cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k3j9kd57k
title: Plant-phenotypic changes induced by parasitoid ichnoviruses enhance the performance of both unparasitized and parasitized caterpillars

description: There is increasing awareness that interactions between plants and insects
 can be mediated by microbial symbionts. Nonetheless, evidence showing that
 symbionts associated with organisms beyond the second trophic level affect
 plant-insect interactions are restricted to a few cases belonging to
 parasitoid-associated bracoviruses. Insect parasitoids harbor a wide array
 of symbionts which, like bracoviruses, can be injected into their
 herbivorous hosts to manipulate their physiology and behavior. Yet, the
 function of these symbionts in plant-based trophic webs remains largely
 overlooked. Here we provide the first evidence of a parasitoid-associated
 symbiont belonging to the group of ichnoviruses which affects the strength
 of plant-insect interactions. A comparative proteomic analysis shows that,
 upon parasitoid injection of calyx fluid containing ichnovirus particles,
 the composition of salivary glands of caterpillars changes both
 qualitatively (presence of two viral-encoded proteins) and quantitatively
 (abundance of several caterpillar-resident enzymes, including elicitors
 such as glucose oxidase). In turn, plant phenotypic changes triggered by
 the altered composition of caterpillar oral secretions affect the
 performance of herbivores. Ichnovirus manipulation of plant responses to
 herbivory leads to benefits for their parasitoid partners in terms of
 reduced developmental time within the parasitized caterpillar.
 Interestingly, plant-mediated ichnoviruses-induced effects also enhance
 the performances of unparasitized herbivores which in natural conditions
 may feed alongside parasitized ones. We discuss these findings in the
 context of ecological costs imposed to the plant by the viral symbiont of
 the parasitoid. Our results provide intriguing novel findings about the
 role played by carnivore-associated symbionts on plant-insect-parasitoid
 systems and underline the importance of placing mutualistic associations
 in an ecological perspective.
description: Exhaustive information
 about dataset collection and processing can be found on the M&M
 section of the associated manuscript ( MEC-21-0710 ) published in
 "Molecular Ecology".
DOI: 10.5061/dryad.nvx0k6dst
title: Data from: Severance of arbuscular mycorrhizal networks in restoration grasslands enhances seedling biomass

description: 1. Establishment and growth of grassland plant species is generally
 promoted by arbuscular mycorrhizal fungi (AMF) when grown in isolation.
 However, in grassland communities AMF form networks that may connect
 individual plants of different ages within and between species. Here, we
 use an in-growth core approach to examine how mycorrhizal networks
 influences performance of seedlings in grasslands. 2. We selected 4 grass
 and 4 forb species with known negative or neutral-positive plant-soil
 feedback and grew them individually in steel mesh cores filled with living
 field soil. Cores were placed in six restored grasslands, three grasslands
 were of relatively young and three were of older successional age. 3.
 Ingrowing mycorrhizal fungal hyphae were severed twice a week in half of
 all cores, which resulted into reduced AMF colonisation and increased
 seedling biomass, irrespective of the fields’ succession stage, and the
 plants’ grass/forb group, or plant-soil feedback type. In the control
 cores, root colonization by AMF was negatively correlated to seedling
 biomass, whereas there was no such relationships in the cores that had
 been lifted. 4. We conclude that connections to arbuscular mycorrhizal
 networks of surrounding plants had a negative impact on biomass of
 establishing forb and grass seedlings.
DOI: 10.5061/dryad.nzs7h44s0
title: Observations of flowering phenology in Concord, Massachusetts, USA, 1963-1993

description: Phenology plays a vital role in understanding the impacts of climate
 change on plants. Observing and recording the dates that plants are in
 flower, over periods of years and decades, can elucidate patterns in how
 plants respond to warming temperatures, shifting precipitation regimes,
 and other effects of a changing climate. Long-term records of plant
 phenology are difficult to find. It is often the case that these records
 do not originate from scientific research studies but instead are the
 product of an individual’s interest in observing natural phases in their
 local environment. Pennie Logemann (1918-2011) was a resident of Concord,
 Massachusetts, United States and a landscape designer. From 1963-1993 she
 recorded the flowering times of plants in her woodland garden, resulting
 in an invaluable dataset of wildflower and shrub phenology. These plants
 were primarily local native plants, but included some non-native species
 as well.  Most likely her garden contained a mixture of species
 occurring naturally on her property and species planted deliberately.
 Logemann’s records have been analyzed in compilation with observations
 made by Henry David Thoreau and contemporary researchers in a study of
 recent climate change in Concord. The dataset provided here includes
 flowering phenology records for 71 species over 30 years (discontinuous
 for most species) at a single location. We encourage the use of these data
 in further studies of plant phenology and hope they may provide
 encouragement for others to record and share their phenology data.
description: Logemann’s methods involved regular surveys of her property where
 she recorded the dates that species were in flower. Her motivation for
 doing so was to inform her garden designs, ensuring a continuous floral
 display. Logemann shared the data directly with Miller-Rushing and Primack
 and these data were used in their 2008 publication. The data provided here
 are the original, raw dates and have not been processed.
description: The dataset includes genus and species along with common name of
 each plant species. Each year has an “s” and an “e” value, representing
 start and end dates of flower. Logemann was not explicit in her definition
 of start and end, but these values have been interpreted as the date when
 the first open flower was observed (start) and the last date that a fresh
 flower was still open (end). Missing values are indicated with
 NA.
DOI: 10.5061/dryad.866t1g1r1
title: Multicellularity and sex helped shape the Tree of Life

description: Across the Tree of Life, there are dramatic differences in species numbers
 among groups. However, the factors that explain the differences among the
 deepest branches have remained unknown. We tested whether multicellularity
 and sexual reproduction might explain these patterns, since the most
 species-rich groups share these traits. We found that groups with
 multicellularity and sexual reproduction have accelerated rates of species
 proliferation (diversification), and that multicellularity has a stronger
 effect than sexual reproduction. Patterns of species richness among clades
 are then strongly related to these differences in diversification rates.
 Taken together, these results help explain patterns of biodiversity among
 groups of organisms at the very broadest scales. They may also help
 explain the mysterious preponderance of sexual reproduction among species
 (the “paradox of sex”) by showing that organisms with sexual reproduction
 proliferate more rapidly.
DOI: 10.5061/dryad.k3j9kd57m
title: GPS data of little owls

description: Advances in bio-logging technology for wildlife monitoring have expanded
 our ability to study space use and behavior of many animal species at
 increasingly detailed scales. However, such data can be challenging to
 analyze due to autocorrelation of GPS positions. As a case study, we
 investigated spatiotemporal movements and habitat selection in the little
 owl (Athene noctua), a bird species that is declining in central Europe
 and verges on extinction in Denmark. We equipped 6 Danish
 food-supplemented little owls and 6 non-supplemented owls in the Czech
 Republic with high-resolution GPS loggers that recorded one position per
 minute. Nightly home ranges, measured as 95% kernel density estimates, of
 Danish male owls were on average 62 ha (± 64 SD, larger than any found in
 previous studies) compared to 2 ha (± 1) in females, and to 3 ± 1 ha
 (males) versus 3 ± 5 ha (females) in the Czech Republic. Foraging Danish
 male owls moved on average 4-fold further from their nest and at almost
 double the distance per hour than Czech males. To create availability data
 for the habitat selection analysis, we accounted for high spatiotemporal
 autocorrelation of the GPS data by simulating correlated random walks with
 the same autocorrelation structure as the actual little owl movement
 trajectories. We found that habitat selection was similar between Danish
 and Czech owls, with individuals selecting for short vegetation and areas
 with high structural diversity. Our limited sample size did not allow us
 to infer patterns on a population level, but nevertheless demonstrates how
 high-resolution GPS data can help to identify critical habitat
 requirements to better formulate conservation actions on a local scale.
description: We captured 6 adult owls from both the Danish (June 2019) and
 Czech populations (June 2020) using mist-nets or traps baited with dead
 chickens (Denmark) or live mice (Czech Republic). Captured owls were sexed
 (based on brood patch and body mass) and fitted with a GPS backpack
 (Technosmart Europe srl., Rome; total mass including Teflon backpack
 harness of ca. 3.2 g; constituting &lt;2.5% of the owls’ body mass).
 GPS units were programmed to record one position per minute, and to start
 recording positions the night after capture (avoiding potential capture
 effects).
description: The data shows the area (Denmark or Czech Republic), owl_ID, the
 latitude and longitude (GPS coordinates), the data and time, sex, distance
 moved between consecutive GPS positions, and distance from the nest (in
 m).
DOI: 10.5061/dryad.k3j9kd57n
title: Data from: The interaction between ambush predators, search patterns of herbivores and aggregations of plants

description: While predators benefit from spatial overlap with their prey, prey strive
 to avoid predators. I used an individual-based simulation comprising
 sit-and-wait predators, widely-foraging herbivores, and plants, to examine
 the link between predator ambush location, herbivore movement, and plant
 aggregation. I used a genetic algorithm to reach the best strategies for
 all players. The predators could ambush herbivores either inside or
 outside plant patches. The herbivores could use movement of varying
 directionality levels, with a change in directionality following the
 detection of plants. When the predators were fixed outside plant patches,
 the herbivores were selected to use a directional movement before plant
 encounter followed by a tortuous movement afterwards. When predators were
 fixed inside patches, herbivores used a continuous directional movement.
 Predators maintained within-patch positions when the herbivores were fixed
 to use the directional-tortuous movement. The predator location inside
 patches led to higher plant aggregations, by changing the herbivore
 movement. Finally, I allowed half of the predators to search for
 herbivores and let them compete with sit-and-wait predators located inside
 plant patches. When plants were clumped and herbivores used a
 directional-tortuous movement, with a movement shift after plant
 detection, ambush predators had a higher success relative to
 widely-foraging predators. In all other scenarios, widely-foraging
 predators did much better than ambush predators. The findings from my
 simulation suggest a behavioral mechanism for several observed phenomena
 of predator-prey interactions, such as a shorter stay by herbivores in
 patches when predators ambush them nearby, and a more directional movement
 of herbivores in riskier habitats.
description: The data are the results of the simulation model, described in
 the manuscript published in Behavioral Ecology.
DOI: 10.5061/dryad.2fqz612ph
title: Agroecosystem diversification with legumes or non-legumes improves differently soil fertility according to soil type

description: Plant diversification through crop rotation or agroforestry is a promising
 way to improve sustainability of agroecosystems. Nonetheless, criteria to
 select the most suitable plant communities for agroecosystems
 diversification facing contrasting environmental constraints need to be
 refined. Here, we compared the impacts of 24 different plant communities
 on soil fertility across six tropical agroecosystems: either on highly
 weathered Ferralsols, with strong P limitation, or on partially weathered
 soils derived from volcanic material, with major N limitation. In each
 agroecosystem, we tested several plant communities for diversification, as
 compared to a matching low diversity management for their cropping system.
 Plant residue restitution, N, P and lignin contents were measured for each
 plant community. In parallel, the soil under each community was analyzed
 for organic C and N, inorganic N, Olsen P, soil pH and nematode community
 composition. Soil potential fertility was assessed with plant bioassays
 under greenhouse controlled climatic conditions. Overall, plant
 diversification had a positive effect on soil fertility across all sites,
 with contrasting effects depending on soil type and legumes presence in
 the community. Communities with legumes improved soil fertility indicators
 of volcanic soils, which was demonstrated through significantly higher
 plant biomass production in the bioassays (+18%) and soil inorganic N
 (+26%) compared to the low diversity management. Contrastingly,
 communities without legumes were the most beneficial in Ferralsols, with
 increases in plant biomass production in the bioassays (+39%), soil Olsen
 P (+46%), soil C (+26%), and pH (+5%). Piecewise structural equation
 models with Shipley’s test revealed that plant diversification impacts on
 volcanic soil fertility were related to soil N availability, driven by
 litter N. Meanwhile, Ferralsols fertility was related to soil P
 availability, driven by litter P. These findings underline the importance
 of multifactorial and multi-sites experiments to inform trait-based
 frameworks used in designing optimal plant diversification in
 agroecological systems.
DOI: 10.5061/dryad.rn8pk0pb2
title: Nanoscale zero-valent iron loaded vermiform expanded graphite for the removal of Cr (VI) from aqueous solution

description: Cr (VI) is indispensable in industrial manufacturing, and its extensive
 use leads to severe heavy-metal pollution in the water environment around
 people, posing a great danger to physical health and living environment of
 multitudinous organisms. Expanded graphite (EG) is considered as a typical
 material for adsorption, while nanoscale zero-valent iron (nZVI) can be
 applied to degrade and sedimentate various organic or inorganic
 pollutants. In this study, a simultaneous collaboration of EG and nZVI is
 carried out, with the investigation on the influence of different test
 conditions for adsorption performances. These findings demonstrate that
 nZVI@EG manifests favorable adsorptive performance on the removal of
 hexavalent chromium efficiently. nZVI, acted as an electron donor, is
 supposed to reduce Cr(VI) to Cr(III), turning itself into iron oxide or
 hydroxide. The whole process is an exothermic reaction, accompanying
 chemical reduction and physical adsorption. And Cr(III) is fastened on the
 appearance by deposition of chromium hydroxide or ferrochromium complex
 precipitation, which greatly reduces the total chromium content in the
 aqueous solution. Herein, as a new composite adsorbent, nZVI@EG shows
 promising prospects of practical applications in water contamination and
 environmental remediation.
DOI: 10.5061/dryad.zkh1893b1
title: Data from: Global induced stress field from large earthquakes since 1900 and chained earthquake occurrence

description: Great earthquakes produce significant damages over large areas.
 The timely identification of impending earthquakes is crucial for
 seismic hazard mitigation. We assess the stress induced from
 neighboring earthquakes for 120 years around the circum-Pacific
 plate boundaries. Large earthquakes perturbed the stress
 fields. We analyze 1,636 earthquakes with moment
 magnitudes greater than or equal to 6.4 in 1900-2020. The
 cumulative Coulomb stress changes reach up to the order of tens
 to hundreds of bar at the plate boundaries. Large earthquakes
 followed in the regions with large lateral gradients of
 cumulative Coulomb stress changes induced by precedent
 earthquakes. Laterally heterogeneous stress fields may play
 an important role in nucleation of great earthquakes.
description: This data set is concerned with the paper "Global induced
 stress field from large earthquakes since 1900 and chained earthquake
 occurrence" submitted to Geochemistry, Geophysics, Geosystems by
 Junhyung Lee, and Tae-Kyung Hong in 2021. We provide data files to produce
 eight figures in the paper: Figures 19, 20, 21, 22, 23, 24, 25, and 26.
 All data files are given in the ASCII format.
description: Please see the file "README" included in the zip
 file.
DOI: 10.5061/dryad.brv15dv9n
title: Arundinella tengchongensis (Poaceae), a name at new rank and newly combined based on morphological and molecular data

description: To clarify the taxonomic status of Arundinella setosa var. tengchongensis
 and its relationships with A. setosa var. setosa and other related
 species, molecular phylogenetic analyses based on nuclear ITS and two
 plastid DNA (matK and trnL-F) sequences, and morphological comparisons
 using one-way ANOVA were carried out. Our results reveal that A. setosa
 var. tengchongensis is recovered within a different clade and separated
 from the type variety. Morphologically, A. setosa var. tengchongensis can
 be easily distinguished from A. setosa var. setosa and other varieties by
 its smaller spikelets, shorter awns, and bearded nodes. Thus, A. setosa
 var. tengchongensis is here elevated to the species rank and newly
 combined as A. tengchongensis.
DOI: 10.5061/dryad.3n5tb2rhw
title: Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity

description: Hoopes G., Meng X., Hamilton J.P., Achakkagari S.R., de Alves Freitas
 Guesdes F., Bolger M.E., Coombs J.J., Esselink D., Kaiser N.R., Kodde L.,
 Kyriakidou M., Lavrijssen B., van Lieshout N., Shereda R., Tuttle H.K.,
 Vaillancourt B., Wood J.C., de Boer J.M., Bornowski N., Bourke P., Douches
 D., van Eck H.J., Ellis D., Feldman M.J., Gardner K.M., Hopman J.C.P.,
 Jiang J., De Jong W.S., Kuhl J.C., Novy R.G., Oome S., Sathuvalli V., Tan
 E.H., Ursum R.A., Vales M.I., Vining K., Visser R.G.F., Vossen J., Yencho
 G.C., Anglin N.L., Bachem C.W.B., Endelman J.B., Shannon L.M., Strömvik
 M.V., Tai H.H., Usadel B., Buell C.R., and Finkers R. (2022). Phased,
 chromosome-scale genome assemblies of tetraploid potato reveals a complex
 genome, transcriptome, and predicted proteome landscape underpinning
 genetic diversity. Mol. Plant. doi:
 https://doi.org/10.1016/j.molp.2022.01.003. Cultivated potato is a
 clonally propagated autotetraploid species with a highly heterogeneous
 genome. Phased assemblies of six cultivars including two chromosome-scale
 phased genome assemblies revealed extensive allelic diversity including
 altered coding and transcript sequences, preferential allele expression,
 and structural variation that collectively result in a highly complex
 transcriptome and predicted proteome which are distributed across the
 homologous chromosomes. Wild species contribute to the extensive allelic
 diversity in tetraploid cultivars, demonstrating ancestral introgressions
 predating modern breeding efforts. As a clonally propagated autotetraploid
 that undergoes limited meiosis, dysfunctional and deleterious alleles are
 not purged in tetraploid potato. Nearly a quarter of the loci bore
 mutations predicted to have a high negative impact on protein function,
 complicating breeder’s efforts to reduce genetic load.
 The StCDF1 locus controls maturity and analysis of six
 tetraploid genomes revealed 12 allelic variants correlated with maturity
 in a dosage dependent manner. Knowledge of the complexity of the
 tetraploid potato genome with its rampant structural variation and
 embedded deleterious and dysfunctional alleles will be key not only to
 implementing precision breeding of tetraploid cultivars but also to the
 construction of homozygous, diploid potato germplasm containing favorable
 alleles to capitalize on heterosis in F1 hybrids.
DOI: 10.5061/dryad.z8w9ghxcj
title: A quantitative analysis of primary dormancy and dormancy changes during burial in seeds of Brassica napus

description: For plants inhabiting unpredictable environments, scheduling germination
 can be challenging. Various responses to environmental conditions have
 been evolved by plants; these responses combine with variation in local
 climate to construct germination niche. Germination process may be
 regulated by a number of factors, among them, the type of seed dormancy
 and dormancy cycling play an important role in promoting survival after
 dispersal. In the present study, seeds of Brassica napus were tested for
 primary conditional dormancy (CD). Dormancy changes were quantified
 through seed population thermal germination parameters to test whether
 different genotypes of B. napus seeds (944, 966, Alestrom, Danube, Okanto
 and Rohan) are non-dormant (ND) at the maturity or if they present primary
 dormancy (D or CD). In a burial experiment, B. napus seeds dormancy
 cycling in the natural soil seedbank was investigated. Germination of all
 genotypes decreased at 5 and &gt;20 oC, showing narrower breadth of
 thermal niche for germination. Dormancy-breaking Treatments lead to the
 widening of thermal range permissive for germination. The lower limit
 (Tl(50)) and higher limit (Th(50)) temperatures for germination decreased
 and increased, respectively, for non-dormant (after-ripened seeds treated
 with GA3) seeds compared with fresh seeds in all genotypes. In fresh
 seeds, the Tl(50) and Th(50) for various genotypes ranged from 3.61 to
 6.5oC and 25.0 to 29.0oC, respectively and ranged  from 0.2 to
 1.8oC and 35 to 41.0oC in non-dormant seeds. Thus, fresh seeds of B. napus
 are dormant at dispersal and adopt delayed germination strategies to avoid
 summer drought. In the burial experiment, the results indicated that B.
 napus must have D/ND cycle in which fresh seeds first become dormant and
 then the cycle begins (CD → D ↔ CD ↔ ND), thus adopting both risk-prone
 and risk- adverse strategies to spread the likelihood of survival over
 time.
description: Experiment 2 was conducted at the research farm of
 Aburaihan Campus, University of Tehran, Pakdasht, Iran. Fresh seeds of
 <i>B. napus</i> (cultivar “Okapi”), which were harvested on 14
 June 2017 from farmer’s field at Varamin, Iran, were buried 5 and 30 cm
 deep in the soil on 23 June 2017. Before burial, the potential of dormancy
 induction (according to the Hohenheim standard dormancy test (HSDT; Weber
 <i>et al.</i> 2010) was determined. The potential of dormancy
 induction is the capability of the responses to seasonal and environmental
 cues (such as temperature and water potential) that allow seeds to enter
 (or re-enter) secondary dormancy. The viability of seeds was also
 determined at the end of HSDT test by crush test (Taab and Andersson 2009;
 Soltani et al<i>.</i> 2017b). Germination of fresh seeds were
 tested in distilled water or GA<sub>3</sub> (100 ppm) in the
 dark.
description: Researchers who are interested in investigating seed bank can use
 the data set to realize how to collect data and perform germination
 trials