cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sj3tx964z
title: Assembled RNA-seq data of Bougainvillea peruviana Thimma

description: Betalain is one of four major plant pigments, which shares some features
 with another major pigment anthocyanin. However, no plant was found to
 biosynthesize both pigments. Previous studies have reported that
 anthocyanin biosynthesis is regulated by post-transcriptional gene
 silencing (PTGS) in some plants, but the importance of PTGS in betalain
 biosynthesis remained unclear. In this study, we report the occurrence of
 PTGS in betalain biosynthesis in bougainvillea (Bougainvillea peruviana)
 ‘Thimma’. ‘Thimma’ produces three different color bracts on the same
 plant, pink, white and pink-white bicolor. This unstable pigmentation
 phenotype resembles the unstable anthocyanin pigmentation associated with
 PTGS, thus PTGS in the betalain biosynthetic pathway was expected. To test
 this hypothesis, we performed pigment analysis, gene expression analysis,
 small RNA analysis and transient overexpression analysis. We demonstrated
 that PTGS of BpCYP76AD1, one of the betalain biosynthetic enzyme genes, is
 responsible for the loss of betalain biosynthesis in ‘Thimma’. Genomic
 background or DNA methylation in the BpCYP76AD1 genome could not explain
 the induction of PTGS implying other locus regulates the unstable
 pigmentation. Our data indicates naturally occurring PTGS contributes to
 color pattern diversification not only in anthocyanin biosynthesis but
 also in betalain biosynthesis. Here, RNA-seq data (5.8 Gb for a pink bract
 and 5.7 Gb for a white bract, respectively) were assembled by Trinity.
 This data was used for identification of betalain-related genes and for
 small RNA mapping analysis.
description: RNA was extracted from around 1.5 cm length bracts (pink and
 white) of 'Thimma' using Sepasol RNA I Super G (Nacalai Tesque,
 Kyoto, Japan). Total RNA was sequenced using a Illumina Hiseq2500
 (Illumina Inc., San Diego, CA, USA) with 101-bp paired end (5.8 Gb for a
 pink bract and 5.7 Gb for a white bract, respectively), and the sequenced
 data were assembled by Trinity, and finally 156,790 contigs were
 obtained. This data was used for identification of betalain-related genes
 and for small RNA mapping analysis.
description: This is FASTA format file for assembled transcript sequence data.
 RNA was extracted from around 1.5 cm length bracts (pink and white) of
 'Thimma' using Sepasol RNA I Super G (Nacalai Tesque, Kyoto,
 Japan). Total RNA was sequenced using a Illumina Hiseq2500 (Illumina Inc.,
 San Diego, CA, USA) with 101-bp paired end (5.8 Gb for a pink bract and
 5.7 Gb for a white bract, respectively), and sequenced data were assembled
 by Trinity, and finally 156,790 contigs were obtained.
DOI: 10.5061/dryad.j9kd51ccg
title: Microsatellite variation in Nordic semi-domestic reindeer

description: We have analyzed DNA microsatellites and the mitochondrial control region
 in reindeer from 31 different husbandry areas in Norway, Sweden and
 Finland in order to better understand the processes that underlie the
 genetic variability of the Nordic domestic herds. The distinct
 differentiation found in the nuclear markers but less so in the
 mitochondrial marker, gives evidence of an origin from a common ancestral
 population which later evolved into the two main gene pools characterizing
 the nuclear genomes of domestic reindeer in Finland and most of Sweden and
 Norway. Analyses of temporal trends in effective population size gives
 evidence of a rapid increase in number of reindeer before the population
 growth associated with the pastoral transition. This implies that the
 ancestry of contemporary domestic reindeer lay among a rapid growing wild
 population possibly located in the boreal areas of eastern Fennoscandia or
 European Russia. The evolution of reindeer husbandry in Finland, perhaps
 with input from European Russia, which later spread to northern Norway
 could explain the shared genomic pattern observed in these areas today.
  The structured selection of productive female-centered herds may
 explain the genetic structure in other parts of Norway and in Sweden. The
 further sub-structuring of the Swedish/ Norwegian gene-pool appears to
 follow the traditional language borders with the South Sámi language
 dominating the southern- and the Central Sámi language in the more
 northern genetic sub-clusters. This suggests that traditional knowledge,
 cultural identities and herd migrations have contributed to shape the
 genetic structure seen today. Ecological gradients are more pronounced
 within as compared to between the genetic clusters, giving further
 evidence that historical and social-cultural processes are important
 drivers for the genetic differentiations found in domestic reindeer across
 the Nordic countries.
description: DNA was extracted from blood and tissue samples using DNeasy
 Blood and Tissue Kits (Qiagen). 904 reindeer samples from 31 reindeer
 herding districts in Norway, Sweden and Finland were analyzed for 18
 microsatellite loci amplified by PCR and scored as product
 sizes.
description: Microsatellites without score are given as 0.
DOI: 10.5061/dryad.1zcrjdfs0
title: Climatic niche shifts in 815 introduced plant species affect their predicted distributions: Data and scripts

description: Aim: Introduced species often occupy different climates in their
 introduced than their native range, but to what degree do such ‘climatic
 niche shifts’ interfere with our ability to predict invasions? Answering
 this question is crucial if we are to understand the threat invasive
 species pose to human and natural systems, especially given the ever
 increasing use of species distribution models as tools for invasive
 species risk assessment and management. Here we investigated how strongly
 climatic niche shifts interfered with the transferability of native- and
 introduced-range species distribution models. Location: Our dataset
 consisted of ~14 million occurrences distributed worldwide. Time Period:
 Occurrence data were collected from online repositories dating from ca.
 1600 with the vast majority being from the 20th century. Climatic data
 represent means between 1970–2000. Major Taxa Studied: Our database
 represented 815 terrestrial plant species. Methods: We used ordination to
 identify climatic niche shifts as species moved between continents. Next,
 we trained separate MAXENT models using native- or introduced-range
 occurrences, and projected those models into each species’ introduced
 range. We compared the ordination and MAXENT models to determine whether
 niche shifts were associated with errors in MAXENT predictions. Results:
 Models trained on native-range occurrences poorly predicted
 introduced-range occurrences, and transferability was lowest in species
 with large climatic niche shifts. Directional shifts in species’ predicted
 geographic distributions mirrored their niche dynamics. This is concerning
 because native-range data are often used to predict introduced-range
 distributions. Main Conclusions: Our results highlight the importance of
 considering niche shifts when modeling the potential geographic
 distributions of introduced species, and cast doubt on the assumption that
 the climatic niche of a species can be transferred between native and
 invasive ranges.
description: Data were generated from GBIF records and Worldclim data. These
 were used to construct MAXENT models which were then analyzed
 statistically. Creation and analysis of the models follows included R
 scripts. Many, but not all of the data generated are included
 here.
description: Scripts can be executed sequentially. Users will need to ensure
 that documents are in the correct folders, following instructions given in
 the R scripts.
DOI: 10.5061/dryad.kh189325w
title: Regionwide temporal gradients of carbon allocation allow for shoot growth and latewood formation in boreal black spruce

description: In boreal ecosystems, phenological events display seasonal patterns. These
 patterns optimize the development of tissues during the short time window
 available for growth in cold climates. Primary and secondary growth, two
 expensive processes for plants, are supposedly modulated in time to
 optimize allocation of carbon to bud and woody tissues. We aimed to assess
 the phenology of primary and secondary meristems, testing their
 relationship over the closed black spruce stands of the commercially
 exploited forest region in Quebec, Canada. Location: Quebec, Canada Time
 period: 2002-2016 Major taxa studied: Gymnospermae We combined weekly
 scaled field observations with Moderate Resolution Imaging
 Spectroradiometer (MODIS) time-series of the Normalized Difference
 Vegetation Index (NDVI) to extract timings of photosynthesis and meristem
 growth in five black spruce [Picea mariana (Mill.) B.S.P.] stands located
 along a latitudinal gradient and to assess their relationship. We then
 tested an empirical relationship based on geographical position and
 seasonal temperatures to predict wood phenology i.e. the onset and ending
 of earlywood and latewood formation, and its spatial patterns were
 compared with existing predictions of bud phenology for the same study
 area. Photosynthesis started at the beginning of May, three weeks before
 bud reactivation and the onset of wood growth. Latewood formation started
 in mid-July, after shoot elongation was completed. For wood phenology
 models, residual standard error ranged from one week up to 12 days. Growth
 dynamics spatialized across the boreal forest of Quebec varied with the
 transition between the subarctic and humid continental climate. Shoot
 elongation and latewood formation were temporally separated, providing
 evidence of a trade-off in structural carbon allocation between primary
 and secondary growth in trees. Wood phenology spatial patterns predicted
 for the black spruce polygons are consistent with bud phenology spatial
 patterns, demonstrating synchronized meristems temporal dynamics at region
 scale.
description: Bud phenology stages have been modelled according to the protocol
 described in Khare et al.; 2019 (https://doi.org/10.3390/rs11232745) in four sites located across a latitudinal gradient and validated on bud phenology observations pubblished in Silvestro et al.; 2019 (https://doi.org/10.1016/j.foreco.2019.01.005)
description: Dataset contains 8 columns corresponding to site, year,
 coordinates of the sites, and phenological stages.
 B1=onset of bud development B6=Onset of shoot
 elongation S1=ending of shoot elongation
 S5=ending of bud development
DOI: 10.6084/m9.figshare.31166350
title: Additional file 3 of Selective vulnerability of the aging cholinergic system to amyloid pathology revealed by induced APP overexpression

description: Supplementary Material 3.
DOI: 10.6084/m9.figshare.31166350.v1
title: Additional file 3 of Selective vulnerability of the aging cholinergic system to amyloid pathology revealed by induced APP overexpression

description: Supplementary Material 3.
DOI: 10.6084/m9.figshare.31166353
title: Additional file 4 of Selective vulnerability of the aging cholinergic system to amyloid pathology revealed by induced APP overexpression

description: Supplementary Material 4.
DOI: 10.6084/m9.figshare.31166353.v1
title: Additional file 4 of Selective vulnerability of the aging cholinergic system to amyloid pathology revealed by induced APP overexpression

description: Supplementary Material 4.
DOI: 10.5061/dryad.c866t1g6t
title: Data reported in: Effects of ozone isotopologue formation on the clumped-isotope composition of atmospheric O2

description: Tropospheric 18O18O is an emerging proxy for past tropospheric ozone and
 free-tropospheric temperatures. The basis of these applications is the
 idea that isotope-exchange reactions in the atmosphere drive 18O18O
 abundances toward isotopic equilibrium. However, previous work used an
 offline box-model framework to explain the 18O18O budget, approximating
 the interplay of atmospheric chemistry and transport. This approach, while
 convenient, has poorly characterized uncertainties. To investigate these
 uncertainties, and to broaden the applicability of the 18O18O proxy, we
 developed a scheme to simulate atmospheric 18O18O abundances (quantified
 as ∆36 values) online within the GEOS-Chem chemical transport model. These
 results are compared to both new and previously published atmospheric
 observations from the surface to 33 km. Simulations using a simplified O2
 isotopic equilibration scheme within GEOS-Chem show quantitative agreement
 with measurements only in the middle stratosphere; modeled ∆36 values are
 too high elsewhere. Investigations using a comprehensive model of the
 O-O2-O3 isotopic photochemical system and proof-of-principle experiments
 suggest that the simple equilibration scheme omits an important pressure
 dependence to ∆36 values: the anomalously efficient titration of 18O18O to
 form ozone. Incorporating these effects into the online ∆36 calculation
 scheme in GEOS-Chem yields quantitative agreement for all available
 observations. While this previously unidentified bias affects the
 atmospheric budget of 18O18O in O2, the modeled change in the mean
 tropospheric ∆36 value since 1850 C.E. is only slightly altered; it is
 still quantitatively consistent with the ice-core ∆36 record, implying
 that the tropospheric ozone burden increased less than ~40% over the
 twentieth century.
DOI: 10.6084/m9.figshare.31166343
title: Additional file 1 of Machine learning-based classification of roses using 18 SNP markers for optimized genebank management

description: Supplementary Material 1. SNP dataset with cultivar labels and unsupervised clustering assignments. The SNP marker panel was adopted from Patzer et al. [17]. The cultivar labels were provided by the Europa-Rosarium Sangerhausen. Unsupervised clustering assignments were added, with samples assigned to a cluster when at least 75% of group membership was consistent with a predominant cluster
DOI: 10.6084/m9.figshare.31166343.v1
title: Additional file 1 of Machine learning-based classification of roses using 18 SNP markers for optimized genebank management

description: Supplementary Material 1. SNP dataset with cultivar labels and unsupervised clustering assignments. The SNP marker panel was adopted from Patzer et al. [17]. The cultivar labels were provided by the Europa-Rosarium Sangerhausen. Unsupervised clustering assignments were added, with samples assigned to a cluster when at least 75% of group membership was consistent with a predominant cluster
DOI: 10.6084/m9.figshare.31166365.v1
title: Additional file 1 of Metabolic transitions along a moisture gradient in a poly-extreme high-altitude desert ecosystem within the Atacama Desert

description: Supplementary Material 1
DOI: 10.5061/dryad.j0zpc86dv
title: Atmospheric and surface gravity wave data for role of surface gravity waves in aquaplanet ocean climates

description: This data corresponds to the runs analysed in the manscript: Role
 of Surface Gravity Waves in Aquaplanet Ocean Climates (JAMES, 2021). In
 this work, we present a set of idealised numerical experiments
 that demonstrate the thermodynamic and dynamic implications of surface
 gravity waves for the oceanic climate of an aquaplanet.
 We study the impact of accounting for modulations by such waves upon
 air-sea momentum fluxes, Langmuir circulation and the Stokes-Coriolis
 force. This dataset is made up of atmospheric, oceanic and surface gravity
 wave simulations. When uncompressed the total dataset is 1.6 TB. The
 atmospheric component is 272 GB, the surface gravity wave component is 9
 GB. See below for further details. See the related works section for the
 corresponding datasets.
description: This data is simulation output of a numerical model of
 the planetary atmosphere and of a spectral model of the
 corresponding surface gravity wave field. The details of the model are
 published in the manuscript (https://doi.org/10.1029/2020MS002202).
description: The data are 6-hourly netcdf files. For a list of computed
 variables see the README file. This is 1 of 4 datasets
 related to this article. Please see the Related Works section for the
 additional datasets.
DOI: 10.5281/zenodo.18397104
title: REVIVING BRAND LOYALTY WITH GEN Z CONSUMERS
DOI: 10.5281/zenodo.18397105
title: REVIVING BRAND LOYALTY WITH GEN Z CONSUMERS
DOI: 10.6084/m9.figshare.31166365
title: Additional file 1 of Metabolic transitions along a moisture gradient in a poly-extreme high-altitude desert ecosystem within the Atacama Desert

description: Supplementary Material 1
DOI: 10.5061/dryad.2jm63xspj
title: Ocean and ice spin-up data for role of surface gravity waves in aquaplanet ocean climates

description: This data corresponds to the runs analysed in the manscript: Role
 of Surface Gravity Waves in Aquaplanet Ocean Climates (JAMES, 2021). In
 this work, we present a set of idealised numerical experiments
 that demonstrate the thermodynamic and dynamic implications of surface
 gravity waves for the oceanic climate of an aquaplanet.
 We study the impact of accounting for modulations by such waves upon
 air-sea momentum fluxes, Langmuir circulation and the Stokes-Coriolis
 force. This dataset is made up of atmospheric, oceanic and surface gravity
 wave simulations. When uncompressed the total dataset is 1.6 TB, the ocean
 spinup component is 242 GB. See below for further
 details. See the related works section for the corresponding datasets.
description: This data is simulation output of the 1 year spin up of a
 numerical model of the planetary ocean and ice field. The details of the
 model are published in the manuscript (https://doi.org/10.1029/2020MS002202).
description: The data are 6-hourly netcdf files. For a list of computed
 variables see the README file. This is 1 of 4 datasets
 related to this article. Please see the Related Works section for the
 additional datasets.
DOI: 10.5061/dryad.1g1jwstw5
title: Ocean and ice with waves data for role of surface gravity waves in aquaplanet ocean climates

description: This data corresponds to the runs analysed in the manscript: Role
 of Surface Gravity Waves in Aquaplanet Ocean Climates (JAMES, 2021). In
 this work, we present a set of idealised numerical experiments
 that demonstrate the thermodynamic and dynamic implications of surface
 gravity waves for the oceanic climate of an aquaplanet.
 We study the impact of accounting for modulations by such waves upon
 air-sea momentum fluxes, Langmuir circulation and the Stokes-Coriolis
 force. This dataset is made up of atmospheric, oceanic and surface gravity
 wave simulations. When uncompressed the total dataset is 1.6 TB, the ocean
 and ice with waves component is 564 GB. See below for
 further details. See the related works section for the corresponding
 datasets.
description: This data is simulation output of year 2 and 3 of a numerical
 model of the planetary ocean and ice field including surface gravity wave
 parameterisation. The details of the model are published in the manuscript
 (https://doi.org/10.1029/2020MS002202).
description: The data are 6-hourly netcdf files. For a list of computed
 variables see the README file. This is 1 of 4 datasets
 related to this article. Please see the Related Works section for the
 additional datasets.
DOI: 10.5061/dryad.0k6djhb0x
title: Ocean and ice without waves data for role of surface gravity waves in aquaplanet ocean climates

description: This data corresponds to the runs analysed in the manscript: Role
 of Surface Gravity Waves in Aquaplanet Ocean Climates (JAMES, 2021). In
 this work, we present a set of idealised numerical experiments
 that demonstrate the thermodynamic and dynamic implications of surface
 gravity waves for the oceanic climate of an aquaplanet.
 We study the impact of accounting for modulations by such waves upon
 air-sea momentum fluxes, Langmuir circulation and the Stokes-Coriolis
 force. This dataset is made up of atmospheric, oceanic and surface gravity
 wave simulations. When uncompressed the total dataset is 1.6 TB, the ocean
 and ice without waves component is 484 GB. See below for
 further details. See the related works section for the corresponding
 datasets.
description: This data is simulation output of year 2 and 3 of a numerical
 model of the planetary ocean and ice field not including surface gravity
 wave parameterisation. The details of the model are published in the
 manuscript (https://doi.org/10.1029/2020MS002202).
description: The data are 6-hourly netcdf files. For a list of computed
 variables see the README file. This is 1 of 4 datasets
 related to this article. Please see the Related Works section for the
 additional datasets.
DOI: 10.5061/dryad.xwdbrv1dc
title: Savannah River NERP songbird tissue, insect, and fruit isotope database

description: Many temperate passerine bird species switch from diets of mostly
 invertebrates in the spring and summer to diets that include fruit and
 seeds in the fall and winter. However, relatively few studies have
 quantified diet composition or the extent of seasonal shifts during the
 non-breeding period, particularly among species and across communities
 with both residents and migrants. We measured carbon and nitrogen stable
 isotope values in food items (fruits, C3 and C4 seeds, and insects from
 various trophic levels and plant communities) and in multiple tissues
 (feathers and plasma/whole blood) from 11 species of songbirds wintering
 in the southeastern U.S. We combined these diet and tissue values with
 empirically derived discrimination factors and used
 concentration-dependent mixing models to quantify seasonal diet shifts. We
 also validated mixing model results with data from fecal samples. Diets in
 this bird community, as delineated N and C isotopic space, diverged in the
 fall and winter relative to the summer as consumption of fruits and seeds
 increased. Across this songbird community, estimated contributions of
 fruit to plasma/whole blood increased from 16.2 ± 7.5% in the fall (mean ±
 SD; range: 4–26%) to 21.7 ± 10.3% (range: 9–37%) in the winter, while
 contributions of seeds increased from 29.4 ± 2.6% (range: 28–32%) in the
 fall to 36.6 ± 4.8% (range: 32–42%) in the winter. Fecal data showed
 qualitatively similar trends to mixing models, but consistently estimated
 higher contributions of fruit. Our work indicates that fruits and seeds
 constitute substantial sources of sustenance for non-breeding songbirds,
 there is considerable separation of resource use among species in the fall
 and winter, and fecal estimates of contributions to songbird tissues
 should be interpreted cautiously.