Markov jump processes in modeling coalescent with recombination

DOI10.1214/14-AOS1227MaRDI QIDQ464186zbMATH OpenOpenAlexFDO

Authors Zhi-Ming Ma, Ying Wang, Xian Chen

Publication date 17 October 2014

Published in The Annals of Statistics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1407.0215, https://projecteuclid.org/euclid.aos/1403715204

zbMATH Keywords

Markov jump processesancestral recombination graphback-in-time algorithmcoalescent processgenetic recombinationspatial algorithm

Mathematics Subject Classification ID

General biostatistics (92B15) Genetics and epigenetics (92D10) Population dynamics (general) (92D25) Continuous-time Markov processes on general state spaces (60J25)

Abstract: Genetic recombination is one of the most important mechanisms that can generate and maintain diversity, and recombination information plays an important role in population genetic studies. However, the phenomenon of recombination is extremely complex, and hence simulation methods are indispensable in the statistical inference of recombination. So far there are mainly two classes of simulation models practically in wide use: back-in-time models and spatially moving models. However, the statistical properties shared by the two classes of simulation models have not yet been theoretically studied. Based on our joint research with CAS-MPG Partner Institute for Computational Biology and with Beijing Jiaotong University, in this paper we provide for the first time a rigorous argument that the statistical properties of the two classes of simulation models are identical. That is, they share the same probability distribution on the space of ancestral recombination graphs (ARGs). As a consequence, our study provides a unified interpretation for the algorithms of simulating coalescent with recombination, and will facilitate the study of statistical inference on recombination.

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Cited in

(6)

• Markov jump processes in modeling coalescent with recombination
• A transformation of Markov jump processes and applications in genetic study
• An adjacent-swap Markov chain on coalescent trees
• Markov genealogy processes
• Markovian approximation to the finite loci coalescent with recombination along multiple sequences
• Markov models for accumulating mutations

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