cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wstqjq2kd
title: Hierarchical genetic structure and implications for conservation of the world’s largest salmonid, Hucho taimen

description: Population genetic analyses can evaluate how evolutionary processes shape
 diversity and inform conservation and management of imperiled species.
 Taimen (Hucho taimen), the world’s largest freshwater salmonid, is
 threatened, endangered, or extirpated across much of its range due to
 anthropogenic activity including overfishing and habitat degradation. We
 generated genetic data using high throughput sequencing of reduced
 representation libraries for taimen from multiple drainages in Mongolia
 and Russia. Nucleotide diversity estimates were within the range
 documented in other salmonids, suggesting moderate diversity despite
 widespread population declines. Similar to other recent studies, our
 analyses revealed pronounced differentiation among the Arctic (Selenge)
 and Pacific (Amur and Tugur) drainages, suggesting historical isolation
 among these systems. However, we found evidence for finer-scale structure
 within the Pacific drainages, including unexpected differentiation between
 tributaries and the mainstem of the Tugur River. Differentiation across
 the Amur and Tugur basins together with coalescent-based demographic
 modeling suggests the ancestors of Tugur tributary taimen likely diverged
 in the eastern Amur basin, prior to eventual colonization of the Tugur
 basin. Our results suggest the potential for differentiation of taimen at
 different geographic scales, and suggest more thorough geographic and
 genomic sampling may be needed to inform conservation and management of
 this iconic salmonid.
description: taimen_allSamples.vcf.gz vcf file after
 stringent filtering steps for the dataset in which all samples from all
 basins were analyzed together. File compressed using gzip.
 taimen_pacificSubset.vcf.gz vcf file after
 stringent filtering steps for the dataset in which the Pacific subset of
 samples from Amur and Tugur basins were analyzed. File compressed using
 gzip. taimen_fastqs.tar.gz
 Directory including all fastq files for each individual included
 in this study. Compressed as a tar archive. 
 fastq_IDs_withPops.csv csv file matching
 individual fastq IDs with populations.
 barcodes.pl Custon Perl script for
 correcting one or two bp sequencing errors in barcode sequences, remove
 barcodes and cut-site associated bases, and match sequences with
 individual sample names. ****We have become aware that some of the MIDs we
 used are 1 bp Levenshtein edit distance from one another and that
 therefore, different MID sets should be used in the future. This was not
 an issue with the MIDs used for this study, but for a larger
 collection.
DOI: 10.7291/d11969
title: Inferred tidal heating distribution and internal structure of Tethys and Enceladus

description: In our submitted paper, "Estimates for Tethys' Moment of
 Inertia, Heat Flux Distribution, and Interior Structure from its
 Long-Wavelength Topography" (Gyalay & Nimmo, 2023), we sought
 to infer the heat flux distribution at the base of Tethys' ice shell.
 This heat flux distribution allows us to infer whether there is a fluid or
 rigid layer interior to the ice shell – the latter of which would suggest
 a global, subsurface ocean. We calculate the heat flux distribution from
 the long-wavelength (spherical harmonic degrees 2 and 4) topography but
 require some assumptions, such as how thick the ice layer is, if the upper
 portion is porous, and what the moment of inertia of Tethys is. Thus we
 fit for the tidal heating distribution for a wide suite of varying
 parameters to find which combination best represents the structure and
 thermal state of Tethys. We also test our procedure on Enceladus, a moon
 for which we already know the moment of inertia and interior structure
 (i.e. that it has a subsurface ocean). This dataset contains the code we
 used to model these icy satellites and generate our data, as well as the
 output data.
description: In our paper, we establish the mathematics behind how we use
 assumed parameters (upper ice shell porosity, total ice shell thickness,
 moment of inertia, basal temperature at the base of the ice shell) to
 infer the average basal heat flux and fit for spatial patterns of tidal
 heating (Beuthe, 2013, Icarus). Using this best-fit tidal heating for each
 set of parameters, we forward model the topography (also described in our
 paper) and calculate its spherical harmonic weights as well as compare
 them to the originally observed topography.
description: The header of each data-output file should describe what each
 column refers to. MoI is the moment of inertia. From these data, one can
 compute density profiles for each model of Tethys (or Enceladus) and judge
 whether it is consistent with the inferred heating pattern weight. Values
 were not printed to file if the calculated average heat flux was NaN, if
 any of chi_A,B,C were not between 0 and 1, or if any of the spherical
 harmonic weights of forward-modeled topography were NaN. Further
 descriptions of parameters and their uses are described in the paper for
 which this dataset was produced. Further, we include files for Enceladus,
 and the code used to generate the data.
DOI: 10.82294/dvndnq71n
title: Datos consolidados de COPUS. Territorio: Cartagena. Sector: Cultura, Educación, Total. Año: 2025

description: En este apartado se presentan los datos consolidados del territorio de Cartagena a partir de las observaciones semiestructuradas realizadas en 2025, esta vez analizadas bajo los criterios del protocolo de observación estructurada COPUS. Este dataset contiene la sumatoria de todas las observaciones COPUS por territorio, por sector, cultura y educación, una sumatoria de estos dos para definir la tendencia en el territorio y una sumatoria de todos los territorios.
DOI: 10.5061/dryad.z8w9ghxbn
title: Etadunna bandicoot tip dated matrices

description: The oldest fossils referrable to the marsupial order Peramelemorphia
 (which includes modern bandicoots and bilbies) dates to the late Oligocene
 of Australia. The earliest geologically speaking of these are from the
 Etadunna Formation in central Australia. Here we describe additional
 peramelemorphian material from the Etadunna Formation, as well as
 specimens from the Namba and Wipajiri Formations. The new material fills
 gaps in the evolutionary history of the order showing that
 peramelemorphians were present in every faunal zones of the Etadunna
 Formation, and demonstrating for the first time the presence of
 Peramelemorphian in the Namba Formation. We describe three new species of
 Bulungu, including the oldest peramelemorphian known to date (from Faunal
 Zone A of Etadunna Formation) and a new genus and species of the family
 Thylacomyidae (which includes modern bilbies), which is ~10 million years
 older than the previous earliest thylacomyid known.  We also
 present a phylogenetic analysis that helps clarify the evolutionary
 relationships of the new taxa described here.
DOI: 10.15468/dl.9wqsu4
title: Occurrence Download

description: A dataset containing 37828 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Mosquito Alert Dataset"
 ]
}

 The dataset includes 37828 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002787-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.fbg79cntg
title: Synchronized file of allele frequencies for: Using seasonal genomic changes to understand historical adaptation to new environments: parallel selection on stickleback in highly-variable estuaries

description: Parallel evolution is considered strong evidence for natural selection.
 However, few studies have investigated the process of parallel selection
 as it plays out in real time. The common approach is to study historical
 signatures of selection in populations already well adapted to different
 environments. Here, to document selection under natural conditions, we
 study six populations of threespine stickleback (Gasterosteus aculeatus)
 inhabiting bar-built estuaries that undergo seasonal cycles of
 environmental changes. Estuaries are periodically isolated from the ocean
 due to sandbar formation during dry summer months, with concurrent
 environmental shifts that resemble the long-term changes associated with
 postglacial colonization of freshwater habitats by marine populations. We
 used pooled whole-genome sequencing (Pool-WGS) to track seasonal allele
 frequency changes in six of these populations and search for signatures of
 natural selection. We found consistent changes in allele frequency across
 estuaries, suggesting a potential role for parallel selection. Functional
 enrichment among candidate genes included transmembrane ion transport and
 calcium binding, which are important for osmoregulation and ion balance.
 The genomic changes that occur in threespine stickleback from bar-built
 estuaries could provide a glimpse into the early stages of adaptation that
 have occurred in many historical marine to freshwater transitions.
description: We sampled stickleback from six bar-built estuaries at two time
 points (i.e., 12 pools). We applied pooled sequencing of whole-genomes (12
 pools). Fst estimates were produced using the fst-sliding.pl program of
 Popoolation2 (https://sourceforge.net/p/popoolation2/wiki/Manual/). The
 scripts used to analyze the results are available
 at https://github.com/garfring.
description: This is the synchronized file created using the mpileup2sync.jar
 program of Popoolation2. The synchronized file contains the allele
 frequencies for all positions in the reference genome and for all
 populations being analyzed. Only informative SNPs have been kept.
 Population order: Waddell T1 = column 1, Waddell T2 = column 7; Lombardi
 T1 = column 2, Lombardi T2 = column 4; Old Dairy T1 = column 3, Old Dairy
 T2 = column 6; Younger T1 = column 5, Younger T2 = column 12; Scott T1 =
 column 8, Scott T2 = column 9; Laguna T1 = column 10, Laguna T2 = column
 11.
DOI: 10.7280/d1s39w
title: Seismic detection of oceanic internal gravity waves from subaerial seismometers

description: Oceanic internal gravity waves propagate along density stratification
 within the water column and are ubiquitous. They can propagate thousands
 of kilometers before breaking in shoaling bathymetry and the ensuing
 turbulent mixing affects coastal processes and climate feedbacks. Despite
 their importance, internal waves are intrinsically difficult to detect as
 they result in only minor amplitudedeflection of the sea surface; the need
 for global detection and long time series of internal waves motivates a
 search for geophysical detection methods. The pressure coupling of a
 propagating internal wave with the sloping seafloor provides a potential
 mechanism to generate seismically observable signals. We use data from the
 South China Sea where exceptional oceanographic and satellite time series
 are available for comparison to identify internal wave signals in an
 onshore passive seismic data set for the first time. We analyze potential
 seismic signals on broadband seismometers in the context of corroborating
 oceanographic and satellite data available near Dongsha Atoll in May–June
 2019 and find a promising correlation between transient seismic tilt
 signals and internal wave arrivals and collisions in oceanic and satellite
 data. It appears that we have successfully detected oceanic internal waves
 using a subaerial seismometer. This initial detection suggests that the
 onshore seismic detection and amplitude determination of oceanic internal
 waves is possible and can potentially be used to expand the historical
 record by capitalizing on existing island and coastal seismic stations.
description: Instrument: Seabird Electronics SBE56 logging
 thermistor.   Deployment details: We use 1-10 second
 sampling rate oceanic temperature measurements in the water column and on
 the ocean bottom during a temporary deployment in May/June 2019 around the
 fore reef of Dongsha Atoll (Figure 1c).  We consider a 20-meter mooring on
 the eastern side of Dongsha Atoll (FRE20) at 19.5 meters depth from May
 13-June 11, 2019 and an ocean bottom temperature sensor at approximately
 16.8 meters depth on the western side of Dongsha Atoll (FRW15) roughly 4.5
 km southwest of a permanent seismic station onshore of Pratas Island from
 May 19-June 6, 2019.
DOI: 10.5061/dryad.b8gtht7bx
title: Genomic divergence in sympatry indicates strong reproductive barriers and cryptic species within Eucalyptus salubris

description: Genetic studies are increasingly detecting cryptic taxa that likely
 represent a significant component of global biodiversity. However, cryptic
 taxa are often criticized because they are typically detected
 serendipitously and may not receive the follow-up study required to verify
 their geographic or evolutionary limits. Here, we follow-up a study of
 Eucalyptus salubris that unexpectedly detected two divergent lineages but
 was not sampled sufficiently to make clear interpretations. We undertook
 comprehensive sampling for an independent genomic analysis (3,605 SNPs) to
 investigate whether the two purported lineages remain discrete genetic
 entities or if they intergrade throughout the species’ range. We also
 assessed morphological and ecological traits, and sequenced chloroplast
 DNA. SNP results showed strong genome-wide divergence (FST=0.252) between
 two discrete lineages: one dominated the north and one the southern
 regions of the species’ range. Within lineages gene flow was high, with
 low differentiation (mean FST=0.056) spanning hundreds of kilometres. In
 the central region, the lineages were interspersed but maintained their
 genomic distinctiveness: an indirect demonstration of reproductive
 isolation. Populations of the southern lineage exhibited significantly
 lower specific leaf area and occurred on soils with lower phosphorus
 relative to the northern lineage. Finally, two major chloroplast
 haplotypes were associated with each lineage but were shared between
 lineages in the central distribution. Together, these results suggest that
 these lineages have non-contemporary origins and that ecotypic adaptive
 processes strengthened their divergence more recently. We conclude that
 these lineages warrant taxonomic recognition as separate species and
 provide fascinating insight to eucalypt speciation.
description: Here, we present three datasets regarding SNP genotypes, specific
 leaf area measurements and soil phosphorus content for a study of cryptic
 species in Eucalyptus salubris. There is additional chloroplast sequence
 data for this study available on GenBank: MT104517-MT104558 .
 1. SNP genotypes: this is the filtered dataset of 3605 SNP loci
 used in all population genomic analyses. The data is in the format of a
 2-row STRUCTURE input file with missing data coded as -9. 
 2. Specific leaf area: individual measurements of specific leaf
 area (ratio of leaf area to dry mass). Ten leaves per tree were measured
 across the same trees sampled for DNA. Lineage classification is also
 indicated. 3. Soil phosphorus: soil phosphorus content
 (mg/kg) for each of the sites sampled. Lineage classification is also
 indicated.
DOI: 10.5061/dryad.dncjsxkzp
title: Landscape-scale dynamics of a threatened species respond to local-scale conservation management

description: Landscape-scale approaches are increasingly advocated for species
 conservation but ensuring landscape level persistence by enlarging the
 size of patches or increasing their physical connectivity is often
 impractical.  Here, we test how such barriers can be overcome by
 management of habitat at the local (site-based) level, using a rare
 butterfly as an exemplar. We used four surveys of the entire UK
 distribution of the Lulworth Skipper (Thymelicus acteon) over 40 years to
 test how local habitat influences population density and colonization /
 extinction dynamics, and parameterized, validated and applied a
 metapopulation model to simulate effects of varying local habitat quality
 on regional persistence. We found the total number of populations in four
 distribution snapshots between 1978 and 2017 varied between 59–84, and
 from 1997 to 2017, 34% of local populations showed turnover (colonization
 or extinction). Population density was closely linked to vegetation
 characteristics indicative of management, namely height and food plant
 frequency, both of which changed through time. Simulating effects of
 habitat quality on metapopulation dynamics 40 years into the future
 suggests coordinated changes to two key components of quality (vegetation
 height and food plant frequency) would increase patch occupancy above the
 range observed in the past 40 years (50–80%). In contrast, deterioration
 of either component below threshold levels leads to metapopulation
 retraction to core sub-networks of patches, or eventual extirpation. Our
 results indicate that changes to habitat quality can overcome constraints
 imposed by habitat patch area and spatial location on relative rates of
 colonization and local extinction, demonstrating the sensitivity of
 regional dynamics to targeted in situ management. Local habitat management
 therefore plays a key role in landscape-scale conservation. 
 Monitoring of population density, and the monitoring and management of
 local (site-level) habitat quality, therefore represent effective and
 important components of conservation strategies in fragmented landscapes.
DOI: 10.5281/zenodo.18372000
title: Succession Data

description: Data on relevant indicators across the successional sequence
DOI: 10.5281/zenodo.18372001
title: Succession Data

description: Data on relevant indicators across the successional sequence
DOI: 10.5061/dryad.ghx3ffbnd
title: Adaptation at different points along antibiotic concentration gradients

description: Antibiotic concentrations vary dramatically in the body and the
 environment. Hence, understanding the dynamics of resistance evolution
 along antibiotic concentration gradients is critical for predicting and
 slowing the emergence and spread of resistance. While it has been shown
 that increasing the concentration of an antibiotic slows resistance
 evolution, how adaptation to one antibiotic concentration correlates with
 fitness at other points along the gradient has not received much
 attention. Here, we selected populations of Escherichia coli at several
 points along a concentration gradient for three different antibiotics,
 asking how rapidly resistance evolved and whether populations became
 specialized to the antibiotic concentration they were selected on.
 Populations selected at higher concentrations evolved resistance more
 slowly but exhibited equal or higher fitness across the whole gradient.
 Populations selected at lower concentrations evolved resistance rapidly,
 but overall fitness in the presence of antibiotics was lower. However,
 these populations readily adapted to higher concentrations upon subsequent
 selection. Our results indicate that resistance management strategies must
 account not only for the rates of resistance evolution but also for the
 fitness of evolved strains.
description: The dataset consists of: a) experimental evolution data tracking
 the development of resistance to three antibiotics in replicate E.coli
 populations. This dataset consists of OD600 measurements taken on each
 daily transfer. b) fitness assays as growth curve measurements of each
 evolved population measured in the presence and absence of
 antibiotics. The uploaded code is the R code used by
 statistical analyses.
DOI: 10.15468/dl.exr8jv
title: Occurrence Download

description: A dataset containing 10156 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Xerochrysum bracteatum"
 ]
}

 The dataset includes 10156 records from 175 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002788-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k98sf7m5h
title: Data from: Does trait-based joint species distribution modelling reveal the signature of competition in stream macroinvertebrate communities?

description: 1. The occupancy and abundance of species are jointly driven by local
 factors, such as environmental characteristics and biotic interactions,
 and regional-scale factors, such as dispersal and climate. Recently, it
 has been shown that biotic interactions shape species occupancies and
 abundances beyond local extents. However, for small ectothermic animals,
 particularly for those occurring in freshwater environments, the
 importance of biotic interactions remains understudied. Species-to-species
 associations from joint species distribution models (i.e. species
 associations while controlling for environmental characteristics) are
 increasingly used to draw hypotheses of which species possibly show biotic
 interactions. 2. We studied whether species-to-species associations from
 joint species distribution models show signs of competition using a
 hypothesis testing framework in stream macroinvertebrate communities at
 regional extent. 3. We sampled aquatic macroinvertebrates from 105 stream
 sites in western Finland encompassing a latitudinal gradient of ca. 500
 kilometers. We hypothesized that if competition drives these associations
 (H1) functionally similar species are mostly negatively associated,
 whereas functionally dissimilar species show random associations. We
 further hypothesized that the relationship between functional
 dissimilarity and the strength of association is more pronounced (H2) for
 abundances rather than occupancies, (H3) at small grain (i.e. stream site)
 rather than at large grain (i.e. river basin), and (H4) among species
 having weak dispersal ability than among species with high dispersal
 ability. 4. Stream macroinvertebrates showed both negative and positive
 species-to-species associations while controlling for habitat
 characteristics. However, the negative associations were mostly at large
 grain (river basin) rather than at small grain (stream site), in occupancy
 rather than abundance, and not related to species functional dissimilarity
 or to their dispersal ability. Thus, all our hypotheses considering
 possible competition (H1-H4) were rejected. 5. Competition does not appear
 to be a major driving force of stream macroinvertebrate communities at the
 spatial grain sizes considered. The observed positive associations in
 occupancy at small grain (stream site) may be attributed to species’
 similar microhabitat preferences, whereas at large grain (river basin),
 they may stem from metacommunity dynamics. Our results highlight that
 species traits were necessary to interpret whether or not
 species-to-species associations from joint species distribution models
 resulted from biotic interactions. 
description: Usage notes in Stream_macroinvertebrates_readme.txt