ArticleNature communications2016
An experimental phylogeny to benchmark ancestral sequence reconstruction.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 82 citations in OpenAlex.
- Highly efficient production ofSynthetic and systems biotechnology · 2027Article
- Ancient enzymes, new biotechnology applications.Nature reviews. Molecular cell biology · 2026Article
- The tree labeling polytope: A unified approach to ancestral reconstruction problems.Cell systems · 2026Article
- High-stoichiometry mRNA (New York, N.Y.) · 2026Article
- A trimer ancestral spike-based mRNA vaccine confers cross-generational protection against SADS-CoV.Journal of nanobiotechnology · 2025Article
- GHIST 2024: The First Genomic History Inference Strategies Tournament.Molecular biology and evolution · 2025Article
- Injectable Hydrogels for Programmable Nanoparticle Release.Advanced functional materials · 2025Article
- Applications of ancestral sequence reconstruction for understanding the evolution of plant specialized metabolism.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Stable monomers in the ancestral sequence reconstruction of the last opisthokont common ancestor of dimeric triosephosphate isomerase.Protein science : a publication of the Protein Society · 2024Article
- Structure, mechanism, and evolution of the last step in vitamin C biosynthesis.Nature communications · 2024Article
- Extant Sequence Reconstruction: The Accuracy of Ancestral Sequence Reconstructions Evaluated by Extant Sequence Cross-Validation.Journal of molecular evolution · 2024Article
- Article
- Performance of tree-building methods using a morphological dataset and a well-supported Hexapoda phylogeny.PeerJ · 2024Article
- An Inferred Ancestral CotA Laccase with Improved Expression and Kinetic Efficiency.International journal of molecular sciences · 2023Article
- Ancestral reconstruction reveals catalytic inactivation of activation-induced cytidine deaminase concomitant with cold water adaption in the Gadiformes bony fish.BMC biology · 2022Article
- Evolutionary gain and loss of a plant pattern-recognition receptor for HAMP recognition.eLife · 2022Article
- Ancestral protein sequence reconstruction using a tree-structured Ornstein-Uhlenbeck variational autoencoder.... International Conference on Learning Representations · 2022Article
- Phylogenetic Articulation of Uric Acid Evolution in Mammals and How It Informs a Therapeutic Uricase.Molecular biology and evolution · 2022Article
- Methodologies for Microbial Ancestral Sequence Reconstruction.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Ancestral Sequence Reconstruction for Exploring Alkaloid Evolution.Methods in molecular biology (Clifton, N.J.) · 2022Article
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Authors and funding
5 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Ancestral sequence reconstruction (ASR) is a still-burgeoning method that has revealed many key mechanisms of molecular evolution. One criticism of the approach is an inability to validate its algorithms within a biological context as opposed to a computer simulation. Here we build an experimental phylogeny using the gene of a single red fluorescent protein to address this criticism. The evolved phylogeny consists of 19 operational taxonomic units (leaves) and 17 ancestral bifurcations (nodes) that display a wide variety of fluorescent phenotypes. The 19 leaves then serve as 'modern' sequences that we subject to ASR analyses using various algorithms and to benchmark against the known ancestral genotypes and ancestral phenotypes. We confirm computer simulations that show all algorithms infer ancient sequences with high accuracy, yet we also reveal wide variation in the phenotypes encoded by incorrectly inferred sequences. Specifically, Bayesian methods incorporating rate variation significantly outperform the maximum parsimony criterion in phenotypic accuracy. Subsampling of extant sequences had minor effect on the inference of ancestral sequences.
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