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Computing the joint distribution of the total tree length across loci in populations with variable size

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  • Miroshnikov, Alexey
  • Steinrücken, Matthias

Abstract

In recent years, a number of methods have been developed to infer complex demographic histories, especially historical population size changes, from genomic sequence data. Coalescent Hidden Markov Models have proven to be particularly useful for this type of inference. Due to the Markovian structure of these models, an essential building block is the joint distribution of local genealogical trees, or statistics of these genealogies, at two neighboring loci in populations of variable size. Here, we present a novel method to compute the marginal and the joint distribution of the total length of the genealogical trees at two loci separated by at most one recombination event for samples of arbitrary size. To our knowledge, no method to compute these distributions has been presented in the literature to date. We show that they can be obtained from the solution of certain hyperbolic systems of partial differential equations. We present a numerical algorithm, based on the method of characteristics, that can be used to efficiently and accurately solve these systems and compute the marginal and the joint distributions. We demonstrate its utility to study the properties of the joint distribution. Our flexible method can be straightforwardly extended to handle an arbitrary fixed number of recombination events, to include the distributions of other statistics of the genealogies as well, and can also be applied in structured populations.

Suggested Citation

  • Miroshnikov, Alexey & Steinrücken, Matthias, 2017. "Computing the joint distribution of the total tree length across loci in populations with variable size," Theoretical Population Biology, Elsevier, vol. 118(C), pages 1-19.
    • Handle: RePEc:eee:thpobi:v:118:y:2017:i:c:p:1-19
    DOI: 10.1016/j.tpb.2017.09.002
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    References listed on IDEAS

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    1. Hobolth, Asger & Jensen, Jens Ledet, 2014. "Markovian approximation to the finite loci coalescent with recombination along multiple sequences," Theoretical Population Biology, Elsevier, vol. 98(C), pages 48-58.
    2. Eriksson, A. & Mahjani, B. & Mehlig, B., 2009. "Sequential Markov coalescent algorithms for population models with demographic structure," Theoretical Population Biology, Elsevier, vol. 76(2), pages 84-91.
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    Cited by:

    1. Arbisser, Ilana M. & Jewett, Ethan M. & Rosenberg, Noah A., 2018. "On the joint distribution of tree height and tree length under the coalescent," Theoretical Population Biology, Elsevier, vol. 122(C), pages 46-56.
    2. Hobolth, Asger & Siri-Jégousse, Arno & Bladt, Mogens, 2019. "Phase-type distributions in population genetics," Theoretical Population Biology, Elsevier, vol. 127(C), pages 16-32.

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