The distribution of waiting distances in ancestral recombination graphs

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Standard

The distribution of waiting distances in ancestral recombination graphs. / Deng, Yun; Song, Yun S.; Nielsen, Rasmus.

In: Theoretical Population Biology, Vol. 141, 2021, p. 34-43.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Deng, Y, Song, YS & Nielsen, R 2021, 'The distribution of waiting distances in ancestral recombination graphs', Theoretical Population Biology, vol. 141, pp. 34-43. https://doi.org/10.1016/j.tpb.2021.06.003

APA

Deng, Y., Song, Y. S., & Nielsen, R. (2021). The distribution of waiting distances in ancestral recombination graphs. Theoretical Population Biology, 141, 34-43. https://doi.org/10.1016/j.tpb.2021.06.003

Vancouver

Deng Y, Song YS, Nielsen R. The distribution of waiting distances in ancestral recombination graphs. Theoretical Population Biology. 2021;141:34-43. https://doi.org/10.1016/j.tpb.2021.06.003

Author

Deng, Yun ; Song, Yun S. ; Nielsen, Rasmus. / The distribution of waiting distances in ancestral recombination graphs. In: Theoretical Population Biology. 2021 ; Vol. 141. pp. 34-43.

Bibtex

@article{b05426bcdac64058867f0156d0cd9e47,

title = "The distribution of waiting distances in ancestral recombination graphs",

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.",

keywords = "Ancestral recombination graph, Recombination evolution, Sequentially Markovian coalescent, Tree inference methods",

author = "Yun Deng and Song, {Yun S.} and Rasmus Nielsen",

note = "Publisher Copyright: {\textcopyright} 2021",

year = "2021",

doi = "10.1016/j.tpb.2021.06.003",

language = "English",

volume = "141",

pages = "34--43",

journal = "Theoretical Population Biology",

issn = "0040-5809",

publisher = "Academic Press",

}

RIS

TY - JOUR

T1 - The distribution of waiting distances in ancestral recombination graphs

AU - Deng, Yun

AU - Song, Yun S.

AU - Nielsen, Rasmus

PY - 2021

Y1 - 2021

N2 - 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.

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.

KW - Ancestral recombination graph

KW - Recombination evolution

KW - Sequentially Markovian coalescent

KW - Tree inference methods

U2 - 10.1016/j.tpb.2021.06.003

DO - 10.1016/j.tpb.2021.06.003

M3 - Journal article

C2 - 34186053

AN - SCOPUS:85110256696

VL - 141

SP - 34

EP - 43

JO - Theoretical Population Biology

JF - Theoretical Population Biology

SN - 0040-5809

ER -

ID: 336746132

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