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423 results for “Haplotypes”
Mitogenome alignment of 159 unique haplotypes representing 455 individual killer whales
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A haplotype-led approach to increase the precision of wheat breeding
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Borrelia infection in bank voles Myodes glareolus is associated with specific DQB haplotypes which affect allelic divergence within individuals
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Data from: Symbiont infection and psyllid haplotype influence phenotypic plasticity during host switching events
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Determining haploblocks and haplotypes in the MAGIC winter wheat population WM-800 based on the wheat 15k Infinium and the 135k Affymetrix SNP arrays
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Data from: Non-random association of MHC-I alleles in favor of high diversity haplotypes in wild songbirds revealed by computer-assisted MHC haplotype inference using the R package MHCtools
<p><strong>Data set from:</strong></p> <p>Roved J., Hansson B., Stervander, M., Hasselquist D., & Westerdahl H. (2020). Non-random association of MHC-I alleles in favor of high diversity haplotypes in wild songbirds revealed by computer-assisted MHC haplotype inference using the R package MHCtools.</p>
Transfer learning enables prediction of CYP2D6 haplotype function
<p>This data here were used to train the models described in the manuscript "Transfer learning enables prediction of CYP2D6 haplotype function". The deep learning model described predicts metabolic function of <em>CYP2D6</em> star alleles. It uses two pretraining steps, first with simulated data, then with sequence data collected from liver microsomes, and finally using sequence data for <em>CYP2D6</em> star alleles.</p> <p> </p> <p>simulated_cyp2d6_diplotypes.tar.gz - This file contains sequence data and labels for simulated <em>CYP2D6 </em>data used in the first training step</p> <p>dalton_2019_cyp2d6_microsomes.txt - This file contains summary statistic data for liver microsome data used in the second pretraining step (originally from <a href="https://doi.org/10.1111/cts.12695">https://doi.org/10.1111/cts.12695)</a></p> <p>star_samples.vcf - This file contains sequence data for <em>CYP2D6 </em>star alleles derived from PharmVar (https://www.pharmvar.org/gene/CYP2D6) used in the final training step.</p>
Diversification or collapse of self-incompatibility haplotypes as a rescue process
In angiosperm self-incompatibility systems, pollen with an allele matching the pollen recipient at the self-incompatibility locus is rejected. Extreme allelic polymorphism is maintained by frequency-dependent selection favoring rare alleles. However, two challenges result in a "chicken-egg"problem for the spread of a new allele (a tightly linked haplotype in this case) under the widespread "collaborative non-self recognition" mechanism. A novel pollen-function mutation alone would merely grant compatibility with a nonexistent style-function allele: a neutral change at best. A novel pistil-function mutation alone could only be fertilized by pollen with a nonexistent pollen-function allele: a deleterious change that would eliminate all seed set. However, a pistil-function mutation complementary to a previously neutral pollen mutation may spread if it restores self-incompatibility to a self-compatible intermediate. We show that novel haplotypes can also drive elimination of existing ones with fewer siring opportunities. We calculate relative probabilities of increase and collapse in haplotype number given the initial collection of incompatibility haplotypes and the population gene conversion rate. Expansion in haplotype number is possible when population gene conversion rate is large, but large contractions are likely otherwise. A Markov chain model derived from these expansion and collapse probabilities generates a stable haplotype number distribution in the realistic range of 10--40 under plausible parameters. However, smaller populations might lose many haplotypes beyond those lost by chance during bottlenecks.
Genome-wide haplotype counting in diatoms S. robusta and P. tricornutum - processed datasets
<p><strong>Datasets used for genome-wide haplotype counting in <em>S. robusta</em> and <em>P. tricornutum</em> next-generation sequencing data.</strong></p> <p>For <em>S. robusta</em> and <em>P. tricornutum </em>genome-wide haplotype counting, reliable SNPs set was first identified in ILLUMINA short-read sequencing datasets and then used for counting of the number of haplotypes in the PacBio RS II and MinION long reads. The ILLUMINA and PacBio data of <em>S. robusta</em> were downloaded from <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB36614">https://www.ebi.ac.uk/ena/browser/view/PRJEB36614</a> and ILLUMINA and Minion data of <em>P. tricornutum</em> were downloaded from <a href="https://www.ebi.ac.uk/ena/browser/view/PRJNA487263">https://www.ebi.ac.uk/ena/browser/view/PRJNA487263</a>.</p> <p>Reference genome assembly for<em> S. robusta</em>: CAICTM010000001-CAICTM010004752 (European Nucleotide Archive) and</p> <p>Reference genome assembly for<em> P. tricornutum</em>: GCA_000150955.2 (European Nucleotide Archive).</p> <p>Uploaded files: </p> <p>-.bam files containing S. robusta PacBio self-corrected CCS reads aligned to reference and processed and P. tricornutum self-corrected MinION reads aligned to reference and processed: </p> <p><em>S_robusta_aligned_corrected_PacBio_reads.bam</em></p> <p><em>P_tricornutum_aligned_corrected_MinION_reads.bam</em></p> <p>-.table files with selected reliable SNPs used for haplotype counting with CHROM, POSITION, REFERENCE and ALTERNATIVE allele </p> <p><em>S_robusta_SNPs.table</em></p> <p><em>P_tricornutum_SNPs.table</em></p> <p> </p>
Recurrent evolution of two competing haplotypes in an insect DNA virus
<p>Hosts and viruses are constantly evolving in response to each other: as hosts attempt to suppress the virus, the virus attempts to evade and suppress the host's immune system. This arms race results in the evolution of novel pathways in both the host and virus to gain the upper hand. Here we describe the coevolution between <i>Drosophila </i>species and a common and virulent DNA virus. We identify two distinct viral types that differ 100-fold in viral titer in infected individuals, with similar effects across multiple species. Our analysis suggests that one of the viral types appears to have recurrently evolved at least 4 times in the past ~30,000 years, including in another geographically distinct species, due to the high effective mutation rate which increases with titer. The higher titer viral type is associated with suppression of the host immune system and an increased transmission rate compared to the low viral titer type. Both types are maintained in all populations, likely due to an increased virulence in the high titer type creating a trade-off between effective transmission and virulence and resulting in nearly equal reproduction rates (R<sub>0</sub>) in both types. Together these results suggest that the reciprocal selective pressures caused by the co-evolution between host and virus has resulted in this recurrently evolving relationship.</p>
DNA sequences for six chloroplast loci concatenated, representing haplotypes found in Colocasia esculenta, and closely related Araceae
<p><span>As an ancient clonal root and leaf crop, taro (<i>Colocasia esculenta</i>) is highly polymorphic with uncertain genetic and geographic origins. We explored chloroplast DNA variation in wild and cultivated taros and other <i>Colocasia</i> species, and found cultivated taro to be polyphyletic, with tropical and temperate clades originating in Southeast Asia. A third clade was found exclusively in wild populations from Southeast Asia to Australia and Papua New Guinea. Our findings do not support the hypothesis of taro domestication in Papua New Guinea. </span></p>
Data from: Reticulate evolution, ancient chloroplast haplotypes, and rapid radiation of the Australian plant genus Adenanthos (Proteaceae)
<p><span><span><span><span><span><span><span><span><span><span><span>Cytonuclear discordance, commonly detected in phylogenetic studies, is often attributed to hybridisation and/or incomplete lineage sorting (ILS). New sequencing technologies and analytical approaches can provide new insights into the relative importance of these processes. Hybridisation has previously been reported in the Australian endemic plant genus <i>Adenanthos </i>(Proteaceae). Like many Australian genera, <i>Adenanthos</i> is of relatively ancient origin, and provides an opportunity to examine long-term evolutionary consequences of gene flow between lineages. Using a hybrid capture approach, we assembled densely sampled low-copy nuclear and plastid DNA sequences for <i>Adenanthos</i>, inferred its evolutionary history, and used a Bayesian posterior predictive approach and coalescent simulations to assess relative contributions of hybridisation and ILS to cytonuclear discordance. Our analyses indicate that strong incongruence detected between our plastid and nuclear phylogenies is not only the result of ILS, but also result from extensive ancient introgression as well as recent chloroplast capture and introgression between extant <i>Adenanthos </i>species<i>. </i>The deep reticulation was also detected from long-persisting chloroplast haplotypes shared between evolutionarily distant species. These haplotypes may have persisted for over 12 Ma in localised populations across southwest Western Australia, indicating that the region is not only an important area for old endemic lineages and accumulation of species, but is also characterized by persistence of high genetic diversity. Deep introgression in <i>Adenanthos</i> coincided with the rapid radiation of the genus during the Miocene, a time when many Australian temperate plant groups radiated in response to large-scale climatic change. This study suggests that ancient introgression may play an important role in the evolution of the Australian flora more broadly. </span></span></span></span></span></span></span></span></span></span></span></p>
FIGURE 4. Combined haplotype networks from CytB data for Laminatubus paulbrooksi n in Laminatubus (Serpulidae, Annelida) from eastern Pacific hydrothermal vents and methane seeps, with description of two new species
FIGURE 4. Combined haplotype networks from CytB data for Laminatubus paulbrooksi n. sp. (top) from Pacific Costa Rica margin and Gulf of California (Mexico) localities and L. joycebrooksae n. sp. (bottom) from Costa Rica. There was little variability among the L. joycebrooksae n. sp. sequences and a distinct break to L. paulbrooksi n. sp. This corresponds to a minimum 6.4% uncorrected distance. Laminatubus paulbrooksi n. sp. showed marked intraspecific variability with distinct breaks among the three main sites; Costa Rica (9°N), Pescadero (23°N) and Guaymas Basin (27°N). * indicates the holotypes for L. paulbrooksi n. sp. and L. joycebrooksae n. sp. respectively.
Data from: Horizontal Transmission of the Heritable Protective Endosymbiont Hamiltonella defensa Depends on Titre and Haplotype
<p></p><p>Secondary endosymbionts of aphids have an important ecological and evolutionary impact on their host, as they provide resistance to natural enemies but also reduce the host's lifespan and reproduction. While secondary symbionts of aphids are faithfully transmitted from mother to offspring, they also have some capacity to be transmitted horizontally between aphids. Here we explore whether 11 isolates from 3 haplotypes of the secondary endosymbiont Hamiltonella defensa differ in their capacity for horizontal transmission. These isolates vary in the protection they provide against parasitoid wasps as well as the costs they inflict on their host, Aphis fabae. We simulated natural horizontal transmission through parasitoid wasps by stabbing aphids with a thin needle and assessed horizontal transmission success of the isolates from one shared donor clone into three different recipient clones. Specifically, we asked whether potentially costly isolates reaching high cell densities in aphid hosts are more readily transmitted through this route. This hypothesis was only partially supported. While transmissibility increased with titre for isolates from two haplotypes, isolates of the H. defensa haplotype 1 were transmitted with greater frequency than isolates of other haplotypes with comparable titres. Thus, it is not sufficient to be merely frequent—endosymbionts might have to evolve specific adaptations to transmit effectively between hosts.</p><p></p>
Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color
<p>The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Access to pan-genome information greatly facilitates the assessment of structural variations and rapid candidate gene identification. Here, we identified the <i>red glume 1</i> (<i>Rg-B1</i>) gene using association genetics and haplotype analyses in ten reference-grade wheat genomes. Glume color is an important trait to characterize wheat cultivars. Red glumes are frequent among Central European spelt, a dominant wheat subspecies in Europe before the 20<sup>th</sup> century. We used genotyping-by-sequencing to characterize a global diversity panel of 267 spelt accessions, which provided evidence for two independent introductions of spelt into Europe. A single region at the <i>Rg-B1</i> locus on chromosome 1BS was associated with glume color in the diversity panel. Haplotype comparisons across ten high-quality wheat genomes revealed a <i>MYB</i> transcription factor as candidate gene. We found extensive haplotype variation across the ten cultivars, with a particular group of <i>MYB</i> alleles that was conserved in red glume wheat cultivars. Genetic mapping and transient infiltration experiments allowed us to validate this particular <i>MYB</i> transcription factor variants. Our study demonstrates the value of multiple high-quality genomes to rapidly resolve copy number and haplotype variations in regions controlling agriculturally important traits.</p>
Data from: PopART: full-feature software for haplotype network construction
1. Haplotype networks are an intuitive method for visualising relationships between individual genotypes at the population level. 2. Here, we present popart, an integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication-ready figure production. 3. popart also provides a platform for the implementation and distribution of new network-based methods – we describe one such new method, integer neighbour-joining. 4. The software is open source and freely available for all major operating systems.
Data from: The genetic structure of Asian corn borer, Ostrinia furnacalis, populations in China: haplotype variance in Northern populations and potential impact on management of resistance to transgenic maize
Asian corn borer, Ostrinia furnacalis (Guenée), is a severe pest that infests cultivated maize in the major production regions of China. Populations show genotype-by-environment variation in voltinism, such that populations with a single generation (univoltine) are fixed in Northern China where growing seasons are short. Low genetic differentiation was found among samples from 33 collection sites across China and one site from North Korea (n = 1,673) using variation at 6 nuclear microsatellite loci (ENA corrected global FST = 0.020; P-value < 0.05). Analysis of molecular variance (AMOVA) indicated that geographic region, number of generations or voltinism accounted for < 0.38% of the total genetic variation at nuclear loci and was corroborated by clustering of co-ancestries among genotypes using the program STRUCTURE. In contrast, a mitochondrial haplotype network identified four distinct clusters, where 70.5% of samples from univoltine populations were within a single group. Univoltine populations were also placed into a unique cluster using Population Graph and Principal Component analyses, which showed significant differentiation with multivoltine populations (ST = 0.400; P-value < 0.01). This study suggests that gene flow among O. furnacalis in China may be high among regions, with the exception of northeastern localities. Haplotype variation may be due to random genetic drift resulting from partial reproductive isolation between univoltine and multivoltine O. furnacalis populations. Such reproductive isolation might impact the potential spread of alleles that confer resistance to transgenic maize in China.
Data from: Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers
Detecting positive selection using genomic data is critical to understanding the role of adaptive evolution. Of particular interest in this context is sex chromosomes since they are thought to play a special role in local adaptation and speciation. We sought to circumvent the challenges associated with statistical phasing when using haplotype-based statistics in sweep scans by benefitting from that whole-chromosome haplotypes of the sex chromosomes can be obtained by re-sequencing of individuals of the hemizygous sex. We analyzed whole Z chromosome haplotypes from 100 females from several populations of four black and white flycatcher species (in birds, females are ZW and males ZZ). Based on integrated haplotype score (iHS) and number of segregating sites by length (nSL) statistics, we found strong and frequent haplotype structure in several regions of the Z chromosome in each species. Most of these sweep signalswere population-specific, with essentially no evidence for regions under selection shared among species. Some completed sweeps were revealed by the cross-population extended haplotype homozygosity (XP-EHH) statistic. Importantly, by using statistically phased Z chromosome data from re-sequencing of males, we failed to recover the signals of selection detected in analyses based on whole-chromosome haplotypes from females; instead, what likely represent false signals of selection were frequently seen. This highlights the power issues in statistical phasing and cautions against conclusions from selection scans using such data. The detection of frequent selective sweeps on the avian Z chromosome supports a large role of sex chromosomes in adaptive evolution.
Data from: The influence of selection on MHC DQA and DQB haplotypes in the endemic New Zealand Hector's and Māui dolphins
Strong balancing selection on the Major Histocompatibility Complex (MHC) can lead to different patterns in gene frequencies and neutral genomic variation within species. We investigated diversity and geographic structure of MHC genes DQA and DQB, as well as their inferred functional haplotypes, from two regional populations (East and West Coast) of the endangered Hector's dolphin (Cephalorhynchus hectori hectori) and the critically endangered Māui dolphin (Cephalorhynchus hectori maui) (West Coast, North Island), and contrasted these results with patterns from neutral microsatellites. The Māui had the lowest number of alleles for DQA (2) and DQB (3), consistent with strong genetic drift acting on this remnant population. However, the two retained DQA alleles are amongst the most divergent combinations of all four alleles found across the Hector's metapopulation, potentially reflecting the retention of divergent alleles due to balancing selection. The high frequency of the divergent DQB04 allele also gave this population the highest nucleotide diversity for DQB. Strong differentiation was evident for DQA, DQB, and DQA-DQB haplotypes between the regional populations of Hector's dolphins (FST>0.213) and both subspecies (FST>0.311). Differentiation was generally greater than observed at neutral microsatellite loci, suggesting the influence of selection between geographically proximate East and West Coast populations. This might be the result of spatial differences in directional selection on those opposite coastlines. Additionally, measures of the ratio of non-synonymous to synonymous substitutions (dN/dS) were consistent with balancing selection over evolutionary time. Together, these results suggest a complex interplay of balancing selection, directional selection, local fidelity, and genetic drift.
Data from: No evidence for MHC class II-based non-random mating at the gametic haplotype in Atlantic salmon
Genes of the major histocompatibility complex (MHC) are a likely target of mate choice because of their role in inbreeding avoidance and potential benefits for offspring immunocompetence. Evidence for female choice for complementary MHC alleles among competing males exists both for the pre- and the postmating stages. However, it remains unclear whether the latter may involve non-random fusion of gametes depending on gametic haplotypes resulting in transmission ratio distortion or non-random sequence divergence among fused gametes. We tested whether non-random gametic fusion of MHC-II haplotypes occurs in Atlantic salmon Salmo salar. We performed in vitro fertilizations that excluded interindividual sperm competition using a split family design with large clutch sample sizes to test for a possible role of the gametic haplotype in mate choice. We sequenced two MHC-II loci in 50 embryos per clutch to assess allelic frequencies and sequence divergence. We found no evidence for transmission ratio distortion at two linked MHC-II loci, nor for non-random gamete fusion with respect to MHC-II alleles. Our findings suggest that the gametic MHC-II haplotypes play no role in gamete association in Atlantic salmon and that earlier findings of MHC-based mate choice most likely reflect choice among diploid genotypes. We discuss possible explanations for these findings and how they differ from findings in mammals.
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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.