cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hmgqnk9k8
title: Physiological control on carbon isotope fractionation in marine phytoplankton

description: One of the great challenges in biogeochemical research over the past half
 a century has been to quantify and understand the mechanisms underlying
 stable carbon isotope fractionation (εp) in phytoplankton in response to
 changing CO2 concentrations. Partly, this interest is grounded in the use
 of fossil photosynthetic organism remains as a proxy for past atmospheric
 CO2 levels. Phytoplankton organic carbon is depleted in 13C compared to
 its source because of kinetic fractionation by the enzyme RubisCO during
 photosynthetic carbon fixation, as well as through physiological pathways
 upstream of RubisCO. Moreover, other factors such as nutrient limitation,
 variations in light regime as well as phytoplankton culturing systems and
 inorganic carbon manipulation approaches may confound the influence of
 aquatic CO2 concentration ([CO2]) on εp. Here, based on experimental data
 compiled from the literature, we assess which underlying physiological
 processes cause the observed differences in εp for various phytoplankton
 groups in response to C-demand/C-supply (i.e., POC production/[CO2]) and
 test potential confounding factors. Culturing approaches and methods of
 carbonate chemistry manipulation were found to best explain the
 differences in εp between studies, although daylength was an important
 predictor for εp in haptophytes. Extrapolating results from culturing
 experiments to natural environments and for proxy applications therefore
 requires caution, and it should be carefully considered whether culture
 methods and experimental conditions are representative of natural
 environments.
DOI: 10.5061/dryad.fxpnvx0v7
title: Estimating abundance in unmarked populations of Golden Eagle

description:  1. Estimates of species abundance are of key importance in
 population and ecosystem level research but can be hard to obtain. Study
 designs using camera-traps are increasingly being used for large-scale
 monitoring of species that are elusive and/or occur naturally at low
 densities. 2. Golden eagle (Aquila chrysaetos) is one such species, and we
 investigate whether existing large-scale monitoring programs using baited
 camera-traps can be used to estimate the abundance of golden eagles, as an
 alternative to traditional labour-intensive searches for active
 territories and nest sites during the breeding period. 3. The camera-trap
 data allowed two measures of abundance to be estimated within each of four
 main study areas in mid and northern Norway; occupancy was measured as the
 probability of camera site use, and population size was measured as the
 number of eagle individuals using the camera sites within a study area.
 Spatial and temporal patterns in occupancy and population size were
 explored and evaluated against independent estimates of the breeding pair
 density in the study areas. 4. Annual estimates of golden eagle occupancy
 showed low precision, while estimates of population size were more precise
 in relation to both estimated and anticipated abundance fluctuations.
 Estimates of population size may therefore be suitable for monitoring
 within study area temporal abundance trends, while estimates of occupancy
 seem unsuitable for such in golden eagles. Across study areas, patterns in
 both average occupancy and average population density estimated from
 population size, were consistent with the spatial pattern in average
 breeding pair densities (r = 0.99, and r = 0.89 respectively). This
 suggests that camera-trap based estimates of occupancy and population
 density reflect territory density at large spatial scales. In conclusion,
 our results suggest that baited camera-traps can be a cost-effective
 strategy for monitoring the abundance of golden eagles.
description: The data used were obtained from two regional research projects
 in Norway targeted towards the conservation of the nationally endangered
 arctic fox (Vulpes lagopus). Both projects use baited camera-traps
 (RECONYX©) during late winter with the primary goal to monitor arctic fox
 abundances as well as other potentially competitive species in the
 scavenger community, including golden eagles. Data from the COAT
 monitoring program originates from the north-eastern part of Finnmark
 County (70 ° N and 26 – 30 ° E) and data from the second monitoring
 program originates from three areas in mid-Norway, Dovrefjell (62°22′ N 95
 and 9°03′ E), Sylan-Forollhogna (63°00′ N and 12°09′ E) and Børgefjell
 (65°15′ and 13°46′). Please see the published article
 for details regarding how the datasets were processed.
description: Please see the published article for details regarding how the
 datasets may be used.
DOI: 10.5061/dryad.1jwstqjx5
title: Data from: No evidence for impaired solitary bee fitness following pre-flowering sulfoxaflor application alone or in combination with a common fungicide in a semi-field experiment

description: Pesticide exposure is considered a major driver of pollinator decline and
 the use of neonicotinoid insecticides has been restricted by regulatory
 authorities due to their risks for pollinators. Impacts of new alternative
 sulfoximine-based compounds on solitary bees and their potential
 interactive effects with other commonly applied pesticides in agriculture
 remain unclear. Here, we conducted a highly replicated full-factorial
 semi-field experiment with the solitary bee Osmia bicornis, an important
 pollinator of crops and wild plants in Europe, and Phacelia tanacetifolia
 as a model crop. We show that spray applications of the insecticide
 sulfoxaflor (product Closer) and the fungicide azoxystrobin (product
 Amistar), both alone and combined, had no significant negative impacts on
 adult female survival or the production, mortality, sex ratio and body
 size of offspring when sulfoxaflor was applied five days before crop
 flowering. Our results indicate that for O. bicornis (1) the risk of
 adverse impacts of sulfoxaflor (Closer) on fitness is small when applied
 at least five days before crop flowering and (2) that azoxystrobin
 (Amistar) has a low potential of exacerbating sulfoxaflor effects under
 field-realistic conditions.
DOI: 10.26165/juelich-data/stu1ll
title: Quota Steiner tree problem for large-scale wind turbine siting including cable routing

description: This data contains the input data for benchmarking the Quota Steiner tree problem in the context of large-scale wind turbine siting including cable routing. The data contains the corresponding .stp problem files. The raw data of turbine and cable connection including values for scenic features of selected regions in Germany can also be found here. The data regarding potential turbine position is based on the work by Ryberg et al. (2019), see https://data.mendeley.com/datasets/vpp7hxhv9m/1. The data corresponding to the value of scenic features is based on the work by Roth (2018), see https://orlis.difu.de/handle/difu/254637. For a detailed description of the data generation, see the manuscript "An efficient solver for large-scale onshore wind farm siting including cable routing" (https://arxiv.org/abs/2304.09658)
DOI: 10.5061/dryad.vhhmgqnwk
title: Large scale across-breed genome-wide association study reveals a variant in HMGA2 associated with inguinal cryptorchidism risk in dogs

description: Cryptorchidism is the most common congenital sex development disorder in
 dogs. Despite this, little progress has been made in understanding its
 genetic background. Extensive genetic testing of dogs through consumer and
 veterinary channels using a high-density SNP genotyping microarray coupled
 with links to clinical records presents the opportunity for a large-scale
 genome-wide association study to elucidate the molecular risk factors
 associated with cryptorchidism in dogs. Using an inter-breed genome-wide
 association study approach, a significant statistical association on
 canine chromosome 10 was identified, with the top SNP pinpointing a
 variant of HMGA2 previously associated with adult weight variance. In
 further analysis we show that incidence of cryptorchidism is skewed
 towards smaller dogs in concordance with the identified variant’s previous
 association with adult weight. This study represents the first putative
 variant to be associated with cryptorchidism in dogs.
DOI: 10.5061/dryad.h44j0zpnm
title: Pollinator loss causes rapid adaptive evolution of selfing and dramatically reduces genome-wide genetic variability

description: While selfing populations harbor little genetic variation limiting
 evolutionary potential, the causes are unclear. We experimentally evolved
 large, replicate populations of Mimulus guttatus for nine generations in
 greenhouses with or without pollinating bees and studied DNA polymorphism
 in descendants. Populations without bees adapted to produce more selfed
 seed yet exhibited striking reductions in DNA polymorphism despite large
 population sizes. Importantly, the genome-wide pattern of variation cannot
 be explained by a simple reduction in effective population size, but
 instead reflects the complicated interaction between selection, linkage,
 and inbreeding. Simulations demonstrate that the spread of favored alleles
 at few loci depresses neutral variation genome-wide in large populations
 containing fully selfing lineages. It also generates greater heterogeneity
 among chromosomes than expected with neutral evolution in small
 populations. Genome-wide deviations from neutrality were documented in
 populations with bees, suggesting widespread influences of background
 selection. After applying outlier tests to detect loci under selection,
 two genome regions were found in populations with bees, yet no adaptive
 loci were otherwise mapped. Large amounts of stochastic change in selfing
 populations compromise evolutionary potential and undermine outlier tests
 for selection. This occurs because genetic draft in highly selfing
 populations makes even the largest changes in allele frequency
 unremarkable.
description: Replicate plant populations were experimentally evolved for nine
 generations in a greenhouse with or without pollinating bees. Descendants
 from these populations had their DNA extracted in pools, which were then
 sequenced. We examined the whole genome response of populations and
 interpreted these patterns in light of simple, chromosome-level
 simulations with and without natural selection. We also identified targets
 of natural selection using SNP outlier methods.
description: The programs we share here require a working knowledge of
 Python3.
DOI: 10.5061/dryad.msbcc2g17
title: A new taxonomist-curated reference library of DNA barcodes for Neotropical electric fishes (Teleostei: Gymnotiformes)

description: DNA barcoding is a useful tool for identifying species; however,
 successful barcode-based identification requires a reference library of
 barcode sequences from accurately identified specimens. Here we present a
 reference library of co1 barcode sequences for the Neotropical
 electric knifefish order Gymnotiformes (Teleostei: Ostariophysi), a model
 taxon for studies of tropical diversification and biogeography, genomics,
 behaviour, and neurobiology. Our library contains barcodes for 167 of the
 ca. 270 valid species of gymnotiforms derived from geo-referenced museum
 voucher specimens, and includes sequences from 26 type specimens and 21
 specimens from type localities, most of which we collected. To assess the
 state of gymnotiform barcodes in two main public barcode repositories,
 GenBank and BOLD, we compared the barcodes in these databases to our
 reference library. Our analysis shows that a considerable proportion of
 gymnotiform barcodes in GenBank and BOLD are mis- or unidentified. We
 encourage taxonomists to develop and publish barcode reference libraries
 composed of carefully curated barcode sequences.
description: We built the Gymnotiformes Barcode Reference Library using
 representative barcode sequences for as many described species as
 possible. We used specimens from the type series of each species when
 possible; if not, we preferentially selected specimens from (within ca. 10
 km) or near (within ca. 500 km) the species type locality. We used tissues
 from voucher specimens deposited in museum collections. Specimens were
 identified using diagnostic keys and species descriptions from the primary
 taxonomic literature (reviewed by Ferraris Jr. <em>et
 al</em>., 2017; Fricke <em>et
 al</em>., 2022). We extracted DNA from each specimen from muscle or
 fin tissue, and then amplified and sequenced <em>co1</em> for
 each specimen.
DOI: 10.5061/dryad.5dv41ns7s
title: Individual dietary specialization in a generalist bee varies across populations but has no effect on the richness of associated microbial communities

description: Despite the increasingly documented occurrence of individual
 specialization, the relationship between individual consumer interactions
 and diet-related microbial communities in wild populations is still
 unclear. Using data from nests of the bee Ceratina australensis from three
 different wild populations, we combine metabarcoding and network
 approaches to explore the existence of individual variation in resource
 use within and across populations, and whether dietary specialization
 affects the richness of pollen-associated microbes. We reveal the
 existence of marked dietary specialization. In the most specialized
 population, we also show that individuals' diet breadth was
 positively related to the richness of fungi, but not bacteria. Overall,
 individual specialization appeared to have a weak or negligible effect on
 the microbial richness of nests, suggesting that different mechanisms
 beyond environmental transmission may be at play regarding microbial
 acquisition in wild bees.
DOI: 10.5061/dryad.xwdbrv1g4
title: Sighting, group composition, and tactile exchange for a study on Atlantic spotted dolphins around Bimini, The Bahamas

description: Interactions between mammalian social groups are generally antagonistic as
 individuals in groups cooperate to defend resources from non-members.
 Members of the family Delphinidae inhabit a three-dimensional habitat
 where resource defense is usually impractical. Here, we describe a
 long-term partial fusion of two communities of Atlantic spotted dolphins
 (Stenella frontalis). The northern community, studied for 30 years,
 immigrated 160 km to the range of the southern community, observed for 20
 years. Both communities featured fission-fusion grouping patterns,
 strongest associations between adult males, and frequent affiliative
 contact between individuals. For the five-year period following the
 immigration, we found members of all age classes and both sexes in mixed
 groups, but there was a strong bias toward finding immigrant males in
 mixed groups. Some association levels between males, and males and
 females, from different communities were as high as the highest
 within-community associations. Affiliative contacts indicate that these
 individuals were forming social bonds. The mixing of two separate social
 groups with new bond formation is rare in terrestrial mammal groups. Such
 mixing between spotted dolphin groups suggests that adaptations to respond
 aggressively to ‘outsiders’ is diminished in this species and possibly
 other ecologically similar dolphins.
description: Sighting data were collected during boat surveys between
 2013-2018 around Bimini, The Bahamas. Group composition data were
 summarized from sighting data collected between 2007 and 2018. Tactile
 exchanges were event sampled from underwater video data recorded during
 boat surveys that had underwater encounters. Tactile exchanges have been
 limited to events that occurred during mixed-origin sightings (i.e.,
 including dolphins from the resident and immigrant group).
description: Analysis of association was completed in Socprog, which runs in
 MatLab. Code from Socprog cannot be provided, but the settings used to
 calculate coefficients of association are included in the Methods section
 of the manuscript.
DOI: 10.5061/dryad.q2bvq83n3
title: Conserved structural elements specialize ATAD1 as a membrane protein extraction machine

description: The mitochondrial AAA protein ATAD1 (in humans; Msp1 in yeast) removes
 mislocalized membrane proteins, as well as stuck import substrates from
 the mitochondrial outer membrane, facilitating their re-insertion into
 their cognate organelles and maintaining mitochondria’s protein import
 capacity. In doing so, it helps to maintain proteostasis in mitochondria.
 How ATAD1 tackles the energetic challenge to extract hydrophobic membrane
 proteins from the lipid bilayer and what structural features adapt ATAD1
 for its particular function has remained a mystery. Previously, we
 determined the structure of Msp1 in complex with a peptide substrate (Wang
 et al., 2020). The structure showed that Msp1’s mechanism follows the
 general principle established for AAA proteins while adopting several
 structural features that specialize it for its function. Among these
 features in Msp1 was the utilization of multiple aromatic amino acids to
 firmly grip the substrate in the central pore. However, it was not clear
 whether the aromatic nature of these amino acids were required, or if they
 could be functionally replaced by aliphatic amino acids. In this work, we
 determined the cryo-EM structures of the human ATAD1 in complex with a
 peptide substrate at near atomic resolution. The structures show that
 phylogenetically conserved structural elements adapt ATAD1 for its
 function while generally adopting a conserved mechanism shared by many AAA
 proteins. We developed a microscopy-based assay reporting on protein
 mislocalization, with which we directly assessed ATAD1’s activity in live
 cells and showed that both aromatic amino acids in pore-loop 1 are
 required for ATAD1’s function and cannot be substituted by aliphatic amino
 acids. A short α-helix at the C-terminus strongly facilitates ATAD1’s
 oligomerization, a structural feature that distinguishes ATAD1 from its
 closely related proteins.
DOI: 10.5061/dryad.zs7h44jc8
title: Estimation of the maximum utilization area including home range and peripheral sites

description: There is increasing evidence that occasional utilization area (peripheral
 sites), in addition to typical utilization area (home range), is important
 for wildlife conservation and management. Here we estimated the maximum
 utilization area (MUA), including both typical and occasional utilization
 areas, based on asymptotic curves of utilization area plotted against
 sample size. In previous studies, these curves have conventionally been
 plots of cumulative utilization area versus sample size, but this
 cumulative method is sensitive to stochastic effects. We propose a new
 method based on simulation studies where outcomes of replicated
 simulations are averaged to reduce stochastic effects. In this averaged
 method, possible combinations of sample size with the same number of
 location data replicated from a dataset were averaged and applied to the
 curves of utilization area. The cumulative method resulted in a large
 variation of MUA estimates, depending on the start date as well as the
 total sample size of the dataset. In the averaged method, MUA estimates
 were robust against changes in the start date and total sample size. The
 large variation of MUA estimates arose because location data on any day
 including the start date are affected by unpredictable effects associated
 with animal activity and environmental conditions. In the averaged method,
 replicates of sample size resulted in a reduction of temporal
 stochasticity, suggesting that the method stably provides reliable
 estimates for MUA.
DOI: 10.5061/dryad.0zpc8670q
title: Data on the Weather and Habitat and Representative results of qPCR and PCR

description: We used weather and habitat characteristics, which collected from studied
 49 sampling sites, to know how those affect ranavirus infection rate in
 amphibian larvae of Dryophytes japonicus (Japanese tree frog), Pelophylax
 nigromaculatus (Black-spotted pond frog), and Lithobates catesbeianus
 (American bullfrog) in South Korea. Description on the method section: To
 investigate the relationship between the ranavirus infection rate and
 habitat characteristics, we analyzed 16 habitat characteristics at each
 sampling location. The land cover rate (urban area, agricultural area,
 forest area, grass area, wetland area, bare area, hydrosphere area) within
 a radius of 3 km2 from the mid-sampling point was calculated on the 2020
 South Korean land cover map(http://egis.me.go.kr ). From the land cover
 data, greenhouse cultivation areas within agricultural areas, salt fields
 and tidal flat areas within wetland areas, and sea areas within
 hydrosphere areas were excluded during data handling because these areas
 are inhabitable for amphibians. Additionally, the shortest distance from
 the mid-sampling point to agricultural land, mountains, water bodies, and
 urban areas was calculated in units of 1 m. When a sampling point was
 located within a specific coverage area, the distance was set to 2 m. All
 land cover rates, distance data, and altitude values of each sampling
 point were calculated using QGIS (ver. 3.4.7, QGIS.org 2021). Furthermore,
 the average air temperature, lowest air temperature, highest air
 temperature, and average precipitation for the immediately preceding
 quarter, based on the sampling date of the tadpoles used in the qPCR
 experiment, were obtained from the local meteorological station closest to
 the sampling point. We also provided the igures of representative positive
 qPCR results of D. japonicus (A, B) collected at Haenam, P. nigromaculatus
 (C, D) collected at Pohang, and L. catesbeianus (E, F) collected at
 Gmchoen, which showing positive ranavirus detection from the samples, and
 the Photographs of representative gel electrophoresis of the MCP fragment
 (~500bp), which confirmed the qPCR result again by sequencing the fragment
 (G, H) in the further study.
description: Data on the weather and habitat characteristics at 49 sampling
 sites to screen ranavirus prevelance in amphibians in South Korea and the
 representative qPCR and PCR (MCP fragment, ~520 bp) reuslts were
 provided.
DOI: 10.5517/ccdc.csd.cc2pw4g6
title: CSD 2498738: Experimental Crystal Structure Determination

description: Related Article: Yucheng Hao, Qiuhui Zhang, Haoran Yu, Xikai Miu, Simin Cai, Xinnan Li, Fengshan Yu, Yuan Lin, Mingyang Cao|2026|Inorg.Chem.Front.|||doi:10.1039/d5qi02229k
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2pw4h7
title: CSD 2498739: Experimental Crystal Structure Determination

description: Related Article: Yucheng Hao, Qiuhui Zhang, Haoran Yu, Xikai Miu, Simin Cai, Xinnan Li, Fengshan Yu, Yuan Lin, Mingyang Cao|2026|Inorg.Chem.Front.|||doi:10.1039/d5qi02229k
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.