Ancestral sequence reconstruction with maximum parsimony
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Abstract: One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference as well as for ancestral sequence inference is Maximum Parsimony (MP). In this manuscript, we focus on this method and on ancestral state inference for fully bifurcating trees. In particular, we investigate a conjecture published by Charleston and Steel in 1995 concerning the number of species which need to have a particular state, say , at a particular site in order for MP to unambiguously return as an estimate for the state of the last common ancestor. We prove the conjecture for all even numbers of character states, which is the most relevant case in biology. We also show that the conjecture does not hold in general for odd numbers of character states, but also present some positive results for this case.
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Cites work
- scientific article; zbMATH DE number 3821741 (Why is no real title available?)
- scientific article; zbMATH DE number 1865935 (Why is no real title available?)
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- Inferring ancestral sequences in taxon-rich phylogenies
- On the balance of unrooted trees
Cited in
(16)- On the accuracy of ancestral sequence reconstruction for ultrametric trees with parsimony
- Minimal Conflicting Sets for the Consecutive Ones Property in Ancestral Genome Reconstruction
- Pairwise sequence alignment at arbitrarily large evolutionary distance
- Cases in which ancestral maximum likelihood will be confusingly misleading
- On characteristics of ancestral character-state reconstructions under the accelerated transformation optimization
- How to infer ancestral genome features by parsimony: dynamic programming over an evolutionary tree
- On the number of binary characters needed to recover a phylogeny using maximum parsimony
- Ancestral state reconstruction with large numbers of sequences and edge-length estimation
- A comparison of ancestral state reconstruction methods for quantitative characters
- Sufficient condition for root reconstruction by parsimony on binary trees with general weights
- Counting ancestral reconstructions in a fixed phylogeny
- Probabilistic ancestral sequences and multiple alignments
- Quantifying the accuracy of ancestral state prediction in a phylogenetic tree under maximum parsimony
- Maximum parsimony on subsets of taxa
- Non-hereditary maximum parsimony trees
- Reconstructing evolution of sequences subject to recombination using parsimony
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