Literature DB >> 19786619

Bayesian computation and model selection without likelihoods.

Christoph Leuenberger1, Daniel Wegmann.   

Abstract

Until recently, the use of Bayesian inference was limited to a few cases because for many realistic probability models the likelihood function cannot be calculated analytically. The situation changed with the advent of likelihood-free inference algorithms, often subsumed under the term approximate Bayesian computation (ABC). A key innovation was the use of a postsampling regression adjustment, allowing larger tolerance values and as such shifting computation time to realistic orders of magnitude. Here we propose a reformulation of the regression adjustment in terms of a general linear model (GLM). This allows the integration into the sound theoretical framework of Bayesian statistics and the use of its methods, including model selection via Bayes factors. We then apply the proposed methodology to the question of population subdivision among western chimpanzees, Pan troglodytes verus.

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Year:  2009        PMID: 19786619      PMCID: PMC2815920          DOI: 10.1534/genetics.109.109058

Source DB:  PubMed          Journal:  Genetics        ISSN: 0016-6731            Impact factor:   4.562


  15 in total

1.  On the number of segregating sites in genetical models without recombination.

Authors:  G A Watterson
Journal:  Theor Popul Biol       Date:  1975-04       Impact factor: 1.570

2.  Markov chain Monte Carlo without likelihoods.

Authors:  Paul Marjoram; John Molitor; Vincent Plagnol; Simon Tavare
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-08       Impact factor: 11.205

3.  Approximate Bayesian computation in population genetics.

Authors:  Mark A Beaumont; Wenyang Zhang; David J Balding
Journal:  Genetics       Date:  2002-12       Impact factor: 4.562

4.  SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history.

Authors:  Guillaume Laval; Laurent Excoffier
Journal:  Bioinformatics       Date:  2004-04-29       Impact factor: 6.937

5.  Comparative evaluation of a new effective population size estimator based on approximate bayesian computation.

Authors:  David A Tallmon; Gordon Luikart; Mark A Beaumont
Journal:  Genetics       Date:  2004-06       Impact factor: 4.562

6.  Inferring coalescence times from DNA sequence data.

Authors:  S Tavaré; D J Balding; R C Griffiths; P Donnelly
Journal:  Genetics       Date:  1997-02       Impact factor: 4.562

7.  Genetic analysis of complex demographic scenarios: spatially expanding populations of the cane toad, Bufo marinus.

Authors:  Arnaud Estoup; Mark Beaumont; Florent Sennedot; Craig Moritz; Jean-Marie Cornuet
Journal:  Evolution       Date:  2004-09       Impact factor: 3.694

8.  Molecular analysis reveals tighter social regulation of immigration in patrilocal populations than in matrilocal populations.

Authors:  Grant Hamilton; Mark Stoneking; Laurent Excoffier
Journal:  Proc Natl Acad Sci U S A       Date:  2005-05-13       Impact factor: 11.205

9.  A new approach to estimate parameters of speciation models with application to apes.

Authors:  Celine Becquet; Molly Przeworski
Journal:  Genome Res       Date:  2007-08-21       Impact factor: 9.043

10.  Divergence population genetics of chimpanzees.

Authors:  Yong-Jin Won; Jody Hey
Journal:  Mol Biol Evol       Date:  2004-10-13       Impact factor: 16.240

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  53 in total

1.  Insights into the origin and distribution of biodiversity in the Brazilian Atlantic forest hot spot: a statistical phylogeographic study using a low-dispersal organism.

Authors:  M Álvarez-Presas; A Sánchez-Gracia; F Carbayo; J Rozas; M Riutort
Journal:  Heredity (Edinb)       Date:  2014-02-19       Impact factor: 3.821

2.  Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary.

Authors:  Faisal Almathen; Pauline Charruau; Elmira Mohandesan; Joram M Mwacharo; Pablo Orozco-terWengel; Daniel Pitt; Abdussamad M Abdussamad; Margarethe Uerpmann; Hans-Peter Uerpmann; Bea De Cupere; Peter Magee; Majed A Alnaqeeb; Bashir Salim; Abdul Raziq; Tadelle Dessie; Omer M Abdelhadi; Mohammad H Banabazi; Marzook Al-Eknah; Chris Walzer; Bernard Faye; Michael Hofreiter; Joris Peters; Olivier Hanotte; Pamela A Burger
Journal:  Proc Natl Acad Sci U S A       Date:  2016-05-09       Impact factor: 11.205

3.  Lack of confidence in approximate Bayesian computation model choice.

Authors:  Christian P Robert; Jean-Marie Cornuet; Jean-Michel Marin; Natesh S Pillai
Journal:  Proc Natl Acad Sci U S A       Date:  2011-08-29       Impact factor: 11.205

4.  An early divergence of KhoeSan ancestors from those of other modern humans is supported by an ABC-based analysis of autosomal resequencing data.

Authors:  Krishna R Veeramah; Daniel Wegmann; August Woerner; Fernando L Mendez; Joseph C Watkins; Giovanni Destro-Bisol; Himla Soodyall; Leslie Louie; Michael F Hammer
Journal:  Mol Biol Evol       Date:  2011-09-01       Impact factor: 16.240

5.  Genomic evidence of survival near ice sheet margins for some, but not all, North American trees.

Authors:  Jordan B Bemmels; L Lacey Knowles; Christopher W Dick
Journal:  Proc Natl Acad Sci U S A       Date:  2019-04-08       Impact factor: 11.205

6.  Demographic factors shaped diversity in the two gene pools of wild common bean Phaseolus vulgaris L.

Authors:  S Mamidi; M Rossi; S M Moghaddam; D Annam; R Lee; R Papa; P E McClean
Journal:  Heredity (Edinb)       Date:  2012-11-21       Impact factor: 3.821

7.  Finding the best resolution for the Kingman-Tajima coalescent: theory and applications.

Authors:  Raazesh Sainudiin; Tanja Stadler; Amandine Véber
Journal:  J Math Biol       Date:  2014-05-14       Impact factor: 2.259

8.  ABCtoolbox: a versatile toolkit for approximate Bayesian computations.

Authors:  Daniel Wegmann; Christoph Leuenberger; Samuel Neuenschwander; Laurent Excoffier
Journal:  BMC Bioinformatics       Date:  2010-03-04       Impact factor: 3.169

9.  Modeling the spatial distribution and fruiting pattern of a key tree species in a neotropical forest: methodology and potential applications.

Authors:  Damien Caillaud; Margaret C Crofoot; Samuel V Scarpino; Patrick A Jansen; Carol X Garzon-Lopez; Annemarie J S Winkelhagen; Stephanie A Bohlman; Peter D Walsh
Journal:  PLoS One       Date:  2010-11-22       Impact factor: 3.240

10.  Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes.

Authors:  Laurent A F Frantz; Joshua G Schraiber; Ole Madsen; Hendrik-Jan Megens; Alex Cagan; Mirte Bosse; Yogesh Paudel; Richard P M A Crooijmans; Greger Larson; Martien A M Groenen
Journal:  Nat Genet       Date:  2015-08-31       Impact factor: 38.330

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