cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.83zwdx
title: Occurrence Download

description: A dataset containing 205 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 GBIF_STRINGARRAYCONTAINS(occurrence.classifications['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c'], '3189883', TRUE)
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence.classificationdetails['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c']['specieskey'] &lt;&gt; '' AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 205 records were derived from 382 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000485-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.s04ng
title: Data from: Mechanisms of thermal adaptation and evolutionary potential of conspecific populations to changing environments

description: Heterogeneous and ever-changing thermal environments drive the evolution
 of populations and species, especially when extreme conditions increase
 selection pressure for traits influencing fitness. However, projections of
 biological diversity under scenarios of climate change rarely consider
 evolutionary adaptive potential of natural species. In this study, we
 tested for mechanistic evidence of evolutionary thermal adaptation among
 ecologically divergent redband trout populations (Oncorhynchus mykiss
 gairdneri) in cardiorespiratory function, cellular response and genomic
 variation. In a common garden environment, fish from an extreme desert
 climate had significantly higher critical thermal maximum (p&lt;0.05)
 and broader optimum thermal window for aerobic scope (&gt;3°C) than
 fish from cooler montane climate. In addition, the desert population had
 the highest maximum heart rate during warming (20% greater than montane
 populations), indicating improved capacity to deliver oxygen to internal
 tissues. In response to acute heat stress, distinct sets of cardiac genes
 were induced among ecotypes, which helps to explain the differences in
 cardiorespiratory function. Candidate genomic markers and genes underlying
 these physiological adaptations were also pinpointed, such as genes
 involved in stress response and metabolic activity (hsp40, ldh-b and
 camkk2). These markers were developed into a multi-variate model that not
 only accurately predicted critical thermal maxima, but also evolutionary
 limit of thermal adaptation in these specific redband trout populations
 relative to the expected limit for the species. This study demonstrates
 mechanisms and limitations of an aquatic species to evolve under changing
 environments that can be incorporated into advanced models to predict
 ecological consequences of climate change for natural organisms.
description: critical thermal
 maximumCTmax of three redband
 trout populations and a hybrid. Heating rate of water was 0.3°C min−1 to
 22°C and 0.1°C min−1 thereafter until CTMAX was
 reached.maximum heart
 rateMaximum heart rate of
 three redband trout populations and a hybrid. Maximum heart rate was
 stimulated by an intraperitoneal injection of atropine sulfate and
 isoproterenol. Heating rate of water was 1 C every 6
 minutes.metabolic rate and
 aerobic scopeStandard and maximum
 metabolic rate of three redband trout populations and a hybrid at 12°C,
 15°C, 18°C, 21°C and 24°C. Maximum metabolic rate was achieved by
 exercise. Aerobic scope was calculated as the difference between standard
 and maximum rate.RAD TAG
 catelogRAD Tag sequence (75 bp
 ) and SNP position of the 5903 genetic markers.
DOI: 10.5061/dryad.n7c42
title: Data from: Stable producer–scrounger dynamics in wild birds: sociability and learning speed covary with scrounging behaviour

description: There has been extensive game-theoretic modelling of conditions leading to
 equilibria of producer–scrounger dichotomies in groups. However there is a
 surprising paucity of experimental evidence in wild populations. Here, we
 examine producer–scrounger games in five subpopulations of birds feeding
 at a socially learnt foraging task. Over four weeks, a bimodal
 distribution of producers and scroungers emerged in all areas, with
 pronounced and consistent individual tactic specialization persisting over
 3 years. Tactics were unrelated to exploratory personality, but correlated
 with latency to contact and learn the foraging task, with the late
 arrivers and slower learners more likely to adopt the scrounging role.
 Additionally, the social environment was also important: at the broad
 scale, larger subpopulations with a higher social density contained
 proportionally more scroungers, while within subpopulations scroungers
 tended to be central in the social network and be observed in larger
 foraging flocks. This study thus provides a rare example of a stable,
 dimorphic distribution of producer–scrounger tactics in a wild population.
 It further gives support across multiple scales for a major prediction of
 social foraging theory; that the frequency of scroungers increases with
 group size.
description: Data_for_GLMMSummary of individual level variables and scrounging propensity across all replicates, data used in GLMM modelsNetwork_PA2012Social network matrix for PA2012 replicateNetwork_CP2012Social network matrix for CP2012 replicateNetwork_GW2012Social network matrix for GW2012 replicateNetwork_BB2013Social network matrix for BB2013 replicateNetwork_MP2013Social network matrix for MP2013 replicate
DOI: 10.5061/dryad.09kf4g02
title: Data from: A computational analysis of locomotor anatomy and body mass evolution in Allosauroidea (Dinosauria Theropoda)

description: We investigate whether musculoskeletal anatomy and three-dimensional (3-D)
 body proportions were modified during the evolution of large (&gt;6000
 kg) body size in Allosauroidea (Dinosauria Theropoda). Three adaptations
 for maintaining locomotor performance at large body size, related to
 muscle leverage, mass, and body proportions, are tested and all are
 unsupported in this analysis. Predictions from 3-D musculoskeletal models
 of medium-sized (Allosaurus) and large-bodied (Acrocanthosaurus)
 allosauroids suggest that muscle leverage scaled close to isometry, well
 below the positive allometry required to compensate for declining muscle
 cross-sectional area with increasing body size. Regression analyses on a
 larger allosauroid data set finds slight positive allometry in the moment
 arms of major hip extensors, but isometry is included within confidence
 limits. Contrary to other recent studies of large-bodied theropod clades,
 we found no compelling evidence for significant positive allometry in
 muscle mass between exemplar medium- and large-bodied allosauroids.
 Indeed, despite the uncertainty in quantitative soft tissue
 reconstruction, we find strong evidence for negative allometry in the
 caudofemoralis longus muscle, the single largest hip extensor in non-avian
 theropods. Finally, we found significant inter-study variability in
 center-of-mass predictions for allosauroids, but overall observe that
 consistently proportioned soft tissue reconstructions produced similar
 predictions across the group, providing no support for a caudal shift in
 the center of mass in larger taxa that might otherwise reduce demands on
 hip extensor muscles during stance. Our data set provides further
 quantitative support to studies that argue for a significant decline in
 locomotor performance with increasing body size in non-avian theropods.
 However, although key pelvic limb synapomorphies of derived allosauroids
 (e.g., dorsomedially inclined femoral head) evolved at intermediate body
 sizes, they may nonetheless have improved mass support.
description: SupportingInformationSupporting information. Additional background on hypotheses, methods and results.
DOI: 10.5061/dryad.c221m
title: Data from: Massive invasion of exotic Barbus barbus and introgressive hybridisation with endemic B. plebejus in Northern Italy: where, how and why?

description: Biological invasions and introgressive hybridisation are major drivers for
 the decline of native freshwater fish. However, the magnitude of the
 problem across a native species range, the mechanisms shaping
 introgression as well as invader’s dispersal and the relative role of
 biological invasions in the light of multiple environmental stressors are
 rarely described. Here, we report extensive (N=665) mtDNA sequence and
 (N=692) microsatellite genotypic data of 32 Northern Adriatic sites aimed
 to unravel the invasion of the European Barbus barbus in Italy, and the
 hybridisation and decline of the endemic B. plebejus. We highlight an
 exceptionally fast breakthrough of B. barbus within the Po River Basin,
 leading to widespread introgressive hybridisation with the endemic B.
 plebejus within few generations. In contrast, adjacent drainage systems
 are still unaffected from B. barbus invasion. We show that barriers to
 migration are inefficient to halt the invasion process and that propagule
 pressure, and not environmental quality, is the major driver responsible
 for B. barbus success. Both introgressive hybridisation and invader’s
 dispersal are facilitated by ongoing fisheries management practices.
 Therefore, immediate changes in fisheries management (i.e. stocking and
 translocation measures) and a detailed conservation plan, focussed on
 remnant purebred B. plebejus populations, are urgently needed.
description: mec13390_genotypesMicrosatellite data set (n=692) follows the Structure input file format (Unix format txt) with individual information on a single line (two columns per marker). The file contains loci names (1st row), individual names (1st column), codes for sampling localities (2nd col.) and 3 additional columns (GenBank Acc. n., haplogroup and haplotype for cyt-b mtDNA sequence).mec13390_SimDataset6000indsMicrosatellite data set (n=6,000) simulated with HYBRIDLAB 1.0 (Nielsen et al. 2001). The file is in Genepop format, with 6 populations representing B. plebejus purebreds, B. barbus purebreds, F1, F2, Backcross F1 X B. plebejus and Backcross F1 X B. barbus.
DOI: 10.5061/dryad.1995
title: Data from: Effects of brooding and broadcasting reproductive modes on the population genetic structure of two Antarctic gastropod molluscs

description: Life-history characteristics exert a profound influence upon the
 population structure of many marine organisms. However, relatively few
 genetic studies have compared direct with indirect-developing species in
 the same ecosystem or geographic region, and none to our knowledge within
 an Antarctic setting. To address this issue we have collected novel
 Amplified Fragment Length Polymorphism (AFLP) data from the
 direct-developing top shell Margarella antarctica to form a comparison
 with previously published data for the broadcast-spawning Antarctic limpet
 Nacella concinna. We scored 270 loci in 240 M. antarctica individuals
 sampled from five populations spanning the full length of the Antarctic
 Peninsula. Profound differences were identified in the strength and
 pattern of population structure between the two species, consistent with
 gene flow being highly restricted in M. antarctica relative to N.
 concinna.
description: Hoffman dryad submission
 16_09_10AFLP datafiles for
 Margarella antarctica and Nacella concina
DOI: 10.5061/dryad.5n00k
title: Data from: When viruses don’t go viral: the importance of host phylogeographic structure in the spatial spread of arenaviruses

description: Many emerging infections are RNA virus spillovers from animal reservoirs.
 Reservoir identification is necessary for predicting the geographic extent
 of infection risk, but rarely are taxonomic levels below the animal
 species considered as reservoir, and only key circumstances in nature and
 methodology allow intrinsic virus-host associations to be distinguished
 from simple geographic (co-)isolation. We sampled and genetically
 characterized in detail a contact zone of two subtaxa of the rodent
 Mastomys natalensis in Tanzania. We find two distinct arenaviruses, Gairo
 and Morogoro virus, each spatially confined to a single M. natalensis
 subtaxon, only co-occurring at the contact zone’s centre. Inter-subtaxon
 hybridization at this centre and a continuum of quality habitat for M.
 natalensis show that both viruses have the ecological opportunity to
 spread into the other substaxon’s range, but do not, strongly suggesting
 host-intrinsic barriers. Such barriers could explain why human cases of
 another M. natalensis-borne arenavirus, Lassa virus, are limited to West
 Africa.
description: FieldLabData_GryseelsPLoSPathogens2016Field information, arenavirus screening data and GenBank accession numbers of Mastomys natalensis as described in the manuscript "When viruses don't go viral: the importance of host phylogeographic structure in the spatial spread of arenaviruses".Microsatellite genotypes_GryseelsPLoSPathogens2016Genotypes of 15 microsatellite loci of 760 Mastomys natalensis individuals from Tanzania.Landscape cost values for GIS and Circuitscape analyses_GryseelsPLoSPathogens2016Cost values of land use elements that occurred in our study area in terms of Mastomys natalensis habitat quality.STRUCTURE parameter settingsParameter settings used in the software STRUCTURE, to infer population genetic structure of Mastomys natalensis based on microsatellite genotypes.MrBayes input filesInput files for the software MrBayes of arenavirus partial L, NP and GPC sequences, containing the used alignments and parameter settings to infer the phylogenetic trees displayed in the manuscript.
DOI: 10.25919/jpx8-0n17
title: Parkes observations for project P1386 semester 2025OCTS_15

description: J0045-7319 is a B star/pulsar binary in the Small Magellanic Cloud (SMC) with an orbital period of 51 days. The system is highly eccentric, with a closest approach of only 6 B-star radii, and it offers an unusual probe into massive stars in the SMC. Although similar systems exhibit strong dispersion measure (DM) variation during periastron arising from the stellar wind, observations in 1996 on the Parkes 70 cm receiver found no evidence of a wind from the B star. We propose a new set of observations on the Ultra-Wide Low-frequency receiver (UWL) designed to measure the wind. A null result will decrease the known upper limit on the B-star wind's contribution to DM by a factor of 9.
DOI: 10.25919/qqe6-ch52
title: Long-term project observations for project P885 semester 2025OCTS_12

description: We propose a modest program to continue monitoring 4 of the 6 known radio magnetars in order to achieve three primary science goals. The first is to characterise magnetar outbursts over long timescales, for which tracking their rotational, flux density, and polarisation properties provide a clear view of the impulse response of their magnetic fields. Second, understanding the links between magnetars the mysterious fast radio burst phenomenon through the discovery of rare emission and propagation effects, shared spectro-temporal phenomenology, and connections to high-energy (X-ray/gamma-ray) phenomena. Lastly, our continued monitoring has enormous benefit to the wider magnetar community, providing rapid alerts to changes in activity, adding context to unusual behaviour detected by high-energy observations, and a host of supplementary science through the teams extensive collaborative networks. The project and its precursors have been running since 2007 and have contributed to 21 publications since then. We are seeking to convert the project to long-term status, thereby also carrying these investigations into the SKA era.
DOI: 10.25919/grkn-ed77
title: Long-term project observations for project P456 semester 2025OCTS_11

description: The Parkes Pulsar Timing Array (PPTA) project has three primary goals: (a) detection of gravitational waves from astronomical sources, (b) establishment of a pulsar timescale, and (c) improvement of our understanding of Solar-system dynamics. We are now in an exciting regime where a signal detected in our (and other data sets) has the form expected for a gravitational wave background. We, along with the international community, are now working hard to either confirm or deny this result, and to determine the astrophysical origin of this signal. With this proposal, we aim to maintain our pre-eminent position in the field. This is a continuing proposal for which observations of millisecond pulsars (MSPs) will continue to improve bounds on ultra-low-frequency gravitational waves until they are detected with confidence. Continued Parkes observations will remain valuable at least until the first stage of the SKA is able to improve on our sensitivity and observing cadence. Even after the gravitational wave background is detected, continued observations will resolve the background origin and individual sources will be identified; advancing the nascent field of gravitational wave astronomy.
DOI: 10.5061/dryad.m62gj
title: Data from: The hydrological legacy of deforestation on global wetlands

description: Increased catchment erosion and nutrient loading are commonly recognized
 impacts of deforestation on global wetlands. In contrast, an increase in
 water availability in deforested catchments is well known in modern
 studies but is rarely considered when evaluating past human impacts. We
 used a Budyko water balance approach, a meta-analysis of global wetland
 response to deforestation, and paleoecological studies from Australasia to
 explore this issue. After complete deforestation, we demonstrated that
 water available to wetlands increases by up to 15% of annual
 precipitation. This can convert ephemeral swamps to permanent lakes or
 even create new wetlands. This effect is globally significant, with 9 to
 12% of wetlands affected, including 20 to 40% of Ramsar wetlands, but is
 widely unrecognized because human impact studies rarely test for it.
description: Database
 S1Database S1 is an Excel
 spreadsheet that contains data from all studies of deforestation in
 wetland catchments during the Holocene. These are the papers used in the
 meta-analysis. All sites examined by each paper are listed. This
 information was extracted from published, peer-reviewed journal
 articlesDatabase
 S2Database S2 contains
 information on specific sites where hydrological changes have occurred
 after deforestation.This information was extracted from published,
 peer-reviewed journal articles listed in Database S1Database
 S3This information was
 extracted from published, peer-reviewed journal articles. Database S3
 contains information relating to the meta-analysis. Database S3 contains
 information from each site where deforestation and wetland change data is
 available. Post-deforestation wetland changes are identified including; a
 change in sedimentation rate, eutrophication or change in
 hydrology.
DOI: 10.5061/dryad.26sb5
title: Data from: Continent-level drivers of African pyrodiversity

description: Pyrodiversity, which describes fire variability over space and time, is
 believed to increase habitat heterogeneity and thereby promote
 biodiversity. However, to date there is no standardised metric for
 quantifying pyrodiversity, and so broad geographic patterns and drivers of
 pyrodiversity remain unexplored. We present the first generalizable method
 to quantify pyrodiversity, and use it to address the fundamental questions
 of what drives pyrodiversity, which fire attributes constrain
 pyrodiversity under different conditions, and whether pyrodiversity is
 spatial grain-dependent. We linked the MODIS burned area and active fire
 products to measure fire size, seasonal timing, return interval, and
 intensity for 2.2 million individual fires in sub-Saharan Africa from
 2000–2015. We then quantified pyrodiversity as a four-dimensional
 hypervolume described by fire attributes within a grid cell, for any
 spatial grain of analysis. Environmental (rainfall, vegetation, soils, and
 topography) and human-associated (cattle biomass, cropland area, and human
 population density) variables were assessed as potential drivers of
 pyrodiversity. Rainfall was the main environmental driver of
 pyrodiversity, with higher pyrodiversity in drier regions (&lt; 650 mm
 yr-1). Pyrodiversity was not strongly associated with human-associated
 variables across Africa. Rainfall and a human influence index had clear
 but contrasting effects on the variability of fire size, seasonal timing,
 return interval, and intensity. Our analyses show that fire size and
 seasonal timing constrain pyrodiversity in wetter regions, whereas none of
 the fire attributes pose a strong constraint in drier regions. We found no
 evidence that pyrodiversity was spatial grain-dependent when recalculated
 at 5-minute grain increments from 15 to 120 minutes. We hypothesise that
 the strongest positive effect of pyrodiversity on biodiversity in all its
 forms will occur at intermediate precipitation (650–1300 mm yr-1), where
 fire plays an important role in shaping vegetation structure and where
 pyrodiversity is still quite high.
description: African_pyrodiversityThe zip archive contains 22 .tif files with pyrodiversity values for sub-Saharan Africa at 5-minute grain increments from 15 to 120 minutes.