IDEAS home Printed from https://ideas.repec.org/a/eee/thpobi/v78y2010i3p165-172.html
   My bibliography  Save this article

Alternatives to the Wright–Fisher model: The robustness of mitochondrial Eve dating

Author

Listed:
  • Cyran, Krzysztof A.
  • Kimmel, Marek

Abstract

Methods of calculating the distributions of the time to coalescence depend on the underlying model of population demography. In particular, the models assuming deterministic evolution of population size may not be applicable to populations evolving stochastically. Therefore the study of coalescence models involving stochastic demography is important for applications. One interesting approach which includes stochasticity is the O’Connell limit theory of genealogy in branching processes. Our paper explores how many generations are needed for the limiting distributions of O’Connell to become adequate approximations of exact distributions. We perform extensive simulations of slightly supercritical branching processes and compare the results to the O’Connell limits. Coalescent computations under the Wright–Fisher model are compared with limiting O’Connell results and with full genealogy-based predictions. These results are used to estimate the age of the so-called mitochondrial Eve, i.e., the root of the mitochondrial polymorphisms of the modern humans based on the DNA from humans and Neanderthal fossils.

Suggested Citation

  • Cyran, Krzysztof A. & Kimmel, Marek, 2010. "Alternatives to the Wright–Fisher model: The robustness of mitochondrial Eve dating," Theoretical Population Biology, Elsevier, vol. 78(3), pages 165-172.
    • Handle: RePEc:eee:thpobi:v:78:y:2010:i:3:p:165-172
    DOI: 10.1016/j.tpb.2010.06.001
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0040580910000493
    Download Restriction: Full text for ScienceDirect subscribers only
    File URL: https://libkey.io/10.1016/j.tpb.2010.06.001?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. Igor V. Ovchinnikov & Anders Götherström & Galina P. Romanova & Vitaliy M. Kharitonov & Kerstin Lidén & William Goodwin, 2000. "Molecular analysis of Neanderthal DNA from the northern Caucasus," Nature, Nature, vol. 404(6777), pages 490-493, March.
    2. Vincent Plagnol & Jeffrey D Wall, 2006. "Possible Ancestral Structure in Human Populations," PLOS Genetics, Public Library of Science, vol. 2(7), pages 1-8, July.
    3. Richard E. Green & Johannes Krause & Susan E. Ptak & Adrian W. Briggs & Michael T. Ronan & Jan F. Simons & Lei Du & Michael Egholm & Jonathan M. Rothberg & Maja Paunovic & Svante Pääbo, 2006. "Analysis of one million base pairs of Neanderthal DNA," Nature, Nature, vol. 444(7117), pages 330-336, November.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Burden, Conrad J. & Wei, Yi, 2018. "Mutation in populations governed by a Galton–Watson branching process," Theoretical Population Biology, Elsevier, vol. 120(C), pages 52-61.
    2. Burden, Conrad J. & Soewongsono, Albert C., 2019. "Coalescence in the diffusion limit of a Bienaymé–Galton–Watson branching process," Theoretical Population Biology, Elsevier, vol. 130(C), pages 50-59.
    3. Burden, Conrad J. & Simon, Helmut, 2016. "Genetic drift in populations governed by a Galton–Watson branching process," Theoretical Population Biology, Elsevier, vol. 109(C), pages 63-74.

    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. Kai Yuan & Xumin Ni & Chang Liu & Yuwen Pan & Lian Deng & Rui Zhang & Yang Gao & Xueling Ge & Jiaojiao Liu & Xixian Ma & Haiyi Lou & Taoyang Wu & Shuhua Xu, 2021. "Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    2. Rogers, Alan R. & Bohlender, Ryan J., 2015. "Bias in estimators of archaic admixture," Theoretical Population Biology, Elsevier, vol. 100(C), pages 63-78.
    3. VanLiere, Jenna M. & Rosenberg, Noah A., 2008. "Mathematical properties of the r2 measure of linkage disequilibrium," Theoretical Population Biology, Elsevier, vol. 74(1), pages 130-137.
    4. Ian J. Wilson & Michael E. Weale & David J. Balding, 2003. "Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities," Journal of the Royal Statistical Society Series A, Royal Statistical Society, vol. 166(2), pages 155-188, June.
    5. Pham, Tuan D., 2012. "Regularity dimension of sequences and its application to phylogenetic tree reconstruction," Chaos, Solitons & Fractals, Elsevier, vol. 45(6), pages 879-887.
    6. Haodong Ye & Jun Wen & Xingpeng Xu & Jiayu Li & Zhaopeng Lv & Yueping Su, 2024. "Study on the Geographical Spatial Characteristics of Forest Health Resorts in Fujian Province, China," Sustainability, MDPI, vol. 16(9), pages 1-13, April.
    7. Hazelton, Martin L. & Cox, Murray P., 2016. "Bandwidth selection for kernel log-density estimation," Computational Statistics & Data Analysis, Elsevier, vol. 103(C), pages 56-67.

    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:78:y:2010:i:3:p:165-172. 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.