cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1jwstqjr3
title: Whistle variation in Mediterranean common bottlenose dolphin: the role of geographical, anthropogenic, social and behavioural factors

description: The studies on the variation of acoustic communication in different
 species have provided insight that genetics, geographic isolation and
 adaptation to ecological and social conditions play important roles in the
 variability of acoustic signals. The dolphin whistles are communication
 signals that can vary significantly among and within populations. Although
 it is known that they are influenced by different environmental and social
 variables, the factors influencing the variation between populations have
 received scant attention. In the present study, we investigated the
 factors associated to the acoustic variability in the whistles of common
 bottlenose dolphin (Tursiops truncatus), inhabiting two Mediterranean
 areas (Sardinia and Croatia). We explored which factors, among 1)
 geographical isolation of populations, 2) different environments in terms
 of noise and boat presence and 3) social factors (including group size,
 behaviour and presence of calves), were associated to whistle
 characteristics. We first applied a principal component analysis to reduce
 the number of collinear whistle frequency and temporal characteristics,
 and then generalised linear mixed models on the first two principal
 components. The study revealed that both geographic distance/isolation and
 local environment are associated to whistle variations between localities.
 The prominent differences in the acoustic environments between the two
 areas, which contributed to the acoustic variability in the first
 principal component (PC1), were found. The calf’s presence and foraging
 and social behaviour were also found to be associated with dolphin whistle
 variation. The second principal component (PC2) was associated only to
 locality and group size, showing that longer and more complex tonal sound
 may facilitate individual recognition and cohesion in social groups. Thus,
 both social and behavioural context influenced significantly the structure
 of whistles, and they should be considered when investigating acoustic
 variability among distant dolphin populations to avoid confounding
 factors.
DOI: 10.5061/dryad.ht76hdrbn
title: Data from: A critical analysis of the potential for EU Common Agricultural Policy measures to support wild pollinators on farmland

description: 1.         Agricultural intensification and associated loss of high-quality habitats are key drivers of insect pollinator declines. With the aim of decreasing the environmental impact of agriculture, the 2014 EU Common Agricultural Policy (CAP) defined a set of habitat and landscape features (Ecological Focus Areas: EFAs) farmers could select from as a requirement to receive basic farm payments. To inform the post-2020 CAP, we performed a European-scale evaluation to determine how different EFA options vary in their potential to support insect pollinators under standard and pollinator-friendly management, as well as the extent of farmer uptake.  2.        A structured Delphi elicitation process engaged 22 experts from 18 European countries to evaluate EFAs options. By considering life cycle requirements of key pollinating taxa (i.e. bumble bees, solitary bees and hoverflies), each option was evaluated for its potential to provide forage, bee nesting sites and hoverfly larval resources. 3.         EFA options varied substantially in the resources they were perceived to provide and their effectiveness varied geographically and temporally. For example, field margins provide relatively good forage throughout the season in Southern and Eastern Europe but lacked early-season forage in Northern and Western Europe. Under standard management, no single EFA option achieved high scores across resource categories and a scarcity of late season forage was perceived. 4.         Experts identified substantial opportunities to improve habitat quality by adopting pollinator-friendly management. Improving management alone was, however, unlikely to ensure that all pollinator resource requirements were met. Our analyses suggest that a combination of poor management, differences in the inherent pollinator habitat quality and uptake bias towards catch crops and nitrogen-fixing crops severely limit the potential of EFAs to support pollinators in European agricultural landscapes. 5.         Policy Implications. To conserve pollinators and help protect pollination services, our study highlights the need to create a variety of interconnected, well-managed habitats that complement each other in the resources they offer. To achieve this the CAP post-2020 should take a holistic view to implementation that integrates the different delivery vehicles aimed at protecting biodiversity (e.g. enhanced conditionality, eco-schemes and Agri-Environment and Climate Measures). To improve habitat quality we recommend an effective monitoring framework with target-orientated indicators and to facilitate the spatial targeting of options collaboration between land managers should be incentivised.
description: Resource Evaluation Scores For Insect Pollinators
DOI: 10.5066/p13xsqwn
title: Assessment of Mercury, Mercury Stable Isotopes, and Trace Metals in Waters, Sediments, and Biota from Great Salt Lake, Utah

description: Great Salt Lake (GSL) is a designated Site of Hemispheric Importance for migratory birds by the Western Hemisphere Shorebird Reserve Network. Elevated mercury (Hg) and methylmercury (MeHg) levels related to current inputs and past industrial contamination pose a potential threat to GSL biota, in addition to waterfowl hunters that utilize GSL and surrounding wetland areas. Sediments, invertebrates (brine shrimp, brine flies, and spiders), and waterfowl (northern shoveler and cinnamon teal) were targeted within these studies to determine relative source contributions of Hg and trace elements to the GSL system, determine which sources of mercury are actively bioaccumulating in GSL food webs, assess controls on mercury cycling within the GSL system, and assess MeHg toxicity risk to waterfowl. Hg stable isotopes were heavily employed as tracers of Hg sources and processing. These data are a part of larger studies and associated with upcoming journal articles.
DOI: 10.5061/dryad.h18931zgk
title: Data from: Human−geographic effects on variations in the population genetics of Sinotaia quadrata (Gastropoda: Viviparidae) that historically migrated from continental East Asia to Japan

description: Background: Anthropogenic factors potentially affect observed
 biogeographical patterns in genetic variations of populations, but the
 effects of ancient human activities on the original patterns that were
 created by natural processes are unknown. Sinotaia quadrata, a widely
 distributed freshwater snail species in East Asia, was used to investigate
 this issue. It is unclear if S. quadrata in Japan was introduced from
 China, and how different human uses and varying geographic patterns affect
 the genetic structure of contemporary populations between the two regions.
 Thus, we investigated the population history of S. quadrata and detected
 its genetic structure in Japan and continental East Asia. Results: S.
 quadrata populations first naturally migrated from continental East Asia
 to Japan, which is associated with the ancient period in Japanese
 geohistory (about 70,000 years ago). They were then artificially
 introduced in association with agriculture expansion by human movements in
 two recent periods (about 8000 and 1200 years ago). Populations in
 different parts of Japan have their own sources. Natural migration in the
 ancient period and artificial introduction in the recent period suggest
 that the population distribution is affected by both the geohistory of
 East Asia and the history of human expansion. In the background of the
 historical migration and introduction, contemporary populations in the two
 regions show different genetic patterns. Population divergence levels were
 significantly correlated with geographical patterns in Japan, and
 significantly correlated with human interventions variables in continental
 East Asia, suggesting that long-term geographical isolation is likely the
 major factor that shaped the genetic structure of contemporary populations
 in Japan, while modern human uses are likely the major factor in
 continental East Asia. Conclusions: Our preliminary results show a complex
 population history and unusual genetic patterns in the contemporary
 populations for a common freshwater snail and are of significance to
 determine the historical formation and contemporary patterns of
 biogeography in Japan and continental East Asia.
description: This data set is used for population genetics analysis for the
 freshwater snail, <em>Sinotaia quadrata</em>. Genetic data set
 is genotyped using 12 microsatellite loci, and divided to three structure
 files of total, Japan, and (East Asia) continent, respectively. The DIYABC
 input file contains 237 randomly sampled individuals representing for the
 four groups in the East Asia continent and Japan. It is used for
 population history analysis in software DIYABC. The variable data are
 extracted from WorldClim (http://worldclim.org) and NASA’s Earth
 Observation system Data and Information System (EOSDIS)
 (https://sedac.ciesin.columbia.edu). Appendix 1 and Appendix 2 are files
 corresponding to the main text.
DOI: 10.5061/dryad.t1g1jwszc
title: Botulinum toxin in the treatment of partially accommodative esotropia with high AC/A ratio

description: Purpose: To study the outcome of botulinum toxin (BTX) treatment (group 1)
 in partially accommodative esotropia with high accommodative
 convergence/accommodation (AC/A) ratio, in comparison with bilateral
 medial rectus muscles recessions and posterior fixation (group 2).
 Methods: In a retrospective comparative study, children aged 3-8 years old
 treated between 2011 and 2016, with partially accommodative esotropia with
 high AC/A ratio, deviation at distance of 10 prism diopters or more, and
 at least 1 year of follow-up, were included. Visual acuity, alternate
 prism and cover test, stereoacuity, biomicroscopy, and cycloplegic
 retinoscopy were carried out at initial, baseline visit, 6 months and 1
 year after BTX injection or surgery. Main outcome variables were deviation
 at distance and near, improvement in stereoacuity, and percentage of
 success. We used multiple regression or proportional odds analysis to
 control for potential confounding variables. Results: Of 95 patients, 84
 were eligible, 48 children in group 1 and 36 in group 2. Deviation and
 stereoacuity were similar in the two groups at 6 months, but significantly
 better in the BTX group at 1 year (median distance deviation 0 prism
 diopters vs 5 prism diopters, p&lt;0.01), although differences were
 not clinically relevant. Percentage of success was also significantly
 better only at 1 year (93% vs 72%, p=0.01). Change in distance-near
 disparity was not significantly different in the two groups in the period
 of study. Conclusions: Botulinum toxin could be superior to, or as
 effective as surgery, at middle term, in the treatment of partially
 accommodative esotropia with high AC/A ratio.
DOI: 10.5061/dryad.pzgmsbcgd
title: Insights from empirical analyses and simulations on using multiple fossil calibrations with relaxed clocks to estimate divergence times

description: Relaxed clock methods account for among-branch-rate-variation when
 estimating divergence times by inferring different rates for individual
 branches. In order to infer different rates for individual branches,
 important assumptions are required. This is because molecular sequence
 data does not provide direct information about rates, but instead provides
 direct information about the total number of substitutions along any
 branch, which is a product of the rate and time for that branch. Often,
 the assumptions required for estimating rates for individual branches
 depend heavily on the implementation of multiple fossil calibrations in a
 single phylogeny. Here, we show that the basis of these assumptions is
 often critically undermined. First, we highlight that the temporal
 distribution of the fossil record often violates key assumptions of
 methods that use multiple fossil calibrations with relaxed clocks. With
 respect to “node calibration” methods, this conclusion is based on our
 inference that different fossil calibrations are unlikely to reflect the
 relative ages of different clades. With respect to the
 fossilised-birth-death-process, this conclusion is based on our inference
 that the fossil recovery rate is often highly heterogeneous. We then
 demonstrate that methods of divergence time estimation that use multiple
 fossil calibrations are highly sensitive to assumptions about the fossil
 record and among-branch-rate-variation. Given the problems associated with
 these assumptions, our results highlight that using multiple fossil
 calibrations with relaxed clocks often does little to improve the accuracy
 of divergence time estimates.
DOI: 10.15468/dl.32rued
title: Occurrence Download

description: A dataset containing 25820 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ochotona"
 ]
}

 The dataset includes 25820 records from 151 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002135-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.b5mkkwh8q
title: Resolving fine-scale population structure and fishery exploitation using sequenced microsatellites in a northern fish

description: The resiliency of populations and species to environmental change is
 dependent on the maintenance of genetic diversity, and as such quantifying
 diversity is central to combatting ongoing wide spread reductions in
 biodiversity. With the advent of next-generation sequencing, several
 methods now exist for resolving fine-scale population structure, but the
 comparative performance of these methods for genetic assignment has rarely
 been tested. Here we evaluate the performance of sequenced microsatellites
 and a single nucleotide polymorphism (SNP) array to resolve fine-scale
 population structure in a critically important salmonid in northeastern
 Canada, Arctic charr (Salvelinus alpinus). We also assess the utility of
 sequenced microsatellites for fisheries applications by quantifying the
 spatial scales of movement and exploitation through genetic assignment of
 fishery samples to rivers of origin and comparing these results with a
 29-year tagging dataset. Self-assignment and simulation-based analyses of
 111 genome-wide microsatellite loci and 500 informative SNPs from 28
 populations of Arctic charr in northeastern Canada identified largely
 river-specific genetic structure. Despite large differences (~4X) in the
 number of loci surveyed between panels, mean self-assignment accuracy was
 similar with the SNP panel and with the microsatellite loci (&gt;90%).
 Subsequent analysis of 996 fishery-collected samples using the
 microsatellite panel revealed that larger rivers contribute greater
 numbers of individuals to the fishery, and that coastal fisheries largely
 exploit individuals originating from nearby rivers, corroborating results
 from traditional tagging experiments. Our results demonstrate the efficacy
 of sequence-based microsatellite genotyping to advance understanding of
 fine-scale population structure and harvest composition in northern and
 understudied species.
description: Files consist of Rubias and genepop input files for
 microsatellite and SNP data
DOI: 10.5061/dryad.tht76hdw0
title: Human walking in the real world: interactions between terrain type, gait parameters, and energy expenditure

description: Humans often traverse real-world environments with a variety of surface
 irregularities and inconsistencies, which can disrupt steady gait and
 require additional effort. Such effects have, however, scarcely been
 demonstrated quantitatively, because few laboratory biomechanical measures
 apply outdoors. Walking can nevertheless be quantified by other means. In
 particular, the foot’s trajectory in space can be reconstructed from
 foot-mounted inertial measurement units (IMUs), to yield measures of
 stride and associated variabilities. But it remains unknown whether such
 measures are related to metabolic energy expenditure. We therefore
 quantified the effect of five different outdoor terrains on foot motion
 (from IMUs) and net metabolic rate (from oxygen consumption) in healthy
 adults (N = 10; walking at 1.25 m/s). Energy expenditure increased
 significantly (P &lt; 0.05) in the order Sidewalk, Dirt, Gravel,
 Grass, and Woodchips, with Woodchips about 27% costlier than Sidewalk.
 Terrain type also affected measures, particularly stride variability and
 virtual foot clearance (swing foot’s lowest height above consecutive
 footfalls). In combination, such measures can also roughly predict
 metabolic cost (adjusted , partial least squares regression), and even
 discriminate between terrain types (10% reclassification error). Body-worn
 sensors can characterize how uneven terrain affects gait, gait
 variability, and metabolic cost in the real world.
DOI: 10.15468/dl.bdeqet
title: Occurrence Download

description: A dataset containing 622 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (c2ecae57-6701-485e-9ebd-5f87b2945cb2, f9b67ad0-9c9b-11d9-b9db-b8a03c50a862, 6ea87510-0561-11d8-b851-b8a03c50a862)",
 "TaxonKey is Melanoplus bruneri",
 "Year 1900-2026"
 ]
}

 The dataset includes 622 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002139-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sjmykv
title: Occurrence Download

description: A dataset containing 22475416 species occurrences available in GBIF matching the query:
{
 "GadmGid" : [
 "is DEU.2_1"
 ]
}

 The dataset includes 22475416 records from 985 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002105-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8cz8w9gkq
title: Independent losses of the Hypoxia-Inducible Factor (HIF) pathway within Crustacea

description: Metazoans respond to hypoxic stress via the Hypoxia Inducible Factor (HIF)
 pathway, a mechanism thought to be extremely conserved due to its
 importance in monitoring cellular oxygen levels and regulating responses
 to hypoxia. However, recent work revealed that key members of the HIF
 pathway have been lost in specific lineages (a tardigrade and a copepod),
 suggesting alternative mechanisms have evolved but are still undescribed.
 Using genomic and transcriptomic data from 70 different species across 12
 major crustacean groups, we assessed the degree to which the gene HIFa,
 the master regulator of the HIF pathway, was conserved. Mining of protein
 domains, followed by phylogenetic analyses of gene families, uncovered
 group-level losses of HIFa, including one across three orders within
 Cirripedia, and in three orders within Copepoda. For these groups,
 additional assessment showed losses of HIF repression machinery (EGLN,
 VHL). These results suggest the existence of alternative mechanisms for
 cellular response to low oxygen, and highlight these taxa as models useful
 for probing these evolutionary outcomes.
description: No additional sequencing was performed for this study, as we
 instead used publically available transcriptomes from both the TSA and
 SRA. Included in this repository are protein files from the transcriptomes
 we assemblied <em>de novo </em>(from SRA sources), alignments
 (in phylip format) and newick files for the phylogenetic trees created.
 For more specific information regarding the generation and analysis,
 please see the "Supplemental Methods" associated with this
 manuscript.
description: NOTE: As stated in the methods, the alignments and newick tree
 files may have residual PAS-only containing protein sequenes and some
 host/fish sequences. We deleted them in post, which is why they are not
 present in the final phylogenetic tree image [Supplementa Methods:
 "In the event that a sequences made it into the final tree and was
 revealed during post-processing to be a member of a PAS-only containing
 gene family, these were pruned from the final phylogenetic tree (though
 are still present in the deposited final alignment and newick
 file)"...]
DOI: 10.15468/dl.m24a5b
title: Occurrence Download

description: A dataset containing 12006234 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Strigiformes"
 ]
}

 The dataset includes 12006234 records from 5674 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002095-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4q7uqh
title: Occurrence Download

description: A dataset containing 261 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Plecturocebus ornatus (Gray, 1866)"
 ]
}

 The dataset includes 261 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009948-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qcbwwx
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Winteria telescopa Brauer, 1901",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((26.9648 -7.1504,17.9648 -7.1504,17.9648 -16.1504,26.9648 -16.1504,26.9648 -7.1504))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009949-250525065834625/datasets/export for details.
DOI: 10.5281/zenodo.17713450
title: PATHOPHYSIOLOGY OF PERIODONTAL TISSUE: CLINICAL FEATURES, ETIOLOGY, AND PATHOGENESIS