Ancestral sequence reconstruction with Maximum Parsimony

Preprint English OPEN
Herbst, Lina ; Fischer, Mareike (2017)
  • Subject: Mathematics - Combinatorics | Quantitative Biology - Populations and Evolution
    arxiv: Quantitative Biology::Genomics | Quantitative Biology::Populations and Evolution
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 $a$, at a particular site in order for MP to unambiguously return $a$ 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.
  • References (15)
    15 references, page 1 of 2

    1. M. Steel and M. Charleston, Five surprising properties of parsimoniously colored trees, Bulletin of Mathematical Biology, Volume 57, page 367-375 (1995)

    2. W. M. Fitch, Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology, Systematic Zoology, Volume 20, page 406-416 (1971)

    3. L. Herbst, Ancestral state reconstruction with parsimony, Master Thesis, Greifswald (2015)

    4. I. P. Goulden and D. M. Jackson, Combinatorial Enumeration, Wiley, New York (1983)

    5. C. Semple and M. Steel, Phylogenetics, Oxford University Press, New York (2003)

    6. J. Felsenstein, Inferring Phylogenies, Sinauer Associates, Inc (2004)

    7. D. A. Liberles (ed), Ancestral Sequence Reconstruction, Oxford University Press, New York (2007)

    8. L. Szekely, P. Erd¨os and M. Steel, The Combinatorics of Evolutionary Trees - a Survey, Journal of Combinatorial Mathematics and Combinatorial Computing, Volume 15, page 241-254 (1994)

    9. O. Gascuel and M.Steel, Predicting the ancestral character changes in a tree is typically easier than predicting the root state, Systematic Biology, Volume 63, page 421-435 (2014)

    10. O. Gascuel and M.Steel, Inferring ancestral sequences in taxon-rich phylogenies, Mathematical Biosciences, Volume 227, page 125-153 (2010)

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