• Analysis of ancestral haplotype blocks revealed that extant mainland populations (i) admixed widely irrespective of ancestry, although admixtures between populations was not always symmetric, and (ii) this practice was rapidly replaced by endogamy about 70 generations ago, among upper castes and Indo-European speakers predominantly. (blogspot.com)
  • For SoS, we used two haplotype-based tests to compare haplotype length variation within admixed and between admixed and East African Shorthorn Zebu cattle populations. (sruc.ac.uk)
  • Haplotype Blocks in Small Populations. (sigmod.org)
  • Moreover, and unlike these approaches, we do not require any prior knowledge of the relationship between sub-groups of donor reference haplotypes and the unseen mixing ancestral populations. (ox.ac.uk)
  • and also offers a way to analyze variation in geographic ancestry without assuming the existence of discrete ancestral populations. (elifesciences.org)
  • Whilst introgression of the B. napus chloroplast type in the wild and weedy B. rapa populations has been proposed by other studies, the presence of this haplotype within the two brocoletto accessions is unexplained. (biomedcentral.com)
  • This contrasted sharply with the distribution of mtDNA haplotypes, which in brown bears is famously characterised by abrupt discontinuities between neighbouring populations and by haplotype sharing between populations separated in time and space. (springernature.com)
  • Africa is inhabited by populations that show high levels of genetic diversity compared to most other continental populations today and it is thought to be the ancestral home of modern humans. (biomedcentral.com)
  • African populations have the largest number of population specific autosomal, X-chromosomal and mitochondrial DNA haplotypes with non-African populations having only a subset of the genetic diversity present in Africa [ 1 ]. (biomedcentral.com)
  • Students and professors that were successfully assigned to haplotypes (70% of sequences clustered to a known haplotype with a posterior probability higher than 65%) are plotted as dots on tips corresponding to their mtDNA haplotypes. (biomedcentral.com)
  • however, most studies that have produced these results have relied only on inferences based on mitochondrial DNA. (uni-bielefeld.de)
  • Etruscans and medieval Tuscans share four mitochondrial haplotypes, and serial coalescent simulations show a clear genealogical continuity between them. (blogspot.com)
  • citation needed] Gusfield has made significant contributions to molecular sequence comparison and analysis, phylogenetic tree and phylogenetic network inference, haplotyping in DNA sequences, the multi-state perfect phylogeny problem using chordal graph theory, and fast algorithms for RNA folding. (wikipedia.org)
  • Inferring Piecewise Ancestral History from Haploid Sequences. (sigmod.org)
  • In non-TRD strains like the research genome the sequences look like present only in the (presumed) ancestral Bax inhibitor peptide, negative control Bax inhibitor peptide, negative control location spread over a 158 kb region (R2d1) ~6 Mb distal from your locus (Fig. 1A). (healthandwellnesssource.org)
  • Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model. (auth.gr)
  • Bayesian inference in phylogeny for genome-scale data. (inria.fr)
  • We estimate the phylogeny of Melanobombus species by including three slower-evolving genes to provide more evidence for deeper relationships, to estimate the time calibration of this phylogeny, and to estimate ancestral distributions, all within a Bayesian framework. (mnhn.fr)
  • Specifically, PrioriTree provides a suite of functions to generate input files for-and summarize output from-BEAST analyses for performing robust Bayesian inference, data-cloning analyses and assessing the relative and absolute fit of candidate discrete-geographic (prior) models to empirical datasets. (nfshost.com)
  • Here, we develop a new program Mongrail that implements a full-likelihood Bayesian hybrid inference method that explicitly models linkage and recombination, generating the posterior probability of different F1 or F2 hybrid, or backcross, genealogical classes. (nfshost.com)
  • We propose two new haplotype-sharing methods for identifying disease loci: the haplotype sharing statistic (HSS), which compares length of shared haplotypes between cases and controls, and the CROSS test, which tests whether a case and a control haplotype show less sharing than two random haplotypes. (biomedcentral.com)
  • In conclusion, haplotype sharing methods, particularly the CROSS test, show great promise for identifying disease gene loci. (biomedcentral.com)
  • Several SNP panels for different purposes as well as novel types of molecular markers, such as the microhaplotype loci that are useful for individual identification, ancestry inference, estimating relationships and deconvoluting mixtures, were developed. (mdpi.com)
  • Because single loci are known to be susceptible to stochastic processes (i.e., random genetic drift of ancestral variation), it initially seemed reasonable to assume that the observed discordant signals of the mitogenome and Y chromosome were simply noise resulting from chance effects. (springernature.com)
  • The size of the reduced ancestral haplotype fragments varies as a result of the uneven nature of such recombination and mutation processes. (biomedcentral.com)
  • The five components they speak of are ANI, ASI, AAA (Ancestral Austro-Asiatic), ATB (Ancestral Tibeto-Burman), and a distinct fifth ancestry in the Andaman archipelago. (blogspot.com)
  • This contrasts with an earlier inference of two ancestries based on limited population sampling. (blogspot.com)
  • This allows inference of the demographic history of the species, properties of admixing groups, identification of signatures of natural selection, and may aid disease gene mapping. (ox.ac.uk)
  • Similarly, a comprehensive overview of the demographic history of the brown bear is achieved by integrating the inferences from the four different datasets. (springernature.com)
  • Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks. (auth.gr)
  • An Overview of Combinatorial Methods for Haplotype Inference. (sigmod.org)
  • A Survey of Computational Methods for Determining Haplotypes. (sigmod.org)
  • However, current GRN inference methods require a total ordering of cells along a linear pseudotemporal axis, which is biologically inappropriate since trajectories with branches cannot be reduced to a single time axis. (bilkent.edu.tr)
  • We hypothesize that there is a difference in haplotype patterns between cases and controls at regions associated with the disease and we present two new methods based on this hypothesis: the haplotype-sharing statistic (HSS), which is an improvement of a statistic described by Van der Meulen et al. (biomedcentral.com)
  • The test statistics of these two haplotype-sharing methods will be described and their performance will be compared to standard association methods. (biomedcentral.com)
  • This year, the sophistication of the analysis methods employed was striking, particularly for drawing inferences from subtle differences in human genetic variation. (biomedcentral.com)
  • Gene regulatory network (GRN) inference that incorporates single-cell RNA-seq (scRNA-seq) differentiation trajectories or RNA velocity can reveal causal links between transcription factors and their target genes. (bilkent.edu.tr)
  • CTG expansion & haplotype analysis in DM1 gene in healthy Iranian population. (cdc.gov)
  • The advantage of single-locus tests is that haplotype inference can be avoided. (biomedcentral.com)
  • However, in the current generation the haplotypes will still share a fragment around the disease locus. (biomedcentral.com)
  • Haplotype analysis of the myotonic dystrophy type 1 (DM1) locus in the Korean population. (cdc.gov)
  • The integrated haplotype score (iHS) analysis identified 16 candidate regions for positive selection in the admixed cattle while the between population Rsb test detected 24 divergently selected regions in the admixed cattle compared to East African Shorthorn Zebu. (sruc.ac.uk)
  • ABC analysis and haplotype networks support earlier inferences of a single out-of-Africa colonization event, while a cline of decreasing genetic diversity indicates that Ae. (iita.org)
  • Therefore, association analysis based on haplotypes is believed to be more powerful, in particular if the common disease-common variant theory applies. (biomedcentral.com)
  • The geographic distribution of Y-chromosomal haplotypes proved even less predictable, with individuals from within the same population often having less in common with each other than with individuals thousands of kilometers away. (springernature.com)
  • Inference under discrete-geographic phylodynamic models-which involve many parameters that must be inferred from minimal information-is inherently sensitive to our prior beliefs about the model parameters. (nfshost.com)
  • We present an interactive utility, PrioriTree, to help researchers identify and accommodate prior sensitivity in discrete-geographic inferences. (nfshost.com)
  • High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability. (harvard.edu)
  • There is a need to predict or visualize the intrinsic dynamics of biomolecular structures in order to make inferences on potential mechanisms of function or dysfunction. (bilkent.edu.tr)
  • Here, we introduce Velorama, a novel conceptual approach to causal GRN inference that newly represents scRNA-seq differentiation dynamics as a partial ordering of cells and operates on the directed acyclic graph (DAG) of cells constructed from pseudotime or RNA velocity measurements. (bilkent.edu.tr)
  • For a global revision of Melanobombus species, we use COI barcodes and seek to reduce the risk from localised over-sampling by filtering the data to include only unique haplotypes. (mnhn.fr)
  • Unique haplotypes give more conservative results than unfiltered data, but still increase the number of species in comparison with recent morphological treatments. (mnhn.fr)
  • For the most widespread and variable species-complexes, our revised species improve the match to the patterns expected of species, both for genetic divergence-with-distance and for sympatry, leading to three main inferences. (mnhn.fr)
  • In the last years, protein interactome comparisons have highlighted conserved modules that might represent common functional cores of ancestral origin. (inria.fr)
  • Dutch myotonic dystrophy type 2 patients and a North-African DM2 family carry the common European founder haplotype. (cdc.gov)
  • Parametric Bootstrap for Assessment of Goodness of Fit of Models for Block Haplotype Structure. (sigmod.org)
  • Consequently, inferences under these models are inherently sensitive to our prior assumptions about the model parameters. (nfshost.com)
  • 5%). Subsequent mutations and recombinations in the ancestral haplotype at which the disease mutation occurred shortened the haplotypes that descended from this ancestor. (biomedcentral.com)
  • The most prevalent haplotype (found in 79% of accessions) was not present within the C genome accessions but was found at low frequencies in B. rapa . (biomedcentral.com)