Find research datasets worth reusing

opennotspecifiedApr 2019View details →

Figure 2 in The taxonomy of aloe xspinosissima hort. ex a.berger (asphodelaceae), a popular hybrid aloe from mediterranean Europe

Figure 2. Aloe ×spinosissima cultivated in the succulent garden of the Botanical Garden of the University of Porto in northwestern coastal Portugal (see Smith & Figueiredo, 2014b). Photograph: Gideon F. Smith.

opennotspecifiedApr 2019View details →

Figure 1 in The taxonomy of aloe xspinosissima hort. ex a.berger (asphodelaceae), a popular hybrid aloe from mediterranean Europe

Figure 1. Aloe ×spinosissima in full flower in the Glasshouse at the Royal Horticultural Society Garden Wisley, Woking, Surrey, United Kingdom. Picture taken on 20th February 2008 by Susan Carter.

opennotspecifiedJun 2020View details →

Figure 2 in Hybrid zone genomics supports candidate species in Iberian Alytes obstetricans

Figure 2. Cline analyses across the almogavarii/pertinax hybrid zone. (A) Cline fitting from a northeast-southwest transect, separately for the genome average (thick black line; 95% CI in red), mtDNA (thick dash line), and 89 species-diagnostic SNPs (thin grey lines). (B) Selective coefficient s ∗ calculated from the cline widths, for a range of dispersal rates (σ). Twelve diagnostic SNPs featured clines with w ∼ 0 km, 11 with w = 2-4 km, while the rest span around the genome average.

opennotspecifiedJun 2020View details →

Figure 1 in Hybrid zone genomics supports candidate species in Iberian Alytes obstetricans

Figure 1. Mitochondrial phylogeny of Alytes obstetricans (left, adapted from Gonçalves et al., 2015), distribution of the main lineages (inset map, adapted from Gonçalves et al., 2015; grey: unclear), and population genomics (433 SNPs) of the Catalonian hybrid zone (right). On the tree, the attributed subspecies (and species, see discussion) are indicated; note that lineage E segregates in almogavarii populations from the Pyrenees, but lacks nuclear differentiation (ghost mtDNA lineage, Maia-Carvalho et al., 2018). The lineages studied here are highlighted in bold. The Catalonian map displays the average nuclear ancestry of each population, based on the STRUCTURE analysis (K = 2). The barplots show individual nuclear and mitochondrial assignments. Photo: Alytes obstetricans (CD).

opennotspecifiedApr 2023View details →

FIGURE 6. Hybrid Catasetum. A–B. C in Catasetum × grasineideae (Orchidaceae: Catasetinae), a new nothospecies from Brazilian Amazon and taxonomic notes for the genus

FIGURE 6. Hybrid Catasetum. A–B. C. × aripuanense. C. C. × dalastranum. D. C. × fergusonii. E–F. C. × mojuense. G–H. C. × yarigii. Photos A–B, D and G–H by J. Fernández G., C by F. Godoy and E–F by E. Pontes.

opencc-zeroMay 2023View details →

Ancient hybridization leads to the repeated evolution of red flowers across a monkeyflower radiation

The re-use of old genetic variation can promote rapid diversification in evolutionary radiations, but in most cases, the historical events underlying this divergence are not known. For example, ancient hybridization can generate new combinations of alleles that sort into descendant lineages, potentially providing the raw material to initiate divergence. In the Mimulus aurantiacus species complex, there is evidence for widespread gene flow among members of this radiation. In addition, allelic variation in the MaMyb2 gene is responsible for differences in flower color between the closely related ecotypes of subspecies puniceus, contributing to reproductive isolation by pollinators. Previous work suggested that MaMyb2 was introgressed into the red-flowered ecotype of puniceus. However, additional taxa within the radiation have independently evolved red flowers from their yellow-flowered ancestors, raising the possibility that this introgression had a more ancient origin. In this study, we used repeated tests of admixture from whole-genome sequence data across this diverse radiation to demonstrate that there has been both ancient and recurrent hybridization in this group. However, most of the signal of this ancient introgression has been removed due to selection, suggesting that widespread barriers to gene flow are in place between taxa. Yet, a roughly 30 kb region that contains the MaMyb2 gene is currently shared only among the red-flowered taxa. Patterns of admixture, sequence divergence, and extended haplotype homozygosity across this region confirm a history of ancient hybridization, where functional variants have been preserved due to positive selection in red-flowered taxa but lost in their yellow-flowered counterparts. The results of this study reveal that selection against gene flow can reduce genomic signatures of ancient hybridization, but that historical introgression can provide essential genetic variation that facilitates the repeated evolution of phenotypic traits between lineages.

opencc-zeroMay 2023View details →

Species, hybrid and genotype effects on leaf litter curling, and their extended consequences for spiders and soil moisture dynamics

This archive contains datasets from a group of studies testing the hypotheses that leaf litter curling is influenced by plant species, hybridization and genotype, and has extended consequences for associated organisms and soil processes. A novel litter curling index (LCI) was used to characterize the curling of newly senesced leaves. There are four distinct datasets represented here. 1) A dataset of LCI from 11 plant species (tall annual forb = Helianthus annuus L.; evergreen shrubs = Arctostaphylos pungens Kunth, Quercus turbinella Greene, Rhus ovata S. Watson; deciduous shrubs = Rhus trilobata Nutt., Ribes cereum Douglas, Acer glabrum Torr.; deciduous trees = Elaeagnus angustifolia L., Quercus gambelii Nutt., Populus tremuloides Michx., Populus fremontii S. Watson) mostly growing in natural habitats of Northern Arizona, USA. 2) A dataset containing LCI from two Populus species (P. fremontii James, P. angustifolia S. Watson) and their F1 hyrbids in a common garden in Ogden, UT, USA (including replicated genotypes of P. angustifolia but not the other tree types). 3) The third dataset examined the relationship between average LCI for a tree and the abundance of agilenid webs under Populus trees growing in a common garden; the LCI values are averages per tree from data collected for dataset 2, and previously published spider web data. 4) The last dataset contains litter and soil moisture values from a litter/soil drying experiment that tested the effect of litter curling on soil moisture dynamics. See the README file for more details on the different datasets.

opencc-zeroMay 2023View details →

Genetic factors predict hybrid formation in the British flora

Natural hybridization can have a profound evolutionary impact, with consequences ranging from the extinction of rare taxa to the origin of new species. Natural hybridization is particularly common in plants; however, our understanding of the general factors that promote or prevent hybridization is hampered by the highly variable outcomes in different lineages. Here, we quantify the influence of different predictors on hybrid formation across species from an entire flora. We combine estimates of hybridization with ecological attributes and a new species-level phylogeny for over 1,100 UK flowering plant species. Our results show that genetic factors, particularly parental genetic distance, as well as phylogenetic position and ploidy, are key determinants of hybrid formation, whereas many other factors such as range overlap and genus size explain much less variation in hybrid formation. Overall, intrinsic genetic factors shape the evolutionary and ecological consequences of natural hybridization across species in a flora.

opencc-by-4.0May 2023View details →

Dataset of Flow Velocity Prediction in Vegetated Alluvial Channels Comparing Empirical and State-of-the-art Hybrid Machine Learning Models

We compiled 447 datasets from different sources and lab- and field-based measurements. These datasets included Einstein and Banks (1950), Fenzl (1962), Kouwen et al. (1969), Ree and Crow (1977), Murota (1984), Tsujimoto and Kitamura (1990), Tsujimoto (1991), Tsujimoto (1993), Shimizu (1994), Dunn et al. (1996), Ikeda and Kanazawa (1996), Meijer (1998), Jarvela (2002), Rowinski and Kubrak (2002), Stone and Shen (2002), Poggi et al. (2004), Carollo et al. (2005), and Murphy et al. (2007).

opencc-zeroJun 2023View details →

Pollinator sharing and hybridization in a pair of dioecious figs sheds light on the pathways to speciation

The dynamics and processes underlying the co-diversification of plant–pollinator interactions are of great interest to researchers of biodiversity and evolution. Co-speciation is generally considered to be a key process in generating the diversity of figs and their pollinating wasps. Groups of closely-related figs pollinated by separate wasps occur frequently and represent excellent opportunities to study ongoing diversification in this textbook mutualism. We study two closely-related sympatric dioecious figs (F. heterostyla and F. squamosa) in Xishuangbanna, southwest China, and aim to document what is likely to be the final stages of speciation between these species using a combination of trait data and experimental manipulation. Thirty-seven and 29 floral volatile compounds were identified from receptive F. heterostyla and F. squamosa figs respectively, with 25 compounds shared by both species. Interspecific variation in chemical dissimilarity was significant but relatively low. Ovipositor lengths lie well within the range required for access to heterospecific ovules, facilitating hybridization. Cross-introduction of wasps into figs was conducted and hybrid seeds were generated for all donor/recipient combinations. Wasps of F. heterostyla produce adult offspring in F. squamosa figs, while wasps of F. squamosa induce gall development in F. heterostyla figs and their offspring fail to mature in synchrony with their novel host. We record limited geographic barriers, limited volatile dissimilarity, compatible morphology, complementary reproductive phenologies and the production of hybrid seeds and wasp offspring. We hypothesize that this incomplete wasp specialization and incomplete reproductive isolation may generalize to other closely-related figs.

opencc-by-4.0Jun 2023View details →

Achieving high hybridization density at DNA biosensor surfaces using branched spacer and click chemistry

Raw data and metadata associated to the study " Achieving high hybridization density at DNA biosensor surfaces using branched spacer and click chemistry". Copy of labbook for synthetic procedures and surface functionalization procedures. Data for surface characterizations (XPS measurements and fluorescent quantification). Data for molecular characterizations: NMR and Mass Spectrometry.

opencc-zeroJun 2023View details →

Data for: Lower survival of hybrid grosbeaks, but not towhees, suggests a molt divide disfavors hybrids

Although avian hybrid zones in the Great Plains have been studied for almost 70 years, we know surprisingly little about the fitness costs for hybrids that keep these zones narrow. We compare age ratios in grosbeaks (Pheucticus ludovicianus and P. melanocephalus) and towhees (Pipilo erythropthalums and P. maculatus), two species pairs that differ in their life-histories and molt schedules, to evaluate survival between hybrids and parentals. We then contrast molt and migratory divides as possible sources of selection against hybrids. Hybrid grosbeaks had 27-33% lower survival relative to their parentals, whereas hybrid towhees had survival rates similar to parentals. Age ratio data for hybrid grosbeaks suggest high mortality in older birds, as expected if selection operates after the first year of life. This pattern is consistent with parental species of grosbeaks having contrasting molt schedules relative to migration, suggesting high mortality costs to hybrids driven by molt biology, which are expressed later in life. Contrasts in molt schedules are absent in towhees. While migratory divides may exist for towhees and grosbeaks, the low adult survival of hybrid grosbeaks suggests that molt may be an important and underappreciated source of selection maintaining this and other narrow avian hybrid zones.

opencc-by-4.0Jun 2023View details →

Dataset accompanying the submission titled "Adaptive covariance hybridization for the assimilation of SST observations within a coupled Earth system reanalysis"

The dataset contains the data accompanying our submission entitled "Adaptive covariance hybridization for the assimilation of SST observations within a coupled Earth system reanalysis". It contains: <ol> <li>The yearly outputs of the free run</li> <li>The observations</li> <li>The yearly outputs of the runs of the standard hybrid</li> <li>The yearly outputs of the runs of the adaptive hybrid</li> <li>The grid of the model</li> <li>The maps of the hybridization coefficients</li> <li>The python and matlab scripts used to plot the figures of the article</li> </ol>

opencc-by-4.0Apr 2023View details →

Hybrid multi-model ensemble learning for reconstructing gridded runoff of Europe for 500 years

1 Introduction The data archive provides the reconstructed dataset capturing the annual runoff across Europe, partitioned into a grid format and preserved in NetCDFv4 (.nc) format for enhanced geospatial information. 1.1 Coordinate system and spatial resolution Each grid cell in the dataset corresponds to a 0.5-degree spatial resolution, using the World Geodetic System 1984 (WGS84) as the standard coordinate frame. 1.2 Temporal resolution The data encapsulates a yearly temporal resolution, offering a comprehensive outlook from 1500 to 1999. For example data for 1500 are represented by the layer 01/01/1500. 1.3 Units Runoff measurements are quantified in millimeters per year (mm/year), providing hydrological data throughout the noted time frame. 1.4 Example library(terra) library(raster) > dt_cc<-rast("HEMMF_ERUN_1500_1999.nc") > dt_cc class       : SpatRaster  dimensions  : 70, 104, 500  (nrow, ncol, nlyr) resolution  : 0.5, 0.5  (x, y) extent      : -12, 40, 35, 70  (xmin, xmax, ymin, ymax) coord. ref. : lon/lat WGS 84 (EPSG:4326)  source      : HEMMF_ERUN_1500_1999.nc  varname     : runoff  names       : runoff_1, runoff_2, runoff_3, runoff_4, runoff_5, runoff_6, ...  unit        :  mm/year,  mm/year,  mm/year,  mm/year,  mm/year,  mm/year, ...  time (days) : 1500-01-01 to 1999-01-01    1.5 Citation The specific data file, named ’HEMMF ERUN 1500 1998.nc,’ is conveniently structured to facilitate easy handling and interpretation of the information. Please ensure to attribute the correct citation when utilizing this dataset, adhering to the subsequent reference: [Singh et al., 2023] References Ujjwal Singh, Petr Maca, Martin Hanel, Yannis Markonis, Rama Rao Nidamanuri, Sadaf Nasreen, Johanna Ruth Bl¨ocher, Filip Strnad, Jiri Vorel, Lubomir Riha, and Akhilesh Singh Raghubanshi. Hybrid multi-model ensemble learning for reconstructing gridded runoff of europe for 500 years. Information Fusion, 97:101807, 2023. ISSN 1566-2535. doi: https://doi.org/10.1016/j.inffus. 2023.101807. URL https://www.sciencedirect.com/science/article/pii/S1566253523001161#d1e5346.

opennotspecifiedOct 2021View details →

Fig. 7 in Unusual matrine-adenine hybrids isolated from Sophora davidii and their inhibitory effects on human cytomegalovirus

Fig. 7. Molecular docking model of 1 (A), 2 (B), 3 (C), and 4 (D) bound to the HCMV protease (PDB: 2WPO). Hydrogen bond interactions are depicted with red dashes, while π–π and π–cation stacking interactions are displayed with green and yellow dashes, respectively. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

opencc-by-4.0Dec 2022View details →

Proximity effect in PbTe-Pb hybrid nanowire Josephson junctions

This repository contains the raw data and processing code of the paper "Proximity effect in PbTe-Pb hybrid nanowire Josephson junctions".

FIGURE 2 in Cymbidium × fugongense (Orchidaceae; Epidendroideae), a new natural hybrid from China: evidence from morphology and molecular analyses

FIGURE 2. Phylogenetic relationships of C. × fugongense based on combined plastid sequence (matK and rbcL). Galeandra devoniana and Eulophia graminea were used as outgroups. The numbers near the nodes are Bayesian posterior probabilities (PP), maximum likelihood bootstrap percentages (BP), and maximum parsimony bootstrap percentages (BP), respectively. "-" indicates that the node ML MP is incongruent between the topology of the Bayesian and MP/ML trees.

FIGURE 4 in Cymbidium × fugongense (Orchidaceae; Epidendroideae), a new natural hybrid from China: evidence from morphology and molecular analyses

FIGURE 4. Cymbidium × fugongense S.Ke, S.R.Lan & Z.J.Liu. A. Habit. B. Flowers, front view. C. Structure of the flower. D-E. Pollinarium. F. C. maguanense flower. G. C. wenshanense flower. H. C. eburneum flowers.

FIGURE 3 in Cymbidium × fugongense (Orchidaceae; Epidendroideae), a new natural hybrid from China: evidence from morphology and molecular analyses

FIGURE 3. Cymbidium × fugongense. A. Habit. B. Flower, front view. C. Lip. D–E. Column. F. Dorsal sepal. G. Petal. H. Lateral sepal. I. Pollinarium.

FIGURE 1 in Cymbidium × fugongense (Orchidaceae; Epidendroideae), a new natural hybrid from China: evidence from morphology and molecular analyses

FIGURE 1. Phylogenetic relationships of C. × fugongense based on the nuclear DNA (ITS). Galeandra devoniana and Eulophia graminea were used as outgroups. The numbers near the nodes are Bayesian posterior probabilities (PP), maximum likelihood bootstrap percentages (BP ML), and maximum parsimony bootstrap percentages (BP MP), respectively. "-" indicates that the node is incongruent between the topology of the Bayesian and MP/ML trees.