Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 561194
Title Bayesian inference of local trees along chromosomes by the sequential Markov coalescent
Author(s) Zheng, Chaozhi; Kuhner, Mary K.; Thompson, Elizabeth A.
Source Journal of Molecular Evolution 78 (2014)5. - ISSN 0022-2844 - p. 279 - 292.
DOI https://doi.org/10.1007/s00239-014-9620-5
Department(s) Mathematical and Statistical Methods - Biometris
Publication type Refereed Article in a scientific journal
Publication year 2014
Keyword(s) Ancestral recombination graph - Bayesian inference - Coalescent - Markov chain Monte Carlo - Sequential Markov coalescent
Abstract

We propose a genealogy-sampling algorithm, Sequential Markov Ancestral Recombination Tree (SMARTree), that provides an approach to estimation from SNP haplotype data of the patterns of coancestry across a genome segment among a set of homologous chromosomes. To enable analysis across longer segments of genome, the sequence of coalescent trees is modeled via the modified sequential Markov coalescent (Marjoram and Wall, Genetics 7:16, 2006). To assess performance in estimating these local trees, our SMARTree implementation is tested on simulated data. Our base data set is of the SNPs in 10 DNA sequences over 50 kb. We examine the effects of longer sequences and of more sequences, and of a recombination and/or mutational hotspot. The model underlying SMARTree is an approximation to the full recombinant-coalescent distribution. However, in a small trial on simulated data, recovery of local trees was similar to that of LAMARC (Kuhner et al. Genetics 156:1393-1401, 2000a), a sampler which uses the full model.

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