Find research datasets worth reusing

Data from: Genomic and bioacoustic variation in a midwife toad hybrid zone: a role for reinforcement?

This data package includes the following datasets and scripts used in the corresponding publication:  <ul> <li>An alignment (fasta format) of the 16S sequences obtained fromt the 221 new A. obstetricans/almogavarii samples barcoded in this study + the A. cisternasii sequence used as outgroup (16S_alignment.fas).</li> <li>A matrix of 1,642 SNPs genotyped in 89 A. obstetricans/almogavarii samples used for ancestry analyses (n89p41r0.5wrs_1642SNP_STRUCTURE.str).</li> <li>The R script used to compute geographic clines with HZAR and their graphical displays (Cline_analyses.r) and the input files it uses (Transect_Q_mtDNA_HZAR.csv; Transect_n57p19r0.5_diag_loci_HZAR.csv; dist_transect.txt; clines_diag_SNPs_1perlocus.csv).</li> <li>The R script used for the bioacoustic analyses (Alytes_FR_Bioacoustics.r) and the corresponding input data extracted from 71 mating calls of A. obstetricans/almogavarii (Alytes_FR_Bioacoustics.csv) the R script used for their analysis.</li> </ul>

Research Data - Nucleation and Arrangement of Abrikosov Vortices in Hybrid Superconductor-Ferromagnetic Nanostructure

Source data from micromagnetic simulations performed in COMSOL Multiphysics and Python codes for data post-processing utilized in the paper "Nucleation and Arrangement of Abrikosov Vortices in Hybrid Superconductor-Ferromagnetic Nanostructure." Square 250-250-205 (nm 3).gif The time evolution of normal-phase indentations and vortex structures in 3D superconducting prism with dimensions \(250 \times 250 \times 205\) nm\(^3\) is analyzed under an inhomogeneous magnetic field generated by a nearby ferromagnetic nanodot with dimensions \(250 \times 250 \times 700\) nm\(^3\), positioned at a distance of \(d\) = 10 nm. Square 250-250-205 (nm 3)- B(H).gif The time evolution of normal-phase indentations and vortex structures in 3D superconducting prism with dimensions \(250 \times 250 \times 205\) nm\(^3\) is analyzed under a homogeneous magnetic field of 315 mT. Sphere radius 200 nm.gif The temporal evolution of vortex structures in a 3D superconducting sphere with a radius of 200 nm is visualized under the effect of a spatially varying magnetic field generated by a ferromagnetic nanodot with dimensions \(350 \times 350 \times 700\) nm\(^3\), positioned 10 nm away. 2D_empty Comsol file The TDGL (Time-Dependent Ginzburg-Landau) model is implemented in COMSOL Multiphysics to simulate 2D superconducting systems, a long wire with a square cross-section and a side length of \(a = 250\) nm, under the influence of homogeneous magnetic fields. 3D-B(H)-dynamic_empty Comsol file The TDGL model is utilized in COMSOL to simulate a 3D superconducting prism with a square cross-section, where the side length is \(a = 250\) nm and the height is either 205 nm or 185 nm, subjected to homogeneous magnetic fields. 3D-350 nm-B(FM)_empty Comsol file The TDGL model is implemented in COMSOL to simulate a 3D superconducting prism with a square cross-section, where the side length is \(a = 350\) nm and the height is 320 nm. The prism is exposed to inhomogeneous magnetic fields produced by a ferromagnetic nanodot with dimensions \(350 \times 350 \times 700\) nm\(^3\), located at varying distances \(d\) from the superconducting prism. 3D-250 nm-B(FM)_empty Comsol file The TDGL model is implemented in COMSOL to simulate a 3D superconducting prism with a square cross-section, where the side length is \(a = 250\) nm and the height is 320 nm. The prism is exposed to inhomogeneous magnetic fields generated by a ferromagnetic nanodot with dimensions \(250 \times 250 \times 700\) nm\(^3\), positioned at varying distances \(d\) from the superconducting prism. The files from Comsol (.mph) are without simulation solutions due to their large size - please contact us if needed.

A hybrid approach to the small unannotated corpus-based language comparison and its application to the Old East Slavic charters - Supplementary material 1 (Old East Slavic)

<h1>Old East Slavic charters (XII - XIV century)</h1> <h2>General description</h2> A set of nine historical Old East Slavic legal texts from Smolensk, Polack and Novgorod from the end of the XII century to the first half of the XIV century. The source for Smolensk charters is Avanesov (1963), which contains original texts as well as their initial deciphering (not machine-readable). The source for Polack charters is Horoshkevich (2015), containing trascribed machine-readable texts that required only an additional check and preparation. The source for Novgorod charters is Napierskij (1857), carrying original texts and their initial non-machine-readable deciphering. All the texts underwent an additional preprocessing of reconstructed and contracted parts deletion in order to better represent the actual texts under consideration and exclude as many research biases as it is possible. The last step was a manual tokenisation and the joining of each text into a single string. The data statement is available among the downloadable files. <h2>How-to</h2> This section contains the tutorials that allow to use this data with the intended pipelines. <h3>Corpus-based distance measurement package</h3> The source code for package is available <a href="https://doi.org/10.5281/zenodo.13958502" target="_blank" rel="noopener">here</a>, the manual is available in the <a href="https://github.com/The-One-Who-Speaks-and-Depicts/corpus_distance/blob/dev/README.md" target="_blank" rel="noopener">README</a> section of the repository. To use this dataset for the measurement of distance between Smolensk, Polack and Novgorod lects, and their subsequent clusterisation, following steps should be completed: <ol> <li>Download the <a href="https://github.com/The-One-Who-Speaks-and-Depicts/corpus_distance/blob/dev/example/Corpus_distance_tutorial.ipynb" target="_blank" rel="noopener">Jupyter notebook</a> that streamlines the package use.</li> <li>Download the dataset.</li> <li>Put the dataset into a selected folder on your computer (make sure there are no other files within this folder).</li> <li>Insert the path to the directory into <code>CONTENT_DIR</code> variable in the Jupyter notebook.</li> <li>Run the notebook, adjusting the parameters, if necessary.</li> </ol> <h2> </h2>

A hybrid approach to the small unannotated corpus-based language comparison and its application to the Old East Slavic charters - Supplementary material 3 (Modern standard Slavic lects)

<h1>Modern standard Slavic lects (Croatian, Slovak, Slovenian)</h1> <h2>General description</h2> The dataset consists of texts, written in three modern stanard Slavic lects: Croatian, Slovak, and Slovenian. The texts are parallel in order to compensate for the possible genre influences. The text is John’s Gospel in each of the given languages. <h3>Sources</h3> Croatian original text is from the <a href="https://www.wordproject.org/bibles/cr/index.htm">Ivan &Scaron;arić’s translation</a> of New Testament. Slovenian text is from the <a href="https://www.bible.com/bible/2319/JHN.1.SSP">standard Slovenian translation</a> of the New Testament. Slovak text is from the modern <a href="https://svatepismo.sk/evanjelium-podla-jana-1">Catholic translation</a> of the New Testament. The data statement is available among the downloadable files. <h2>How-to</h2> This section contains the tutorials that allow to use this data with the intended pipelines. <h3>Corpus-based distance measurement package</h3> The source code for package is available <a href="https://doi.org/10.5281/zenodo.13958502" target="_blank" rel="noopener">here</a>, the manual is available in the <a href="https://github.com/The-One-Who-Speaks-and-Depicts/corpus_distance/blob/dev/README.md" target="_blank" rel="noopener">README</a> section of the repository. To use this dataset for the measurement of distance between Slovak, Croatian and Slovenian lects, and their subsequent clusterisation, following steps should be completed: <ol> <li>Download the <a href="https://github.com/The-One-Who-Speaks-and-Depicts/corpus_distance/blob/dev/example/Corpus_distance_tutorial.ipynb" target="_blank" rel="noopener">Jupyter notebook</a> that streamlines the package use.</li> <li>Download the dataset.</li> <li>Put the dataset into a selected folder on your computer (make sure there are no other files within this folder).</li> <li>Insert the path to the directory into <code>CONTENT_DIR</code> variable in the Jupyter notebook.</li> <li>Run the notebook, adjusting the parameters, if necessary.</li> </ol> <h2> </h2>

Dataset of the publication: Hybrid Heterostructures of a Spin Crossover Coordination Polymer on MoS2: Elucidating the Role of the 2D Substrate. Small 2023, 19, e2304954.

Dataset of the publication: Hybrid Heterostructures of a Spin Crossover Coordination Polymer on MoS2: Elucidating the Role of the 2D Substrate. A. Núñez-López, R. Torres-Cavanillas, M. Morant-Giner, N. Vassilyeva, R. Mattana, S. Tatay, P. Ohresser, E. Otero, E. Fonda, M. Paulus, V. Rubio-Giménez, A. Forment-Aliaga, E. Coronado, Small 2023, 19, e2304954. doi: 10.1002/smll.202304954 10.1002/smll.20230495410.1002/smll.20230495410.1002/smll.202304954

Dataset of the publication: Two-dimensional magnetic behaviour in hybrid NiFe-layered double hydroxides by molecular engineering

Dataset of the publication: Two-dimensional magnetic behaviour in hybrid NiFe-layered double hydroxides by molecular engineering DOI: 10.1039/D2DT03804H A. Seijas-Da Silva, J. A. Carrasco, B. J. Vieira, J. C. Bentes Waerenborgh, E. Coronado, G. Abellán Dalton Trans., 2023,52, 1219-1228

opencc-by-4.0Nov 2013View details →

Fig. 1 in Origine hybride de Arthropteris boutoniana (Hook.) Pic. Serm. (Arthropteridaceae) de l'île Maurice et de Madagascar

Fig. 1. – Distribution de Arthropteris monocarpa (Cordem.) C. Chr. (carrés), Arthropteris orientalis (J. F. Gmel.) Posth. var. orientalis (triangles) et Arthropteris ×boutoniana (Hook.) Pic. Serm. (étoiles) sur la carte bioclimatique de Madagascar (CORNET, 1974) et la carte de Maurice. Chaque point représente une station dans laquelle le taxon est présent 1 à x-fois.

Fig. 6. – Deparia septentrionalis Rakotondr. A in Révision du genre Deparia Hook. & Grev. (Pteridophyta, Athyriaceae) à Madagascar: trois espèces nouvelles, une synonymie nouvelle et des hybrides présumés

Fig. 6. – Deparia septentrionalis Rakotondr. A. Aspect général; B. Rachis et base d'une penne, face adaxiale: remarquer la discontinuité entre les canalicules du rachis et des costae; C. Détail du limbe fertile, face abaxiale; D. Ecaille du rhizome; E. Poil vermiculaire de la face adaxiale de la costa et de la nervure principale; F. Poil plus long parfois présent sur le rachis. [A-C, E, F: Rakotondrainibe 3445, P; D: Rakotondrainibe et al. 6278, P] [Dessin: A. Jouy]

Fig. 5 in Révision du genre Deparia Hook. & Grev. (Pteridophyta, Athyriaceae) à Madagascar: trois espèces nouvelles, une synonymie nouvelle et des hybrides présumés

Fig. 5. – Deparia parvisora (C. Chr.) M. Kato. A. Aspect général; B. Détail du limbe fertile, face abaxiale; C. Ecaille de la base du pétiole; D. Poil caténé de la face abaxiale du rachis; E. Poil vermiculaire, fréquent sur tous les axes du limbe. [Humbert 25046, P] [Dessin: A. Jouy]

Fig. 4 in Révision du genre Deparia Hook. & Grev. (Pteridophyta, Athyriaceae) à Madagascar: trois espèces nouvelles, une synonymie nouvelle et des hybrides présumés

Fig. 4. – Deparia marojejyensis (Tardieu) M. Kato. A. Apex d'une fronde; B. Trois segments d'une penne distale; C. Penne moyenne; D. Deux pinnules d'une penne moyenne; E. Nervures et sores; F. Ecaille du rhizome; G. Poil vermiculaire présent sur tous les axes du limbe. [A-E: Rasolohery 281, P; F, G: Humbert et al. 17851, P].

Fig. 2. – Deparia florensiae Rakotondr. A in Révision du genre Deparia Hook. & Grev. (Pteridophyta, Athyriaceae) à Madagascar: trois espèces nouvelles, une synonymie nouvelle et des hybrides présumés

Fig. 2. – Deparia florensiae Rakotondr. A. Pétiole et pennes proximales; B. Pennes moyennes; C. Apex de la fronde; D. Deux lobes de la penne moyenne, face abaxiale; E. Détail des nervures et des sores; F. Ecaille de la base du pétiole; G. Poil caténé présents sur toute la surface du limbe et de ses axes. [A-E, G:Rakotondrainibe & Florens 4887, P; F: Rakotondrainibe & Florens 4887 bis, P] [Dessin: A. Jouy]

Fig. 1 in Révision du genre Deparia Hook. & Grev. (Pteridophyta, Athyriaceae) à Madagascar: trois espèces nouvelles, une synonymie nouvelle et des hybrides présumés

Fig. 1. – Deparia boryana (Willd.) M. Kato. A. Pétiole et pennes proximales; B. Deux segments ultimes, face adaxiale; C. Poils longs, apprimés, insérés sur la face adaxiale des nervures; D. Poil vermiculaire sur les marges du canalicule des costae et costulae; E. Sores jeunes avec des indusies réniformes fugaces. [Andrianantoandro et al. 124, P] [Dessin: A. Jouy]

opencc-by-4.0Jun 2012View details →

Fig. 1 in Study of some European wild hybrids of Erica L. (Ericaceae), with descriptions of a new nothospecies: Erica nelsonii Fagúndez and a new nothosubspecies: Erica veitchii nothosubsp. asturica Fagúndez

Fig. 1. – Erica ×nelsonii Fagúndez. A. Synflorescence of upper left fragment (typus); B. General view of upper right fragment. [P. F. Hunt 1636, K] [Drawn by the author]

opencc-by-4.0Jun 2012View details →

Fig. 2 in Study of some European wild hybrids of Erica L. (Ericaceae), with descriptions of a new nothospecies: Erica nelsonii Fagúndez and a new nothosubspecies: Erica veitchii nothosubsp. asturica Fagúndez

Fig. 2. – Seeds of different species of Erica L. A: Erica tetralix L.; B: E. tetralix (detail of surface cells); C: E. tetralix × E. ciliaris; D: E. tetralix × E. ciliaris (detail of surface cells); E: E. ciliaris L.; F: E. ciliaris (detail of surface cells). [A: Fagúndez s.n., SANT-BG [119]; B: Fagúndez s.n., SANT-BG [211]; C-D: Fagúndez 3266, SANT; E: Fagúndez & Reyes s.n., SANT-BG [266]; F: Fagúndez & Reyes s.n., SANT-BG [273]]

opencc-by-4.0Jan 2022View details →

Genomic signatures of isolation, hybridization, and selection during speciation of island finches

Data associated to the study Genomic signatures of isolation, hybridization, and selection during speciation of island finches Contents <ul> <li>Table_S9_samples_accession_nos.xlsx: Editable Excel matrix with sample names and accession numbers.</li> <li>RAD_SNPs_stacks_42424_loci.vcf.tar.gz: VCF file (gzip-compressed tarball) containing SNPs in 42,424 loci, based on analyses of restriction site-associated DNA (RAD) sequencing using Stacks.</li> <li>RAD_SNPs_standard_variant_calling.vcf.tar.gz: VCF file (gzip-compressed tarball) containing 131,661 SNPs from standard variant calling pipelines.</li> <li>mitochondrial_markers_full_data.nex: Nexus file containing mitochondrial (mt) sequences used for mt-phylogeny. Partitioned for COX2, tRNA-Lys, ATP8, and ATP6. </li> <li>sequences_nuclear_genotype_with_zebra_finch_TG.tar.gz: Directory (gzip-compressed tarball) containing genotype sequence (heterozygous sites with IUPAC codes) alignments of nuclear markers in nexus files. In addition to the study species, the sequence for zebra finch Taeniopygia guttata is included with sample code TG.</li> <li>sequences_nuclear_phased_and_mitochondrial_haplotypes_matching.tar.gz: Directory (gzip-compressed tarball) containing phased sequence (haplotype) alignments of nuclear markers in nexus files. These include only those individuals that match individuals sequenced for mitochondrial markers (also included here). In case of recombining loci, both the full locus and the largest non-recombining block are represented.</li> <li>sequences_nuclear_phased_haplotypes_all.tar.gz: Directory (gzip-compressed tarball) containing phased sequence (haplotype) alignments of nuclear markers in nexus files. These include all individuals. In case of recombining loci, both the full locus and the largest non-recombining block are represented.</li> <li>microsatellite_dataset.xlsx: Microsatellite datasets for the study species and additional outgroups. <ul> </ul> Sequences and short read datasets available from NCBI; accession numbers in Table S9 (Table_S9_samples_accession_nos.xlsx). </li> </ul>   Study summary Sister species occurring sympatrically on islands are rare and offer unique opportunities to understand how speciation can proceed in the face of gene flow. The São Tomé grosbeak is a massive-billed, ‘giant’ finch endemic to the island of São Tomé in the Gulf of Guinea, where it has diverged from its co-occurring sister species the Príncipe seedeater, an average-sized finch that also inhabits two neighbouring islands. Here, we show that the grosbeak carries a large number of unique alleles different from all three Príncipe seedeater populations, but also shares many alleles with the sympatric São Tomé population of the seedeater, a genomic signature signifying divergence in isolation as well as subsequent introgressive hybridization. Furthermore, genomic segments that remain unique to the grosbeak are situated close to genes, including genes that determine bill morphology, suggesting the preservation of adaptive variation through natural selection during divergence with gene flow. This study reveals a complex speciation process whereby genetic drift, introgression, and selection during periods of isolation and secondary contact all have shaped the diverging genomes of these sympatric island endemic finches.

dryad40/100

Frequency-dependent hybridization contributes to habitat segregation in monkeyflowers

Spatial segregation of closely related species is usually attributed to differences in stress tolerance and competitive ability. For both animals and plants, reproductive interactions between close relatives can impose a fitness cost that is more detrimental to the rarer species. Frequency-dependent mating interactions may thus prevent the establishment of immigrants within heterospecific populations, maintaining spatial segregation of species. Despite strong spatial segregation in natural populations, two sympatric California monkeyflowers (Mimulus nudatus and M. guttatus) survive and reproduce in the other's habitat when transplanted reciprocally. We hypothesized that a frequency-dependent mating disadvantage maintains spatial segregation of these monkeyflowers during natural immigration. To evaluate this hypothesis, we performed two field experiments. First, we experimentally added immigrants in varying numbers to sites dominated by heterospecifics. Second, we reciprocally transplanted arrays of varying resident and immigrant frequency. Immigrant seed viability decreased with conspecific rarity for M. guttatus, but not M. nudatus. We observed immigrant minority disadvantage for both species, but driven by different factors– frequency-dependent hybridization for M. guttatus, and competition for resources and/or pollinators for M. nudatus. Overall, our results suggest a major role for reproductive interference in spatial segregation that should be evaluated along with stress tolerance and competitive ability.

opencc-zeroJan 2022View details →

opencc-by-4.0Jan 2022View details →

A Deep Learning-Based Hybrid Model of Global Terrestrial Evaporation

This repository contains the datasets used in the research article "A Deep Learning-Based Hybrid Model of Global Terrestrial Evaporation". The repository contains the following files: 1) Input - contains all the processed input used for training the deep learning models and the datasets used for creating the figures in the article. 2) Output - contains the final deep learning models and the outputs (evaporation and transpiration stress factor) outputs from the hybrid model developed in the study. Formats: All scripts are in the programming language Python. The datasets are in HDF5 and NetCDF file formats. The codes related to the research article and deep learning model are available in the following repository: https://github.com/akashkoppa/StressNet

dryad40/100

Predictors of genomic differentiation within a hybrid taxon

Hybridization is increasingly recognized as an important evolutionary force. Novel genetic methods now enable us to address how the genomes of parental species are combined in hybrid lineages. However, we still do not know the relative importance of admixed proportions, genome architecture and local selection in shaping hybrid genomes. Here, we take advantage of the genetically divergent island populations of Italian sparrow on Crete, Corsica and Sicily to investigate the predictors of genomic variation within a hybrid taxon. We test if differentiation is affected by recombination rate, selection, or variation in ancestry proportions. We find that the relationship between recombination rate and differentiation is less pronounced within hybrid lineages than between the parent species, as expected if purging of minor parent ancestry in low recombination regions reduces the variation available for differentiation. In addition, we find that differentiation between islands is correlated with differences in signatures of selection in two out of three comparisons. Signatures of selection within islands are correlated across all islands, suggesting that shared selection may mould genomic differentiation. The best predictor of strong differentiation within islands is the degree of differentiation from house sparrow, and hence loci with Spanish sparrow ancestry may vary more freely. Jointly, this suggests that constraints and selection interact in shaping the genomic landscape of differentiation in this hybrid species.

opencc-zeroFeb 2022View details →

dryad40/100

Genome-wide sequence data show no evidence of hybridization and introgression among pollinator wasps associated with a community of Panamanian strangler figs

The specificity of pollinator host choice influences opportunities for reproductive isolation in their host plants. Similarly, host plants can influence opportunities for reproductive isolation in their pollinators. For example, in the fig and fig wasp mutualism, offspring of fig pollinator wasps mate inside the inflorescence that the mothers pollinate. Although often host specific, multiple fig pollinator species are sometimes associated with the same fig species, potentially enabling hybridization between wasp species. Here we study the 19 pollinator species (Pegoscapus spp.) associated with an entire community of 16 Panamanian strangler fig species (Ficus subgenus Urostigma, section Americanae) to determine whether the previously documented history of pollinator host switching and current host sharing predicts genetic admixture among the pollinator species, as has been observed in their host figs. Specifically, we use genome-wide ultraconserved element (UCE) loci to estimate phylogenetic relationships and test for hybridization and introgression among the pollinator species. In all cases, we recover well-delimited pollinator species that contain high interspecific divergence. Even among pairs of pollinator species that currently reproduce within syconia of shared host fig species, we found no evidence of hybridization or introgression. This is in contrast to their host figs, where hybridization and introgression have been detected within this community, and more generally, within figs worldwide. Consistent with general patterns recovered among other obligate pollination mutualisms (e.g., yucca moths and yuccas), our results suggest that while hybridization and introgression are processes operating within the host plants, these processes are relatively unimportant within their associated insect pollinators.

opencc-zeroFeb 2022View details →