ArticleGenetics2015
Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution.
Article in Genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Dinucleotide preferences underlie apparent codon preference reversals in theProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Extant Sequence Reconstruction: The Accuracy of Ancestral Sequence Reconstructions Evaluated by Extant Sequence Cross-Validation.Journal of molecular evolution · 2024Article
- DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies.Systematic biology · 2023Article
- The diverse terminology of reptile eggshell microstructure and its effect on phylogenetic comparative analyses.Journal of anatomy · 2022Review
- Evidence for a force favoring GC over AT at short intronic sites in Drosophila simulans and Drosophila melanogaster.G3 (Bethesda, Md.) · 2021Article
- Investigation of ancestral alleles in the Bovinae subfamily.BMC genomics · 2021Article
- Alignment-Integrated Reconstruction of Ancestral Sequences Improves Accuracy.Genome biology and evolution · 2020Article
- A Darwinian Uncertainty Principle.Systematic biology · 2020Article
- Impact of C-terminal amino acid composition on protein expression in bacteria.Molecular systems biology · 2020Article
- Noncoding regions underpin avian bill shape diversification at macroevolutionary scales.Genome research · 2020Article
- Allele-specific nonstationarity in evolution of influenza A virus surface proteins.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Methods for Estimating Demography and Detecting Between-Locus Differences in the Effective Population Size and Mutation Rate.Molecular biology and evolution · 2019Article
- Mitochondrial genome diversity and evolution in Branchiopoda (Crustacea).Zoological letters · 2019Article
- Ancestral Function and Diversification of a Horizontally Acquired Oomycete Carboxylic Acid Transporter.Molecular biology and evolution · 2018Article
- Inferring the Probability of the DerivedGenetics · 2018Article
- Alignment Modulates Ancestral Sequence Reconstruction Accuracy.Molecular biology and evolution · 2018Article
- Distinguishing Among Evolutionary Forces Acting on Genome-Wide Base Composition: Computer Simulation Analysis of Approximate Methods for Inferring Site Frequency Spectra of Derived Mutations.G3 (Bethesda, Md.) · 2018Article
- Determinants of the Efficacy of Natural Selection on Coding and Noncoding Variability in Two Passerine Species.Genome biology and evolution · 2017Article
- Variation in the Intensity of Selection on Codon Bias over Time Causes Contrasting Patterns of Base Composition Evolution in Drosophila.Genome biology and evolution · 2017Article
- An experimental phylogeny to benchmark ancestral sequence reconstruction.Nature communications · 2016Article
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Authors and funding
3 authors.
Funding
Abstract
Inference of gene sequences in ancestral species has been widely used to test hypotheses concerning the process of molecular sequence evolution. However, the approach may produce spurious results, mainly because using the single best reconstruction while ignoring the suboptimal ones creates systematic biases. Here we implement methods to correct for such biases and use computer simulation to evaluate their performance when the substitution process is nonstationary. The methods we evaluated include parsimony and likelihood using the single best reconstruction (SBR), averaging over reconstructions weighted by the posterior probabilities (AWP), and a new method called expected Markov counting (EMC) that produces maximum-likelihood estimates of substitution counts for any branch under a nonstationary Markov model. We simulated base composition evolution on a phylogeny for six species, with different selective pressures on G+C content among lineages, and compared the counts of nucleotide substitutions recorded during simulation with the inference by different methods. We found that large systematic biases resulted from (i) the use of parsimony or likelihood with SBR, (ii) the use of a stationary model when the substitution process is nonstationary, and (iii) the use of the Hasegawa-Kishino-Yano (HKY) model, which is too simple to adequately describe the substitution process. The nonstationary general time reversible (GTR) model, used with AWP or EMC, accurately recovered the substitution counts, even in cases of complex parameter fluctuations. We discuss model complexity and the compromise between bias and variance and suggest that the new methods may be useful for studying complex patterns of nucleotide substitution in large genomic data sets.
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