs from HTsequencing
 data.xlsxP. nigra Genotype
 dataGenotype calling of P.
 nigra individuals originating from 12 western european river basins and
 full sib progenies. The individuals are listed in Tables
 S1Input files for
 ADMIXTURE and PCAInput files for
 ADMIXTURE and PCA analysis see Material and methods
 sectionP. nigra reference
 sequenceThis .zip file contains
 the fasta-formatted and compressed complete sequence of Populus nigra
 genotype 71077-308.Consensus_71077-308_version0915-MER.fa.zip
DOI: 10.5281/zenodo.18391888
title: Données des fouilles archéologiques menées au site paléolithique de la Tute du Pèlerin, Fabas, France

description: Ce dépôt contient les données des fouilles menées entre 2021 et 2025 sur le site paléolithique de la Tute du Pèlerin, à Fabas (France). Il se compose de plusieurs tableaux :



tute-du-pelerin.csv : données des fouilles 2021-2024, une ligne correspond à un objet archéologique

tute-du-pelerin_2025.csv : données des fouilles 2021-2024, une ligne correspond à un objet archéologique

tute-du-pelerin-refits.csv : remontages observés entre fragments d'objets ; une ligne du tableau documente une relation de remontages.
DOI: 10.5281/zenodo.18391889
title: Données des fouilles archéologiques menées au site paléolithique de la Tute du Pèlerin, Fabas, France

description: Ce dépôt contient les données des fouilles menées entre 2021 et 2025 sur le site paléolithique de la Tute du Pèlerin, à Fabas (France). Il se compose de plusieurs tableaux :



tute-du-pelerin.csv : données des fouilles 2021-2024, une ligne correspond à un objet archéologique

tute-du-pelerin_2025.csv : données des fouilles 2021-2024, une ligne correspond à un objet archéologique

tute-du-pelerin-refits.csv : remontages observés entre fragments d'objets ; une ligne du tableau documente une relation de remontages.
DOI: 10.5061/dryad.tr85d
title: Data from: Conserved but attenuated parental gene expression in allopolyploids: constitutive zinc hyperaccumulation in the allotetraploid Arabidopsis kamchatica

description: Allopolyploidization combines parental genomes and often confers broader
 species distribution. However, little is known about parentally
 transmitted gene expression underlying quantitative traits following
 allopolyploidization because of the complexity of polyploid genomes. The
 allopolyploid species Arabidopsis kamchatica is a natural hybrid of the
 zinc hyperaccumulator A. halleri and of the nonaccumulator A. lyrata. We
 found that A. kamchatica retained the ability to hyperaccumulate zinc from
 A. halleri and grows in soils with both low and high metal content.
 Hyperaccumulation of zinc by A. kamchatica was reduced to about half of A.
 halleri, but is 10-fold greater than A. lyrata. Homeologs derived from A.
 halleri had significantly higher levels of expression of genes such as
 HEAVY METAL ATPASE4 (HMA4), METAL TRANSPORTER PROTEIN1 and other metal ion
 transporters than those derived from A. lyrata, which suggests
 cis-regulatory differences. A. kamchatica has on average half the
 expression of these genes compared with A. halleri due to fixed
 heterozygosity inherent in allopolyploids. Zinc treatment significantly
 changed the ratios of expression of 1% of homeologous pairs, including
 genes putatively involved in metal homeostasis. Resequencing data showed a
 significant reduction in genetic diversity over a large genomic region
 (290 kb) surrounding the HMA4 locus derived from the A. halleri parent
 compared with the syntenic A. lyrata-derived region, which suggests
 different evolutionary histories. We also estimated that three A.
 halleri-derived HMA4 copies are present in A. kamchatica. Our findings
 support a transcriptomic model in which environment-related
 transcriptional patterns of both parents are conserved but attenuated in
 the allopolyploids.
description: HMA4 homeologs and
 flanking gene alignments13 CDS alignments used
 in polymorphism analysis of HMA4 in A. kamchatica.Akam_all.fastaSupplementaryFile5A. kamchatica Murodo (MUR) genotype whole genome leaf (5.2) and root (5.3) expression and statistics, and only heavy metal annotated genes (5.4).SupplementaryFile6A. kamchatica Potter (PAK) genotype whole genome leaf (6.2) and root (6.3) expression and statistics.SupplementaryFile7A. halleri and A. lyrata leaf and root expression and statistics.
DOI: 10.15468/hpmk35
title: University of California Santa Cruz Fungal Herbarium

description: The UCSC Fungal Herbarium, hosted at the Kenneth S. Norris Center for Natural History, is a small but powerful collection comprising hundreds of collections from the Pacific states, as well as a few from farther abroad (including the eastern United States and Mexico). Our herbarium is set apart by the high quality of photography and metadata accompanying the collections. The breadth and depth of collections from the Redwood Coast bioregion in particular makes this an excellent resource for ecologists. Contributions of funding and logistial support from the Fungus Federation of Santa Cruz and ongoing work by students of the UCSC MycoTeam have made it possible to pair microscopic data, and in many cases, DNA sequences with our collections.
DOI: 10.5061/dryad.k6j0h
title: Data from: Higher fungal diversity is correlated with lower CO2 emissions from dead wood in a natural forest

description: Wood decomposition releases almost as much CO2 to the atmosphere as does
 fossil-fuel combustion, so the factors regulating wood decomposition can
 affect global carbon cycling. We used metabarcoding to estimate the fungal
 species diversities of naturally colonized decomposing wood in subtropical
 China and, for the first time, compared them to concurrent measures of CO2
 emissions. Wood hosting more diverse fungal communities emitted less CO2,
 with Shannon diversity explaining 26 to 44% of emissions variation.
 Community analysis supports a ‘pure diversity’ effect of fungi on
 decomposition rates and thus suggests that interference competition is an
 underlying mechanism. Our findings extend the results of published
 experiments using low-diversity, laboratory-inoculated wood to a
 high-diversity, natural system. We hypothesize that high levels of
 saprotrophic fungal biodiversity could be providing globally important
 ecosystem services by maintaining dead-wood habitats and by slowing the
 atmospheric contribution of CO2 from the world’s stock of decomposing
 wood. However, large-scale surveys and controlled experimental tests in
 natural settings will be needed to test this hypothesis.
description: otutable_first200_taxTop 200 most reads OTUs with their taxonomy assignment and reads numberSequence dataRaw 454 sequencing dataBioinformatic command scriptAn example bioinformatic scriptS1 fungus_CROP_R_script_nonrarefiedThe HTML outputs of the R scripts using the non-rarefied CROP datasetsS1 fungus_CROP_R_script_rarefiedThe HTML outputs of the R scripts using the rarefied CROP datasetsS1 fungus_uclust_R_script_nonrarefiedThe HTML outputs of the R scripts using the non-rarefied UCLUST datasetsS1 fungus_uclust_R_script_rarefiedThe HTML outputs of the R scripts using the rarefied UCLUST datasetsMapping filesMapping files to link MID sequences to sample metadata. Used in the QIIME split_libraries.py scriptmapping_files.zip
DOI: 10.5061/dryad.qm4j1.1
title: Data from: Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales

description: Comparative genetic studies of non-model organisms are transforming
 rapidly due to major advances in sequencing technology. A limiting factor
 in these studies has been the identification and screening of orthologous
 loci across an evolutionarily distant set of taxa. Here, we evaluate the
 efficacy of genomic markers targeting ultraconserved DNA elements (UCEs)
 for analyses at shallow evolutionary timescales. Using sequence capture
 and massively parallel sequencing to generate UCE data for five
 co-distributed Neotropical rainforest bird species, we recovered 776–1516
 UCE loci across the five species. Across species, 53–77% of the loci were
 polymorphic, containing between 2.0 and 3.2 variable sites per polymorphic
 locus, on average. We performed species tree construction, coalescent
 modeling, and species delimitation, and we found that the five
 co-distributed species exhibited discordant phylogeographic histories. We
 also found that species trees and divergence times estimated from UCEs
 were similar to the parameters obtained from mtDNA. The species that
 inhabit the understory had older divergence times across barriers,
 contained a higher number of cryptic species, and exhibited larger
 effective population sizes relative to the species inhabiting the canopy.
 Because orthologous UCEs can be obtained from a wide array of taxa, are
 polymorphic at shallow evolutionary timescales, and can be generated
 rapidly at low cost, they are an effective genetic marker for studies
 investigating evolutionary patterns and processes at shallow timescales.
description: Supplemental
 FiguresSupplemental-data-
 GPhoCS-outputSupplementary
 TablesSupplementary
 MethodsSupp
 Methods.docxSupplemental
 FiguresSupplemental-data-
 GPhoCS-outputSupplementary
 TablesSupplementary
 MethodsSupp
 Methods.docxSupplemental
 FiguresSupplemental-data-
 GPhoCS-outputSupplementary
 TablesSupplementary
 MethodsSupp
 Methods.docxfullFasta alignments of
 sequences from ultraconserved elements containing up to eight individuals
 from each of five study species. All alignments in a given species that
 contain at least one individual in each of four areas of endemism are
 included.orthologsFasta alignments of sequences from ultraconserved elements containing up to eight individuals from each of five study species. Only the 166 loci that are present in all five full datasets are included.interspecies_fullFasta alignments of sequences from ultraconserved elements containing up to thirty-six individuals from five study species. Alignments include samples from all species, and any loci for which data was recovered for at least two individuals.interspecies_reducedFasta alignments of sequences from ultraconserved elements containing up to thirty-six individuals from five study species. Alignments include samples from all species, but only loci for which at least one individual is represented in every area of endemism in all study species.
DOI: 10.5061/dryad.k95j3
title: Data from: Spatial spread of the West Africa Ebola epidemic

description: Controlling Ebola outbreaks and planning an effective response to future
 emerging diseases are enhanced by understanding the role of geography in
 transmission. Here we show how epidemic expansion may be predicted by
 evaluating the relative probability of alternative epidemic paths. We
 compared multiple candidate models to characterize the spatial network
 over which the 2013–2015 West Africa epidemic of Ebola virus spread and
 estimate the effects of geographical covariates on transmission during
 peak spread. The best model was a generalized gravity model where the
 probability of transmission between locations depended on distance,
 population density and international border closures between Guinea,
 Liberia and Sierra Leone and neighbouring countries. This model
 out-performed alternative models based on diffusive spread, the force of
 infection, mobility estimated from cell phone records and other
 hypothesized patterns of spread. These findings highlight the importance
 of integrated geography to epidemic expansion and may contribute to
 identifying both the most vulnerable unaffected areas and locations of
 maximum intervention value.
description: DataAndCodeIncludes all data and code used in the manuscript. This includes data manipulation, data analysis and figures.DataTrajectories of Ebola infection probability in West Africa.data.zip
DOI: 10.5061/dryad.5q1sb
title: Data from: Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment

description: The fruit fly Drosophila is a classic model organism to study adaptation
 as well as the relationship between genetic variation and phenotypes.
 Although associated bacterial communities might be important for many
 aspects of Drosophila biology, knowledge about their diversity,
 composition, and factors shaping them is limited. We used 454-based
 sequencing of a variable region of the bacterial 16S ribosomal RNA gene to
 characterize the bacterial communities associated with wild and laboratory
 Drosophila isolates. In order to specifically investigate effects of food
 source and host species on bacterial communities, we analyzed samples from
 wild Drosophila melanogaster and D. simulans collected from a variety of
 natural substrates, as well as from adults and larvae of nine
 laboratory-reared Drosophila species. We find no evidence for host species
 effects in lab-reared flies; instead, lab of origin and stochastic
 effects, which could influence studies of Drosophila phenotypes, are
 pronounced. In contrast, the natural Drosophila–associated microbiota
 appears to be predominantly shaped by food substrate with an additional
 but smaller effect of host species identity. We identify a core member of
 this natural microbiota that belongs to the genus Gluconobacter and is
 common to all wild-caught flies in this study, but absent from the
 laboratory. This makes it a strong candidate for being part of what could
 be a natural D. melanogaster and D. simulans core microbiome. Furthermore,
 we were able to identify candidate pathogens in natural fly isolates.
description: Staubachetal2The file contains a metadata spreadsheet that provides detailed information about samples and another zip file that contains a fasta formatted sequence file for each sample in the study as well as a sequence quality file for each sampleStaubachetal.zip
DOI: 10.5061/dryad.h8972
title: Data from: The mating behaviour of the seed shrimp Parapolycope spiralis (Ostracoda: Cladocopina), with insight into the evolution of mating systems in cryptic interstitial habitats

description: The mating behaviour of the interstitial ostracod Parapolycope spiralis
 Tanaka & Tsukagoshi, 2010 is reported here for the first time.
 This species is adapted to an interstitial environment, and is typified by
 having tiny body size and being completely blind. In this paper it is
 presumed that the characteristics of the mating behaviour are typical for
 species in an interstitial environment. Observations by microscopy on
 mating behaviour in the laboratory showed various distinct stages: (1) the
 male captures the female by a sucker on the antennula; (2) the male clasps
 and maintains the mating position using the endopodite, the endopodite
 claw, and the exopodite of the antenna; (3) the male makes contact using
 the distal part of the upper lip; and (4) copulation takes place. These
 observations indicate that the sequence of stages of the mating behaviour
 of miniaturized animals is not necessarily always a simplified process.
 During the process, it seems that the male upper lip establishes physical
 contact stimuli with the female. Because the interstitial environment is
 cryptic and consists of a three-dimensional space with reduced
 connectivity, direct physical contact is likely to be one of the most
 effective and successful courtship behaviours.
description: Video_S1MPEG video clip of the mating behaviour of Parapolycope spiralis (Ostracoda). Stage 1: male captures female by sucker on the antennula.Video_S2MPEG video clip of the mating behaviour of Parapolycope spiralis (Ostracoda). Stage 2: male (right side) clasps female (left side) and maintains the mating position by the endopodite, endopodite claw, and exopodite of the antenna.Video_S3MPEG video clip of the mating behaviour of Parapolycope spiralis (Ostracoda). Stage 3: male (upper side) repeatedly makes contact with the lateral side of female (lower side) posterior body, by the distal part of upper lip. Male upper lip is viewable (00:05 and 00:31).Video_S4MPEG video clip of the mating behaviour of Parapolycope spiralis (Ostracoda). Stage 4:male (right side) flexes the posterior of its body back and forth and then inserts the ejaculatory duct into the female (left side) genital opening, in reversed ventral-ventral mating position. Anterior of the male is in the direction of the lower left of the screen. Anterior of the female is in the direction of the upper left corner of the screen.
DOI: 10.5061/dryad.cm28r
title: Data from: Phylogenomics using formalin-fixed and 100+ year old intractable natural history specimens

description: Museum specimens provide a wealth of information to biologists, but
 obtaining genetic data from formalin-fixed and fluid-preserved specimens
 remains challenging. While DNA sequences have been recovered from such
 specimens, most approaches are time-consuming and produce low data quality
 and quantity. Here we use a modified DNA extraction protocol combined with
 high-throughput sequencing to recover DNA from formalin-fixed and
 fluid-preserved snakes that were collected over a century ago and for
 which little or no modern genetic materials exist in public collections.
 We successfully extracted DNA and sequenced ultraconserved elements (x̄ =
 2,318 loci) from 10 fluid-preserved snakes and included them in a
 phylogeny with modern samples. This phylogeny demonstrates the general use
 of such specimens in phylogenomic studies and provides evidence for the
 placement of enigmatic snakes, such as the rare and never-before sequenced
 Indian Xylophis stenorhynchus. Our study emphasizes the relevance of
 museum collections in modern research and simultaneously provides a
 protocol that may prove useful for specimens that have been previously
 intractable for DNA sequencing.
description: Phylips&treesIncludes the 50% missing data alignment/resulting tree and the 35% missing data (i.e., 65% complete) alignment/resulting tree .ESM3_Phylips&trees.zipExtraction_protocolExtraction protocol followed in the manuscript.Abyss contigsThe assembled contigs for each sequenced individual from Abyss, including the negative control.contigs.zipall_snakes_dataset1_informative_sites.inf.taxonTab delimited text files with information for resulting UCE loci for both the 50% missing data matrix and the 35% missing data matrix (i.e., 65% complete).Final_Specimen&LibraryPrepExcel file (with two tabs) with details on specimens and library prep information.
DOI: 10.15468/dl.hbkdf7
title: Occurrence Download

description: A dataset containing 738 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (c8d737e0-2ff8-42e8-b8fc-6b805d26fc5f, 28eb1a3f-1c15-4a95-931a-4af90ecb574d)",
 "TaxonKey is Cornu aspersum",
 "Year 1000-2021"
 ]
}

 The dataset includes 738 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001729-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.67s40
title: Data from: Borneo and Indochina are major evolutionary hotspots for Southeast Asian biodiversity

description: Tropical Southeast Asia harbors extraordinary species richness and in its
 entirety comprises four of the Earth’s 34 biodiversity hotspots. Here, we
 examine the assembly of the Southeast Asian biota through time and space.
 We conduct meta-analyses of geological, climatic and biological (including
 61 phylogenetic) datasets to test which areas have been the sources of
 long-term biological diversity in SE Asia, particularly in the
 pre-Miocene, Miocene and Plio-Pleistocene, and whether the respective
 biota have been dominated by in situ diversification, immigration and/or
 emigration, or equilibrium dynamics. We identify Borneo and Indochina, in
 particular, as major ‘evolutionary hotspots’ for a diverse range of fauna
 and flora. While most of the region’s biodiversity is a result of both the
 accumulation of immigrants and in situ diversification, within-area
 diversification and subsequent emigration have been the predominant
 signals characterizing Indochina and Borneo’s biota since at least the
 early Miocene. In contrast, colonization events are comparatively rare
 from younger volcanically active emergent islands such as Java, which show
 increased levels of immigration events. Few dispersal events were observed
 across the major biogeographic barrier of Wallace’s Line. Accelerated
 efforts to conserve Borneo’s flora and fauna in particular, currently
 housing the highest levels of Southeast Asian plant and mammal species
 richness, are critically required.
description: Data from: Borneo and
 Indochina are major evolutionary hotspots for Southeast Asian
 biodiversityThis file contains
 Supplementary Data (scroll-down pdf showing SE Asia’s tectonic evolution
 from 160 Ma until present).Supplementary Data
 1.pdfData from: Borneo and
 Indochina are major evolutionary hotspots for Southeast Asian
 biodiversityThis file contains
 Supplementary Data (scroll-down pdf showing tectonics in the Banda region
 from 30 Ma until present).Supplementary Data
 2.pdfData from: Borneo and
 Indochina are major evolutionary hotspots for Southeast Asian
 biodiversitySupplementary Text,
 Figures and TablesdeBruyn_SI.pdfData from: Borneo and Indochina are major evolutionary hotspots for Southeast Asian biodiversityFolder includes sequence files for each dataset analysis performed in the present study (*.fas), BEAST input files for relaxed clock analyses (*.xml), BEAST MCC tree files used for Lagrange (*.tre), and Lagrange input and output files including area codes (*_lagrange.py, *_codes.txt, *_results.txt) if performed for the respective dataset.BEAST_Lagrange.zip