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Fast Bayesian Haplotype Inference Via Context Tree Weighting [chapter]

Pasi Rastas, Jussi Kollin, Mikko Koivisto
Lecture Notes in Computer Science  
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

Katalin Csilléry, Michael G.B. Blum, Oscar E. Gaggiotti, Olivier François
2010 Trends in Ecology & Evolution  
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

Yann X C Bourgeois, Ben H Warren
2021 Molecular Ecology  
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

Yi-Jun Zhang, Matthias Stöck, Peng Zhang, Xiu-Ling Wang, Hui Zhou, Liang-Hu Qu
2008 Genetica  
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]

Marina Petkovic, Thomas BK Watkins, Emma C Colliver, Sofya Laskina, Charles Swanton, Kerstin Haase, Roland F Schwarz
2021 bioRxiv   pre-print
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

Eric P. Xing, Kyung-Ah Sohn
2007 Bayesian Analysis  
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

K.-F. Chung, C.-I Peng, S. R. Downie, K. Spalik, B. A. Schaal
2005 American Journal of Botany  
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

Robert G. Trujillo, John C. Patton, Duane A. Schlitter, John W. Bickham
2009 Journal of Mammalogy  
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

Guimin Gao, David B. Allison, Ina Hoeschele
2009 Human Heredity  
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

David W. Weisrock, Rodin M. Rasoloarison, Isabella Fiorentino, José M. Ralison, Steven M. Goodman, Peter M. Kappeler, Anne D. Yoder, Manfred Kayser
2010 PLoS ONE  
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

Kyung-Ah Sohn, Eric P. Xing
2009 Annals of Applied Statistics  
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

Susanne Horn, Stefan Prost, Mathias Stiller, Daniel Makowiecki, Tatiana Kuznetsova, Norbert Benecke, Erich Pucher, Anne K. Hufthammer, Charles Schouwenburg, Beth Shapiro, Michael Hofreiter
2014 Molecular Ecology  
(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

T. LEE, D. Ó FOIGHIL
2004 Molecular Ecology  
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]

Vladimir Makarenkov, Dmytro Kevorkov, Pierre Legendre
2006 Applied Mycology and Biotechnology  
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

Taehwan Lee, Diarmaid Ó Foighil
2005 Evolution  
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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