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

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  • 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
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    Citations

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    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. 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.
    6. Steel, Mike, 2015. "Reflections on the extinction–explosion dichotomy," Theoretical Population Biology, Elsevier, vol. 101(C), pages 61-66.

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