cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k3j9kd55x
title: Genetic barcoding of museum eggshell improves data integrity of avian biological collections

description: Natural history collections are often plagued by missing or inaccurate
 metadata for collection items, particularly for specimens that are
 difficult to verify or rare. Avian eggshell in particular can be
 challenging to identify due to extensive morphological ambiguity among
 taxa. Species identifications can be improved using DNA extracted from
 museum eggshell; however, the suitability of current methods for use on
 small museum eggshell specimens has not been rigorously tested, hindering
 uptake. In this study, we compare three sampling methodologies to
 genetically identify 45 data-poor eggshell specimens, including a
 putatively extinct bird’s egg. Using an optimised drilling technique to
 retrieve eggshell powder, we demonstrate that sufficient DNA for molecular
 identification can be obtained from even the tiniest eggshells without
 significant alteration to the specimen’s appearance or integrity. This
 method proved superior to swabbing the external surface or sampling the
 interior; however, we also show that these methods can be viable
 alternatives. We then applied our drilling method to confirm that a
 purported clutch of Paradise Parrot eggs collected 40 years after the
 species’ accepted extinction date were falsely identified, laying to rest
 a 53-year-old ornithological controversy. Thus, even the smallest museum
 eggshells can offer new insights into old questions.
description: DNA was extracted from museum eggshell specimens. Two
 mitochondrial mini barcodes (12S rDNA) were amplified via PCR and
 sequenced via NGS. 
description: The dataset provided includes demultiplexed, quality filtered and
 dereplicated .fasta sequence files, and BLAST tables in .txt
 format.  The naming convention is as follows: Sample ID
 - DNA extraction ID - Substrate - Barcode - Forward index ID - Reverse
 index ID - "Quality Filtered" - <br>
 "Dereplicated" - "Chimera filtered" -
 "Denoised" - "Abundance Filtered".fasta
DOI: 10.5061/dryad.fn2z34tsg
title: Phylogenomics of Perityleae (Compositae) provides new insights into morphological and chromosomal evolution of the rock daisies

description: Rock daisies (Perityleae; Compositae) are a diverse clade of seven genera
 and ca. 84 minimum-rank taxa that mostly occur as narrow endemics on sheer
 rock-cliffs throughout the southwest U.S. and northern Mexico. Taxonomy of
 Perityleae has traditionally been based on morphology and cytogenetics. To
 test taxonomic hypotheses and utility of characters emphasized in past
 treatments, we present the first densely sampled molecular phylogenies of
 Perityleae and reconstruct trait and chromosome evolution. We inferred
 phylogenetic trees from whole chloroplast genomes, nuclear ribosomal
 cistrons, and hundreds of low-copy nuclear genes using genome skimming and
 target-capture. Discordance between sources of molecular data suggests a
 underappreciated history of hybridization in Perityleae. Phylogenies
 support the monophyly of subtribe Peritylinae, a distinctive group
 possessing a four-lobed disc corolla; however, all of the phylogenetic
 trees generated in this study reject the monophyly of the most
 species-rich genus, Perityle as well as its sections Perityle sect.
 Perityle, Perityle sect. Laphamia, and Perityle sect. Pappothrix. Using
 reversible jump MCMC, our results suggest that morphological characters
 traditionally used to classify members of Perityleae have evolved multiple
 times within the group. A base chromosome number of x=18 gave rise to
 lower base numbers in subtribe Peritylinae (x=12, 13, 16, 17, and 19) by
 descending dysploidization. Most taxa constitute a monophyletic lineage
 with a base chromosome number of x=17, with many polyploidization events.
 These results demonstrate the advantages and obstacles to next-generation
 sequencing approaches in synantherology while laying the foundation for
 taxonomic revision and comparative study of the evolutionary ecology of
 Perityleae
DOI: 10.5061/dryad.866t1g1pp
title: DNA sequences of transgenes detected via environmental DNA (raw ABI files, processed FASTA files, and reference alignments)

description: We demonstrate that simple, non-invasive environmental DNA (eDNA) methods
 can detect transgenes of genetically modified (GM) animals from
 terrestrial and aquatic sources in invertebrate and vertebrate systems. We
 detected transgenic fragments between 82-234 bp through targeted PCR
 amplification of environmental DNA extracted from food media of GM fruit
 flies (Drosophila melanogaster), feces, urine, and saliva of GM laboratory
 mice (Mus musculus), and aquarium water of GM tetra fish (Gymnocorymbus
 ternetzi). With rapidly growing accessibility of genome-editing
 technologies such as CRISPR, the prevalence and diversity of GM animals
 will increase dramatically. GM animals have already been released into the
 wild with more releases planned in the future. eDNA methods have the
 potential to address the critical need for sensitive, accurate, and
 cost-effective detection and monitoring of GM animals and their transgenes
 in nature.
description: Bi-directional Sanger sequencing was conducted on an ABI 3730xl
 96-capillary sequencer by the Centre d’expertise et de services Génome
 Québec. DNA sequences were aligned using BioEdit v.7.2.5 and
 ClustalW.
description: "F-", "GF-", "M-" files are raw
 transgene sequences from fruit fly, GloFish, and mouse respectively.
 "_final.fas" files are alignments of trimmed transgene sequences
 (three different fluorescent genes for GloFish). ABI
 files can be opened through software such as FinchTV or any other DNA
 sequence electropherogram software.
DOI: 10.7280/d1b38g
title: Peromyscus WGCNA supplement

description: P. leucopus also (deer mouse) is a known reservoir for infectious disease
 such as lyme disease and it is able to survive infections that other
 rodent models cannot. In this paper we explore P. lecucopus transcriptomic
 response after LPS stimulus in blood, liver and spleen using RNA-seq and
 compare it to M. musculus response. When comparing gene response to LPS
 from different species and tissues, neutrophil associated terms are
 enriched in the P. leucopus response, while mouse response is enriched for
 cytokine signaling. To compare intra species and tissue gene patterns, we
 identified gene networks that were associated with specie specific
 upregulation response to LPS. Interestingly majority of the genes that
 were upregulated in P. leucopus response originated from blood, whereas
 most of the M. musculus genes originated from liver. Both of these gene
 modules uphold the Neutrophil associated pathways for P. leucopus and
 cytokine mediated response for mouse that originated from independent
 analysis. We characterized and identify key genes for LPS response in P.
 leucopus and M. musculus, additionally we identify biological processes
 characteristic for each specie that pointed to inflammation, oxidative
 stress, phagocytosis, and metabolism. Thanks to its robust immune response
 and alternative pathways, P. leucopus stands out as a novel model to
 evaluate a broader range of infectious diseases.
description: After performing RNA-seq on three different tissues, We used
 WGCNA {Langfelder, 2008 #1404} to identify densely interconnected genes
 (modules) for the 6 datasets across species and tissues by building a
 matrix of gene expression with genes TPM &gt;1 in one or more
 individual. We selected a power (b) of 13 for a soft threshold for the
 weighted network and specified a minimum of 100 genes per module. To merge
 modules with similar gene expression profiles, we carried out a dynamic
 tree cut, with an eigengene dissimilarity threshold of 0.2 that generated
 the final eigengene profiles, where eigengene is the first principal
 component of module expression matrix {Foroushani, 2017 #1406}. The
 inferred modules were distinguished by different color names, e.g.
 cyan.
DOI: 10.15468/dl.jmh2nw
title: Occurrence Download

description: A dataset containing 141 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cullen corylifolium",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 141 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002699-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.18931zcw2
title: Data from: Changes in seed predation along a 2300-m elevational gradient on a tropical mountain in Myanmar: a standardized test with 32 non-native plant species

description: It has been hypothesized that biotic interactions are stronger towards
 lower latitudes and elevations. However, results vary among interaction
 systems and experimental protocols. Our goal was to examine the validity
 of this prediction by using a standardized method to investigate
 seed–animal interaction. We assessed removal by animals for 40960 seeds
 belonging to 32 non-native tree species along an elevation gradient from
 600 m to 2910 m on Mount Victoria (Nat Ma Taung), western Myanmar. We
 analyzed the elevational trends of seed removal at both individual seed
 level (probability of depot encounter, proportion of seeds removed after
 encounter and total proportion of seeds removed) and community level
 (Shannon diversity and species evenness indices). The dry and wet seasons
 had opposite relationships between seed removal and elevation, i.e.
 hump-shaped in the dry season and U-shaped in the wet season. Individual
 plant species displayed almost all possible patterns: U-shaped and
 hump-shaped, monotonic decrease and increase, and elevation-independent
 patterns. As a consequence of the hump-shaped seed removal pattern with
 elevation in the dry season, the diversity and evenness of surviving seeds
 showed U-shaped patterns. Our study shows that elevational trends in
 seed–animal interactions do not follow a constant rule, but differ between
 seasons and among species, suggesting that a one-off survey with few
 species might give misleading information on overall macroecological
 patterns. Future studies of trends in biotic interactions along gradients
 should bear this in mind.
description: Details about how the dataset was collected, please see the
 published paper (DOI: 10.1111/ecog.05385).
description: Obs: the observation ID of our 8192 seed releasing depots in
 total elevation: the elevation of a depot where it was
 released latitude and longtitude: the GPS position of a
 depot where it was released transect: the transect ID
 in each elevation depot:  the depot ID in each
 transect speciesID: the species ID for each
 species Species name: the scientific name for each
 species Harvest: number of seeds removed by animals at
 each depot Left: number of seeds left intact in situ at
 each depot Day: survey time (i.e., Day 1 or Day
 2) Season: season when the experiments were conducted,
 dry (dry season) and wet (wet season)
DOI: 10.5061/dryad.cz8w9gj2k
title: Data from: Reciprocal facilitation between annual plants and burrowing crabs: implications for the restoration of degraded salt marshes

description: ​​​​​​Increasing evidence shows that facilitative interactions between
 species play an essential role in coastal wetland ecosystems. However,
 there is a lack of understanding of how such interactions can be used for
 restoration purposes in salt marsh ecosystems. We, therefore, studied the
 mechanisms of reciprocal facilitative interactions between native annual
 plants, Suaeda salsa, and burrowing crabs, Helice tientsinensis, in a
 middle-elevation salt marsh (with generally high plant density and
 moderate tides) in the Yellow River Delta of China. We investigated the
 relationship between the densities of the plants and crab burrows in
 different seasons. Then, we tested whether and how salt marsh plants and
 crabs indeed facilitate each other in a series of field and laboratory
 experiments. Finally, we applied the results by creating a field-scale
 artificial approach for microtopographic modification to restore a
 degraded salt marsh. We found that the density of plant seedlings in
 spring was positively correlated with the density of crab burrows in the
 previous autumn; moreover, the density of crab burrows was correlated with
 the density of plants in summer. The concave-convex surface
 microtopography created by crabs promoted seed retention and seedling
 establishment of salt marsh plants in winter and spring. These plants in
 turn facilitated crabs by inhibiting predators, providing food, and
 reducing physical stresses for crabs in summer and autumn. The
 experimental removal of salt marsh plants decreased crab burrow density,
 while both transplanting and simulating plants in bare patches promoted
 crabs. The microtopographic modification, inspired by our new
 understanding of the interactions between salt marsh plants and crabs,
 showed that these degraded salt marsh ecosystems can be restored by a
 single ploughing intervention. Synthesis. Our results suggest a reciprocal
 facilitation between annual plants and burrowing crabs in a
 middle-elevation salt marsh ecosystem. This knowledge yielded new
 restoration options for degraded coastal salt marshes through the one-time
 ploughing initiation of microtopographic variation, which could promote
 the re-establishment of ecosystem engineers and lead to the efficient
 recovery of pioneer coastal vegetation and associated fauna.
DOI: 10.5061/dryad.k0p2ngf76
title: Data from: Species abundance fluctuations over 31 years are associated with plant-soil feedback in a species-rich mountain meadow

description: 1. Increasing evidence suggest that plant-soil interactions play an
 essential role in plant community assembly processes. Empirical
 investigations show that plant species abundance in the field is often
 related to plant-soil biota interactions, however, the direction of these
 relations have yielded inconsistent results. 2. We combined unique 31-year
 long field data on species abundances from a species-rich mountain meadow
 with single time point plant-soil feedback greenhouse experiments of 24
 co-occurring plant species. We tested whether these relations were dynamic
 in time, whether coupled increases and decreases in abundance between
 years were related to plant-soil feedback and whether these changes were
 underlain by years in which manuring was applied. 3. The prevailingly
 negative relationship between plant-soil feedback and plant relative
 abundance in the field was significantly time-dependent, which may
 reconcile the contrasting results in literature. Furthermore, significant
 coupled oscillations appeared between species relative abundance changes
 and plant-soil feedback, which were likely moderated by years in which
 manuring was applied. Our results are consistent with the notion that the
 more abundant species are stabilised by negative plant-soil feedback, and
 the less abundant species co-vary with the fluctuations of these more
 competitive species. 4. Synthesis: Our results project plant-soil feedback
 as an important regulatory mechanism in plant communities, operating in
 conjunction with a species’ competitive ability and soil nutrient
 availability. We suggest that negative feedback is particularly prominent
 in more abundant plant species that profit from more readily available
 soil nutrients than less abundant species with positive feedback. Negative
 plant-soil feedback may thus prevent more abundant plant species from
 outcompeting less abundant plant species, facilitating stable species
 co-existence.
description: Data from the plant-soil feedback experiment. Field data on plant
 species abundances were obtained from the LOng Term Vegetation Sampling
 (LOTVS) database of Valencia et al., (2020). Valencia,
 E., de Bello, F., Lepš, J., Galland, T., E-Vojtkó, A., Conti, L., …
 Götzenberger, L. (2020). Directional trends in species composition over
 time can lead to a widespread overemphasis of year-to-year asynchrony.
 Journal of Vegetation Science, 31(5), 792–802. doi:
 10.1111/jvs.12916.
DOI: 10.5061/dryad.zpc866t7h
title: Lattice Boltzmann simulations on the tumbling to tank-treading transition: effects of membrane viscosity

description: The tumbling to tank-treading (TB-TT) transition for red blood cells
 (RBCs) has been widely investigated, with a main focus on the effects of
 the viscosity ratio λ (i.e., the ratio between the
 viscosities of the fluids inside and outside the membrane) and the shear
 rate γ ̇ applied to the RBC. However, the
 membrane viscosity μm plays a major role in a realistic
 description of RBC’s dynamics, and only a few works have systematically
 focused on its effects on the TB-TT transition. In this work, we provide a
 parametric investigation on the effect of membrane
 viscosity μm on the TB- TT transition, for a single RBC.
 It is found that, at fixed viscosity ratios λ, larger values
 of μm lead to an increased range of values of capillary
 number at which the TB-TT transition occurs. We systematically quantify
 such an increase by means of mesoscale numerical simulations based on the
 lattice Boltzmann models.
DOI: 10.5061/dryad.sj3tx963m
title: Data from: With a little help from my friends – Physiological integration facilitates invasion of wetland grass Elymus athericus into flooded soils

description: Tidal wetlands worldwide are undergoing rapid invasions by tall-growing
 clonal grasses. Prominent examples are invasions by species of the genera
 Spartina, Phragmites, and Elymus. The responsible physiological and
 ecological drivers of these invasions are poorly understood. Physiological
 integration (PI) is a key trait of clonal plants, which enables the
 exchange of resources among ramets. We investigated PI in Elymus
 athericus, which has been rapidly spreading from high-marsh into low-marsh
 environments of European salt marshes during the last decades. We applied
 a nitrogen-stable-isotope approach to trace nutrient translocation between
 ramets in a factorial mesocosm experiment. The experiment was set up to
 mimic an invasion pattern commonly found in tidal wetlands, i.e. from
 high-elevated and rarely flooded into low-elevated and frequently flooded
 microenvironments. We tested for intraspecific variability in PI by
 including two genotypes of Elymus that naturally occur at different
 elevations within the tidal frame, a high-marsh (HM) and a low-marsh (LM)
 genotype. PI strongly increased offspring ramet aboveground and
 belowground biomass by 62 and 81%, respectively. Offspring ramets under
 drained conditions had 95% greater belowground biomass than those under
 flooded conditions. LM genotype offspring ramets produced 27% more
 aboveground biomass than HM genotypes. Offspring ramets were clearly more
 enriched in 15N under flooded vs. drained conditions; however, this
 positive effect of flooding on δ15N was only significant in the LM
 genotype. Our findings demonstrate the importance of PI for the growth of
 Elymus offspring ramets and thereby for the species’ capacity for fast
 vegetative spread. We show that offspring ramets under stressful flooded
 conditions are more dependent on nutrient supply from parent ramets than
 those under drained conditions. Our data furthermore suggest a higher
 degree of adaptation to flooding via PI in the LM vs. HM genotype. In
 conclusion, we highlight the importance of assessing PI and intraspecific
 trait variability to understand invasion processes within ecosystems.
DOI: 10.5281/zenodo.18395932
title: SuperDARN data in netCDF format (2006-Apr)

description: 2006-Apr SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'
DOI: 10.5061/dryad.98sf7m0hg
title: Data for: Both Conifer II and Gnetales are characterized by a high frequency of ancient mitochondrial gene transfer to the nuclear genome

description: Background: Mitochondrial gene transfer/loss is common in land plants, and
 therefore the fate of missing mitochondrial genes has attracted more and
 more attention. The gene content of gymnosperm mitochondria varies
 greatly, supplying a system for studying the evolutionary fate of missing
 mitochondrial genes. Results: Here we studied the tempo and pattern of
 mitochondrial gene loss/transfer in gymnosperms represented by all 13
 families, using high-throughput sequencing of both DNA and cDNA. All 41
 mitochondrial protein-coding genes were found in cycads, Ginkgo and
 Pinaceae, whereas multiple mitochondrial genes were absent in Conifer II
 and Gnetales. In Conifer II, gene transfer from mitochondria to the
 nucleus followed by loss of the mitochondrial copy was common, but
 complete loss of a gene in both mitochondrial and nuclear genomes was
 rare. In contrast, both gene transfer and loss were commonly found in
 Gnetales. Notably, in Conifer II and Gnetales, the same five mitochondrial
 genes were transferred to the nuclear genome, and these gene transfer
 events occurred, respectively, in ancestors of the two lineages. A
 two-step transfer mechanism (retroprocessing and subsequent DNA-mediated
 gene transfer) may be responsible for mitochondrial gene transfer in
 Conifer II and Gnetales. Moreover, the mitochondrial gene content
 variation is correlated with gene length, GC content, hydrophobicity, and
 nucleotide substitution rates in land plants. Conclusions: This study
 reveals a complete evolutionary scenario for mitochondrial genes of
 gymnosperms and the factors responsible for mitochondrial gene content
 variation in land plants.
description: To avoid the influence of RNA editing sites, cDNA sequences were
 used in the phylogenetic analysis. Two basal angiosperms with all 41
 mitochondrial genes, i.e., <em>Amborella trichopoda</em> and
 <em>Liriodendron tulipifera</em>, were selected to represent
 angiosperms, and two ferns, i.e., <em>Ophioglossum
 californicum</em> and <em>Psilotum nudum</em>, were
 selected as outgroups. All mitochondrial genes were concatenated directly.
 If one gene was proven to be transferred to the nucleus in a species, we
 first reconstructed the single-gene trees so that we could infer when and
 how many times this gene was transferred to the nuclear genome. The
 GTRGAMMA and PROTGAMMAAUTO models were used in the nucleotide and AA
 matrices, respectively, and RaxML v. 8.2.12 was used to reconstruct the
 phylogenetic relationships with 100 bootstrap replicates.