Ancestral state reconstruction with large numbers of sequences and edge-length estimation

DOI10.1007/S00285-022-01715-5MaRDI QIDQ2113521zbMATH OpenOpenAlexWikidataFDO

Authors Lam Si Tung Ho, Edward Susko

Publication date 14 March 2022

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

Full work available at URL https://arxiv.org/abs/2104.00151

zbMATH Keywords

ancestral state reconstructionconsistencyempirical Bayes estimatorevolutionmaximum likelihood estimatorphylogenetics

Mathematics Subject Classification ID

Problems related to evolution (92D15)

Abstract: Likelihood-based methods are widely considered the best approaches for reconstructing ancestral states. Although much effort has been made to study properties of these methods, previous works often assume that both the tree topology and edge lengths are known. In some scenarios the tree topology might be reasonably well known for the taxa under study. When sequence length is much smaller than the number of species, however, edge lengths are not likely to be accurately estimated. We study the consistency of the maximum likelihood and empirical Bayes estimators of ancestral state of discrete traits in such settings under a star tree. We prove that the likelihood-based reconstruction is consistent under symmetric models but can be inconsistent under non-symmetric models. We show, however, that a simple consistent estimator for the ancestral states is available under non-symmetric models. The results illustrate that likelihood methods can unexpectedly have undesirable properties as the number of sequences considered get very large. Broader implications of the results are discussed.

Review text

The main goal of the present work using likelihood-based methods is to study the consistency of the maximum likelihood and empirical Bayes estimators of the ancestral state of discrete traits in such settings under a star tree. The authors prove that the likelihood-based reconstruction is consistent under symmetric models but can be inconsistent under non-symmetric models. More preciously speaking they show that in this setting the maximum likelihood estimator (MLE) and empirical Bayes estimator (sometimes also referred to as the maximum a posteriori (MAP) estimator) converge upon the same solution. Consequently, it suffices to consider the MLE. The MLE is shown to be consistent under symmetric models but there exists a zone of inconsistency under non-symmetric models. They show, also, that a simple consistent estimator for the ancestral states is available under non-symmetric models. It is noted by them that in some species, for which sequence length is much smaller than the number of species, edge lengths are not likely to be accurately estimated, whatever is the tree topology is reasonable or not. The results illustrate that the likelihood methods can unexpectedly have undesirable properties as the number of sequences considered gets very large. Broader implications of the results are discussed.

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Cites work

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Cited in

(11)

• Multi-task learning improves ancestral state reconstruction
• Choosing the best ancestral character state reconstruction method
• On the convergence of the maximum likelihood estimator for the transition rate under a 2-state symmetric model
• Statistically consistent and computationally efficient inference of ancestral DNA sequences in the TKF91 model under dense taxon sampling
• Cases in which ancestral maximum likelihood will be confusingly misleading
• A comparison of ancestral state reconstruction methods for quantitative characters
• Efficient estimation of the accuracy of the maximum likelihood method for ancestral state reconstruction
• Ancestral sequence reconstruction for co-evolutionary models
• When can we reconstruct the ancestral state? Beyond Brownian motion
• When can we reconstruct the ancestral state? A unified theory
• Inferring ancestral sequences in taxon-rich phylogenies

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