cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s4mw6m9c2
title: Distance to the edge and other landscape features influence nest predation in grey partridges

description: Predation and habitat deterioration are the main reasons for the strong
 decline of ground-nesting farmland birds such as the grey partridge Perdix
 perdix in Europe. Grey partridge nests and incubating females are
 especially vulnerable to predation. We have previously demonstrated that
 predator activity is much lower inside flower blocks (agri-environment
 schemes sown with a flower seed mix) than at their edges and that predator
 activity in flower blocks depends on the surrounding landscape. Here, we
 investigate whether these differences in predator activity translate into
 differences in grey partridge nest predation and assess predation patterns
 relative to landscape and nest site characteristics. We recorded the
 success of 56 nests of radio-tagged grey partridges between 2009–2017 in
 an agricultural landscape in Central Germany. We used Bayesian logistic
 regression to analyse the effects of nest site and landscape
 characteristics on nest predation on a subset of 46 nests (21 nests
 successful, 25 predated). Distance to the edge of the nesting habitat was
 the most important predictor, reducing predation probability from 66.8% at
 the edge to 18.5% at 85.5 m. Predation probability decreased with
 increasing length of habitat borders, habitat diversity and the area of
 permanent grasslands and fallows. Predation probability was higher further
 from settlements and increased with increasing woodland area in the
 agricultural matrix. When considering linear landscape structures, nest
 predation patterns matched the patterns of predator activity from our
 previous studies. Results suggest that the distance to the edge of the
 nesting habitat is most important, and that nest predation may be reduced
 by providing sufficiently broad nesting habitats. Nest predation may
 further be minimized by increasing habitat diversity and coverage of
 extensive vegetation types and by establishing conservation measures for
 grey partridges further away from woodlands. These measures may also
 benefit other ground-nesting farmland birds. 
description: Please see the corresponding article for information on data
 collection and analysis.
description: R and JAGS are required to run the code. Additionally the
 packages jagsUI, dplyr, lubridate and loo are necessary to run the
 code.
DOI: 10.5061/dryad.4qrfj6qg6
title: Genotype likelihood (beagle file) and genotype (vcf) files of North Atlantic and Black Sea Harbour porpoises (Phocoena phocoena)

description: The Harbour porpoise (Phocoena phocoena) is a highly mobile cetacean
 species primarily occurring in coastal and shelf waters across the
 Northern hemisphere. It inhabits heterogeneous seascapes broadly varying
 in salinity and temperature. Here we produced 74 whole genomes at
 intermediate coverage to study Harbour porpoise’s evolutionary history and
 investigate the role of local adaptation in the diversification into
 subspecies and populations. We identified ~6 million high-quality SNPs
 sampled at 8 localities across the North Atlantic and adjacent waters,
 which we used for population structure, demographic, and
 genotype-environment association analyses. Our results suggest a genetic
 differentiation between three subspecies (P.p. relicta, P.p. phocoena, and
 the recently proposed P.p meridionalis), and three distinct populations
 within the subspecies P.p. phocoena: Atlantic, Belt Sea, and Proper Baltic
 Sea. Effective population size and Tajima’s D levels suggest a population
 contraction in Black Sea and Iberian porpoises, but a population expansion
 in the P.p. phocoena populations. Phylogenetic trees indicate a
 post-glacial colonization from a southern refugium. Genotype-environment
 association analysis identified salinity as a major driver in genomic
 variation and we identified candidate genes putatively underlying
 adaptation to different salinity levels. Our study highlights the value of
 whole genome resequencing to unravel subtle population structure in highly
 mobile species, shows how strong environmental gradients and local
 adaptation may lead to population differentiation and how neutral and
 adaptive markers give different perspectives on population subdivision.
 The results have great conservation implications as we found inbreeding
 and low genetic diversity in the endangered Black Sea subspecies and
 identified the critically endangered Proper Baltic Sea porpoises as a
 separate population.
description: # Genotype likelihood (beagle file) and genotype (vcf) files of North
 Atlantic and Black Sea Harbour porpoises (Phocoena phocoena)
 [https://doi.org/10.5061/dryad.4qrfj6qg6](https://doi.org/10.5061/dryad.4qrfj6qg6) This dataset contains resequencing data used in harbour porpoise genomics research. In this project, we analyzed population structure, demographic history, and signatures of selection. ## Description of the data and file structure Data uploaded here contain: - Genotype likelihoods of the 72 samples: 72_porpoises_unlinked.beagle - Genotypes of 72 samples: Filtered_SNPs_72_samples.vcf - Adaptive_SNPs_no_including_BLS: Pcadapt_adaptive_SNPs_unlinked_67_porpoises.vcf - Neutral_SNPs_no_including_BLS: Neutral_SNPs_unlinked_67_porpoises_in_HWE.vcf - RDA_Pcadapt_overalpping_SNPS_no_including_BLS: RDA-Pcadapt_adaptive_SNPs_unlinked_67_porpoises.vcf ## Sharing/Access information Raw sequecing data can be downloaded from the NCBI Bio Project PRJNA997110
DOI: 10.18742/31038256
title: PSYD_2801: UCLA

description: <i>This record is part of the Psy-ShareD database. The Psy-ShareD database will host pre-existing structural MRI data collected at different global sites that will be suitable for region of interest, voxel-based morphometry, cortical thickness and surface area analytical approaches. To access this database, complete the Data Access Request Form by following the link on this page under the Licence ‘Psy-ShareD Data Access Request’. For more information, follow the link listed in Related Materials.</i><b>Title: </b><b>C</b><b>ross-Sectional</b><b> Study of Individuals w</b><b>ith A</b><b>dult ADHD, Bipolar Disorder, and Schizophrenia</b><b>Contributors and PI’s:</b> Russell A. Poldrack, Krzysztof J. Gorgolewski, Joke DurnezStanford University, USA (Openneuro) <b>Key Details & Variables</b><pre></pre><b>Age Range</b>21-50<b>Number of Participants</b>265<b>Diagnostic Criteria</b>SCZ, BPD, ADHD<b>Number of Clinical Subjects</b>50, 49, 41<b>Number of Clinical Subjects (follow-up)</b>No<b>Number of Control Subjects</b>125<b>Number of Control Subjects (follow-up)</b>No<b>Demographic Information</b>Age, Sex, Ethnicity<b>Clinical Measures</b>SAPS, SANS, BPRS<b>Cognitive Measures</b>Color Trails Test (CTT), CPT, CVLT-II, MPQ, WAIS, Wechsler Memory Scale, Verbal working memory capacity, SMMT<b>Clinical Functioning Measures</b>N/A<b>Antipsychotic Medication Information Recorded</b>Yes<b>Antipsychotic Medication Name/ Antipsychotic Type</b>Yes<b>Antipsychotic Dose Recorded</b>Yes<b>CPZ Equivalents Recorded</b>N/A<b>Other Medication Variables Recorded</b>No<b>Recreational Drug/ Alcohol Use</b>No<br>
DOI: 10.18742/31038256.v1
title: PSYD_2801: UCLA

description: <i>This record is part of the Psy-ShareD database. The Psy-ShareD database will host pre-existing structural MRI data collected at different global sites that will be suitable for region of interest, voxel-based morphometry, cortical thickness and surface area analytical approaches. To access this database, complete the Data Access Request Form by following the link on this page under the Licence ‘Psy-ShareD Data Access Request’. For more information, follow the link listed in Related Materials.</i><b>Title: </b><b>C</b><b>ross-Sectional</b><b> Study of Individuals w</b><b>ith A</b><b>dult ADHD, Bipolar Disorder, and Schizophrenia</b><b>Contributors and PI’s:</b> Russell A. Poldrack, Krzysztof J. Gorgolewski, Joke DurnezStanford University, USA (Openneuro) <b>Key Details & Variables</b><pre></pre><b>Age Range</b>21-50<b>Number of Participants</b>265<b>Diagnostic Criteria</b>SCZ, BPD, ADHD<b>Number of Clinical Subjects</b>50, 49, 41<b>Number of Clinical Subjects (follow-up)</b>No<b>Number of Control Subjects</b>125<b>Number of Control Subjects (follow-up)</b>No<b>Demographic Information</b>Age, Sex, Ethnicity<b>Clinical Measures</b>SAPS, SANS, BPRS<b>Cognitive Measures</b>Color Trails Test (CTT), CPT, CVLT-II, MPQ, WAIS, Wechsler Memory Scale, Verbal working memory capacity, SMMT<b>Clinical Functioning Measures</b>N/A<b>Antipsychotic Medication Information Recorded</b>Yes<b>Antipsychotic Medication Name/ Antipsychotic Type</b>Yes<b>Antipsychotic Dose Recorded</b>Yes<b>CPZ Equivalents Recorded</b>N/A<b>Other Medication Variables Recorded</b>No<b>Recreational Drug/ Alcohol Use</b>No<br>
DOI: 10.5061/dryad.cnp5hqcb0
title: Data matrix for phylogeography of Euphorbia jolkinii

description: In this study, we conducted phylogenomic analyses on the plastome and
 genome-wide nuclearSNP of Euphorbia jolkinii and its relative. We archived
 the data matrix for the analyses.
description: Euphorbia_jolkinii_plastome.fas: plasome sequences assembled and
 aligned from NGS short
 reads.<br>Euphorbia_jolkinii_plastome_CDS.fas: plasome sequences CDS
 only assembled and aligned from NGS short
 reads.<br>Euphorbia_jolkinii_MIGseq.phylip: SNPs calling by stacks
 from the MIG-seq.
description: Euphorbia_jolkinii_plastome.fas: MEGA, RAxML,
 PopART.<br>Euphorbia_jolkinii_plastome_CDS.fas:
 BEAST.<br>Euphorbia_jolkinii_MIGseq.phylip: STRUCTURE, TreeMix,
 DIYABC.
DOI: 10.18120/65ga-ke41
title: StaticDynamicGraspForce
DOI: 10.5061/dryad.sj3tx969q
title: Data from: Evolution of a cross-feeding interaction following a key innovation in a long-term evolution experiment with Escherichia coli

description: The evolution of a novel trait can profoundly change an organism’s effects
 on its environment, which can in turn affect the further evolution of that
 organism and any coexisting organisms. We examine these effects and
 feedbacks following the evolution of a novel function in the Long-Term
 Evolution Experiment (LTEE) with Escherichia coli. A characteristic
 feature of E. coli is its inability to grow aerobically on citrate (Cit−).
 Nonetheless, a Cit+ variant with this capacity evolved in one LTEE
 population after 31,000 generations. The Cit+clade then coexisted stably
 with another clade that retained the ancestral Cit− phenotype. This
 coexistence was shaped by the evolution of a cross-feeding relationship
 based on C4-dicarboxylic acids, particularly succinate, fumarate, and
 malate, that the Cit+ variants release into the medium. Both the
 Cit− and Cit+ cells evolved to grow on these excreted resources. The
 evolution of aerobic growth on citrate thus led to a transition from an
 ecosystem based on a single limiting resource, glucose, to one with at
 least five resources that were either shared or partitioned between the
 two coexisting clades. Our findings show that evolutionary novelties can
 change environmental conditions in ways that facilitate diversity by
 altering ecosystem structure and the evolutionary trajectories of
 coexisting lineages.
DOI: 10.5061/dryad.0gb5mkm6t
title: Eutrophication, water quality, and fisheries: a wicked management problem with insights from a century of change in Lake Erie

description: The datasets here were used to examine relationships between the overall
 productivity of Lake Erie and the commercial harvest of lake whitefish
 (Coregonus clupeaformis), walleye (Sander vitreus), and yellow perch
 (Perca flavescens) during 1915–2011. Here, we provide the two datasets
 used in the paper by Sinclair et al. titled "Eutrophication, water
 quality, and fisheries: a wicked management problem with insights from a
 century of change in Lake Erie". Each dataset is provided as a
 separate tab in a single Excel worksheet. The first dataset
 ("Productivity") provides the annual values of the five metrics
 used to develop the index of overall Lake Erie productivity. The second
 dataset ("Commercial harvest") provides the total annual
 commercial harvest (kg) of the three fish species, which were obtained
 from the Great Lakes Fishery Commission
 (http://www.glfc.org/great-lakes-databases.php). A summary and explanation
 of each variable is provided in the "Info" tab. Further
 information on how values were calculated (and transformed if necessary)
 is provided in either the info tab or the methods and supporting
 information of the associated article.
description: Please refer to the associated article for data collection
 methods and information on variable transformations.
description: Any spreadsheet software that can open ".xlsx" formats
 (e.g., Microsoft Excel or Google Sheets).
DOI: 10.15468/dl.3w2ubk
title: Occurrence Download

description: A dataset containing 71378 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-79.24224 -3.93835,-79.1012 -4.04835,-78.933 -4.00572,-78.88797 -3.86627,-79.0248 -3.73733,-79.23899 -3.78627,-79.26583 -3.87311,-79.24224 -3.93835))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 71378 records from 227 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003542-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.z08kprrjz
title: Limited outbreak of highly pathogenic influenza A(H5N1) virus in a Herring Gull colony, Canada, 2022

description: In summer 2022, highly pathogenic influenza A(H5N1) virus reached the
 Herring Gull (Larus argentatus) breeding colony on Kent Island, New
 Brunswick, Canada. Real-time monitoring revealed a self-limiting outbreak
 with low mortality. Proactive seabird surveillance is crucial for
 monitoring such limited outbreaks, protecting vulnerable seabirds, and
 tracing potential zoonotic transmission routes.
description: Images and videos of deceased or live, symptomatic American
 Herring Gulls recorded during the highly pathogenic avian influenza (HPAI)
 outbreak on Kent Island, New Brunswick, Canada in summer 2022.
DOI: 10.5061/dryad.gf1vhhmvj
title: Data from: Housework or vigilance? Bilbies alter burrowing activity under threat of predation by feral cats

description: Behavioral adjustments to predation risk not only impose costs on prey
 species themselves but can also have cascading impacts on whole
 ecosystems. The greater bilby (Macrotis lagotis) is an important ecosystem
 engineer, modifying the physical environment through their digging
 activity, and supporting a diverse range of sympatric species that use its
 burrows for refuge and food resources. The bilby has experienced severe
 decline over the last 200 years, and the species is now restricted to
 approximately 20% of its former distribution. Introduced predators, such
 as the feral cat (Felis catus), have contributed to this decline. We used
 camera traps to monitor bilby burrows at four sites in Western Australia,
 where bilbies were exposed to varying levels of cat predation threat. We
 investigated the impact of feral cats on bilby behavior at burrows,
 particularly during highly vulnerable periods when they dig and clear away
 soil or debris from the burrow entrance as they perform burrow
 maintenance. There was little evidence that bilbies avoided burrows that
 were visited by a feral cat; however, bilbies reduced the time spent
 performing burrow maintenance in the days following a cat visit (p=0.010).
 We found the risk posed to bilbies varied over time, with twice the cat
 activity around full moon compared with dark nights. Bilby burrows are
 such valuable resources for ecosystem functioning that bilby predation by
 feral cats, as well as even indirect impacts on bilby behavioral responses
 to perceived predation risk, together may have a substantial ecosystem
 impact.
description: This dataset was collected using Reconyx camera traps. The images
 were imported into DigiKam, and tagged accordingly. The metadata of the
 images were then exported into an Excel spreadsheet using R package
 "camtrapR".
DOI: 10.5061/dryad.79cnp5j1t
title: List of Erinaceidae and Dimylidae from the Late Miocene of Slovakia

description: The families Erinaceidae and Dimylidae are represented in the Late Miocene
 localities of Slovakia (Borský Svätý Jur, Krásno, Pezinok, Šalgovce,
 Studienka, Triblavina) by at least six hedgehog species (“Schizogalerix”
 voesendorfensis, Schizogalerix cf. moedlingensis, Lantanotherium
 sanmigueli, Atelerix cf. depereti, Atelerix aff. depereti, cf.
 Postpalerinaceus sp., Erinaceinae gen. and sp. indet.) and two dimylid
 species (Plesiodimylus chantrei, Metacordylodon aff. schlosseri). The
 material of Lantanotherium sanmigueli from the western Carpathians is
 investigated, revealing a broad variability in all samples. Additionally,
 deciduous premolars of Lantanotherium are described for the first
 time. Erinaceid species are frequent in the Vallesian but their abundance
 strongly declines afterwards. As an exception, Schizogalerix reentered the
 Danube and Vienna basins during MN11, likely from eastern Europe.
 Erinaceinae displays a low diversity during the Late Miocene of central
 Europe, which tends to support a pan-European diversity phenomenon. The
 humidity-dependent Dimylidae species are abundant during the late
 Vallesian. Rare finds of Plesiodimylus confirm the survival of this family
 into early MN11 in the Pannonian region.
DOI: 10.5061/dryad.8gtht76vh
title: Woodland expansion in the presence of deer: 30 years of evidence from the Cairngorms Connect landscape restoration partnership

description: Restoring native woodlands to areas where they have been lost is a key
 element for tackling the nature and climate crises. Natural regeneration
 offers the potential to achieve this cheaply and at scale, but browsing
 ungulates like deer can inhibit this or alter the pattern of regeneration.
 This issue is particularly pronounced in the Scottish Highlands, a heavily
 deforested region with high deer numbers. We describe the work of the 600
 km2 landscape restoration partnership, Cairngorms Connect, in speeding up
 natural woodland expansion. We use 30 years of regeneration monitoring to
 show a consistent, large-scale expansion of native woodland, largely
 through natural regeneration alongside deer culling, without the use of
 fences. This was achieved across the partnership, despite differing
 management histories and land-managing organisations (comprising two
 statutory agencies, one private landowner and one non-governmental
 organisation). During peak periods of woodland expansion, the area of new
 woodland (i.e. exceeding 100 trees per hectare) increased by 1.2%, 1.7%,
 2.7% and 6.0% annually in the four landholdings’ regeneration zones,
 equating to a total of approximately 164 ha annually of new woodland.
 Natural regeneration is however patchy and hard to predict. Higher levels
 of management intervention may be needed to increase species that are
 rarer, more palatable or further from seed sources; we recommend long-term
 field trials to inform this, such as those underway in Cairngorms Connect.
 Further research should develop techniques for remote-sensing of woodland
 expansion, verified against field data, combined with development of
 process-based models to enable us to predict the outcomes of different
 management scenarios. Synthesis and applications: We show that
 collaborative deer management across multiple adjoining landholdings can
 achieve rapid landscape-scale native woodland expansion with minimal need
 for planting or fencing. Our results show the power of monitoring
 regeneration directly, to inform deer management for an area. We
 demonstrate that by uniting over a shared vision, organisations with
 differing management approaches and histories can build understanding
 alongside landscape-scale ecological restoration.
description: Full methods are described in the paper and Supplementary
 Information
description: MS Excel or similar, such as LibreOffice Calc.
DOI: 10.5061/dryad.8kprr4xtf
title: Physiology of the widespread pulsating soft coral Xenia umbellata is affected by food sources, but not by water flow

description: Coral energy and nutrient acquisition strategies are complex and sensitive
 to environmental conditions such as water flow. While high water flow can
 enhance feeding in hard corals, knowledge about the effects of water flow
 on the feeding of soft corals, particularly those pulsating, is still
 limited. In this study, we thus investigated the effects of feeding and
 water flow on the physiology of the pulsating soft coral Xenia umbellata.
 We crossed three feeding treatments i) no feeding, ii) particulate organic
 matter [POM] as phytoplankton, and iii) dissolved organic carbon [DOC] as
 glucose, with four water volume exchange rates (200, 350, 500 and 650
 Lh-1) over 15 days. Various ecophysiological parameters were assessed
 including pulsation rate, growth rate, isotopic and elemental ratios of
 carbon (C) and nitrogen (N) as well as photo-physiological parameters of
 the Symbiodiniaceae (cell density, chlorophyll-a and mitotic index). Water
 flow had no significant effect but feeding had a substantial impact on the
 physiology of the X. umbellata holobiont. In the absence of food, corals
 exhibited significantly lower pulsation rates, lower Symbiodiniaceae cell
 density, and lower mitotic indices compared to the fed treatments, yet
 significantly higher chlorophyll-a per cell and total N content.
 Differences were also observed between the two feeding treatments, with
 significantly higher pulsation rates and lower chlorophyll-a per cell in
 the DOC treatment, but higher C and N content in the POM treatment. Our
 findings suggest that the X. umbellata holobiont can be viable under
 different trophic strategies, though favouring mixotrophy. Additionally,
 the physiology of the X. umbellata may be regulated through its own
 pulsating behaviour without any positive nor negative effects from
 different water flow. Thus, this study contributes to our understanding of
 soft coral ecology, particularly regarding the competitive success and
 widespread distribution of X. umbellata.
description: An aquarium experiment was carried out on soft coral
 <em>Xenia</em> <em>umbellata</em> at the
 University of Bremen, Germany, crossing 3 feeding treatments (no feeding,
 phytoplankton and DOC) with four water flow treatments (200, 350, 500 and
 650 Lh<sup>-1</sup>). Various physiological parameters were
 assessed. Data was subsequently analysed using R statistical
 software.
description: Microsoft Excel
DOI: 10.15468/dl.s38c3c
title: Occurrence Download

description: A dataset containing 241550 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Field Museum of Natural History (Zoology) Mammal Collection"
 ]
}

 The dataset includes 241550 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003568-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.