Species tree estimation under joint modeling of coalescence and duplication: sample complexity of quartet methods

DOI10.1214/22-AAP1799zbMATH Open1505.92139arXiv2007.06697OpenAlexW3042991511MaRDI QIDQ2108905FDOQ2108905

Authors: Max Hill, Brandon Legried, Sebastien Roch 

Publication date: 20 December 2022

Published in: The Annals of Applied Probability (Search for Journal in Brave)

Abstract: We consider species tree estimation under a standard stochastic model of gene tree evolution that incorporates incomplete lineage sorting (as modeled by a coalescent process) and gene duplication and loss (as modeled by a branching process). Through a probabilistic analysis of the model, we derive sample complexity bounds for widely used quartet-based inference methods that highlight the effect of the duplication and loss rates in both subcritical and supercritical regimes.

Full work available at URL: https://arxiv.org/abs/2007.06697

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zbMATH Keywords

phylogeneticsincomplete lineage sortingstatistical consistencygene duplication and loss

Mathematics Subject Classification ID

Problems related to evolution (92D15) Applications of branching processes (60J85) Coalescent processes (60J90)

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Cited In (3)

• Identifying species network features from gene tree quartets under the coalescent model
• Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss
• Statistically consistent rooting of species trees under the multispecies coalescent model

Uses Software

• BEAST
• ASTRAL-II
• BUCKy
• MSCquartets

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