Bayesian estimation of the number of inversions in the history of two chromosomes

Thomas L. York; Richard Durrett; Rasmus Nielsen

doi:10.1089/10665270260518281

Bayesian estimation of the number of inversions in the history of two chromosomes

Thomas L. York, Richard Durrett, Rasmus Nielsen^*

^*Corresponding author for this work

19 Citations (Scopus)

Abstract

We present a Bayesian approach to the problem of inferring the history of inversions separating homologous chromosomes from two different species. The method is based on Markov Chain Monte Carlo (MCMC) and takes full advantage of all the information from marker order. We apply the method both to simulated data and to two real data sets. For the simulated data, we show that the MCMC method provides accurate estimates of the true posterior distributions and in the analysis of the real data we show that the most likely number of inversions in some cases is considerably larger than estimates obtained based on the parsimony inferred number of inversions. Indeed, in the case of the Drosophila repleta-D. melanogaster comparison, the lower boundary of a 95% highest posterior density credible interval for the number of inversions is considerably larger than the most parsimonious number of inversions.

Original language	English
Journal	Journal of Computational Biology
Volume	9
Issue number	6
Pages (from-to)	805-818
Number of pages	14
ISSN	1066-5277
DOIs	https://doi.org/10.1089/10665270260518281
Publication status	Published - 1 Dec 2002

Keywords

Bayesian estimation
Breakpoint graph
Inversions
MCMC

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10.1089/10665270260518281

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abstract = "We present a Bayesian approach to the problem of inferring the history of inversions separating homologous chromosomes from two different species. The method is based on Markov Chain Monte Carlo (MCMC) and takes full advantage of all the information from marker order. We apply the method both to simulated data and to two real data sets. For the simulated data, we show that the MCMC method provides accurate estimates of the true posterior distributions and in the analysis of the real data we show that the most likely number of inversions in some cases is considerably larger than estimates obtained based on the parsimony inferred number of inversions. Indeed, in the case of the Drosophila repleta-D. melanogaster comparison, the lower boundary of a 95% highest posterior density credible interval for the number of inversions is considerably larger than the most parsimonious number of inversions.",

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T1 - Bayesian estimation of the number of inversions in the history of two chromosomes

AU - York, Thomas L.

AU - Durrett, Richard

AU - Nielsen, Rasmus

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N2 - We present a Bayesian approach to the problem of inferring the history of inversions separating homologous chromosomes from two different species. The method is based on Markov Chain Monte Carlo (MCMC) and takes full advantage of all the information from marker order. We apply the method both to simulated data and to two real data sets. For the simulated data, we show that the MCMC method provides accurate estimates of the true posterior distributions and in the analysis of the real data we show that the most likely number of inversions in some cases is considerably larger than estimates obtained based on the parsimony inferred number of inversions. Indeed, in the case of the Drosophila repleta-D. melanogaster comparison, the lower boundary of a 95% highest posterior density credible interval for the number of inversions is considerably larger than the most parsimonious number of inversions.

AB - We present a Bayesian approach to the problem of inferring the history of inversions separating homologous chromosomes from two different species. The method is based on Markov Chain Monte Carlo (MCMC) and takes full advantage of all the information from marker order. We apply the method both to simulated data and to two real data sets. For the simulated data, we show that the MCMC method provides accurate estimates of the true posterior distributions and in the analysis of the real data we show that the most likely number of inversions in some cases is considerably larger than estimates obtained based on the parsimony inferred number of inversions. Indeed, in the case of the Drosophila repleta-D. melanogaster comparison, the lower boundary of a 95% highest posterior density credible interval for the number of inversions is considerably larger than the most parsimonious number of inversions.

KW - Bayesian estimation

KW - Breakpoint graph

KW - Inversions

KW - MCMC

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JO - Journal of Computational Biology

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Bayesian estimation of the number of inversions in the history of two chromosomes

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Keywords

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