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78 results for “hybridization sequencing”
Strong sequence dependence in RNA/DNA hybrid strand displacement kinetics supplementary data and code
<p>Supplementary data and code needed to replicate figures and results for the paper: Strong sequence-dependence in RNA/DNA hybrid strand displacement kinetics - Francesca G. Smith, John P. Goertz, Molly M. Stevens and Thomas E. Ouldridge. README is included to explain each folder and file in the repository.</p>
Variant Data from Pooled Sequencing of Hybrid Kiwifruit
<p>Variant data from pooled sequencing of hybrid <em>Actinidia</em> families segregating for fruit size and Vitamin C Content.</p>
Genome-wide sequence data show no evidence of hybridization and introgression among pollinator wasps associated with a community of Panamanian strangler figs
<p>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 (<em>Pegoscapus</em> spp.) associated with an entire community of 16 Panamanian strangler fig species (<em>Ficus</em> subgenus <em>Urostigma</em>, section <em>Americanae</em>) 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 (<em>e.g.</em>, 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.<br> </p>
Data for: Range and niche expansion through multiple interspecific hybridization - a genotyping by sequencing analysis of Cherleria (Caryophyllaceae)
<p><b>Background:</b> <i>Cherleria</i> (Caryophyllaceae) is a circumboreal genus that also occurs in the high mountains of the northern hemisphere. In this study, we focus on a clade that diversified in the European High Mountains, which was identified using nuclear ribosomal (nrDNA) sequence data in a previous study. With the nrDNA data, all but one species was monophyletic, with little sequence variation within most species. Here, we use genotyping by sequencing (GBS) data to determine whether the nrDNA data showed the full picture of the evolution in the genomes of these species.</p> <p><b>Results:</b> The overall relationships found with the GBS data were congruent with those from the nrDNA study. Most of the species were still monophyletic and many of the same subclades were recovered, including a clade of three narrow endemic species from Greece and a clade of largely calcifuge species. The GBS data provided additional resolution within the two species with the best sampling, <i>C. langii</i> and <i>C. laricifolia</i>, with structure that was congruent with geography. In addition, the GBS data showed significant hybridization between several species, including species whose ranges did not currently overlap.</p> <p><b>Conclusions:</b> The hybridization led us to hypothesize that lineages came in contact on the Balkan Peninsula after they diverged, even when those lineages are no longer present on the Balkan Peninsula. Hybridization may also have helped lineages expand their niches to colonize new substrates and different areas. Not only do genome-wide data provide increased phylogenetic resolution of difficult nodes, they also give evidence for a more complex evolutionary history than what can be depicted by a simple, branching phylogeny.</p>
Hybrid sequencing reveals insight into heat sensing and signaling of bread wheat
<p>Wheat (<em>Triticum aestivum</em> L.), a globally important crop, is challenged by increasing temperatures (heat stress, HS); however, its polyploid nature, the incompleteness of its genome sequences and annotation, the lack of comprehensive HS-responsive transcriptomes and the unexplored heat sensing and signaling of wheat hinder our full understanding of its adaptations to HS. The recently released genome sequences of wheat, as well as the emerging single-molecular sequencing technologies, provides an opportunity to thoroughly investigate the molecular mechanisms of the wheat response to HS. We generated a high-resolution spatio-temporal transcriptome map of wheat flag leaves and filling grain under HS at 0 minute (m), 5 m, 10 m, 30 m, 1 hour (h) and 4 h by combining full-length single-molecular sequencing and Illumina short reads sequencing. This hybrid sequencing newly discovered 4,947 loci and 70,285 transcripts, generating the comprehensive and dynamic list of HS-responsive full-length transcripts and complementing the recently released wheat reference genome.</p>
Figure 1 in Evolutionary systematics of the Indian mouse Mus famulus Bonhote, 1898: molecular (DNA/DNA hybridization and 12S rRNA sequences) and morphological evidence
Figure 1. Phylogenetic trees derived from the DNA/DNA hybridization analysis. A and B: Consensus trees resulting from the bootstrap analysis of delta-Tm (A) and delta-mode (B) 12*12 matrices. BP values are indicated when different from 100%. The lengths of the branches correspond to one tree arbitrarily selected among those of the consensus. C and D: Average consensus trees resulting from the weighted jacknife procedure for delta-Tm (C) and delta-mode (D) 13*13 matrices. The thin lines represent nodes that were not present in maximum and minimum consensus trees or that are not supported for all combinations of single deletion analysis. uUnlabelled taxa. The names in bold indicate the differences that can be observed between the two distance estimators (Tm, Mode).
Figure 4 in Evolutionary systematics of the Indian mouse Mus famulus Bonhote, 1898: molecular (DNA/DNA hybridization and 12S rRNA sequences) and morphological evidence
Figure 4. Fifty per cent majority rule consensus of 52 trees derived from the morphological analysis. Each mostparsimonious tree is 54 steps long, and has a Consistency Index of 0.52, a Retention Index of 0.72, and a Rescaled Consistency Index of 0.37. Values given below the branches represent the percentage of trees containing the specified clades.
Figure 3. Synthetic tree derived from the 12S in Evolutionary systematics of the Indian mouse Mus famulus Bonhote, 1898: molecular (DNA/DNA hybridization and 12S rRNA sequences) and morphological evidence
Figure 3. Synthetic tree derived from the 12S rRNA datasets with the inclusion of all substitutions (TV + TI). The thin lines indicate nodes that are not robustly supported by all kinds of analysis. The robustness of the different nodes are indicated as follows: [BP(BPweighted analysis)/BSI (Parsimony)]/[BP(NJ)/Reliability Percentage (ML)].
Data for: Range and niche expansion through multiple interspecific hybridization - a genotyping by sequencing analysis of Cherleria (Caryophyllaceae)
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Genome-wide sequence data show no evidence of hybridization and introgression among pollinator wasps associated with a community of Panamanian strangler figs
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DAS Data for the figure in the paper entitled "A Hybrid Earthquake Detection Method for Distributed Acoustic Sensing Array Data and Its Application to the 2022 Menyuan Earthquake Sequence"
<p>The DAS data can be loaded using numpy. The sampling rate is 100 Hz, and each row is a time series for that channel.</p>
Solidago hybrid-sequence capture probe set
<p><em>Premise of the study</em>: The phylogenetic relationships among the ca. 138 species of goldenrods (<em>Solidago</em>; Asteraceae) have been difficult to infer due to species richness, and shallow interspecific genetic divergences. This study aims to overcome these obstacles by combining extensive sampling of goldenrod herbarium specimens with the use of a custom <em>Solidago</em> hybrid-sequence capture probe set.</p> <p><em>Methods</em>: A set of tissues from herbarium samples comprising ca. 90% of <em>Solidago</em> species was assembled, and DNA was extracted. A custom hybrid-sequence capture probe set was designed, and data from 854 nuclear regions were obtained and analyzed from 209 specimens. Maximum likelihood and coalescent approaches were used to estimate the genus phylogeny for 157 diploid samples.</p> <p><em>Key results</em>: Although DNAs from older specimens were both more fragmented and produced fewer sequencing reads, there was no relationship between specimen age and our ability to obtain sufficient data at the target loci. The <em>Solidago</em> phylogeny was generally well supported, with 88/155 (57%) nodes receiving ≥95% bootstrap support. <em>Solidago</em> was supported as monophyletic, with <em>Chrysoma</em> <em>pauciflosculosa</em> identified as sister. A clade comprising <em>Solidago</em> <em>ericameriodes</em>, <em>Solidago</em> <em>odora</em>, and <em>Solidago</em> <em>chapmanii</em> was identified as the earliest diverging <em>Solidago</em> lineage. The previously segregated genera <em>Brintonia</em> and <em>Oligoneuron</em> were identified as placed well within <em>Solidago</em>. These and other phylogenetic results were used to establish four subgenera and fifteen sections within the genus.</p> <p><em>Conclusions</em>: The combination of expansive herbarium sampling and hybrid-sequence capture data allowed us to quickly and rigorously establish the evolutionary relationships within this difficult, species-rich group.</p>
Exome sequencing of a hybrid pine species complex on the Qinghai-Tibetan Plateau
<p>This study investigates the evolutionary history of <em>Pinus</em> <em>densata</em> on the Qinghai-Tibetan Plateau (QTP) and genomic heterogeneity across a zone of species transition to understand contemporary dynamics of selection and evolution of species barriers. We analyzed the genetic diversity in a range-wide collection of <em>P. densata</em> and representative populations of its progenitors <em>P. tabuliformis</em> and <em>P. yunnanensis</em> using 40,000 exome probe capture sequencing.</p>
Solidago hybrid-sequence capture probe set
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Exome sequencing of a hybrid pine species complex on the Qinghai-Tibetan Plateau
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Data from: Genetic incompatibilities in reciprocal hybrids between populations of Tigriopus californicus with low to moderate mitochondrial sequence divergence
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Data from: Development of diagnostic microsatellite markers from whole-genome sequences of Ammodramus sparrows for assessing admixture in a hybrid zone
Studies of hybridization and introgression and, in particular, the identification of admixed individuals in natural populations benefit from the use of diagnostic genetic markers that reliably differentiate pure species from each other and their hybrid forms. Such diagnostic markers are often infrequent in the genomes of closely related species, and genomewide data facilitate their discovery. We used whole-genome data from Illumina HiSeqS2000 sequencing of two recently diverged (600,000 years) and hybridizing, avian, sister species, the Saltmarsh (Ammodramus caudacutus) and Nelson's (A. nelsoni) Sparrow, to develop a suite of diagnostic markers for high-resolution identification of pure and admixed individuals. We compared the microsatellite repeat regions identified in the genomes of the two species and selected a subset of 37 loci that differed between the species in repeat number. We screened these loci on 12 pure individuals of each species and report on the 34 that successfully amplified. From these, we developed a panel of the 12 most diagnostic loci, which we evaluated on 96 individuals, including individuals from both allopatric populations and sympatric individuals from the hybrid zone. Using simulations, we evaluated the power of the marker panel for accurate assignments of individuals to their appropriate pure species and hybrid genotypic classes (F1, F2, and backcrosses). The markers proved highly informative for species discrimination and had high accuracy for classifying admixed individuals into their genotypic classes. These markers will aid future investigations of introgressive hybridization in this system and aid conservation efforts aimed at monitoring and preserving pure species. Our approach is transferable to other study systems consisting of closely related and incipient species.
Modeling Sequences of Earthquakes and Aseismic Slip (SEAS) in Elasto-Plastic Fault Zones With a Hybrid Finite Element Spectral Boundary Integral Scheme
<p>This repository contains the results of 2D simulations of the earthquake cycles accounting for off-fault plasticity.</p> <p>Folder Case1 contains the slip rate and time history for all simulations with cohesion c = 47 MPa</p> <p>Folder Case2 contains the slip rate and time history for all simulations with cohesion c = 25 MPa</p> <p>the mat files contain equivalent plastic strain of each element stored at the start and end of each event with element connectivity and node coordinates.</p>
Data from: Inconsistency between morphological traits and ancestry of individuals in the hybrid zone between two Rhododendron japonoheptamerum varieties revealed by a genotyping-by-sequencing approach
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Data from: Restriction site-associated DNA sequencing generates high-quality single nucleotide polymorphisms for assessing hybridization between bighead and silver carp in the United States and China
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.