cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zw3r2285n
title: Genomic prediction enables rapid selection of high-performing genets in an intermediate wheatgrass (Thinopyrum intermedium) breeding program

description: In an era of constrained and depleted natural resources, perennial grains
 could provide sustainable food production in addition to beneficial
 ecosystem services like reduced erosion and increased atmospheric carbon
 capture. One such perennial, intermediate wheatgrass (IWG; Thinopyrum
 intermedium) has been undergoing continuous breeding for domestication and
 improvement to develop a perennial grain crop since the 1980’s. However,
 as a perennial species, IWG has required 2-5 years per selection
 generation. Therefore, starting in 2017 genomic selection was initiated in
 the breeding program at The Land Institute, Salina, KS, enabling one
 complete cycle per year. For each cycle, ~4,000 seedlings were profiled
 using genotyping-by-sequencing and genomic estimated breeding values were
 calculated. Selection identified 100 individuals to advance as parents
 each generation, while validation populations for model updating
 consisting of 1,000-1,200 were also selected. The crossing block
 populations were randomly intermated in a greenhouse to form the
 subsequent cycle, while the validation populations were transplanted to
 irrigated and non-irrigated field sites for phenotypic evaluations in the
 following years. For priority breeding traits of seed mass, free
 threshing, and non-shattering, correlations between predicted values and
 observed data were greater than 0.51 and all traits ranged from 0.02-0.76.
 The realized selection differential ranged from 19-23% for selected
 traits, and the expected genetic gains for these traits, including spike
 yield, ranged from 5-15% per year. Genomic selection is a powerful tool to
 speed the domestication and development of intermediate wheatgrass and
 likely other perennial crops with extended breeding timelines.
description: See manuscript and readme file.
description: Read me file documents data and process.
DOI: 10.5061/dryad.n8pk0p2s3
title: Nutritional developmental history and its consequences for reproductive success in Drosophila suzukii (Diptera: Drosophilidae)

description: The characteristics of the juvenile developmental environment of an
 individual can have many important consequences for their adult
 reproductive success as it may shape the development and expression of
 phenotypes that are relevant to the later operation of sexual selection.
 Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is an economically
 important invasive pest species that lays its eggs in many types of soft
 fruits and potentially experiences large intra-population spatial and
 temporal variation in its nutritional developmental environments. Here, we
 examine whether the larval nutritional developmental environment
 influences D. suzukii mate choice, egg production, and offspring
 performance. Using D. suzukii raised on diets differing in their
 nutritional quality, we examined mating preferences, fecundity, and
 offspring survivorship in “no-choice”, “female choice”, and “male choice”
 reproductive contexts. We found evidence for both adaptive and
 non-adaptive mate choice behaviours associated with the phenotypes of D.
 suzukii that had developed in different nutritional environments. These
 results reveal the complex nature of the relationship between the
 developmental environment and individual reproductive success in D.
 suzukii, which has important potential implications for future management
 plans involving this species.
description: This data contains information on mating outcome, mating latency,
 copulation duration, offpsring production and egg-to-adult survivorship of
 spotted wing fruit flies, Drosophila suzukii from 3 different mate choice
 assays (no choice, male choice and female choice). The data from the 3
 assay files is also reorganized by the 4 possible combinations of the
 nutritional developmental histories of the mating pairs to faciliate
 comparisons between the choice and no-choice treatments.
DOI: 10.5061/dryad.zw3r2285p
title: Data from: Life-history traits of Tubastraea coccinea: reproduction, development, and larval competence

description: The sun coral Tubastraea coccinea Lesson, 1829 (Dendrophylliidae) is a
 widely distributed shallow-water scleractinian that has extended its range
 to non-native habitats in recent decades. With its rapid spread, this
 coral is now one of the main invasive species in Brazil. Its high invasive
 capability is related to opportunistic characteristics, including several
 reproductive strategies that have allowed it to disperse rapidly and
 widely. To better understand the reproductive biology of T. coccinea and
 aid in developing management strategies for invaded areas, we investigated
 aspects of its reproductive performance and life cycle, including the
 effects of colony size, seawater temperature and salinity, and lunar
 periodicity on offspring production and larval metamorphosis competence. A
 total of 18,139 offspring were released in different developmental stages,
 mainly from the larger colonies, which also produced larvae with longer
 competence periods. The main reproductive peak occurred during the First
 Quarter and New Moon phases and was highest in water temperatures around
 26°C. Together, these results help to explain the rapid expansion of T.
 coccinea into non-native habitats such as the Caribbean and southwestern
 Atlantic, and will inform actions of the recent Brazilian National Plan
 for the prevention, eradication, control, and monitoring of sun corals.
description: Embryonic stages and larvae released from each colony of
 <em>Tubastraea coccinea </em>kept in open water aquarium
 system were sampled once a day and placed in separate aquaria according to
 their respective release dates. These larvae were monitored every 24 h for
 sampling different ontogenetic stages (newly settled, settled, early
 metamorphosis, metamorphosed, and recruit), which were then transferred to
 new aquaria (300 to 500 ml) according to the stage (also kept separated by
 parent colony). The time for larvae to reach each developmental stage was
 tracked. To assess the reproductive performance of
 <i>T. coccinea</i> and the potential effects of biotic and
 abiotic factors on its fitness, released offspring were monitored for 91
 d. During the experiment, we tested the number of offspring released
 (number of embryos and larvae per day) as the response variable, and lunar
 periodicity, temperature, and salinity as explanatory variables.
 Temperature and salinity were measured with a YSI Model 30 Handheld
 Conductivity, Salinity, & Temperature meter, once a day in surface
 water at the location where the water used in the experiment was
 obtained.
description: All necessary information are in the spreadsheets as comments to
 some cells and also in the scientific paper.
DOI: 10.5061/dryad.dr7sqv9vw
title: Thistle-down velvet ants in the Desert Mimicry Ring and the evolution of white coloration: Müllerian mimicry, camouflage, and thermal ecology

description: Adaptive coloration among animals is one of the most recognizable outcomes
 of natural selection. Here we investigate evolutionary drivers of white
 coloration in velvet ants (Hymenoptera: Mutillidae), which has previously
 been considered camouflage with the fruit of creosote bush. Our analyses
 indicate instead that velvet ants evolved white coloration millions of
 years before creosote bush was widespread in North America’s hot deserts.
 Furthermore, velvet ants and the creosote fruit exhibit different spectral
 reflectance patterns, which appear distinct to potential insectivorous
 predators. While the white coloration in velvet ants likely did not evolve
 as camouflage, we find that white-colored species remain cooler than their
 red/orange relatives, and therefore we infer the white coloration likely
 evolved in response to Neogene desertification. This study shows the
 importance of cross-disciplinary investigation and the importance of
 testing multiple hypotheses when investigating evolutionary drivers of
 adaptive coloration.
DOI: 10.21223/p3/sfxxdc
title: Dataset for: Advanced clones of B3C0, group B3, population B in Oxapampa-Peru

description: B3C0 is the initial cycle of recombination of group B3- Population B. This population has been derived from population A. R genes have been eliminated from this group and horizontal resistance has been retained. Currently, these clones are being used on the variety selection in developing countries. This group of clones were planted under a randomized complete block design (RCBD) with 2 replicates in Oxapampa (1810 masl Pasco-Peru) the Eastern mountain ranges facing the Amazon. Oxampapa is similar to the target environments due to the high disease pressure of late blight present in the area and used to screen selected potato genotypes for resistance to this disease.
DOI: 10.5061/dryad.r4xgxd28r
title: Data from: The ecological implications of rubber-based agroforest: insect conservation and invasion control

description: 1. Protected areas are increasingly threatened by biological invasions,
 especially in Tropical Asia where extensive areas of natural habitats have
 been converted to monoculture plantations. Such disturbance provides a
 gateway for exotic species invasions, highlighting an urgent need for
 cross-boundary solutions to mitigate invasion impacts. 2. Agroforests,
 with multi-storied trees and crops resembling the complex structure of
 natural forest, are well-known to promote native species compared to
 monoculture plantations. Yet our knowledge on their roles in controlling
 exotic species is limited to plant invaders, with effects on animal
 invaders still unknown. Given that protected areas are increasingly
 threatened by invaders from surrounding plantations, with a majority of
 them represented by insects, it is important to evaluate the effect of
 agroforestry practice, and mechanisms of associated management to control
 invasions. 3. By using both taxonomic and functional trait-based
 approaches, we studied leaf litter ant communities in 12 rubber
 monoculture (mono-rubber), 9 rubber plantation with understory crops
 (agro-rubber), 16 secondary, and 12 old-growth secondary forest plots in
 and around protected areas in Hainan, China. Sampled ants were further
 classified into groups based on their invasive potential (tramp vs
 non-tramp) to determine the ecological values of agro-rubber. 4. We found
 that despite mono-rubber and agro-rubber presenting similar species
 richness, the latter 1) supports species composition and functional
 diversity more similar to secondary forests, and 2) reduces tramp ant
 species occurrence, a novel management incentive. Nonetheless, agro-rubber
 is not comparable to secondary forest in terms of non-tramp ant species
 composition. 5. Synthesis and applications. If it is not feasible
 to preserve natural forests in human-dominated landscapes against the
 growing threat of biological invasion, proactive mitigation through
 increasing the area of agro-rubber at the periphery of protected areas can
 reduce invasive species’ establishment and spread. Plantation-based
 agroforestry has emerged as a potential management avenue and incentive
 for transforming monoculture plantations into a less “harmful”
 alternative.
DOI: 10.15468/dl.9834h4
title: Occurrence Download

description: A dataset containing 398 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anthonotha fragrans",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 398 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002320-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jh9w0vt7t
title: Data from: Peak vertical jump power predicts radial bone strength better than hand grip strength in healthy individuals

description: Osteoporosis is considered a pediatric disease with geriatric
 consequences. However, measuring bone strength in children is complex and
 creates a practical problem for health professionals, teachers and
 parents.  A non-invasive measure of muscle fitness that
 correlates to bone strength may provide a means to monitor bone strength
 throughout the lifespan.  Therefore, the purpose of this study
 was to investigate the relationship between common muscle function tests
 (relative grip strength (RGS), peak vertical jump power (PP)) and bone
 strength in the radial diaphysis and epiphysis of a healthy population.
 Healthy participants (n=147 (81 female)) performed a bilateral grip
 strength test using a hand dynamometer, and a maximal vertical jump test.
 Peak vertical jump power was calculated from maximal jump height using the
 Sayer’s equation. Moment of inertia (MoI), cortical area (CoA), cortical
 bone mineral density (cBMD), and polar strength-strain index (SSIp) were
 measured using peripheral Quantitative Computed Tomography (pQCT) to
 determine bone strength parameters at the 66% radial site (predominantly
 cortical bone). At the 4% site (trabecular bone site), bone mineral
 content (vBMC.tb), bone mineral density (vBMD.tb), total area (ToA.tb) and
 bone strength index (BSIc) were measured.  Hierarchical multiple
 regression analyses determined the relationship of each muscle function
 test for each bone envelope (cortical and trabecular). For the cortical
 bone measurements: RGS, and PP were both significantly correlated with
 CoA, MoI, and SSIp. Peak vertical jump power predicted bone strength
 parameters to a greater extent compared to RGS. For the trabecular bone
 envelope, RGS was not a predictor of bone strength however peak power was
 a significant predictor of bone strength parameters. Peak vertical jump
 power was a significant predictor of bone strength at both trabecular and
 cortical radial sites.  Interestingly PP, a lower limb
 measurement explained the most variance in the bone strength of the upper
 limb.
DOI: 10.5061/dryad.h44j0zpgk
title: Data from: First evidence for allotriploid hybrids between Juniperus thurifera and J. sabina in a sympatric area in the French Alps

description: At Saint Crépin location (French Alps), where sympatry between the
 tetraploid Juniperus thurifera and the
 diploid Juniperus sabina occurs, three individuals with
 an atypical morphology, have been observed. AFLP markers were
 used to unravel hybridization and potential introgression events in this
 population. In total, 147 polymorphic loci remained after the process of
 peak selection. This dataset demonstrates hybrids originated from a cross
 between J. sabina and J. thurifera and
 suggests that back-cross at least to J. thurifera is
 possible. This study shed light on a rare case of hybridization of
 two Juniperus species with different ploidy levels in
 natural sympatric population.
description: The AFLP experiment was conducted according to Vos et al. (1995) with slight modifications. Around 200 ng of genomic DNA of each sampled individual was used for digestion and ligation. The PCR selective amplifications were elaborated using two different primer combinations given in the table 6 of the related manuscript. Each forward primer used in the selective amplification was labelled with 6-FAM modification at the 5’ extremity. To test fragment detection repeatability, eight negative controls were included in the PCR and genotyping steps. In addition, 7 individuals randomly chosen (2 from<i> J. thurifera </i>and 5 from<i> J. sabina</i>) were repeated three times: two repetitions were done at the stage of extraction and kept all over the process, and the third one was included after the digestion-ligation step at PCR and genotyping steps. AFLP migration profiles were analyzed using GeneMapper v.5 (Thermo Fisher Scientific) using the GS500 (-250) LIZ control to scale for fragment size. Markers selection was conducted as following: Peak selection and phenotype assignment was done using the default options in GeneMapper v.5 for AFLP data. Peaks having a size between 60 bp and 500 bp were exclusively kept for the analysis. Manual examination of peaks for each individual was done and individuals that displayed bad profiles (weak signals or strong background noise) were discarded from the analysis. All peaks detected in negative controls were removed. Bonin Error rate (Bonin et al. 2004) using repetitions of control samples were estimated and all peaks that had an Error &gt; 0% were rejected. Locus displaying alternative phenotypes (presence or absence of the detected peak in only one individual among the whole sample (singletons)) were also discarded.
DOI: 10.25934/pr00012559.0
title: Available datapackage for study 'Supporting COVID-19 Prevention and Testing for Marginalized and Minoritized Youth and Young Adults'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.5061/dryad.9s4mw6mch
title: The genome sequence of Samia ricini, a new model species of lepidopteran insect

description: Samia ricini, a gigantic saturniid moth, has the potential to be a novel
 lepidopteran model species. Since S. ricini is much more
 tough and resistant to diseases than the current model
 species Bombyx mori, the former can be easily reared compared to
 the latter. In addition, genetic resources available for S.
 ricini rival or even exceed those for B. mori: at least
 26 eco-races of S. ricini are reported and S.
 ricini can hybridize with wild Samia species,
 which are distributed throughout Asian countries, and produce fertile
 progenies. Physiological traits such as food preference, integument
 colour, larval spot pattern, etc. are different between S.
 riciniand wild Samia species so that those traits can be
 the target for forward genetic analysis.
               In order to facilitate genetic research in S. ricini, we determined the whole genome sequence of S. ricini. The assembled genome of S. ricini was 458 Mb with 155 scaffolds, and the N50 length of the assembly was approximately 21 Mb. 16,702 protein coding genes were predicted in the assembly. Although the gene repertoire of S. ricini was not so different from that of B. mori, some genes, such as chorion genes and fibroin genes, seemed to have specifically evolved in S. ricin​​​​​​i.
DOI: 10.5061/dryad.dv41ns1vd
title: Data from: Ovarian BDNF promotes survival, migration, and attachment of tumor precursors originated from p53 mutant fallopian tube epithelial cells

description: High-grade serous ovarian carcinoma (HGSOC) is the most lethal
 gynecological malignancy. New evidence supports a hypothesis that HGSOC
 can originate from fallopian tube epithelium (FTE). It is unclear how
 genetic alterations and pathophysiological processes drive the progression
 of FTE tumor precursors into widespread HGSOCs. In this study, we
 uncovered that brain-derived neurotrophic factor (BDNF) in the follicular
 fluid stimulates the tropomyosin receptor kinase B (TrkB)-expressing FTE
 cells to promote their survival, migration, and attachment. Using in vitro
 and in vivo models, we further identified that the acquisition of common
 TP53 gain-of-function (GOF) mutations in FTE cells led to enhanced
 BDNF/TrkB signaling comparing to that of FTE cells with TP53
 loss-of-function (LOF) mutations. Different mutant p53 proteins can either
 increase TrkB transcription or enhance TrkB endocytic recycling. Our
 findings have demonstrated possible interplays between genetic alterations
 in FTE tumor precursors (i.e., p53 gain-of-function mutations) and
 pathophysiological processes (i.e., the release of follicular fluid upon
 ovulation) during the initiation of HGSOC from the fallopian tube. Our
 data revealed molecular events underlying the link between HGSOC
 tumorigenesis and ovulation, a physiological process that has been
 associated with risk factors of HGSOC.
description: FTE240 cells were treated with BDNF 50ng/ml in 3D culture for 24
 hours. Untreated cells were cultured under the same condition as control.
 Three biological repeats were included in the experiment, in which three
 different batches of FTE240 cells were utilized. Each repeat included
 untreated control and BDNF-treated groups. RNA was extracted and analysed
 using Clariom D Human Transcriptome Array and GeneChip Scanner 3000 7G
 system (Thermo Fisher Scientific, Waltham, MA). Transcriptome Analysis
 Console software was used to analyse the array data. The RNA expression
 was compared between the paired samples of untreated control and
 BDNF-treated groups.
DOI: 10.5061/dryad.08kprr503
title: Data from: Species-specific variation in germination rates contributes to spatial coexistence more than adult plant water use in four closely-related annual flowering plants

description: 1. Spatial partitioning is a classic hypothesis to explain plant species
 coexistence, but evidence linking local environmental variation to spatial
 sorting, demography, and species’ traits is sparse. If co-occurring
 species’ performance is optimized differently along environmental
 gradients because of trait variation, then spatial variation might
 facilitate coexistence. 2. We used a system of four naturally co-occurring
 species of Clarkia (Onagraceae) to ask if distribution patchiness
 corresponds to variation in two environmental variables that contribute to
 hydrological variation. We then reciprocally sowed Clarkia into each patch
 type and measured demographic rates in the absence of congeneric
 competition. Species sorted in patches along one or both gradients, and in
 three of the four species, germination rate in the “home” patch was higher
 than all other patches. 3. Spatially variable germination resulted in the
 same three species exhibiting the highest population growth rates in their
 home patches. 4. Species’ trait values related to plant water use, as well
 as indicators of water stress in home patches, differed among species and
 corresponded to home patch attributes. However, post-germination survival
 did not vary among species or between patch types, and fecundity did not
 vary spatially. 5. Synthesis Our research demonstrates the likelihood that
 within-community spatial heterogeneity affects plant species coexistence,
 and presents novel evidence that differential performance in space is
 explained by what happens in the germination stage. Despite the seemingly
 obvious link between adult plant water-use and variation in the
 environment, our results distinguish the germination stage as important
 for spatially variable population performance.
description: See ReadMe file included with data files