Distributions of 4-subtree patterns for uniform random unrooted phylogenetic trees

Choi, Kwok Pui, Kaur, Gursharn, Thompson, Ariadne and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2024) Distributions of 4-subtree patterns for uniform random unrooted phylogenetic trees. Journal of Theoretical Biology, 584. ISSN 0022-5193

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Abstract

Tree shape statistics based on peripheral structures have been utilized to study evolutionary mechanisms and inference methods. Partially motivated by a recent study by Pouryahya and Sankoff on modeling the accumulation of subgenomes in the evolution of polyploids, we present the distribution of subtree patterns with four or fewer leaves for the unrooted Proportional to Distinguishable Arrangements (PDA) model. We derive a recursive formula for computing the joint distributions, as well as a Strong Law of Large Numbers and a Central Limit Theorem for the joint distributions. This enables us to confirm several conjectures proposed by Pouryahya and Sankoff, as well as provide some theoretical insights into their observations. Based on their empirical datasets, we demonstrate that the statistical test based on the joint distribution could be more sensitive than those based on one individual subtree pattern to detect the existence of evolutionary forces such as whole genome duplication.

Item Type:	Article
Additional Information:	Funding information: K.P. Choi acknowledges the support of Singapore Ministry of Education Academic Research Fund, Singapore [Grant number R-155-000-222-114]. G. Kaur acknowledges the support provided by NSF Expeditions in Computing Grant, USA [CCF-1918656 and CCF-191781]. A. Thompson is supported by the UKRI Biotechnology and Biological Sciences Research Council Norwich Research Park Biosciences Doctoral Training Partnership, UK [Grant number BB/M011216/1].
Faculty \ School:	Faculty of Science > School of Computing Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Computational Biology Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation Faculty of Science > Research Groups > Data Science and AI
Depositing User:	LivePure Connector
Date Deposited:	15 Mar 2024 09:30
Last Modified:	10 Dec 2024 01:43
URI:	https://ueaeprints.uea.ac.uk/id/eprint/94703
DOI:	10.1016/j.jtbi.2024.111794

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