cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.crjdfn33r
title: Data from: Genotyping SNPs and inferring ploidy by amplicon sequencing for polyploid, ploidy-variable organisms

description: Whole genome duplication is hypothesized to have played a critical role in
 the evolution of several major organism groups, including vertebrates, and
 while many lineages have rediploidized, some retain polyploid genomes.
 Additionally, variation in ploidy can occur naturally or be artificially
 induced within select plant and animal species. Modern genetic techniques
 have not been widely applied to polyploid or ploidy-variable species, in
 part due to the difficulty of obtaining genotype data from polyploids. In
 this study we provide a strategy for developing an amplicon sequencing
 panel of single nucleotide polymorphisms for high-throughput genotyping of
 polyploid organisms. We then developed a method to infer ploidy of
 individuals from amplicon sequencing data that is generalized to apply to
 any ploidy and does not require prior identification of heterozygous
 genotypes. Combining these two techniques will allow researchers to both
 infer ploidy and generate ploidy-aware genotypes with the same amplicon
 sequencing panel. We demonstrated this approach with white sturgeon
 Acipenser transmontanus, a ploidy-variable (octoploid, decaploid, and
 dodecaploid) imperiled species under conservation management in the
 Pacific Northwest and obtained a panel of 325 loci. These loci were
 validated by examining inheritance in known-cross families, and the ploidy
 inference method was validated with known ploidy samples. We provide
 scripts that adapt existing pipelines to genotype polyploids and an R
 package for application of the ploidy inference method. We expect that
 these techniques will empower studies of genetic variation and inheritance
 in polyploid organisms that vary in ploidy level, either naturally or as a
 result of artificial propagation practices.
description: These are read counts and genotypes for biallelic SNPs genotyped
 by amplicon sequencing (GT-seq).
description: The rda files are to be loaded into R statistical software. All
 files have two matrices, one of read counts for reference alleles and one
 for read counts of alternate alleles. Rows are samples and columns are
 loci. 10n_sturgeon_readCounts.rda: presumed 10N white
 sturgeon 8n_12n_sturgeon_readCounts.rda: confirmed 8N
 and 12N white sturgeon at various subsampling levels. Rownames indicate
 the sample number, subsampling level as a percentage, and the true
 ploidy. 2n_3n_Chinook_readCounts.rda: confirmed 2N and
 3N Chinook salmon. Rownames indicate the true ploidy.
 white_sturgeon_genos: ".genos" files produced by the
 GT-seq pipeline with genotypes and read counts for all samples in this
 study
DOI: 10.5061/dryad.j0zpc86dh
title: Data from: The relationship between native species richness and exotic species richness or occurrence will always be negative when the total number of species is accounted for in statistical models: A response to Beaury et al.

description: Beaury et al. (2020) attempt to address the scale dependence of evidence
 for biotic resistance by including environmental covariates that can
 account for total species richness. However, this approach will
 incorrectly estimate relationships, driven by the accuracy of the
 covariates rather than the true relationship between native and non-native
 species.
description: This data set includes the script required to recreate and run
 the simulation and analyses described in the associated
 manuscript. 
description: See the included README.txt file and model description in the
 associated manuscript (Muthukrishnan, R. 2021. The relationship between
 native species richness and exotic species richness or occurrence will
 always be negative when the total number of species is accounted for in
 statistical models: A response to Beaury et al. Ecology Letters)
DOI: 10.25338/b8wg9s
title: Pictures of unmanned aerial vehicle (UAV) experiments on testing paper

description: Our computational developments and analyses on experimental images are
 designed to evaluate the effectiveness of chemical spraying via unmanned
 aerial vehicle (UAV). Our evaluations are in accord with the two
 perspectives of color-complexity: color variety within a color system and
 color distributional geometry on an image. First, by working within RGB
 and HSV color systems, we develop a new color-identification algorithm
 relying on highly associative relations among three color-coordinates to
 lead us to exhaustively identify all targeted color-pixels. A color-dot is
 then identified as one isolated network of connected color-pixel. All
 identified color-dots vary in shapes and sizes within each image. Such a
 pixel-based computing algorithm is shown robustly and efficiently
 accommodating heterogeneity due to shaded regions and lighting conditions.
 Secondly, all color-dots with varying sizes are categorized into three
 categories. Since the number of small color-dot is rather large, we
 spatially divide the entire image into a 2D lattice of rectangular. As
 such, each rectangle becomes a collective of color-dots of various sizes
 and is classified with respect to its color-dots intensity. We
 progressively construct a series of minimum spanning trees (MST) as
 multiscale 2D distributional spatial geometries in a decreasing-intensity
 fashion. We extract the distributions of distances among connected
 rectangle-nodes in the observed MST and simulated MSTs generated under the
 spatial uniformness assumption. We devise a new algorithm for testing 2D
 spatial uniformness based on a Hierarchical clustering tree upon all
 involving MSTs. This new tree-based p-value evaluation has the capacity to
 become exact.
DOI: 10.5061/dryad.02v6wwq2w
title: Data from: Prolonged impacts of past agriculture and ungulate overabundance on soil fungal communities in restored forests

description: Soil fungi can help improve ecosystem restoration, yet our understanding
 of how they reassemble in degraded land is limited. Here, using DNA
 metabarcoding, we studied the fungal community structure in reforested
 sites following agricultural abandonment and ungulate overabundance. Two
 treatments, namely ‘reforestation using different numbers of tree species’
 and ‘deer exclusion,’ have been applied for multiple decades in the study
 sites. We found that local fungal richness (alpha diversity) and total
 fungal richness (gamma diversity) were 1.9–2.9 and 1.3–1.9 times greater,
 respectively, in reforested stands than in natural forests. These results
 were regardless of the number of tree species planted in the reforested
 stands. Conversely, reforested stands had a spatially homogenized
 community structure with relatively lower degrees of compositional
 dissimilarity among sites within each stand (beta diversity). These
 findings were attributable to lower environmental heterogeneity, stronger
 dispersal limitation, and a comparatively shorter time since the onset of
 community assembly in reforested stands. Deer exclosures had no detectable
 effect on fungal community structure. Overall, the agricultural legacy in
 fungal community structure appears to have persisted for decades, even
 under proactive restoration of aboveground vegetation. Direct human
 intervention belowground may therefore be necessary for the recovery of
 soil biota once altered.
description: In May 2013, we collected soil samples at 72 locations across a
 restoration landscape in northern Japan. The topsoil from 0–5 cm depth
 were collected using a soil core. Soil samples were put into separate
 zip-lock bags, transported from the field on ice, frozen within 3 hours of
 collection, and kept at −20°C until further analysis.
 Total DNA was extracted from each of the 72 soil samples (0.25 g
 sample<sup>−1</sup>) using the Soil DNA Isolation kit (Norgen
 Biotek Corp., Canada). A semi-nested polymerase chain reaction (PCR) was
 then performed to amplify the nuclear internal transcribed spacer 1 (ITS1)
 region. The pooled amplicons were sequenced with a GS Junior sequencer
 (454 Life Sciences, USA).
description: The dataset consists of a fungal community matrix (389 OTU × 72
 sites), species’ functional groups, a list of literature we used to
 determine the functional groups, and consensus sequences.
DOI: 10.5061/dryad.2rbnzs7n9
title: Novel anatomical apical dissection utilizing puboprostatic open-collar technique: Impact on apical surgical margin and early continence recovery

description: Purpose: To evaluate the impact of modifications to anatomical
 apical dissection including a puboprostatic open-collar technique, which
 visualizes the lateral aspect of the apex and dorsal vein complex (DVC)
 covering the rhabdosphincter while preserving the puboprostatic collar, on
 positive surgical margin (PSM) and continence recovery.
 Methods: One-hundred-and-sixty-seven patients underwent gasless
 single-port retroperitoneoscopic radical prostatectomy using a
 three-dimensional head-mounted display system. Sequentially modified
 surgical techniques comprised puboprostatic open-collar technique,
 sutureless transection of the DVC, retrograde urethral dissection, and
 anterior reconstruction. The associations of these modifications with PSM
 and continence recovery were assessed. Results: The puboprostatic
 open-collar technique, sutureless DVC transection, and retrograde urethral
 dissection were significantly associated with lower apical PSM (P=0.003,
 0.003, and 0.010, respectively). The former two also showed similar
 associations in 84 patients with anterior apical tumor (P=0.021 and 0.030,
 respectively). Among 92 patients undergoing all of these three procedures,
 overall and apical PSM rates were 13.0% and 3.3%, respectively. Retrograde
 urethral dissection (odds ratio [OR] 2.73, P=0.004) together with nerve
 sparing (OR 2.77, P=0.003) and anterior apical tumor (OR 0.45, P=0.017)
 were independently associated with immediate continence recovery. A
 multivariable model for 3-month continence recovery included anterior
 apical tumor (OR 0.28, P=0.003) and puboprostatic open-collar technique
 (OR 3.42, P=0.062). Immediate and 3-month continence recovery rates were
 56.3% and 85.4%, respectively, in 103 patients undergoing both the
 puboprostatic open-collar technique and retrograde urethral dissection.
 Conclusion: Novel anatomical apical dissection utilizing a
 puboprostatic open-collar technique may favorably impact on both apical
 surgical margin and continence recovery.
DOI: 10.5061/dryad.0vt4b8gzk
title: Data from: Within-species trait variation can lead to size limitations in seed dispersal of small-fruited plants

description: The inability of small-gaped animals to consume very large fruits may
 limit seed dispersal of the respective plants. This has often been shown
 for large-fruited plant species that remain poorly dispersed when
 large-gaped animal species are lost due to anthropogenic pressure. Little
 is known about whether gape-size limitations similarly influence seed
 dispersal of small-fruited plant species that can show a large variation
 in fruit size within species. In this study, fruit sizes of 15 plant
 species were compared with the gape sizes of their 41 animal dispersers in
 the temperate, old-growth Białowieża Forest, Poland. The effect of
 gape-size limitations on fruit consumption was assessed at the plant
 species level, and for a subset of nine plant species, also at the
 individual level, and subindividual level (i.e., fruits of the same plant
 individual). In addition, for the species subset, fruit-seed trait
 relationships were investigated to determine whether a restricted access
 of small-gaped animals to large fruits results in the dispersal of fewer
 or smaller seeds per fruit. Fruit sizes widely varied among plant species
 (74.2%), considerably at the subindividual level (17.1%), and to the
 smallest extent among plant individuals (8.7%). Key disperser species
 should be able to consume fruits of all plant species and all individuals
 (except those of the largest-fruited plant species), even if they are able
 to consume only 28-55% of available fruits. Fruit and seed traits were
 positively correlated in eight out of nine plant species, indicating that
 gape size limitations will result in 49% fewer (in one plant species) or
 16-21% smaller seeds (in three plant species) dispersed per fruit by
 small-gaped than by large-gaped main dispersers, respectively. Our results
 show that a large subindividual variation in fruit size is characteristic
 for small-fruited plant species, and increases their connectedness with
 frugivores at the level of plants species and individuals. Simultaneously,
 however, the large variation in fruit size leads to gape-size limitations
 that may induce selective pressures on fruit size if large-gaped
 dispersers become extinct. This study emphasizes the mechanisms by which
 gape-size limitation at the species, individual and subindividual level
 shape plant-frugivore interactions and the co-evolution of small-fruited
 plants.
description: Please see manuscript for more information.
DOI: 10.5061/dryad.qrfj6q5ff
title: Data from: Competitive ability of native and alien plants: effects of residence time and invasion status

description: Competition is commonly thought to underlie the impact of plant invasions.
 However, competitive effects of aliens and competitive response of natives
 may also change over time. Indeed, as with time the novelty of an invader
 decreases, the accumulated eco-evolutionary experience of resident species
 may eventually limit invasion success. We aimed to gain insights on
 whether directional changes in biotic interactions over time, or more
 general differences between natives and aliens, for instance resulting
 from an introduction bias, are relevant in determining competitive
 ability. We conducted a pairwise competition experiment in a
 target-neighbour design, using 47 Asteraceae species with residence times
 between 8-12,000 years in Germany. We first tested whether there are
 differences in performance in intraspecific competition among invasion
 status groups, that is casual and established neophytes, archaeophytes, or
 native species. We then evaluated whether competitive response and effects
 depend on residence time or invasion status. Lastly, we assessed whether
 competitive effects influence range sizes. We found only limited evidence
 that native target species tolerate neighbours with longer potential
 coexistence times better, whereas differences in competitive ability were
 mostly better explained by invasion status than residence time. Although
 casual neophytes produced most biomass in intraspecific competition, they
 had the weakest per-capita competitive effects on natives. Notably, we did
 not find differences between established neophytes and natives, both of
 which ranked highest in interspecific competitive ability. This lack of
 differences might be explained by a biased selection of highly invasive or
 rare native species in previous studies, or because invasion success may
 result from mechanisms other than interspecific competitive superiority.
 Accordingly, interspecific per-capita competitive effects did not
 influence range sizes. Further studies across a broader range of
 environmental conditions, involving other biotic interactions that
 indirectly influence plant-plant interactions, may clarify when
 eco-evolutionary adaptations to new invaders are a relevant mechanism.
description: The dataset contains two files. The file
 "SheppardBrendelNeoBiota_Experimentaldata.csv" contains data
 collected on Asteraceae plants in each pot of a competition experiment
 conducted at the Heidfeldhof experimental station of the Faculty of
 Agricultural Sciences, University of Hohenheim, Stuttgart, in summer 2017.
 The file "SheppardBrendelNeoBiota_CompeffectsRangesize.csv"
 contains data from the results of species-specific regressions to
 determine competitive effects and data on range sizes of competitor
 species.
description: Detailed description of the variables in this dataset is
 available in the uploaded Metadata file. Further explanations and
 descriptions of the analysis of the data is explained in the Methods
 section and Supplementary File of the research article.
DOI: 10.5061/dryad.qrfj6q5fg
title: Pure species discriminate against hybrids in the Drosophila melanogaster species subgroup

description: Introgression, the exchange of alleles between species, is a common event
 in nature. This transfer of alleles between species must happen through
 fertile hybrids. Characterizing the traits that cause defects in hybrids
 illuminate how and when gene flow is expected to occur. Inviability and
 sterility are extreme examples of fitness reductions but are not the only
 type of defects in hybrids. Some traits specific to hybrids are more
 subtle but are important to determine their fitness. In this report, we
 study whether F1 hybrids between two species pairs of Drosophila are as
 attractive as the parental species. We find that in both species pairs,
 the sexual attractiveness of the F1 hybrids is reduced and that pure
 species discriminate strongly against them. We also find that the
 cuticular hydrocarbon (CHC) profile of the females hybrids is intermediate
 between the parental species. Perfuming experiments show that modifying
 the CHC profile of the female hybrids to resemble pure species improves
 their chances of mating. Our results show that behavioral discrimination
 against hybrids might be an important component of the persistence of
 species that can hybridize.
DOI: 10.5061/dryad.f7m0cfxvz
title: Patterns of genetic diversity vary among shoot and root functional traits in Norway spruce (Picea abies) along a latitudinal gradient

description: Roots constitute a major segment of plant biomass, and variation in
 belowground traits in situ correlates with environmental gradients at
 large spatial scales. Local adaptation of populations maintains
 intraspecific genetic variation in various shoot traits, but the
 contribution of genetic factors to adaptation to soil heterogeneity
 remains poorly known. I established a common-garden experiment with three
 Norway spruce (Picea abies) populations sampled between 60° and 67° N in
 Finland, each represented by 13 or 15 maternal families, to determine
 whether belowground traits are as genetically differentiated among
 populations as those in the shoot along a collective latitudinal gradient
 of temperature and soil heterogeneity. Two growing season simulations
 enabled testing for among-population differences in phenotypic plasticity.
 I phenotyped 777 first-year seedlings from shoot to root to capture
 functional traits that may influence survival in the wild: autumn
 phenology, shoot growth, root system size, root architecture, root
 morphology and growth allocation. All traits exhibited within-population
 genetic diversity, but among-population differentiation ranged from strong
 in shoot traits to nonexistent in root system architecture and morphology
 that are scaled to root system size. However, latitudinal trends
 characterised root-to-shoot ratio and root tip-to-shoot ratio that account
 for among-population differences in aboveground growth. Overall trait
 variability was multidimensional with variable among- vs.
 within-population trends: for example, phenology and shoot growth covaried
 across populations, but their association within individual populations
 was variable. Shoot growth correlated positively with root system size,
 but not with root architecture or morphology. Finally, the two
 higher-latitude populations exhibited greater phenotypic plasticity in
 shoot traits and growth allocation. The results demonstrate varying
 patterns of genetic variation in functional traits of Norway spruce in the
 boreal zone, suggesting simultaneous adaptation to multiple environmental
 factors. Functional traits that exhibit phenotypic plasticity, genetic
 diversity and little covariation will promote long-term survival of
 populations in fluctuating environments.
DOI: 10.5061/dryad.ht76hdrfg
title: Global resorption efficiencies of trace elements in leaves of terrestrial plants

description: 1. Leaf nutrient resorption is a critical nutrient conservation strategy.
 Previous studies focus mainly on resorption patterns of macronutrients,
 but resorption patterns of trace elements remain poorly understood. 2. A
 meta-analysis was conducted to explore the general patterns of the leaf
 resorption of eight trace elements [i.e., copper (Cu), molybdenum (Mo),
 zinc (Zn), boron (B), manganese (Mn), sodium (Na), aluminum (Al), and iron
 (Fe)], and a macronutrient [i.e., sulfur (S)] using data collected from 53
 published studies. 3. Sulfur (49.6%) had the highest average resorption
 efficiency followed by Cu (30.3%), Mo (29.5%), Zn (19.5%), and B (17.6%).
 Two structural elements, Na and Mn, were not resorbed, whereas two
 potentially toxic elements, Al (–55.6%) and Fe (–25.4%), were accumulated
 in senesced leaves. Both climatic factors and growth types affected leaf
 nutrient resorption efficiency, but the magnitudes and directions of the
 effects differed greatly between S and the trace elements. The resorption
 efficiencies of S, Cu, Mo, and Zn decreased as leaf nutrient
 concentrations increased, but the structural or potentially toxic elements
 (i.e., B, Mn, Na, Fe, and Al) presented no response or opposite trends. 4.
 Our results provide global mean resorption efficiencies of trace elements
 for the first time, and highlight that structural and potentially toxic
 elements have relatively lower or no leaf resorption, which should be
 fully considered in biogeochemical models.
DOI: 10.5281/zenodo.18396917
title: TALABANING RAQAMLI PORTFELI VA KOMPETENSIYALARNI BAHOLASH TIZIMI
DOI: 10.5281/zenodo.18396918
title: TALABANING RAQAMLI PORTFELI VA KOMPETENSIYALARNI BAHOLASH TIZIMI
DOI: 10.15468/dl.9ypzhy
title: Occurrence Download

description: A dataset containing 3418 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Calligonum"
 ]
}

 The dataset includes 3418 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002856-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.