Literature DB >> 23788830

PADÉ APPROXIMANTS AND EXACT TWO-LOCUS SAMPLING DISTRIBUTIONS.

Paul A Jenkins1, Yun S Song.   

Abstract

For population genetics models with recombination, obtaining an exact, analytic sampling distribution has remained a challenging open problem for several decades. Recently, a new perspective based on asymptotic series has been introduced to make progress on this problem. Specifically, closed-form expressions have been derived for the first few terms in an asymptotic expansion of the two-locus sampling distribution when the recombination rate ρ is moderate to large. In this paper, a new computational technique is developed for finding the asymptotic expansion to an arbitrary order. Computation in this new approach can be automated easily. Furthermore, it is proved here that only a finite number of terms in the asymptotic expansion is needed to recover (via the method of Padé approximants) the exact two-locus sampling distribution as an analytic function of ρ; this function is exact for all values of ρ ∈ [0, ∞). It is also shown that the new computational framework presented here is flexible enough to incorporate natural selection.

Entities:  

Keywords:  Padé approximants; asymptotic expansion; population genetics; recombination; sampling distribution

Year:  2012        PMID: 23788830      PMCID: PMC3685441          DOI: 10.1214/11-AAP780

Source DB:  PubMed          Journal:  Ann Appl Probab            Impact factor:   1.872


  11 in total

1.  Two-locus sampling distributions and their application.

Authors:  R R Hudson
Journal:  Genetics       Date:  2001-12       Impact factor: 4.562

2.  A coalescent-based method for detecting and estimating recombination from gene sequences.

Authors:  Gil McVean; Philip Awadalla; Paul Fearnhead
Journal:  Genetics       Date:  2002-03       Impact factor: 4.562

3.  AN ASYMPTOTIC SAMPLING FORMULA FOR THE COALESCENT WITH RECOMBINATION.

Authors:  Paul A Jenkins; Yun S Song
Journal:  Ann Appl Probab       Date:  2010-06       Impact factor: 1.872

4.  Analytic computation of the expectation of the linkage disequilibrium coefficient r2.

Authors:  Yun S Song; Jun S Song
Journal:  Theor Popul Biol       Date:  2006-09-23       Impact factor: 1.570

5.  Estimation of selection intensity under overdominance by Bayesian methods.

Authors:  Erkan Ozge Buzbas; Paul Joyce; Zaid Abdo
Journal:  Stat Appl Genet Mol Biol       Date:  2009-06-30

6.  Closed-form two-locus sampling distributions: accuracy and universality.

Authors:  Paul A Jenkins; Yun S Song
Journal:  Genetics       Date:  2009-09-07       Impact factor: 4.562

7.  Diffusion approximations of the two-locus Wright-Fisher model.

Authors:  S N Ethier; T Nagylaki
Journal:  J Math Biol       Date:  1989       Impact factor: 2.259

8.  The sampling theory of selectively neutral alleles.

Authors:  W J Ewens
Journal:  Theor Popul Biol       Date:  1972-03       Impact factor: 1.570

9.  Linkage disequilibrium at steady state determined by random genetic drift and recurrent mutation.

Authors:  T Ohta; M Kimura
Journal:  Genetics       Date:  1969-09       Impact factor: 4.562

10.  The fine-scale structure of recombination rate variation in the human genome.

Authors:  Gilean A T McVean; Simon R Myers; Sarah Hunt; Panos Deloukas; David R Bentley; Peter Donnelly
Journal:  Science       Date:  2004-04-23       Impact factor: 47.728

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  8 in total

1.  Inferring Demographic History Using Two-Locus Statistics.

Authors:  Aaron P Ragsdale; Ryan N Gutenkunst
Journal:  Genetics       Date:  2017-04-16       Impact factor: 4.562

2.  CLOSED-FORM ASYMPTOTIC SAMPLING DISTRIBUTIONS UNDER THE COALESCENT WITH RECOMBINATION FOR AN ARBITRARY NUMBER OF LOCI.

Authors:  Anand Bhaskar; Yun S Song
Journal:  Adv Appl Probab       Date:  2012-06       Impact factor: 0.690

3.  APPROXIMATE SAMPLING FORMULAS FOR GENERAL FINITE-ALLELES MODELS OF MUTATION.

Authors:  Anand Bhaskar; John A Kamm; Yun S Song
Journal:  Adv Appl Probab       Date:  2012-06       Impact factor: 0.690

4.  Two-Locus Likelihoods Under Variable Population Size and Fine-Scale Recombination Rate Estimation.

Authors:  John A Kamm; Jeffrey P Spence; Jeffrey Chan; Yun S Song
Journal:  Genetics       Date:  2016-05-10       Impact factor: 4.562

5.  A numerical framework for genetic hitchhiking in populations of variable size.

Authors:  Eric Friedlander; Matthias Steinrücken
Journal:  Genetics       Date:  2022-03-03       Impact factor: 4.562

6.  TRACTABLE DIFFUSION AND COALESCENT PROCESSES FOR WEAKLY CORRELATED LOCI.

Authors:  Paul A Jenkins; Paul Fearnhead; Yun S Song
Journal:  Electron J Probab       Date:  2016-06-04       Impact factor: 1.151

7.  On the Recombination Rate Estimation in the Presence of Population Substructure.

Authors:  Julian Hecker; Dmitry Prokopenko; Christoph Lange; Heide Löhlein Fier
Journal:  PLoS One       Date:  2015-12-30       Impact factor: 3.240

8.  Genome-wide fine-scale recombination rate variation in Drosophila melanogaster.

Authors:  Andrew H Chan; Paul A Jenkins; Yun S Song
Journal:  PLoS Genet       Date:  2012-12-20       Impact factor: 5.917

  8 in total

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