Bayesian inference of local trees along chromosomes by the sequential Markov coalescent

Chaozhi Zheng, Mary K. Kuhner, Elizabeth A. Thompson*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

7 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)279-292
Number of pages14
JournalJournal of Molecular Evolution
Volume78
Issue number5
DOIs
Publication statusPublished - 11 May 2014

Keywords

  • Ancestral recombination graph
  • Bayesian inference
  • Coalescent
  • Markov chain Monte Carlo
  • Sequential Markov coalescent

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