Find research datasets worth reusing

opencc-by-4.0Apr 2023View details →

Data set for "Electrical control of hybrid exciton transport in a van der Waals heterostructure"

Data set for "Electrical control of hybrid exciton transport  in a van der Waals heterostructure"

A complex genomic architecture underlies reproductive isolation in a North American Oriole hybrid zone

Natural hybrid zones provide powerful opportunities for identifying the mechanisms that facilitate and inhibit speciation. Documenting the extent of genomic admixture allows us to discern the architecture of reproductive isolation through the identification of isolating barriers. This approach is particularly powerful for characterizing the accumulation of isolating barriers in systems exhibiting varying levels of genomic divergence. Here, we use a hybrid zone between two species--the Baltimore (Icterus galbula) and Bullock's (I. bullockii) orioles--to investigate this architecture of reproductive isolation. We combine whole genome re-sequencing with data from an additional 313 individuals amplityped at ancestry-informative markers to characterize fine-scale patterns of admixture, and to quantify links between genes and the plumage traits. On a genome-wide scale, we document several putative barriers to reproduction, including elevated peaks of divergence above a generally high genomic baseline, a large putative inversion on the Z chromosome, and complex interactions between melanogenesis-pathway candidate genes. Concordant and coincident clines for these different genomic regions further suggest the coupling of pre- and post-mating barriers. Our findings of complex and coupled interactions between pre- and post-mating barriers suggest a relatively rapid accumulation of barriers between these species, and they demonstrate the complexities of the speciation process.

Limited hybridization and introgression despite stocking among endemic Interior Highlands black basses (Centrarchidae: Micropterus)

Aim Smallmouth Bass (Micropterus dolomieu; SMB) are globally popular among anglers and have been widely introduced (i.e., stocked) for population management and sportfishing. Importantly, stocking was prevalent before cryptic diversity within the SMB complex was known, which now includes three newly elevated species: Neosho Bass (M. velox; NB), Little River Bass (M. sp. cf. dolomieu Little River; LRB), and Ouachita Bass (M. sp. cf. dolomieu Ouachita River; OB). We sought to quantify population structure and hybridization and introgression in these three recently described species. Location Species-level diversity, particularly in the basin-restricted LRB and OB in the Ouachita Mountains within the Central Interior Highlands (CIH), North America, suggests the presence of distinct genetic variation that could be eroded by introgression. Methods We estimated interspecific introgression and intraspecific population differentiation in the Smallmouth Bass species complex (SMB-C) using 472 specimens comprising SMB, NB, LRB, and OB, including the naturally sympatric Spotted Bass (M. punctulatus; SPB). Genomic samples were genotyped on a SNP panel of 192 loci designed to detect allele-sharing on multiple hierarchical levels. Results We found low range-wide hybridization between species in the SMB-C and SPB (mostly SMB-C backcrosses), and interspecific heterozygosity varied, indicating differential introgression. Range-wide hybridization between species in the CIH and SMB was similar overall (but mostly F2 and CIH backcrosses) and was observed in streams with known SMB stocking in connected reservoirs. Interspecific heterozygosity in SMB hybrids was also generally lower, indicating later-generation backcrosses. We found strong population structure in the Ouachita Mountains (LRB and OB). Main Conclusions Despite isolated incidences of natural (SPB) and human-mediated (SMB) introgression, genomic identity appears intact in endemic LRB and OB, suggesting potential ecological or behavioral isolating mechanisms preventing cross-species reproduction. Our findings reveal that genetic variation remains in cryptic, basin-restricted species in the Ouachita Mountains ecoregion that may be managed for long-term conservation.

opencc-by-4.0Jun 2023View details →

Control over epitaxy and the role of the InAs/Al interface in hybrid two-dimensional electron gas systems

Raw and processed 'transport' data for paper the paper "Control over epitaxy and the role of the InAs/Al interface in hybrid two-dimensional electron gas systems". A short readme is given, data organized according to figures of the Main Text and Supplemental Material.

Can cryptic female choice prevent invasive hybridization in external fertilizing fish?

Polyandrous mating systems result in females mating with multiple males, generating opportunities for strong pre-mating and post-mating sexual selection. Polyandry also creates the potential for unintended matings and subsequent sperm competition with hybridizing species. Cryptic female choice allows females to bias paternity towards preferred males under sperm competition and may include conspecific sperm preference when under hybridization risk. The potential for hybridization becomes particularly important in context of invasive species that can novelly hybridize with natives, and by definition, have evolved allopatrically. We provide the first examination of conspecific sperm preference in a system of three species with the potential to hybridize: North American native Atlantic salmon (Salmo salar) and brook char (Salvelinus fontinalis), and invasive brown trout (Salmo trutta) from Europe. Using naturalized populations on the island of Newfoundland, we measured changes in sperm swimming performance, a known predictor of paternity, to determine the degree of modification in sperm swimming to female cues related to conspecific sperm preference. Compared to water alone, female ovarian fluid, in general, had a pronounced effect and changed sperm motility (by a mean of 53%) and swimming velocity (mean 30%), but not linearity (mean 6%). However, patterns in the degree of modification suggest there is no conspecific sperm preference in the North American populations. Furthermore, female cues from both native species tended to boost the sperm of invasive males more than their own. We conclude that cryptic female choice via ovarian fluid mediated sperm swimming modification is too weak in this system to prevent invasive hybridization and is likely insufficient to promote or maintain reproductive isolation among the native North American species.

Climate change outpaces adaptive potential via hybridization in nesting female Saltmarsh and Nelson's Sparrows

Hybridization and introgression can promote adaptive potential and evolutionary resilience in response to increased pressures of climate change; they can also disrupt local adaptation and lead to outbreeding depression. We investigated female fitness consequences of hybridization in two sister species that are endemic to a threatened tidal marsh ecosystem: Saltmarsh (Ammospiza caudacutus) and Nelson's Sparrows (A. nelsoni). We found increasing nest flooding rates due to rising sea levels are outpacing potential adaptive benefits of hybridization due to very low overall nesting success in both the Nelson's and Saltmarsh Sparrows. In the center of the hybrid zone across two years, we determined the success of 201 nests of 104 pure and admixed Saltmarsh and Nelson's Sparrow females, genotyped using a panel of Single Nucleotide Polymorphisms (SNPs) from double digest restriction-site associated DNA (ddRAD) Sequencing. We evaluated five metrics of female fitness and modeled nesting success in relation to genotypic, environmental, and nesting characteristics. We found differential fitness among Saltmarsh, Nelson's, and hybrid females, such that birds with predominantly Saltmarsh Sparrow alleles had higher reproductive success than birds with predominantly Nelson's Sparrow alleles, and hybrids were intermediate. Fledging success increased with two known tidal marsh nesting adaptations: nest height and nesting synchrony with tidal cycles. We found a positive relationship between hybrid index and fitness in daily nest survival in 2016, but not in 2017, likely due to differing levels of precipitation and nest flooding between years. The strongest and most consistent predictors of daily nest survival were nesting synchrony with lunar tidal flooding cycles and daily maximum tide height. Fitness patterns suggest there may be an adaptive benefit of interspecific geneflow for the Nelson's Sparrow at the detriment of the Saltmarsh Sparrow; however, flooding rates are so high in many years they mask any fitness differences between the species, and all females had poor nesting success, regardless of genetic makeup.

opencc-zeroAug 2023View details →

Supporting information for: Integrating morphological, molecular, and cytogenetic data for F2 sea turtle hybrids diagnosis revealed balanced chromosomal sets

Hybridization could be considered part of the evolutionary history of many species. The hybridization among sea turtle species on the Brazilian coast is atypical and occurs where nesting areas and reproductive seasons overlap. Integrated analysis of morphology and genetics is still scarce, and there is no evidence of the parental chromosome set distribution in sea turtle interspecific hybrids. In this study, chromosome markers previously established for pure sea turtle species were combined with morphological and molecular analyses aiming to recognize genetic composition and chromosome sets in possible interspecific hybrids initially identified by mixed morphology. The data showed that one hybrid could be an F2 individual among Caretta caretta × Eretmochelys imbricata × Chelonia mydas, and another is resulting from backcross between C. caretta × Lepidochelys olivacea. Native alleles of different parental lineages were reported in the hybrids, and, despite this, it was verified that the hybrid chromosome sets were still balanced. Thus, how sea turtle hybridism can affect genetic features in the long term is a concern, as the implications of the crossing-over in hybrid chromosomal sets and the effects on genetic function are still unpredictable.

opencc-by-4.0Aug 2023View details →

Discovery of enhanced lattice dynamics in a single-layered hybrid perovskite

This repository presents the raw data for the paper "Discovery of enhanced lattice dynamics in a single-layered hybrid perovskite", published as an open-access article in Science Advances at <a href="https://www.science.org/doi/10.1126/sciadv.adg4417">https://www.science.org/doi/10.1126/sciadv.adg4417</a>. Data presented in the Supplementary Materials will be provided upon request. For such requests or general questions regarding the paper, please contact Zhuquan Zhang (<a href="mailto:zhuquan@mit.edu">zhuquan@mit.edu</a>), Keith Nelson (<a href="mailto:kanelson@mit.edu">kanelson@mit.edu</a>), or Edoardo Baldini (<a href="mailto:edoardo.baldini@austin.utexas.edu">edoardo.baldini@austin.utexas.edu</a>).

opencc-zeroAug 2023View details →

Data for Geographic variation in phenotypic divergence between two hybridizing field cricket species

Patterns of morphological divergence across species' ranges can provide insight into local adaptation and speciation. In this study, we compare phenotypic divergence among 4,221 crickets from 337 populations of two closely related species of field cricket, Gryllus firmus and G. pennsylvanicus and their hybrids. We find that these species differ across their geographic range in key morphological traits, such as body size and ovipositor length, and we directly compare phenotype with genotype for a subset of crickets to demonstrate nuclear genetic introgression, phenotypic intermediacy of hybrids, and essentially unidirectional mitochondrial introgression. We discuss how these morphological traits relate to life history differences between these two species. Our comparisons across geographic areas support prior research that suggested that cryptic variation within G. firmus may represent different species. Overall, our study highlights how variable morphology can be across wide ranging species, and the importance of studying reproductive barriers in more than one or two transects of a hybrid zone.

opencc-by-4.0Aug 2023View details →

Data from Quantitative Analyses of Coupling in Hybrid Zones

This data set comprises simulated and empirical genetic data and associated metadata that were analyzed for the publication "Quantitative Analyses of Coupling in Hybrid Zones" (doi:10.1101/cshperspect.a041434). The data set includes two compressed directories (tar.gz files). dfuseSims.tar.gz contains the simulated data. These are the main (.main) output files from the program dfuse. The simulation conditions are encoded in the file names, this includes the number of demes (number after d), the number of loci (number after L), theta (number after theta) and the replicate number (number after rep). The genetic map size (M) is given if not 1 and the migration rate (m) is given if not 0.1. The directory includes 2250 simulated data sets. data.tar.gz contains the empirical data sets re-analyzed for this paper. We specifically include the final input files needed for analysis. The file formats vary slightly but are described in detail in the supplemental material for the publication and in the R scripts used for analysis. The latter are available from GitHub (https://github.com/zgompert/ClineCoupling). There is one directory per data set within the main compressed directory.

opencc-by-4.0Aug 2023View details →

Tailoring the hybridization density of DNA biosensors through tunable surface functionalization

Raw data and metadata associated to the study "Tailoring the hybridization density of DNA biosensors through tunable surface functionalization" Metadata file. Raw data for molecular characterization (NMR and MS analyses). Raw data for surface characterization (XPS analyses and fluorescence quantification). Copy of labbook for synthesis and surface functionalization protocols.

opencc-by-4.0Sep 2023View details →

Hybrid Machine Learning Model for Ultra-Short-Term Wind Power Forecasting with Multi-Model Training Approach

This is the core data code of the "Hybrid Machine Learning Model for Ultra-Short-Term Wind Power Forecasting with Multi-Model Training Approach".

opencc-by-4.0Jul 2023View details →

GTnum PERSEUS #InteractionHybridation - Vidéos sur l'hybridation Physique-Numérique

Vous trouverez, via les liens de téléchargement, 7 vidéos reliées aux différents bulletins de l'axe 2 "Hybridation physique/numérique" du GTnum #InteractionHybridation. Ces vidéos à visée pédagogique présentent les grands concepts et les principales technologies associées à l'hybridation des mondes physiques et numériques dans le cadre des recherches actuelles en Interaction Humain-Machine pour l'éducation :  - Interface Humain-Machine ; - Interaction Humain-Machine ; - Interface graphique ; - Interface tactile ; - Interface tangible ; - Réalité virtuelle ; - Réalité augmentée.

opencc-by-4.0Feb 2023View details →

Subgap spectroscopy along hybrid nanowires by nm-thick tunnel barriers

These are datasets and codes used for the manuscript with a title : Subgap spectroscopy along hybrid nanowires by nm-thick tunnel barriers

opencc-zeroSep 2023View details →

Population genomic analyses reveal hybridization and marked differences in genetic structure and demographic history of Scurria limpet sister species with parapatric distributions across the southeastern pacific

The study of sister species that occur in parapatry around biogeographic transition zones can help understand the evolutionary processes that underlie the changes in species composition across biogeographic transition zones. The South Eastern Pacific (SEP) coast is a highly productive coastal system that exhibits a broad biogeographic transition zone around 30–35ºS. Here, we present a comparative genome-wide analysis of the sister species Scurria viridula and Scurria zebrina, that occur in parapatry and whose poleward and equatorward range edges intersect in the 30–35ºS SEP biogeographic transition zone. We sampled 118 specimens sourced from nine sites from Tocopilla (22ºS) to Chiloé (41ºS) including one site where both species overlap and analyzed over 8,000 biallelic single nucleotide polymorphisms. We found evidence of hybridization between these species in the contact zone and found significant but contrasting population structures for both species. Our results indicate that the genetic structure in S. viridula, which is currently expanding its range poleward, follows a simple isolation-by-distance model with no traces of natural selection (no evidence of outlier loci). In contrast, S. zebrina, which finds its equatorward range edge at the transition zone, displayed a pronounced genetic break approximately at 32-34ºS, along a region of marked environmental heterogeneity in association with a semi-permanent coastal upwelling regime. For S. zebrina, we also found 43 outlier loci associated with this genetic break, with a significant proportion of them clustering in a single linkage group. This marked difference in the presence of outlier loci between species suggests that they could be responding differently to local environmental challenges found at their overlapping geographic range edges, thus providing important new insights about genomic changes around biogeographic transition zones in sister species and the forces that shape genetic diversity in intertidal marine species.

opencc-by-4.0Oct 2023View details →

Dataset of A User-driven Hybrid Neuro-symbolic Approach for Knowledge Graph Creation from Relational Data

This dataset contains the following: 1. achieved percentage values of the generated RML rules using LXS and manually 2. basic information about the example used and with which creation type users started 3. all answers of users to the User Experience Questionnaire 4. Answers to the structured part of the user interview

opencc-zeroOct 2023View details →

Importance of mega-environments in evaluation and identification of climate resilient maize hybrids (Zea mays L.)

Multi-location experiments on maize were conducted from 2016 to 2019 at ten locations distributed across two agro-climatic zones (ACZ) i.e., ACZ-3 and ACZ-8 of Karnataka, India. Individual analysis of variance for each location-year combination showed significant differences among the hybrids; similarly, combined analysis showed a higher proportion of GE interaction variance than due to genotype. Mega-environments were identified using biplot approaches such as AMMI, GGE, and WAASB methodologies for the years 2016 to 2019. The BLUP method revealed a high correlation between grain yield and stability indices ranging from 0.67 to 1.0. Considering all three methods together, the three location pairs Arabhavi-Belavatagi, Bailhongal-Belavatagi, and Hagari-Sirguppa had three occurrences in the same mega-environment with a value of 0.67, and these location combinations consistently produced winning genotypes. Among the common winning genotypes identified, it was G7 during 2016 and 2017 and G10 during 2018 and 2019, based on WAASBY. The likelihood of Arabhavi-Nippani, Hagari-Mudhol, and Dharwad-Hagari occurring in the same mega-environment is minimal because they did not share the same winning genotype, with the exception of a small number of events. Despite being in the same agro-climatic zone, Arabhavi, Hagari, and Mudhol rarely had a winning genotype in common. An agro-climatic zone is grouped based on climatic and soil conditions which doesn't consider GE interaction of cultivars thus, releasing the cultivars for commercial cultivation considering mega environments pattern would enhance the yield for the given target region.

opencc-by-4.0Sep 2023View details →

Data for the publication "In Situ Observation of Room-Temperature Magnesium Metal Deposition on a NASICON/IL Hybrid Solid Electrolyte"

Datasets are obtained from X-ray diffraction (XRD), Rietveld analysis, Scanning electron microscopy (SEM), Electrochemicla impedance spectroscopy (EIS), Nudged Elastic Band (NEB), Chronopotentiometry (CP), Linear sweep voltammetry (LSV), X-ray photoelectron spectroscopy (XPS), Energy-dispersive X-ray spectroscopy (EDS). Abstract: Secondary batteries using multivalent cations as ionic charge carriers have attracted increasing attention in recent years due to the high theoretical energy density provided by multi-electron redox reactions. However, the high charge density of these cations inevitably leads to sluggish kinetics of ion migration at room temperature, which poses a challenge for the development of solid-state batteries using multivalent ions. Here, we prepared a magnesium ion conducting hybrid solid electrolyte (HSE) consisting of a new NASICON-structured material, Mg0.5Sn2(PO4)3, and a small amount of Mg ionic liquid. The HSE shows superior room-temperature ionic conductivity of 1.11 · 10−4 S cm−1 and an activation energy of 0.36 eV. Due to good compatibility of the HSE with the magnesium metal anode, symmetric MgǀHSE|Mg cells show stable Mg plating and stripping behavior at room temperature. Using in situ electrochemical scanning electron microscopy measurements the room temperature growth-induced fracture of the HSE was observed, giving unequivocal evidence for magnesium deposition. These results may serve as starting point for understanding the magnesium deposition mechanism on solid electrolyte in solid-state batteries.

opencc-by-nc-nd-4.0May 2023View details →

A global hybrid tropical cyclone risk model based upon statistical and coupled climate models - Supporting figures and data

IntroductionThis contribution consists of 1) supporting figures and 2) supporting data for the submitted manuscript "A Global Hybrid Tropical Cyclone Risk Model based upon Statistical and Coupled Climate Models." Supporting figures are presented in two interactive HTML documents. The supporting datasets contain tropical cyclone event sets, catalogs, and an example analysis that plots summaries of the simulated catalogs and compares them to historical observations. All files are provided for the 400 ensemble members (event sets) that represent climate model years 1981-2020 (40 years) from the first 10 CESM-LE members.Contents./Catalog/sim_650Tropical cyclone annual catalog for each basin based on the CESM-LE distribution of ENSO phases. 650 simulations are provided for each of 400 event sets. Each file contains the catalog for a single basin and is written as catalog_tc_(BASIN)_sim650_my400_nbinom_condmeanensojma.csv., where BASIN can be NA, EP, WP, NI, SI, SP../DocumentationTCMODEL_UQAM_EXAMPLE.html: Analysis script showing example of use of the tropical cyclone catalogs and comparison to historical observations.UQAM_TC_Model_Data_Supplement_Dictionary.xlsx: Data dictionary of all data supplement file contents../IBTRACSSummary of IBTrACS data required in the analysis script../TrajectoryBanksContains subdirectories for each basin (EP, NAT, NI, SI, SP, WP)Each subdirectory contains several files summarizing the event sets, or banks, of tropical cyclone trajectories.VersionsVersion 1.0.1: Updated TCMODEL_UQAM_SUPPORTING_FIGURES.zip for revisions to submitted manuscript.Version 1.0.0: Original version.