IDEAS home Printed from https://ideas.repec.org/a/eee/thpobi/v90y2013icp113-128.html
   My bibliography  Save this article

Birth–death models and coalescent point processes: The shape and probability of reconstructed phylogenies

Author

Listed:
  • Lambert, Amaury
  • Stadler, Tanja

Abstract

Forward-in-time models of diversification (i.e., speciation and extinction) produce phylogenetic trees that grow “vertically†as time goes by. Pruning the extinct lineages out of such trees leads to natural models for reconstructed trees (i.e., phylogenies of extant species). Alternatively, reconstructed trees can be modelled by coalescent point processes (CPPs), where trees grow “horizontally†by the sequential addition of vertical edges. Each new edge starts at some random speciation time and ends at the present time; speciation times are drawn from the same distribution independently. CPPs lead to extremely fast computation of tree likelihoods and simulation of reconstructed trees. Their topology always follows the uniform distribution on ranked tree shapes (URT).

Suggested Citation

  • Lambert, Amaury & Stadler, Tanja, 2013. "Birth–death models and coalescent point processes: The shape and probability of reconstructed phylogenies," Theoretical Population Biology, Elsevier, vol. 90(C), pages 113-128.
  • Handle: RePEc:eee:thpobi:v:90:y:2013:i:c:p:113-128
    DOI: 10.1016/j.tpb.2013.10.002
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0040580913001056
    Download Restriction: Full text for ScienceDirect subscribers only

    File URL: https://libkey.io/10.1016/j.tpb.2013.10.002?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.

    Citations

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


    Cited by:

    1. Ho, Lam Si Tung & Dinh, Vu, 2022. "When can we reconstruct the ancestral state? A unified theory," Theoretical Population Biology, Elsevier, vol. 148(C), pages 22-27.
    2. Lambert, Amaury, 2018. "The coalescent of a sample from a binary branching process," Theoretical Population Biology, Elsevier, vol. 122(C), pages 30-35.
    3. Ignatieva, Anastasia & Hein, Jotun & Jenkins, Paul A., 2020. "A characterisation of the reconstructed birth–death process through time rescaling," Theoretical Population Biology, Elsevier, vol. 134(C), pages 61-76.
    4. Wiuf, Carsten, 2018. "Some properties of the conditioned reconstructed process with Bernoulli sampling," Theoretical Population Biology, Elsevier, vol. 122(C), pages 36-45.
    5. Steel, Mike, 2015. "Reflections on the extinction–explosion dichotomy," Theoretical Population Biology, Elsevier, vol. 101(C), pages 61-66.
    6. Crespo, Fausto F. & Posada, David & Wiuf, Carsten, 2021. "Coalescent models derived from birth–death processes," Theoretical Population Biology, Elsevier, vol. 142(C), pages 1-11.

    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:90:y:2013:i:c:p:113-128. 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.

    We have no bibliographic references for this item. You can help adding them by using 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.