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

DOI10.1007/S00285-022-01715-5zbMATH Open1493.92039arXiv2104.00151OpenAlexW3141301832WikidataQ113905408 ScholiaQ113905408MaRDI QIDQ2113521FDOQ2113521

Authors: Lam Si Tung Ho, Edward Susko 

Publication date: 14 March 2022

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

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.

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

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zbMATH Keywords

consistencyphylogeneticsmaximum likelihood estimatorevolutionancestral state reconstructionempirical Bayes estimator

Mathematics Subject Classification ID

Problems related to evolution (92D15)

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Cited In (5)

• Inferring ancestral sequences in taxon-rich phylogenies
• When can we reconstruct the ancestral state? A unified theory
• When can we reconstruct the ancestral state? Beyond Brownian motion
• Choosing the best ancestral character state reconstruction method
• Statistically consistent and computationally efficient inference of ancestral DNA sequences in the TKF91 model under dense taxon sampling

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