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423 results for “t haplotype”
Data from: Lack of evidence for selection favouring MHC haplotypes that combine high functional diversity
High rates of gene duplication and the highest levels of functional allelic diversity in vertebrate genomes are the main hallmarks of the major histocompatibility complex (MHC), a multigene family with a primordial role in pathogen recognition. The usual tight linkage among MHC gene duplicates may provide an opportunity for the evolution of haplotypes that associate functionally divergent alleles and thus grant the transmission of optimal levels of diversity to coming generations. Even though such associations may be a crucial component of disease resistance, this hypothesis has been given little attention in wild populations. Here, we leveraged pedigree data from a barn owl (Tyto alba) population to characterize MHC haplotype structure across two MHC class I (MHC-I) and two MHC class IIB (MHC-IIB) duplicates, in order to test the hypothesis that haplotypes' genetic diversity is higher than expected from randomly associated alleles. After showing that MHC loci are tightly linked within classes, we found limited evidence for shifts towards MHC haplotypes combining high diversity. Neither amino acid nor functional within-haplotype diversity were significantly higher than in random sets of haplotypes, regardless of MHC class. Our results therefore provide no evidence for selection towards high-diversity MHC haplotypes in barn owls. Rather, high rates of convergent evolution may constrain the evolution of high-diversity haplotypes at MHC-I, while, in contrast, for MHC-IIB, fixed differences among loci may provide barn owls with already optimized functional diversity. This suggests that at the MHC-I and MHC-IIB, respectively, different evolutionary dynamics may govern the evolution of within-haplotype diversity.
Frequent paternal mitochondrial inheritance and rapid haplotype frequency shifts in copepod hybrids
<p>Mitochondria are assumed to be maternally inherited in most animal species, and this foundational concept has fostered advances in phylogenetics, conservation, and population genetics. Like other animals, mitochondria were thought to be solely maternally inherited in the marine copepod <i>Tigriopus californicus, </i>which has served as a useful model for studying mitonuclear interactions, hybrid breakdown, and environmental tolerance. However, we present PCR, Sanger sequencing, and Illumina Nextera sequencing evidence that extensive paternal mitochondrial DNA (mtDNA) transmission is occurring in inter-population hybrids of <i>T. californicus</i>. PCR on four types of crosses between three populations (total sample size of 376 F1 individuals) with 20% genome-wide mitochondrial divergence showed 2% to 59% of F1 hybrids with both paternal and maternal mtDNA, where low and high paternal leakage values were found in different cross directions of the same population pairs. Sequencing methods further verified nucleotide similarities between F1 mtDNA and paternal mtDNA sequences. Interestingly, the paternal mtDNA in F1s from some crosses inherited haplotypes that were uncommon in the paternal population. Compared to some previous research on paternal leakage, we employed more rigorous methods to rule out contamination and false detection of paternal mtDNA due to non-functional nuclear mitochondrial DNA fragments. Our results raise the potential that other animal systems thought to only inherit maternal mitochondria may also have paternal leakage, which would then affect the interpretation of past and future population genetics or phylogenetic studies that rely on mitochondria as uniparental markers.</p>
Genome assembly of a commercial tomato hybrid (Funtelle) for haplotyping an introgression that confers TMV resistance
<p>Plant crop genome assemblies facilitate the characterization of genetically diverse cultivated and wild germplasm. </p> <p>The cultivated tomato (Solanum lycopersicum) has been improved through the introgression of genetic material from related wild species, including genetic resistance to pandemic strains of Tobacco Mosaic virus (TMV) and tomato mosaic virus (ToMV) originating from Solanum peruvianum. The exact size and the structure of the introgression from Solanum peruvianum containing the TMV/ToMV resistance gene (Tm-2^2 gene) has remained unknown, although it was known to include at least half of the physical length of chromosome 9.<br> <br> We selected a commercial cultivated tomato cultivar called Funtelle, which contains the Tm-2^2 resistance introgression in a hemizygous state, and generated Oxford Nanopore sequencing reads. Using Flye, a genome assembly tool, we assembled the reads. The assembled DNA sequences (contigs) from the Flye assembly are made available here. Subsequently, as described in detail in the associated manuscript, we made use of the assembled contigs for comprehensive haplotyping of the chromosome 9 introgression region in this commercial hybrid.<br> <br> The raw Oxford Nanopore sequencing reads of the Funtelle variety are available via the European Nucleotide Archive under project number PRJEB44956.</p>
FIGURE 5. Haplotype analysis for C in The Oracle of Delphi-a molecular phylogenetic approach to Greek Cordulegaster Leach in Brewster, 1815 (Odonata: Anisoptera: Cordulegastridae)
FIGURE 5. Haplotype analysis for C. heros (TCS-network made in PopART 1.7).
FIGURE 6. Haplotype analysis for the Clade II in The Oracle of Delphi-a molecular phylogenetic approach to Greek Cordulegaster Leach in Brewster, 1815 (Odonata: Anisoptera: Cordulegastridae)
FIGURE 6. Haplotype analysis for the Clade II (TCS-network made in PopART 1.7).
Haplotype-phasing of long-read HiFi data to enhance structural variant detection through a Skip-Gram model
<p>Example dataset for DipPAV</p>
FIGURE 22. Haplotype array for A in DNA barcodes reveal different speciation scenarios in the four North American Anthocharis Boisduval, Rambur, [Duménil] & Graslin, [1833] (Lepidoptera: Pieridae: Pierinae: Anthocharidini) species groups
FIGURE 22. Haplotype array for A. lanceolata group.
Datasets used in "Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat"
Open the record for dataset details and reuse information.
Fig. 1 in Haplotype variation in the Physa acuta group (Basommatophora): genetic diversity and distribution in Serbia Abstract
Fig. 1: Distribution of P. acuta group in Canada, North America, Mexico and Cuba (A), Europe (B) and Serbia (C). Distribution of P. acuta in North and Central America (white circles) was compiled from the data of Wethington et al. (2009), Wethington & Guralnick (2004) and Kraus et al. (2014). The European (white circles) range is based on Wethington & Lydeard (2007), data and distribution in Serbia is based on Novaković (2014, black circles), and on our field sampling data (white circles).
Fig. 4 in Variation In Cone And Seed Morphology Traits Among The Mitochondrial Dna Haplotypes Of Scots Pine (Pinus Sylvestris L.)
Fig. 4. Dependence of seed number per cone on cone width for the type A and type B mitotypes of Scots pine. Individual cone values are shown.
Fig. 3. Maximum likelihood phylogeny for 72 unique haplotypes obtained from O. hatcheri, O in Populations of Odontesthes (Teleostei: Atheriniformes) in the Andean region of Southern South America: body shape and hybrid individuals
Fig. 3. Maximum likelihood phylogeny for 72 unique haplotypes obtained from O. hatcheri, O. bonariensis, and O. smitti. Haplotype labels indicate their sampling locality (as explained in Fig. 1 and Table 1) and the number of individuals (in parentheses). Several common haplotypes were recovered from several individuals from the same or different localities (most significantly haplotype 5). Monophyly of haplotypes from each species is supported by 100% bootstrap values, and two groups of O. hatcheri haplotypes (from EPU and CDP, indicated by heavier lines) also received strong bootstrap support. All other nodes were weakly supported by bootstrap analyses. *: presumptive hybrids individuals identified on meristic and morphological characters (Table 2).
Figures 2–3. Mitochondrial cytochrome c oxidase subunit 1 in Molecular confirmation of the occurrence of Anguilla interioris (Actinopterygii: Anguilliformes) in North Maluku of Indonesia and mitochondrial DNA haplotype diversity among existing specimens
Figures 2–3. Mitochondrial cytochrome c oxidase subunit 1 (CO1) 551 bp sequence analyses. (2) Phylogenetic analysis based on maximum likelihood algorithm with the sample codes, GenBank or BOLD accession numbers and sample sites shown. Bootstrap percentages are shown at the tree nodes. (3) Haplotype network with the haplotypes labelled as H1 to H9. The circle size is proportional to the number of samples, and different sample sites are represented by different colours. Small white circle represents median vector which is the hypothesized or missing haplotype. Each dash on the line symbolizes one mutational step.
Figure 2. CAD haplotype network. TCS Network based off 814 in Low Variation in Nuclear and Mitochondrial DNA Inhibits Resolution of Invasion Pathways across the Pacific for the Coconut Rhinoceros Beetle (Scarabeidae: Oryctes rhinoceros)
Figure 2. CAD haplotype network. TCS Network based off 814 base pairs of the CAD gene region from a total of 117 samples (8 to 39 from any given location) representing 234 total haplotypes. Hash marks represent a single base pair change. A PHASE algorithm was used to generate haplotypes from ambiguities present in the sequence data of a multi-copy nuclear gene, resulting in twice as many haplotypes as samples.
Data from: Contribution of Asian haplotype of KCNJ18 to susceptibility to and ethnic differences in thyrotoxic periodic paralysis
Context and Objectives: Thyrotoxic periodic paralysis (TPP) is an acute complication of thyrotoxicosis that can be lethal. TPP is relatively rare in Caucasians but often affects young males in East Asian populations. This study aimed to clarify the contribution of KCNJ18 to susceptibility to TPP in East Asian populations. Participants and Methods: The study comprised 635 participants including 13 Japanese patients with TPP, 208 Japanese patients with Graves' disease without TPP, and 414 healthy control subjects from the Japanese [n=208], Korean [n=111], and Caucasian populations [n=95]. DNA samples from 29 subjects (13 with TPP, 8 with Graves' disease, and 8 controls) were sequenced for KCNJ18, and all subjects (n=635) were genotyped for six variants of KCNJ18 and a polymorphism of KCNJ2 (rs312691). Results: Six single nucleotide variants (SNVs) with amino acid substitutions were identified by direct sequencing of KCNJ18. Among these, four SNVs comprised three haplotypes under strong linkage disequilibrium. Haplotype 1 (AAAG) of KCNJ18 was significantly associated with susceptibility to TPP in the Japanese population (odds ratio [95%CI]: 19.6 [1.5–256.9], p=0.013). Haplotype frequencies in the general East Asian (Japanese and Korean) and Caucasian populations differed significantly (Haplotype 1: 80.8% vs. 48.4%, p= 1.1×10-27). Conclusion: A major haplotype of KCNJ18 in East Asian populations is significantly associated with susceptibility to thyrotoxic periodic paralysis. The haplotype is much more frequent in East Asian than Caucasian populations, suggesting its contribution to the high prevalence of TPP in East Asian populations.
Data from: RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling
Reduced representation genome-sequencing approaches based on restriction digestion are enabling large-scale marker generation and facilitating genomic studies in a wide range of model and nonmodel systems. However, sampling chromosomes based on restriction digestion may introduce a bias in allele frequency estimation due to polymorphisms in restriction sites. To explore the effects of this nonrandom sampling and its sensitivity to different evolutionary parameters, we developed a coalescent-simulation framework to mimic the biased recovery of chromosomes in restriction-based short-read sequencing experiments (RADseq). We analysed simulated DNA sequence datasets and compared known values from simulations with those that would be estimated using a RADseq approach from the same samples. We compare these 'true' and 'estimated' values of commonly used summary statistics, π, θw, Tajima's D and FST. We show that loci with missing haplotypes have estimated summary statistic values that can deviate dramatically from true values and are also enriched for particular genealogical histories. These biases are sensitive to nonequilibrium demography, such as bottlenecks and population expansion. In silico digests with 102 completely sequenced Drosophila melanogaster genomes yielded results similar to our findings from coalescent simulations. Though the potential of RADseq for marker discovery and trait mapping in nonmodel systems remains undisputed, our results urge caution when applying this technique to make population genetic inferences.
Data from: Introgression of Chinese haplotypes contributed to the improvement of Danish Duroc pigs
The distribution of Asian ancestry in the genome of Danish Duroc pigs was investigated using whole-genome sequencing data from European wild boars, Danish Duroc, Chinese Meishan and Bamaxiang pigs. Asian haplotypes deriving from Meishan and Bamaxiang occur widely across the genome. Signatures of selection on Asian haplotypes are common in the genome, but few of these haplotypes have been fixed. By defining 50 kb windows with more than 50% Chinese ancestry, which did not exhibit extreme genetic differentiation between Meishan and Bamaxiang as candidate regions, the enrichment of quantitative trait loci in candidate regions support that Asian haplotypes under selection play an important role in contributing genetic variation underlying production, reproduction, meat and carcass, and exterior traits. Gene annotation of regions with the highest proportion of Chinese ancestry revealed genes of biological interest, such as NR6A1. Further haplotype clustering analysis suggested that a haplotype of Chinese origin around the NR6A1 gene was introduced to Europe and then underwent a selective sweep in European pigs. Besides, functional genes in candidate regions, such as AHR and PGRMC2, associated with fertility, and SAL1, associated with meat quality were identified. Our results demonstrate the contribution of Asian haplotypes to the genomes of European pigs. Findings herein facilitate further genomic studies such as genome-wide association study and genomic prediction by providing ancestry information of variants.
Data from: Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees
Understanding the genetic basis of adaption is a central task in biology. Populations of the honey bee Apis mellifera that inhabit the mountain forests of East Africa differ in behavior and morphology from those inhabiting the surrounding lowland savannahs, which likely reflects adaptation to these habitats. We performed whole genome sequencing on 39 samples of highland and lowland bees from two pairs of populations to determine their evolutionary affinities and identify the genetic basis of these putative adaptations. We find that in general, levels of genetic differentiation between highland and lowland populations are very low, consistent with them being a single panmictic population. However, we identify two loci on chromosomes 7 and 9, each several hundred kilobases in length, which exhibit near fixation for different haplotypes between highland and lowland populations. The highland haplotypes at these loci are extremely rare in samples from the rest of the world. Patterns of segregation of genetic variants suggest that recombination between haplotypes at each locus is suppressed, indicating that they comprise independent structural variants. The haplotype on chromosome 7 harbors nearly all octopamine receptor genes in the honey bee genome. These have a role in learning and foraging behavior in honey bees and are strong candidates for adaptation to highland habitats. Molecular analysis of a putative breakpoint indicates that it may disrupt the coding sequence of one of these genes. Divergence between the highland and lowland haplotypes at both loci is extremely high suggesting that they are ancient balanced polymorphisms that greatly predate divergence between the extant honey bee subspecies.
Reproductive fitness of Callosobruchus maculatus mtDNA haplotypes
<p><span><span><span><span><span><span><span><span><span><span><span>Mitochondrial DNA (mtDNA) consists of few but vital maternally inherited genes that interact closely with nuclear genes to produce cellular energy. How important mtDNA polymorphism is for adaptation is still unclear. The assumption in population genetic studies is often that segregating mtDNA variation is selectively neutral. This contrasts with empirical observations of mtDNA haplotypes affecting fitness related traits and thermal sensitivity, and latitudinal clines in mtDNA haplotype frequencies. Here we experimentally test whether ambient temperature affects selection on mtDNA variation, and whether such thermal effects are influenced by intergenomic epistasis due to interactions between mitochondrial and nuclear genes, using replicated experimental evolution in <i>Callosobruchus maculatus</i> seed beetle populations seeded with a mixture of different mtDNA haplotypes. We also test for sex-specific consequences of mtDNA evolution on reproductive success, given that mtDNA mutations can have sexually antagonistic fitness effects. Our results demonstrate natural selection on mtDNA haplotypes, with some support for thermal environment influencing mtDNA evolution through mitonuclear epistasis. The changes in male and female reproductive fitness were both aligned with changes in mtDNA haplotype frequencies, suggesting that natural selection on mtDNA is sexually concordant in stressful thermal environments. We discuss the implications of our findings for the evolution of mtDNA. </span></span></span></span></span></span></span></span></span></span></span></p>
Figure 3. Bayesian phylogram for cytochrome b sequences. Upper Sacramento River basin haplotypes are distributed among clades A–D in Extensive diversification of pebblesnails (Lithoglyphidae: Fluminicola) in the upper Sacramento River basin, northwestern USA
Figure 3. Bayesian phylogram for cytochrome b sequences. Upper Sacramento River basin haplotypes are distributed among clades A–D. Posterior probability values ≥ 90% are shown. Upper Sacramento River basin lineages newly discovered in this study are highlighted by the larger font. Specimen codes are from Table 1.
Assemblies generated in the paper "phasebook: haplotype-aware de novo assembly of diploid genomes from long reads"
<p>Assemblies generated in the paper "phasebook: haplotype-aware de novo assembly of diploid genomes from long reads"</p>
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.