Ancestral state reconstruction with large numbers of sequences and edge-length estimation
From MaRDI portal
Publication:2113521
DOI10.1007/S00285-022-01715-5zbMATH Open1493.92039arXiv2104.00151OpenAlexW3141301832WikidataQ113905408 ScholiaQ113905408MaRDI QIDQ2113521FDOQ2113521
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
Recommendations
- Efficient estimation of the accuracy of the maximum likelihood method for ancestral state reconstruction
- A comparison of ancestral state reconstruction methods for quantitative characters
- Global alignment of molecular sequences via ancestral state reconstruction
- Ancestral sequence reconstruction with maximum parsimony
- Time-dependent-asymmetric-linear-parsimonious ancestral state reconstruction
- Fast phylogeny reconstruction through learning of ancestral sequences
- Ancestral sequence reconstruction for co-evolutionary models
- Reconstructing ancestral character states under Wagner parsimony
- Multi-task learning improves ancestral state reconstruction
- Quantifying the accuracy of ancestral state prediction in a phylogenetic tree under maximum parsimony
consistencyphylogeneticsmaximum likelihood estimatorevolutionancestral state reconstructionempirical Bayes estimator
Cites Work
- Consistent Estimates Based on Partially Consistent Observations
- Consistency of the Maximum Likelihood Estimator in the Presence of Infinitely Many Incidental Parameters
- Analysis of comparative data with hierarchical autocorrelation
- Choosing the best ancestral character state reconstruction method
- Majority rule has transition ratio 4 on Yule trees under a 2-state symmetric model
- A few logs suffice to build (almost) all trees (I)
- A few logs suffice to build (almost) all trees. II
- Links between maximum likelihood and maximum parsimony under a simple model of site substitution
- Inferring ancestral sequences in taxon-rich phylogenies
- On the accuracy of ancestral sequence reconstruction for ultrametric trees with parsimony
- Necessary and sufficient conditions for consistent root reconstruction in Markov models on trees
- Multi-task learning improves ancestral state reconstruction
- Quantifying the accuracy of ancestral state prediction in a phylogenetic tree under maximum parsimony
- Consistency and convergence rate of phylogenetic inference via regularization
Cited In (3)
This page was built for publication: Ancestral state reconstruction with large numbers of sequences and edge-length estimation
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2113521)
