cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jb01f
title: Data from: Persistent reproductive isolation between sympatric lineages of fall Chinook salmon in White Salmon River, Washington

description: Populations of fall Chinook salmon Oncorhynchus tshawytscha in the
 Columbia River are divided among two evolutionarily significant units:
 lower Columbia River fall Chinook salmon (or “tules”) in the lower portion
 of the river and upriver “brights” (URBs) in the upper portion. The two
 lineages migrate together through portions of the lower Columbia River but
 spawn allopatrically. Little White Salmon National Fish Hatchery has been
 releasing URBs adjacent to what was historically exclusively tule spawning
 habitat in the White Salmon River for approximately 22 years. Tules and
 URBs now spawn in sympatry in the adjacent White Salmon River, and
 potential introgression between these two lineages has been identified as
 a genetic risk of the hatchery program. To assess the extent of
 introgression, we analyzed 13 microsatellite loci in juveniles taken from
 the White Salmon River in three consecutive years. Assignment tests
 revealed that juveniles leaving the White Salmon River from March to early
 May resembled tules, while those leaving from late May to June resembled
 URBs. Model-based hybrid detection revealed that between 4.3% and 15.0% of
 the juveniles in each year were tule × URB hybrids. No hybrid adults were
 detected in any of the collections examined. The divergence between the
 tule and URB populations in the White Salmon River was comparable to that
 between allopatric populations representing the two lineages. Although
 hybrid juveniles are produced in the wild, we found no evidence that they
 survive to return as adults or successfully cross back into the parental
 populations. The separation between the two fall Chinook salmon lineages
 thus appears to be based on intrinsic as well as extrinsic factors.
description: genotype data in Convert
 formatNote that the mixture
 collections from White Salmon River are listed twice. The first version
 includes all individuals, and the second version (marked by "ns"
 in the data) has all but one individual from each sibling group
 removed.
DOI: 10.5281/zenodo.18315043
title: GESMA: A Dataset of Ghanaian Environmental Soundscapes for Machine Learning Applications

description: The GESMA dataset is a large-scale collection of real-world Ghanaian environmental soundscapes designed to support machine learning research in acoustic scene analysis and sound event classification, particularly in low-resource and underrepresented contexts. It comprises 22,193 uncompressed 44.1 kHz/16-bit WAV audio recordings (approximately 62.24 hours) captured across diverse urban, institutional, and community environments in Ghana, including markets, transport hubs, educational settings, public spaces, and human non-verbal acoustic contexts.

Audio recordings were collected in situ using consumer-grade smartphones under natural acoustic conditions to preserve authentic background noise, reverberation, and overlapping sound events. All files are organized using a hierarchical labeling structure (category → class → subclass) and are accompanied by a structured CSV metadata file containing contextual information such as location, environment type, time of day, and recording device. Annotations were manually verified through a multi-stage validation process to ensure label accuracy and consistency, and recordings containing intelligible speech or poor signal quality were excluded.

The dataset addresses a significant geographic and cultural gap in existing environmental audio resources, which are predominantly derived from Western contexts. GESMA can be reused for a wide range of applications, including environmental monitoring, sound event detection, accessibility and assistive technologies, smart-city research, and the development and benchmarking of context-aware machine listening models. Its use of consumer-grade recording devices also enables reproducibility and extension by other researchers.
DOI: 10.5281/zenodo.18315044
title: GESMA: A Dataset of Ghanaian Environmental Soundscapes for Machine Learning Applications

description: The GESMA dataset is a large-scale collection of real-world Ghanaian environmental soundscapes designed to support machine learning research in acoustic scene analysis and sound event classification, particularly in low-resource and underrepresented contexts. It comprises 22,193 uncompressed 44.1 kHz/16-bit WAV audio recordings (approximately 62.24 hours) captured across diverse urban, institutional, and community environments in Ghana, including markets, transport hubs, educational settings, public spaces, and human non-verbal acoustic contexts.

Audio recordings were collected in situ using consumer-grade smartphones under natural acoustic conditions to preserve authentic background noise, reverberation, and overlapping sound events. All files are organized using a hierarchical labeling structure (category → class → subclass) and are accompanied by a structured CSV metadata file containing contextual information such as location, environment type, time of day, and recording device. Annotations were manually verified through a multi-stage validation process to ensure label accuracy and consistency, and recordings containing intelligible speech or poor signal quality were excluded.

The dataset addresses a significant geographic and cultural gap in existing environmental audio resources, which are predominantly derived from Western contexts. GESMA can be reused for a wide range of applications, including environmental monitoring, sound event detection, accessibility and assistive technologies, smart-city research, and the development and benchmarking of context-aware machine listening models. Its use of consumer-grade recording devices also enables reproducibility and extension by other researchers.
DOI: 10.5061/dryad.4nt8m
title: Data from: Phylogenomics and analysis of shared genes suggest a single transition to mutualism in Wolbachia of nematodes

description: Wolbachia, endosymbiotic bacteria of the order Rickettsiales, are
 widespread in arthropods but also present in nematodes. In arthropods, A
 and B supergroup Wolbachia are generally associated with distortion of
 host reproduction. In filarial nematodes, including some human parasites,
 multiple lines of experimental evidence indicate that C and D supergroup
 Wolbachia are essential for the survival of the host, and here the
 symbiotic relationship is considered mutualistic. The origin of this
 mutualistic endosymbiosis is of interest for both basic and applied
 reasons: How does a parasite become a mutualist? Could intervention in the
 mutualism aid in treatment of human disease? Correct rooting and
 high-quality resolution of Wolbachia relationships are required to resolve
 this question. However, because of the large genetic distance between
 Wolbachia and the nearest outgroups, and the limited number of genomes so
 far available for large-scale analyses, current phylogenies do not provide
 robust answers. We therefore sequenced the genome of the D supergroup
 Wolbachia endosymbiont of Litomosoides sigmodontis, revisited the
 selection of loci for phylogenomic analyses, and performed a phylogenomic
 analysis including available complete genomes (from isolates in
 supergroups A, B, C and D). Using ninety orthologous genes with reliable
 phylogenetic signals, we obtained a robust phylogenetic reconstruction,
 including a highly supported root to the Wolbachia phylogeny between an
 (A+B) clade and a (C+D) clade. While we currently lack data from several
 Wolbachia supergroups, notably F, our analysis supports a model wherein
 the putatively mutualist endosymbiotic relationship between Wolbachia and
 nematodes originated from a single transition event.
description: For_DRYADThe file is a zip archive of four files: Wolbachia_phylogenomic_90genes_concatenate.faa (the catenated aminoacid alignemtn of 90 genes), Wolbachia_phylogenomic_90genes_concatenate.ffn (the catenated nucleic acid alignemtn of 90 genes), Wolbachia_phylogenomic_OrthoMCL_cluster_aminoacidic_multifastas.zip (a zip file of the amino acid/protein sequences of clusters generated from the Wolbachia genomes using orthoMCL) and Wolbachia_phylogenomic_OrthoMCL_cluster_nucleotidic_multifastas.zip (a zip file of the nucleic acid sequences of clusters generated from the Wolbachia genomes using orthoMCL)
DOI: 10.5061/dryad.4tb7301
title: Data from: 100-year time-series reveal little morphological change following impoundment and predator invasion in two Neotropical characids

description: Human activities are dramatically altering ecosystems worldwide, often
 resulting in shifts in selection regimes. In response, natural populations
 sometimes undergo rapid phenotypic changes, which if adaptive, can
 increase their probability of persistence. However, in many instances,
 populations fail to undergo any phenotypic change, which might indicate a
 variety of possibilities, including maladaptation. In freshwater
 ecosystems, the impoundment of rivers and the introduction of exotic
 species are among the leading threats to native fishes. We examined how
 the construction of the Panama Canal, which formed Lake Gatun, and the
 subsequent invasion of the predatory Cichla monoculus influenced the
 morphology of two native fishes: Astyanax ruberrimus and Roeboides spp.
 Using a 100-year time series, we studied variation in overall body shape
 over time (pre vs. post impoundment and invasion) as well as across space
 (between an invaded and an uninvaded reservoir). In addition, we examined
 variation in linear morphological traits associated with swim performance
 and predator detection/avoidance. Notwithstanding a few significant
 changes in particular traits in particular comparisons, we found only
 limited evidence for morphological change associated with these two
 stressors. Most observed changes were subtle, and tended to be site and
 species-specific. The lack of a strong morphological response to these
 stressors, coupled with dramatic population declines in both species,
 suggests they may be maladapted to the anthropogenically-perturbed
 environment of Lake Gatun, but direct measures of fitness would be needed
 to test this. In general, our results suggest that morphological responses
 to anthropogenic disturbances can be very limited and when they do occur,
 are often complex and context-dependent.
description: Geladi_et_al_2019_Raw_data_fileHistorical specimens were collected from NMNH (National Museum of Natural History. Modern specimens were either collected by Diana Sharpe, Luis Fernando De León or/and Rigoberto Gonzalez. If not, they were in the inventory of STRI (Smithsonian Tropical Research institute).
DOI: 10.5061/dryad.hm7k5
title: Data from: Contrasting drivers of reproductive ageing in albatrosses

description: 1.Age-related variation in reproductive performance is ubiquitous in wild
 vertebrate populations and has important consequences for population and
 evolutionary dynamics. 2.The ageing trajectory is shaped by both
 within-individual processes, such as improvement and senescence, and by
 the among-individual effects of selective appearance and disappearance. To
 date, few studies have compared the role of these different drivers among
 species or populations. 3.In this study, we use nearly 40 years of
 longitudinal monitoring data to contrast the within- and among-individual
 processes contributing to the reproductive ageing patterns in three
 albatross species (two biennial and one annual breeder), and test whether
 these can be explained by differences in life-histories. 4.Early life
 performance in all species increased with age, and was predominantly
 influenced by within-individual improvements. However, reproductive
 senescence was detected in only two of the species. In the species
 exhibiting senescent declines, we also detected a terminal improvement in
 breeding success. This is suggestive of a trade-off between reproduction
 and survival, which was supported by evidence of selective disappearance
 of good breeders. 5.We demonstrate that comparisons of closely-related
 species which differ in specific aspects of their life-history can shed
 light on the ecological and evolutionary forces shaping variation in
 ageing patterns.
description: MeanAnnualBSData used to calculate mean annual breeding success for each species (Figure S1)FailureStageNest outcomes, used to calculate proportion of failures that occurred during incubation vs chick rearing for each speciesAFRALRData used to calculate mean age at first and last reproduction for each sex and species (Table 1)BreedingSucAgeData for the population-level analysis, used to model age-related variation in breeding success for each sex and species (Figure 2; Table S1; Table S2)BreedingSucAgeBothSexesData for the population-level analysis where the age of both parents was known, used to compare the explanatory power of male and female age for each species (Table S3)EarlyAdulthoodData for the analysis of factors underpinning breeding success in early adulthood for each sex and species (controlling for selective appearance) (Table 2a; Table S4)LateAdulthoodData for the analysis of factors underpinning breeding success in late adulthood for each sex and species (controlling for selective disappearance) (Table 2b; Table S5; Table S6; Table S7)GENERAL STATEMENT PLEASE READ THIS BEFORE USING THE DATADATA DESCRIPTION
DOI: 10.34740/kaggle/dsv/14631307
title: Berita UNNES
DOI: 10.5061/dryad.3r8p4
title: Data from: A proteomic strategy for global analysis of plant protein complexes

description: Global analyses of protein complex assembly, composition, and location are
 needed to fully understand how cells coordinate diverse metabolic,
 mechanical, and developmental activities. The most common methods for
 proteome-wide analysis of protein complexes rely on affinity
 purification-mass spectrometry or yeast two-hybrid approaches. These
 methods are time consuming and are not suitable for many plant species
 that are refractory to transformation or genome-wide cloning of open
 reading frames. Here, we describe the proof of concept for a method
 allowing simultaneous global analysis of endogenous protein complexes that
 begins with intact leaves and combines chromatographic separation of
 extracts from subcellular fractions with quantitative label-free protein
 abundance profiling by liquid chromatography-coupled mass spectrometry.
 Applying this approach to the crude cytosolic fraction of Arabidopsis
 thaliana leaves using size exclusion chromatography, we identified
 hundreds of cytosolic proteins that appeared to exist as components of
 stable protein complexes. The reliability of the method was validated by
 protein immunoblot analysis and comparisons with published size exclusion
 chromatography data and the masses of known complexes. The method can be
 implemented with appropriate instrumentation, is applicable to any
 biological system, and has the potential to be further developed to
 characterize the composition of protein complexes and measure the dynamics
 of protein complex localization and assembly under different conditions.
description: Program to compute
 protein abundance in mass spectrometryThe program is to
 compute protein abundance from spectral counts from mass spectrometry. It
 computes protein abundance from unique peptides and hared peptides among
 proteins considered. It is also available at
 http://kiharalab.org/RACalculator/RACalculator.zip
DOI: 10.5061/dryad.mn3g7
title: Data from: Myosin XI is associated with fitness and adaptation to aridity in wild pearl millet

description: Phenotypic changes in plants can be observed along many environmental
 gradients and are determined by both environmental and genetic factors.
 The identification of alleles associated with phenotypic variations is a
 rapidly developing area of research. We studied the genetic basis of
 phenotypic variations in 11 populations of wild pearl millet (Pennisetum
 glaucum) on two North-South aridity gradients, one in Niger and one in
 Mali. Most of the 11 phenotypic traits assessed in a common garden
 experiment varied between the populations studied. Moreover, the size of
 the inflorescence, the number of flowers and aboveground dry mass
 co-varied positively with a decrease in rainfall. To decipher the genetic
 basis of these phenotypes, we used an association mapping strategy with a
 mixed model. We found two SNPs on the same myosin XI contig significantly
 associated with variations in the average number of flowers. Both the
 allele frequency of the two SNPs and the average number of flowers
 co-varied with the rainfall gradient on the two gradients. Interestingly,
 this gene was also a target of selection during domestication. The Myosin
 XI gene is thus a good candidate for fitness-related adaptation in wild
 populations.
description: Table_Genotype_phenotype_dataThis file is an excel file containing the individual genotype of each plants, and its phenotype assess during two years (see article for more details).This dataset was used to performed association studies of wild pearl millet populations.
DOI: 10.5061/dryad.4s209
title: Data from: Prescribed fire and conifer removal promote positive understorey vegetation responses in oak woodlands

description: Fire-prone woodlands and savannas world-wide face management challenges
 resulting from fire exclusion and subsequent encroachment of
 fire-sensitive trees. In the Pacific Northwest (USA), Quercus garryana oak
 woodlands and savannas are threatened by encroachment from the native
 conifer Pseudotsuga menziesii in the absence of fire. In the Bald Hills of
 Redwood National Park (California, USA), prescribed fire and conifer
 removal have been used to restore encroached woodlands. We examined the
 effects of encroachment and restoration on understorey vegetation,
 comparing four treatments: prescribed fire, prescribed fire and conifer
 removal, conifer removal, and encroached (control). Treatments including
 prescribed fire had the greatest native species richness. These two
 treatments also had the greatest non-native species richness, at both the
 site level and the treatment level. Woodlands treated with conifer removal
 and no prescribed fire were intermediate in species richness and diversity
 compared to burned treatments and encroached woodlands. Encroached
 woodlands had diminished richness and diversity compared to all
 restoration treatments. Non-metric multidimensional scaling (NMS)
 ordination demonstrated that conifer basal area, conifer litter and fine
 wood were associated with low species richness and diversity and that
 elevation and thatch were associated with higher species richness and
 diversity. Indicator species analysis identified that most native species
 and non-native species were associated with burned woodlands that were
 never encroached. Synthesis and applications. Our results suggest that
 both prescribed fire and conifer removal have benefits for understorey
 plant communities, increasing species richness, diversity and cover in oak
 woodlands and shifting understorey communities from forest-associated
 species to more woodland-associated species. Restoration of remnant
 Quercus garryana oak woodlands is complicated by the persistence and
 abundance of non-native herbaceous plants.
description: Sampling
 dataData was collected in
 the field.Livingston_Amy_JPE_5_15_16_Data.xlsxSpatial data for site locations.LivingstonA_JournalofAppliedEcology_SiteLocations.shp.WIN7_T530.21420.22140.sr.zip
DOI: 10.15482/usda.adc/28849928
title: Data from: Electrical geophysical monitoring of subsurface solute transport in low-relief agricultural landscapes in response to a simulated major rainfall event

description: This dataset derives from an intensive field experiment that involved the use of time-lapse electrical resistivity imaging (ERI) to track the fate and transport of an injected salt tracer (KBr) in shallow groundwater during a simulated rainfall event (150 mm in 12 hours) in a ditch-drained field. The study was led by a team of researchers from Rutgers University, USDA-ARS, University of Delaware, Morehead State University, and Landcare Research. The research team conducted the experiment in a 1.5-ha agricultural field located on the University of Maryland Eastern Shore Research and Teaching Farm in Princess Anne, MD. The experiment lasted four days (06/20/2022 to 06/23/2022) and focused on a 150-m2 plot that was situated in the southwestern corner of the field near an open drainage ditch. Resources in this dataset include the following:<i>1D Vertical Electrical Sound</i><i> – vertical electrical resistivity tomography surveys; data were collected during the simulated rainfall event.</i><i>3D Time domain induced polarization survey</i><i> - time domain complex conductivity (TDIP) survey using the 96 Syscal Pro/Switch (Iris Instruments, France); data were collected as background data prior to the simulated rainfall event.</i><i>3D Timelapse electrical resistivity imaging</i><i> - electrical conductivity surveys using a radial array configuration with a total radial spread of ∼24 degrees; data were collected during and after the simulated rainfall event.</i><i>Ground penetrating radar</i><i> - ground penetrating radar was collected for Robinson et. al. 2020 and for Thompson et al. 2025; data were collected as background data prior to the simulated rainfall event.</i><i>Hydrologic data</i><i> - water levels in shallow wells measured by HOBO pressure transducers and time domain reflectometry (TDR) measurement of volumetric soil moisture content; data were collected during and after the simulated rainfall event.</i><i>Soil data</i><i> - soils data (texture) and geophysical measurements of soil cores for characterization of field site; data were collected as background data prior to the simulated rainfall event</i><i>Tracer data</i><i> – concentrations of Br- measured in ten multilevel groundwater samplers; data were collected after the simulated rainfall event</i>For more information about this dataset contact: Josh Thompson (jht51@scarletmail.rutgers.edu); Anthony Buda (anthony.buda@usda.gov); Amy Shober (ashober@udel.edu). Also see publications by Thompson et al. (2025) and Robinson et al. (2019) for detailed methodology.<br>