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Fast Bayesian Haplotype Inference Via Context Tree Weighting
[chapter]
Lecture Notes in Computer Science
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We present a new, Bayesian method for inferring haplotypes for unphased genotypes. ...
Specifically, we make use of the Context Tree Weighting algorithm to efficiently compute the posterior probability of any given haplotype assignment; we employ a simulated annealing scheme to rapidly find ...
The Context Tree Weighting Algorithm We apply the CTW algorithm [16] -originally developed for compressing a single binary string -to efficiently evaluate the sum over context trees for haplotype (1 ...
doi:10.1007/978-3-540-87361-7_22
fatcat:563ennrhgzhgxjd5zo3ddx4voy
Approximate Bayesian Computation (ABC) in practice
2010
Trends in Ecology & Evolution
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Hierarchical models are central to modern Bayesian statistics and allow an objective approach to inference. ...
Individuals may represent molecular marker loci, genes, or chromosomes depending on the context. ...
Various approximations to the coalescent allow for fast simulation of recombining haplotypes [89, 90] . ...
doi:10.1016/j.tree.2010.04.001
pmid:20488578
fatcat:4zvdd3x5r5hg3ijsdu5ddccste
An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes
2021
Molecular Ecology
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We summarise the strategies they use to infer demographic history and selection, and discuss some of their limitations. A website listing these methods is available at www.methodspopgen.com. ...
Future versions should allow gene flow inference (e.g., structure; Fast, handles VCF format. ...
frequencies and can be Fast and accurate Outputs a species tree instead of used for pooled data Included in paml. ...
doi:10.1111/mec.15989
pmid:34009688
fatcat:q5ctfy5uvzbu7j24s26ai764me
Phylogeography of a widespread terrestrial vertebrate in a barely-studied Palearctic region: green toads (Bufo viridis subgroup) indicate glacial refugia in Eastern Central Asia
2008
Genetica
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Genetic structure of Bufo pewzowi is strongly affected by landscape: we found three haplotype groups in eastern Kazakhstan, Dzungaria and Tarim Basin, divided by the Tian Shan and Dzungarian Alatau ranges ...
Glacial refugia were inferred in the Tarim Basin (around the Turpan depression), in southern Dzungaria (Urumqui region), at the northern foot of the Tian Shan (Gongnaisi) and perhaps at the Altai range ...
Outgroup weight calculations indicated that clade 1-5 contained the inferred ancestral haplotype (H27, loc. 10). ...
doi:10.1007/s10709-008-9243-0
pmid:18301990
fatcat:qr2g4xsgqjgajdvgyfklfa4dsm
Whole-genome doubling-aware copy number phylogenies for cancer evolution with MEDICC2
[article]
2021
bioRxiv
pre-print
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MEDICC2 can identify WGD events and quantify SCNA burden in single-sample studies and infer phylogenetic trees and ancestral genomes in multi-sample scenarios. ...
While SCNAs can provide a rich source of phylogenetic information, so far no method exists for phylogenetic inference from SCNAs that includes WGD events. ...
After inferring the tree topology, ancestral CNPs at the internal nodes of the tree are inferred using an upward and downward pass on the tree, analogous to Felsenstein's Pruning algorithm for maximum-likelihood ...
doi:10.1101/2021.02.28.433227
fatcat:lpmmiy6tcbbmjkuekfryfp76ne
Hidden Markov Dirichlet process: modeling genetic inference in open ancestral space
2007
Bayesian Analysis
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it also infers the ancestral genetic patterns and offers a highly accurate map of ancestral compositions of modern populations. ...
The problem of inferring the population structure, linkage disequilibrium pattern, and chromosomal recombination hotspots from genetic polymorphism data is essential for understanding the origin and characteristics ...
This nonparametric Bayesian formalism forms the technical foundation of the haplotype modeling and inference algorithms to be developed in this paper. ...
doi:10.1214/07-ba220
fatcat:yn25v527vvgqxbdwjppxf2ehla
Molecular systematics of the trans-Pacific alpine genus Oreomyrrhis (Apiaceae): phylogenetic affinities and biogeographic implications
2005
American Journal of Botany
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The structure of the ITS haplotype network suggests that a rapid range expansion via long-distance dispersal had been crucial in generating the trans-Pacific disjunction of Oreomyrrhis. ...
Phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian inference revealed that species of Oreomyrrhis form a weakly supported monophyletic clade that is nested within Chaerophyllum ...
(B) Bayesian inference tree. Bayesian posterior probabilities that are greater or equal to 50% are shown around nodes. ...
doi:10.3732/ajb.92.12.2054
pmid:21646123
fatcat:n5opowputrefbf4miszl7ahuvm
Molecular Phylogenetics of the Bat GenusScotophilus(Chiroptera: vespertilionidae): Perspectives from Paternally and Maternally Inherited Genomes
2009
Journal of Mammalogy
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All trees have S. kuhlii from Asia as the most basal species followed by S. nux from Africa. ...
The large-bodied S. nigrita is closely related to S. dinganii with a similar mtDNA haplotype but distinct zfy haplotype, suggesting a possible hybridization event in the most recent common ancestor that ...
Starting trees were obtained via stepwise addition. Data were polarized via the outgroup method, and the outgroup taxa were chosen based on the study of Hoofer and Van Den Bussche (2003) . ...
doi:10.1644/08-mamm-a-239r2.1
fatcat:hvcaqvx7ufe53n3625dcv6uxgu
Haplotyping Methods for Pedigrees
2009
Human Heredity
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With the dramatic increase in the number of available single nucleotide polymorphism (SNP) markers, haplotype inference (haplotyping) using observed genotype data has become an important component of genetic ...
In the past twenty years, many haplotyping methods for family and pedigree data have been developed. ...
We note that the purpose of these extended methods is to infer haplotypes and estimate haplotype frequencies for parents (founders), rather than to infer haplotype configurations for entire families (or ...
doi:10.1159/000194978
pmid:19172084
pmcid:PMC2692835
fatcat:fl6zfs7ehfbs7pssi4jyypfyoy
Delimiting Species without Nuclear Monophyly in Madagascar's Mouse Lemurs
2010
PLoS ONE
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However, delimiting recently diverged species is challenging due to insufficient time for the differential evolution of characters-including morphological differences, reproductive isolation, and gene tree ...
Conclusions: The resolution of a large number of geographically defined clades in the mtDNA gene tree provides strong initial evidence for recognizing a high diversity of population-level lineages in mouse ...
All mouse lemur lineages delimited via mtDNA monophyly and nuclear clustering have significant patterns of genealogical exclusivity in their nuclear gene trees, as measured by gsi values for the Bayesian ...
doi:10.1371/journal.pone.0009883
pmid:20360988
pmcid:PMC2847600
fatcat:c2mt4mxpxrfcpd4uiirnxyp35m
A hierarchical Dirichlet process mixture model for haplotype reconstruction from multi-population data
2009
Annals of Applied Statistics
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Other Versions
In this paper we present a hierarchical nonparametric Bayesian model to address this problem in the context of multi-population haplotype inference. ...
Underlying Haploi is a new haplotype distribution model based on a nonparametric Bayesian formalism known as the hierarchical Dirichlet process, which represents a tractable surrogate to the coalescent ...
Posterior inference via Gibbs sampling. ...
doi:10.1214/08-aoas225
fatcat:nrwjulnsofd4znwrsfthfnuqaq
Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe
2014
Molecular Ecology
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(B) Maximum clade credibility (MCC) tree with Bayesian posterior support values provided at the nodes. The genealogy was generated using BEAST with the dated ancient and 152 modern sequences. ...
histories than that inferred from the mitochondrion. ...
doi:10.1111/mec.12691
pmid:24795996
fatcat:lldmxdcj3jgrnjrbkiivkh4pd4
Hidden Floridian biodiversity: mitochondrial and nuclear gene trees reveal four cryptic species within the scorched mussel, Brachidontes exustus, species complex
2004
Molecular Ecology
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Characters were unordered and equally weighted, and inferred sequence gaps were considered as missing data. ...
Smaller unlabelled circles represent inferred 'missing' haplotypes. ...
doi:10.1111/j.1365-294x.2004.02337.x
pmid:15488009
fatcat:4uo7zglnpjhmriivcildbhcdcu
Phylogenetic Network Construction Approaches
[chapter]
2006
Applied Mycology and Biotechnology
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Distance-based methods Distance-based methods estimate pairwise distances prior to computing a branch-weighted phylogenetic tree. ...
If the rate of evolution is constant over the entire tree and the "molecular clock" hypothesis holds, corrections to the pairwise distances required during inference of the phylogenetic tree may be small ...
This technique is extremely fast and is able to process thousands of haplotypes in reasonable time. It can also be applied to amino acid sequences. ...
doi:10.1016/s1874-5334(06)80006-7
fatcat:m5bu6onibfaozjmexhwibubh44
PLACING THE FLORIDIAN MARINE GENETIC DISJUNCTION INTO A REGIONAL EVOLUTIONARY CONTEXT USING THE SCORCHED MUSSEL, BRACHIDONTES EXUSTUS, SPECIES COMPLEX
2005
Evolution
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Smaller unlabeled circles represent inferred missing haplotypes. Branch lengths connecting tip clades are from a minimum spanning tree computed using Arlequin 2.001 (Schneider et al. 2000) . ...
Comparative molecular studies can yield important and novel insights into marine biodiversification processes by placing the genetic structuring of taxa into an inferred historical context (Grosberg and ...
doi:10.1554/05-193.1
pmid:16405159
fatcat:wswznx2sibhqxmbgkuapvrtxce
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