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On cherry and pitchfork distributions of random rooted and unrooted phylogenetic trees

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  • Choi, Kwok Pui
  • Thompson, Ariadne
  • Wu, Taoyang

Abstract

Tree shape statistics are important for investigating evolutionary mechanisms mediating phylogenetic trees. As a step towards bridging shape statistics between rooted and unrooted trees, we present a comparison study on two subtree statistics known as numbers of cherries and pitchforks for the proportional to distinguishable arrangements (PDA) and the Yule–Harding–Kingman (YHK) models. Based on recursive formulas on the joint distribution of the number of cherries and that of pitchforks, it is shown that cherry distributions are log-concave for both rooted and unrooted trees under these two models. Furthermore, the mean number of cherries and that of pitchforks for unrooted trees converge respectively to those for rooted trees under the YHK model while there exists a limiting gap of 1∕4 for the PDA model. Finally, the total variation distances between the cherry distributions of rooted and those of unrooted trees converge for both models. Our results indicate that caution is required for conducting statistical analysis for tree shapes involving both rooted and unrooted trees.

Suggested Citation

  • Choi, Kwok Pui & Thompson, Ariadne & Wu, Taoyang, 2020. "On cherry and pitchfork distributions of random rooted and unrooted phylogenetic trees," Theoretical Population Biology, Elsevier, vol. 132(C), pages 92-104.
    • Handle: RePEc:eee:thpobi:v:132:y:2020:i:c:p:92-104
    DOI: 10.1016/j.tpb.2020.02.001
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    References listed on IDEAS

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    1. Wu, Taoyang & Choi, Kwok Pui, 2016. "On joint subtree distributions under two evolutionary models," Theoretical Population Biology, Elsevier, vol. 108(C), pages 13-23.
    2. Arbisser, Ilana M. & Jewett, Ethan M. & Rosenberg, Noah A., 2018. "On the joint distribution of tree height and tree length under the coalescent," Theoretical Population Biology, Elsevier, vol. 122(C), pages 46-56.
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    Cited by:

    1. Kaur, Gursharn & Choi, Kwok Pui & Wu, Taoyang, 2023. "Distributions of cherries and pitchforks for the Ford model," Theoretical Population Biology, Elsevier, vol. 149(C), pages 27-38.

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    1. Kaur, Gursharn & Choi, Kwok Pui & Wu, Taoyang, 2023. "Distributions of cherries and pitchforks for the Ford model," Theoretical Population Biology, Elsevier, vol. 149(C), pages 27-38.
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