Inferring metric trees from weighted quartets via an intertaxon distance

DOI10.1007/S11538-020-00773-4MaRDI QIDQ786063zbMATH OpenOpenAlexWikidataFDO

Authors Samaneh Yourdkhani, John A. Rhodes

Publication date 12 August 2020

Published in Bulletin of Mathematical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/2002.04564

zbMATH Keywords

phylogenetic treedistancemultispecies coalescentquartetconsensus tree

Mathematics Subject Classification ID

Problems related to evolution (92D15) Taxonomy, cladistics, statistics in mathematical biology (92B10) Computational methods for problems pertaining to biology (92-08)

Abstract: A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these weights, and shown to exactly fit the same tree topology, but with edge weights rescaled by certain factors dependent on the associated split size. These distances are analogs for metric trees of similar ones recently introduced for topological trees that are based on induced unweighted rooted triples and quartets. The distances introduced here lead to new statistically consistent methods of inferring a metric species tree from a collection of topological gene trees generated under the multispecies coalescent model of incomplete lineage sorting. Simulations provide insight into their potential.

Recommendations

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Cites work

• Encoding phylogenetic trees in terms of weighted quartets
• Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent
• Reconstructing trees from subtree weights.
• Some uses of the Farris transform in mathematics and phylogenetics -- A review
• X-trees and weighted quartet systems

Cited in

(4)

• A distance-based model for convergent evolution
• Fast and accurate species trees from weighted internode distances
• Bayesian-weighted triplet and quartet methods for species tree inference
• Distributions of topological tree metrics between a species tree and a gene tree

Describes a project that uses

Uses Software

• MSCquartets
• FastMe
• ASTRID
• ASTRAL-II
• ape

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