The distribution of waiting distances in ancestral recombination graphs

Yun Deng*, Yun S. Song, Rasmus Nielsen

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

2 Citations (Scopus)

Abstract

The ancestral recombination graph (ARG) contains the full genealogical information of the sample, and many population genetic inference problems can be solved using inferred or sampled ARGs. In particular, the waiting distance between tree changes along the genome can be used to make inference about the distribution and evolution of recombination rates. To this end, we here derive an analytic expression for the distribution of waiting distances between tree changes under the sequentially Markovian coalescent model and obtain an accurate approximation to the distribution of waiting distances for topology changes. We use these results to show that some of the recently proposed methods for inferring sequences of trees along the genome provide strongly biased distributions of waiting distances. In addition, we provide a correction to an undercounting problem facing all available ARG inference methods, thereby facilitating the use of ARG inference methods to estimate temporal changes in the recombination rate.

Original languageEnglish
JournalTheoretical Population Biology
Volume141
Pages (from-to)34-43
Number of pages10
ISSN0040-5809
DOIs
Publication statusPublished - 2021
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2021

Keywords

  • Ancestral recombination graph
  • Recombination evolution
  • Sequentially Markovian coalescent
  • Tree inference methods

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