IDEAS home Printed from https://ideas.repec.org/a/eee/thpobi/v141y2021icp34-43.html
   My bibliography  Save this article

The distribution of waiting distances in ancestral recombination graphs

Author

Listed:
  • Deng, Yun
  • Song, Yun S.
  • Nielsen, Rasmus

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.

Suggested Citation

  • Deng, Yun & Song, Yun S. & Nielsen, Rasmus, 2021. "The distribution of waiting distances in ancestral recombination graphs," Theoretical Population Biology, Elsevier, vol. 141(C), pages 34-43.
    • Handle: RePEc:eee:thpobi:v:141:y:2021:i:c:p:34-43
    DOI: 10.1016/j.tpb.2021.06.003
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0040580921000484
    Download Restriction: Full text for ScienceDirect subscribers only
    File URL: https://libkey.io/10.1016/j.tpb.2021.06.003?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    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. Carmi, Shai & Wilton, Peter R. & Wakeley, John & Pe’er, Itsik, 2014. "A renewal theory approach to IBD sharing," Theoretical Population Biology, Elsevier, vol. 97(C), pages 35-48.
    3. Matthew D Rasmussen & Melissa J Hubisz & Ilan Gronau & Adam Siepel, 2014. "Genome-Wide Inference of Ancestral Recombination Graphs," PLOS Genetics, Public Library of Science, vol. 10(5), pages 1-27, May.
    4. Gustavo V. Barroso & Nataša Puzović & Julien Y Dutheil, 2019. "Inference of recombination maps from a single pair of genomes and its application to ancient samples," PLOS Genetics, Public Library of Science, vol. 15(11), pages 1-21, November.
    5. Heng Li & Richard Durbin, 2011. "Inference of human population history from individual whole-genome sequences," Nature, Nature, vol. 475(7357), pages 493-496, July.
    6. Jerome Kelleher & Alison M Etheridge & Gilean McVean, 2016. "Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes," PLOS Computational Biology, Public Library of Science, vol. 12(5), pages 1-22, May.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Kerdoncuff, Elise & Lambert, Amaury & Achaz, Guillaume, 2020. "Testing for population decline using maximal linkage disequilibrium blocks," Theoretical Population Biology, Elsevier, vol. 134(C), pages 171-181.
    2. Per Unneberg & Mårten Larsson & Anna Olsson & Ola Wallerman & Anna Petri & Ignas Bunikis & Olga Vinnere Pettersson & Chiara Papetti & Astthor Gislason & Henrik Glenner & Joan E. Cartes & Leocadio Blan, 2024. "Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins," Nature Communications, Nature, vol. 15(1), pages 1-29, December.
    3. Ali Mahmoudi & Jere Koskela & Jerome Kelleher & Yao-ban Chan & David Balding, 2022. "Bayesian inference of ancestral recombination graphs," PLOS Computational Biology, Public Library of Science, vol. 18(3), pages 1-15, March.
    4. Carmi, Shai & Wilton, Peter R. & Wakeley, John & Pe’er, Itsik, 2014. "A renewal theory approach to IBD sharing," Theoretical Population Biology, Elsevier, vol. 97(C), pages 35-48.
    5. Jerome Kelleher & Alison M Etheridge & Gilean McVean, 2016. "Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes," PLOS Computational Biology, Public Library of Science, vol. 12(5), pages 1-22, May.
    6. Johndrow, James E. & Palacios, Julia A., 2019. "Exact limits of inference in coalescent models," Theoretical Population Biology, Elsevier, vol. 125(C), pages 75-93.
    7. Gideon S Bradburd & Peter L Ralph & Graham M Coop, 2016. "A Spatial Framework for Understanding Population Structure and Admixture," PLOS Genetics, Public Library of Science, vol. 12(1), pages 1-38, January.
    8. Juraj Bergman & Rasmus Ø. Pedersen & Erick J. Lundgren & Rhys T. Lemoine & Sophie Monsarrat & Elena A. Pearce & Mikkel H. Schierup & Jens-Christian Svenning, 2023. "Worldwide Late Pleistocene and Early Holocene population declines in extant megafauna are associated with Homo sapiens expansion rather than climate change," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    9. Cotter, Daniel J. & Severson, Alissa L. & Rosenberg, Noah A., 2021. "The effect of consanguinity on coalescence times on the X chromosome," Theoretical Population Biology, Elsevier, vol. 140(C), pages 32-43.
    10. Nicola F. Müller & Kathryn E. Kistler & Trevor Bedford, 2022. "A Bayesian approach to infer recombination patterns in coronaviruses," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    11. Ya-Mei Ding & Xiao-Xu Pang & Yu Cao & Wei-Ping Zhang & Susanne S. Renner & Da-Yong Zhang & Wei-Ning Bai, 2023. "Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    12. Romain Fournier & Zoi Tsangalidou & David Reich & Pier Francesco Palamara, 2023. "Haplotype-based inference of recent effective population size in modern and ancient DNA samples," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    13. Steinrücken, Matthias & Paul, Joshua S. & Song, Yun S., 2013. "A sequentially Markov conditional sampling distribution for structured populations with migration and recombination," Theoretical Population Biology, Elsevier, vol. 87(C), pages 51-61.
    14. Barton, N.H. & Etheridge, A.M. & Kelleher, J. & Véber, A., 2013. "Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks," Theoretical Population Biology, Elsevier, vol. 87(C), pages 105-119.
    15. Sergio F. Nigenda-Morales & Meixi Lin & Paulina G. Nuñez-Valencia & Christopher C. Kyriazis & Annabel C. Beichman & Jacqueline A. Robinson & Aaron P. Ragsdale & Jorge Urbán R. & Frederick I. Archer & , 2023. "The genomic footprint of whaling and isolation in fin whale populations," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    16. Ralph, Peter L., 2019. "An empirical approach to demographic inference with genomic data," Theoretical Population Biology, Elsevier, vol. 127(C), pages 91-101.
    17. Guangping Huang & Lingyun Song & Xin Du & Xin Huang & Fuwen Wei, 2023. "Evolutionary genomics of camouflage innovation in the orchid mantis," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    18. Legried, Brandon & Terhorst, Jonathan, 2022. "Rates of convergence in the two-island and isolation-with-migration models," Theoretical Population Biology, Elsevier, vol. 147(C), pages 16-27.
    19. Zihao Wang & Wenxi Wang & Xiaoming Xie & Yongfa Wang & Zhengzhao Yang & Huiru Peng & Mingming Xin & Yingyin Yao & Zhaorong Hu & Jie Liu & Zhenqi Su & Chaojie Xie & Baoyun Li & Zhongfu Ni & Qixin Sun &, 2022. "Dispersed emergence and protracted domestication of polyploid wheat uncovered by mosaic ancestral haploblock inference," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    20. Hobolth, Asger & Siri-Jégousse, Arno & Bladt, Mogens, 2019. "Phase-type distributions in population genetics," Theoretical Population Biology, Elsevier, vol. 127(C), pages 16-32.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:thpobi:v:141:y:2021:i:c:p:34-43. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: https://www.journals.elsevier.com/intelligence .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.