RT Journal Article
SR Electronic
T1 The distribution of waiting distances in ancestral recombination graphs and its applications
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.12.24.424361
DO 10.1101/2020.12.24.424361
A1 Yun Deng
A1 Yun S. Song
A1 Rasmus Nielsen
YR 2020
UL http://biorxiv.org/content/early/2020/12/26/2020.12.24.424361.abstract
AB 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.Competing Interest StatementThe authors have declared no competing interest.