Quantifying the accuracy of ancestral state prediction in a phylogenetic tree under maximum parsimony
- 158 Downloads
In phylogenetic studies, biologists often wish to estimate the ancestral discrete character state at an interior vertex v of an evolutionary tree T from the states that are observed at the leaves of the tree. A simple and fast estimation method—maximum parsimony—takes the ancestral state at v to be any state that minimises the number of state changes in T required to explain its evolution on T. In this paper, we investigate the reconstruction accuracy of this estimation method further, under a simple symmetric model of state change, and obtain a number of new results, both for 2-state characters, and r-state characters (\(r>2\)). Our results rely on establishing new identities and inequalities, based on a coupling argument that involves a simpler ‘coin toss’ approach to ancestral state reconstruction.
KeywordsPhylogenetic tree Markov process Maximum parsimony Coupling
Mathematics Subject Classification05C05 92D15
Lina Herbst thanks the University of Greifswald for the Landesgraduiertenförderung studentship and the German Academic Exchange Service (DAAD) for the DAAD-Doktorandenstipendium. Mike Steel thanks the New Zealand Marsden Fund (UOC-1709). We also thank Mareike Fischer for several helpful comments, Santiago Catalano for references to some recent biological studies, and the two anonymous reviewers for numerous helpful comments on an earlier version of this manuscript.
- Felsenstein J (2004) Inferring phylogenies. Sinauer Press, SunderlandGoogle Scholar
- Steel M, Penny D (2005) Maximum parsimony and the phylogenetic information in multi-state characters. In: Albert VA (ed) Parsimony, phylogeny and genomics. Oxford University Press, Oxford, pp 163–178Google Scholar
- Yang Z, Kumar S, Nei M (1995) A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641–1650Google Scholar