Exact and approximate limit behaviour of the Yule tree's cophenetic index
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Publication:1711952
Random graphs (graph-theoretic aspects) (05C80) Strong limit theorems (60F15) Applications of branching processes (60J85) Markov processes: hypothesis testing (62M02) Applications of statistics to biology and medical sciences; meta analysis (62P10) Computational methods for problems pertaining to biology (92-08) Taxonomy, cladistics, statistics in mathematical biology (92B10) Problems related to evolution (92D15)
Abstract: In this work we study the limit distribution of an appropriately normalized cophenetic index of the pure-birth tree conditioned on contemporary tips. We show that this normalized phylogenetic balance index is a submartingale that converges almost surely and in L2. We link our work with studies on trees without branch lengths and show that in this case the limit distribution is a contraction-type distribution, similar to the Quicksort limit distribution. In the continuous branch case we suggest approximations to the limit distribution. We propose heuristic methods of simulating from these distributions and it may be observed that these algorithms result in reasonable tails. Therefore, we propose a way based on the quantiles of the derived distributions for hypothesis testing, whether an observed phylogenetic tree is consistent with the pure-birth process. Simulating a sample by the proposed heuristics is rapid, while exact simulation (simulating the tree and then calculating the index) is a time-consuming procedure. We conduct a power study to investigate how well the cophenetic indices detect deviations from the Yule tree and apply the methodology to empirical phylogenies.
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Cites work
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Cited in
(4)- On a problem of Yekutieli and Mandelbrot about the bifurcation ratio of binary trees
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- Squaring within the Colless index yields a better balance index
- Limit distribution of the quartet balance index for Aldous's \((\beta \ge 0)\)-model
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