cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j3t86
title: Data from: Spatio-temporal models reveal subtle changes to demersal communities following the Exxon Valdez oil spill

description: Toxic pollutants such as crude oil have direct negative effects for a wide
 array of marine life. While mortality from acute exposure to oil is
 obvious, sub-lethal consequences of exposure to petroleum derivatives for
 growth and reproduction are less evident and sub-lethal effects in fish
 populations are obscured by natural environmental variation, fishing, and
 measurement error. We use fisheries independent surveys in the Gulf of
 Alaska to examine the consequences of the 1989 Exxon Valdez oil spill
 (EVOS) for demersal fish. We delineate areas across a range of exposure to
 EVOS and use spatio-temporal models to quantify the abundance of 53
 species-groups over 31 years. We compare multiple community metrics for
 demersal fish in EVOS and Control areas. We find that areas more exposed
 to EVOS have more negative trends in total groundfish biomass than
 non-EVOS areas, and that this change is driven primarily by reductions in
 the abundance of the apex predator guild. We show no signature of
 increased variability or increased levels of synchrony within EVOS areas.
 Our analysis supports mild consequences of EVOS for groundfish
 communities, but suggests that long time-series and assessments of changes
 at the community level may reveal sub-lethal effects in marine
 communities.
description: Datafiles and scripts
 for Shelton et al. 2017This file is composed of
 four sub-files. The "READ ME.zip" contains two word files that
 describe how the data files and R scripts interact to provide. "Csv
 data files.zip" contains four csv files including raw data used in
 the analysis, a spatial projection data file required to generate
 predictions used in the analysis, a file detailing the spatial locations
 used in the analysis, and the final output from the statistical model used
 to create figures. "Gulf of Alaska shapefile.zip" contains the
 files needed to open and manipulate the spatial data layers for the Gulf
 of Alaska. "R scripts.zip" contains seven R scripts that
 interact to produce the analysis and plot in the manuscript (see ReadMe
 for more details).Data_Scripts_and_Shapefiles.zip
DOI: 10.5061/dryad.7gp59
title: Data from: The ecology of avian influenza viruses in wild dabbling ducks (Anas spp.) in Canada

description: Avian influenza virus (AIV) occurrence and transmission remain important
 wildlife and human health issues in much of the world, including in North
 America. Through Canada's Inter-Agency Wild Bird Influenza Survey,
 close to 20,000 apparently healthy, wild dabbling ducks (of seven species)
 were tested for AIV between 2005 and 2011. We used these data to identify
 and evaluate ecological and demographic correlates of infection with low
 pathogenic AIVs in wild dabbling ducks (Anas spp.) across Canada.
 Generalized linear mixed effects model analyses revealed that risk of AIV
 infection was higher in hatch-year birds compared to adults, and was
 positively associated with a high proportion of hatch-year birds in the
 population. Males were more likely to be infected than females in British
 Columbia and in Eastern Provinces of Canada, but more complex
 relationships among age and sex cohorts were found in the Prairie
 Provinces. A species effect was apparent in Eastern Canada and British
 Columbia, where teal (A. discors and/or A. carolinensis) were less likely
 to be infected than mallards (A. platyrhynchos). Risk of AIV infection
 increased with the density of the breeding population, in both Eastern
 Canada and the Prairie Provinces, and lower temperatures preceding
 sampling were associated with a higher probability of AIV infection in
 Eastern Canada. Our results provide new insights into the ecological and
 demographic factors associated with AIV infection in waterfowl.
description: Ecology of Avian
 Influenza Viruses in Wild Dabbling Ducks in CanadaDryad_revised.csv
DOI: 10.5061/dryad.p82f2
title: Data from: Scale and direction of adaptive introgression between black cottonwood (Populus trichocarpa) and balsam poplar (P. balsamifera)

description: Introgression can introduce novel genetic variation at a faster rate than
 mutation alone, and result in adaptive introgression when adaptive alleles
 are maintained in the recipient genome over time by natural selection. A
 previous study from our group demonstrated adaptive introgression from
 Populus balsamifera into P. trichocarpa in a target genomic region. Here
 we expanded our local ancestry analysis to the whole genome of both
 parents to provide a comprehensive, unbiased view of introgression
 patterns and to identify additional candidate regions for adaptive
 introgression genome-wide. Populus trichocarpa is a large, fast-growing
 tree of mild coastal regions of the Pacific northwest, whereas P.
 balsamifera is a smaller stature tree of continental and boreal regions
 with intense winter-cold. The species are parapatric with extensive
 hybridization. Here, using local ancestry analysis, we detected asymmetric
 patterns of introgression across the whole genome of these two species of
 poplar trees adapted to contrasting environments, with stronger
 introgression from P. balsamifera to P. trichocarpa than vice versa.
 Admixed P. trichocarpa individuals showed more genomic regions with
 unusually high levels of introgression (19 regions) compared with admixed
 P. balsamifera (9 regions) but also the largest introgressed peak (1.02
 Mb). Our analysis also revealed numerous candidate regions for adaptive
 introgression with strong signals of selection, notably related to disease
 resistance, and enriched for genes that may play crucial roles for
 survival and adaptation. Furthermore, we revealed overrepresentation of
 subtelomeric regions in P. balsamifera introgression into P. trichocarpa
 and possible protection of the sex-determining regions from interspecific
 gene flow.
description: annotation_introgressed_genesAnnotation of candidate genes for adaptive introgression across the whole genome of P. trichocarpa (balsa in tricho) and P. balsamifera (tricho in balsa) based on local ancestry analysis in RASPberry. Gene annotation was retrived using Popgenie (Sjödin et al. 2009)TajimasD_wg_Pt_PbTajima’s D values across all the introgressed regions for the 50 pure species individuals (P. trichocarpa and P. balsamifera), using 20-kb windows. Tajimas' D in P. balsamifera quantile 0.05 =-1.35871; 0.95 = 1.49239. Tajimas' D in P. trichocarpa quantile 0.05 =-1.22174; 0.95 = 1.29456
DOI: 10.5281/zenodo.18388287
title: 2026 Europlanet GMAP Winter School - Lava tubes hands-on

description: Training datasets for the Europlanet Winter School 2026. This is the repository for the excersize about lava tubes, contains an image, a DTM, and test shapefiles located in Arsia Mons, in Mars.
DOI: 10.5281/zenodo.18269005
title: 2026 Europlanet GMAP Winter School - Lava tubes hands-on

description: Training datasets for the Europlanet Winter School 2026. This is the repository for the excersize about lava tubes, contains an image, a DTM, and test shapefiles located in Arsia Mons, in Mars.
DOI: 10.6084/m9.figshare.31157668
title: Supplementary data S3

description: 18S dataset for 37 rhabdocoel taxa in fasta format, after removing alignment-ambiguous sites and shortening.
DOI: 10.5061/dryad.1vr54
title: Data from: The role of exotic ladybeetles in the decline of native ladybeetle populations: evidence from long-term monitoring

description: Ladybeetles (Coleoptera: Coccinellidae) are ubiquitous predators which
 play an important role in suppressing pest insects. In North America, the
 coccinellid community is increasingly dominated by exotic species, and the
 abundance of some native species has declined dramatically since the
 1980s. Several hypotheses have been proposed to describe the mechanism of
 invasion coupled with native species declines, e.g. vacant niche
 exploitation, intraguild predation, competitive exploitation and habitat
 compression. We analyze a 24-year dataset of coccinellid community
 structure in southwestern Michigan to elucidate the most likely
 mechanism(s) of native coccinellid decline and implications for their
 conservation. Correlation analyses indicated that impact of exotic species
 on native coccinellids varies with their degree of interaction. Although
 several native species were observed to be in numerical decline, only
 Adalia bipunctata and Coleomegilla maculata had declines that were
 statistically significant. The magnitude of decline in these two species
 varied with the degree of dietary overlap with invaders, thus their
 decline is most likely driven by competitive exploitation. Habitat use
 patterns by some native species (A. bipunctata and Coccinella trifasciata)
 changed during years when the exotic Harmonia axyridis reached high
 numbers, lending support to the habitat compression hypothesis, where
 native species survive in ancestral (i.e. natural or semi-natural)
 habitats when invaders dominate cultivated habitats. Coccinellid
 communities occurring in semi-natural forested habitats were unique in
 both composition and variability from those occurring in cultivated
 habitats. Such semi-natural habitats can act as refuges for native
 coccinellids and may play a role in maintaining the functional resilience
 of coccinellid communities.
description: Ladybeetle captures at
 Kellogg Biological Station, 1989-2012Counts of 13 ladybeetle
 species collected from yellow sticky cards at sampling stations in the
 Main Cropping System Experiment at Kellogg biological station in
 southwestern Michiganraw_data_Bahlai_BINV_2015.csv
DOI: 10.6084/m9.figshare.31157668.v2
title: Supplementary data S3

description: 18S dataset for 37 rhabdocoel taxa in fasta format, after removing alignment-ambiguous sites and shortening.
DOI: 10.6084/m9.figshare.31157668.v1
title: Sekiguchi & Kakui 2026 - <b>Supplementary data S3.</b>

description: 18S dataset for 37 rhabdocoel taxa in fasta format, after removing alignment-ambiguous sites and shortening.
DOI: 10.5061/dryad.r7q86
title: Data from: Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens

description: Laboratory techniques for high-throughput sequencing have enhanced our
 ability to generate DNA sequence data from millions of natural history
 specimens collected prior to the molecular era, but remain poorly tested
 at shallower evolutionary time scales. Hybridization capture using
 restriction site-associated DNA probes (hyRAD) is a recently developed
 method for population genomics with museum specimens. The hyRAD method
 employs fragments produced in a restriction site-associated double
 digestion as the basis for probes that capture orthologous loci in samples
 of interest. While promising in that it does not require a reference
 genome, hyRAD has yet to be applied across study systems in independent
 laboratories. Here, we provide an independent assessment of the
 effectiveness of hyRAD on both fresh avian tissue and dried tissue from
 museum specimens up to 140 years old and investigate how variable
 quantities of input DNA affect sequencing, assembly, and population
 genetic inference. We present a modified bench protocol and bioinformatics
 pipeline, including three steps for detection and removal of microbial and
 mitochondrial DNA contaminants. We confirm that hyRAD is an effective tool
 for sampling thousands of orthologous SNPs from historic museum specimens
 to describe phylogeographic patterns. We find that modern DNA performs
 significantly better than historical DNA better during sequencing but that
 assembly performance is largely equivalent. We also find that the quantity
 of input DNA predicts %GC content of assembled contiguous sequences,
 suggesting PCR bias. We caution against sampling schemes that include
 taxonomic or geographic autocorrelation across modern and historic
 samples.
description: S. torotoro
 pseudo-reference genomePseudo-reference genome
 for clean read alignment, consisting of assembled loci from probe library
 (S. t. ochracea, CAS ORN 97943) merged with on-target assemblies and 100
 bp flanking regions from other modern DNA samples.syma_torotoro_pseudoreference.fastaS. torotoro 100% SNP matrix for adegenet100% complete SNP matrix of 19 Syma torotoro samples formatted for import to R package adegenet.syma_torotoro_SNPs_noMD_adegenethyRAD performance metricsTable with information on numerous enrichment, sequencing, and assembly statistics for both modern and historic S. torotoro hyRAD libraries.syma_torotoro_hyRAD_performance.csvS. torotoro full data SNP matrixFull data (39,105 SNPs) matrix for 19 individuals of S. torotoro, in Eigenstrat (.geno) format.syma_torotoro_SNPs_full.geno
DOI: 10.5061/dryad.70mt1
title: Data from: Vegetation response to control of invasive Tamarix in southwestern US rivers: a collaborative study including 416 sites

description: Most studies assessing vegetation response following control of invasive
 Tamarix trees along southwestern U.S. rivers have been small in scale
 (e.g., river reach), or at a regional scale but with poor spatial-temporal
 replication, and most have not included testing the effects of a now
 widely-used biological control. We monitored plant composition following
 Tamarix control along hydrologic, soil and climatic gradients in 244
 treated and 172 reference sites across six U.S. States. This represents
 the largest comprehensive assessment to date on the vegetation response to
 the four most common Tamarix control treatments. Biocontrol by a
 defoliating beetle (treatment #1) reduced the abundance of Tamarix less
 than active removal by mechanically using hand and chain-saws (#2), heavy
 machinery (#3) or burning (#4). Tamarix abundance also decreased with
 lower temperatures, higher precipitation, and follow-up treatments for
 Tamarix resprouting. Native cover generally increased over time in active
 Tamarix removal sites, however, the increases observed were small and was
 not consistently increased by active revegetation. Overall, native cover
 was correlated to permanent stream flow, lower grazing pressure, lower
 soil salinity and temperatures, and higher precipitation. Species
 diversity also increased where Tamarix was removed. However, Tamarix
 treatments, especially those generating the highest disturbance (burning
 and heavy machinery), also often promoted secondary invasions of exotic
 forbs. The abundance of hydrophytic species was much lower in treated than
 in reference sites, suggesting that management of southwestern U.S. rivers
 has focused too much on weed control, overlooking restoration of fluvial
 processes that provide habitat for hydrophytic and floodplain vegetation.
 These results can help inform future management of Tamarix-infested rivers
 to restore hydrogeomorphic processes, increase native biodiversity and
 reduce abundance of noxious species.
description: Tamarix
 "Chorus" DatasetPlant composition
 (species abundance) following Tamarix control and environmental variables
 including management, hydrology, soil and climate in 244 treated and 172
 reference sites across six U.S. States.TamarixChorusDataset for
 Dryad.xlsx
DOI: 10.5061/dryad.rm7dd
title: Data from: Epigenomic study identifies a novel mesenchyme homeobox2-GLI1 transcription axis involved in cancer drug resistance, overall survival and therapy prognosis in lung cancer patients

description: Several homeobox-related gene (HOX) transcription factors such as
 mesenchyme HOX-2 (MEOX2) have previously been associated with cancer drug
 resistance, malignant progression and/or clinical prognostic responses in
 lung cancer patients; however, the mechanisms involved in these responses
 have yet to be elucidated. Here, an epigenomic strategy was implemented to
 identify novel MEOX2 gene promoter transcription targets and propose a new
 molecular mechanism underlying lung cancer drug resistance and poor
 clinical prognosis. Chromatin immunoprecipitation (ChIP) assays derived
 from non-small cell lung carcinomas (NSCLC) hybridized on gene promoter
 tiling arrays and bioinformatics analyses were performed, and
 quantitative, functional and clinical validation were also carried out. We
 statistically identified a common profile consisting of 78 gene promoter
 targets, including Hedgehog-GLI1 gene promoter sequences (FDR≤0.1 and
 FDR≤0.2). The GLI-1 gene promoter region from -2,192 to -109 was occupied
 by MEOX2, accompanied by transcriptionally active RNA Pol II and was
 epigenetically linked to the active histones H3K27Ac and H3K4me3; these
 associations were quantitatively validated. Moreover, siRNA genetic
 silencing assays identified a MEOX2-GLI1 axis involved in cellular
 cytotoxic resistance to cisplatinum in a dose-dependent manner, as well as
 cellular migration and proliferation. Finally, Kaplan-Maier survival
 analyses identified significant MEOX2-dependent GLI-1 protein expression
 associated with clinical progression and poorer overall survival using an
 independent cohort of NSCLC patients undergoing platinum-based oncological
 therapy with both epidermal growth factor receptor (EGFR)-non-mutated and
 EGFR-mutated status. In conclusion, this is the first study to investigate
 epigenome-wide MEOX2-transcription factor occupation identifying a novel
 overexpressed MEOX2-GLI1 axis and its clinical association with
 platinum-based cancer drug resistance and EGFR-tyrosine kinase inhibitor
 (TKI)-based therapy responses in NSCLC patients.
description: Lung Cancer Epigenomics
 Data_MEOX2/RNA Pol II_ratio_peaksIdentification of
 Fluorescence peaks derived from the MEOX2 and RNA POL II
 Immuno-precipitation assays, derived from lung carcinoma patients, using
 gene promoter tiling microarrays (NIMBLEGEN Platform, 3X720K format).
 Shown peak ID, chromosome, start and end of peaks, score and FDR, and
 Access number.Epigenomic_data_MEOX2_ratio_peaks.zip
DOI: 10.15468/kh5bwe
title: New species of Afagrilaxia Bílý & Bellamy, 1999 (Coleoptera: Buprestidae) from South Africa

description: This dataset contains the digitized treatments in Plazi based on the original journal article Obořil, Martin, Sekerka, Lukáš (2025): New species of Afagrilaxia Bílý & Bellamy, 1999 (Coleoptera: Buprestidae) from South Africa. Zootaxa 5719 (1): 133-138, DOI: 10.11646/zootaxa.5719.1.8, URL: https://doi.org/10.11646/zootaxa.5719.1.8AbstractAfagrilaxia magorgori Obořil & Sekerka, sp. nov. from South Africa and Zimbabwe is described, illustrated, and compared with the yet only known species of the genus, Afagrilaxia natalensis (Bellamy, 1986), which is also illustrated.
DOI: 10.5061/dryad.c4t44
title: Data from: The effects of climate warming and disturbance on the colonization potential of ornamental alien plant species

description: 1. A large number of alien plant species have been introduced as
 ornamental garden plants to Europe, but relatively few have become
 invasive. Low climatic suitability may be limiting the current invasion
 potential of many alien ornamental species. However, with ongoing
 disturbance and climate change, this barrier may be reduced for some
 species. 2. Here we tested how colonization ability (a prerequisite for
 invasion) of frequently planted alien ornamentals depends on disturbance
 and heating, and on their species characteristics. We sowed seeds of 37
 non-naturalized alien herbaceous garden-plant species into native
 grassland plots with and without disturbance, and with and without
 infrared heating lamps. To assess whether their responses differ from
 those within the regional wild flora, we also sowed 14 native species and
 12 naturalized alien species. During two years, we assessed the
 likelihoods of germination, first-year survival, second-year survival and
 flowering of these 63 study species. 3. The heating treatment, which also
 reduced soil moisture, decreased all measures of colonization success, but
 more so for sown native species than for the non-naturalized and
 naturalized alien ones. The disturbance treatment increased colonization
 success, and because heating decreased productivity of the undisturbed
 grassland plots, it also increased invasibility of these plots. Average
 colonization success of non-naturalized aliens was reduced by heating, but
 some species were not affected or performed even better with heating,
 particularly those with an annual life span and a high seed mass. Winter
 hardiness improved colonization ability of non-naturalized aliens, but
 this advantage was reduced in the heated plots. 4. Synthesis. Disturbance
 increased and heating decreased the absolute colonization success of most
 of the 63 species sown. However, heating had stronger adverse effects on
 the resident grassland and sown native species than either type of sown
 alien species. Together, these results suggest that some alien plants may
 have greater colonization success relative to native plants under a warmer
 climate.
description: IR2017_EH_WD_MvK_dataComplete primary and supplementary data: sown species colonization data, temperature differences between heating treatments, soil moisture measurements, sown species optimal germination rates, grassland species composition, grassland biomass
DOI: 10.5061/dryad.501ps
title: Data from: Learning from the past to prepare for the future: felids face continued threat from declining prey richness

description: Many contemporary species of large-felids (&gt;15 kg) feed upon prey
 that are endangered, raising concern that prey population declines
 (defaunation) will further threaten felids. We assess the threat that
 defaunation presents by investigating a late Quaternary (LQ),
 ‘present-natural’ counterfactual scenario. Our present-natural
 counterfactual is based on predicted ranges of mammals today in the
 absence of any impacts of modern humans (Homo sapiens) through time. Data
 from our present-natural counterfactual are used to understand firstly how
 megafauna extinction has impacted felid communities to date and secondly
 to quantify the threat to large-felid communities posed by further
 declines in prey richness in the future. Our purpose is to identify
 imminent risks to biodiversity conservation and their cascading
 consequences and, specifically, to indicate the importance of preserving
 prey diversity. We pursue two lines of enquiry; first, we test whether the
 loss of prey species richness is a potential cause of large-felid
 extinction and range loss. Second, we explore what can be learnt from the
 large-scale large-mammal LQ losses, particularly in the Americas and
 Europe, to assess the threat any further decline in prey species presents
 to large-felids today, particularly in Africa and Asia. Large-felid
 species richness was considerably greater under our present-natural
 counterfactual scenario compared to the current reality. In total, 86% of
 cells recorded at least one additional felid in our present-natural
 counterfactual, and up to 4-5 more large-felids in 10% of the cells. A
 significant positive correlation was recorded between the number of prey
 species lost and the number of large-felids lost from a cell. Extant
 felids most at risk include lion and Sunda clouded leopard, as well as
 leopard and cheetah in parts of their range. Our results draw attention to
 the continuation of a trend of megafauna decline that began with the
 emergence of hominins in the Pleistocene.
description: Felid mammalian prey
 over present-natural range“Felid mammalian prey
 over present-natural range” is a dataset listing all the mammals that
 occur in each extant and recently extinct felid’s present-natural range.
 It also records an estimate of the importance as a prey species of each
 mammal to each felid.Sandom Appendix 1
 240117.csv