Rooting gene trees without outgroups: EP rooting

Abstract

Gene sequences are routinely used to determine the topologies of unrooted phylogenetic trees, but many of the most important questions inevolutionrequire knowingboththe topologies andthe rootsof trees.However,general algorithms for calculatingrooted trees from gene and genomic sequences in the absence of gene paralogs are few.Using the principles of evolutionary parsimony (EP) (Lake JA. 1987a. A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Mol Biol Evol. 4:167-181) and its extensions (Cavender, J. 1989. Mechanized derivation of linear invariants. Mol Biol Evol. 6:301-316; Nguyen T, Speed TP. 1992. A derivation of all linear invariants for a nonbalanced transversion model. J Mol Evol. 35:60-76), we explicitly enumerate all linear invariants that solely contain rooting information and derive algorithms for rooting gene trees directly fromgene and genomic sequences. These newEP linear rooting invariants allowone to determine rooted trees, even in thecomplete absence of outgroups and gene paralogs. EP rooting invariants are explicitly derived for three taxon trees, and rules for their extension to four or more taxa are provided. The method is demonstrated using 18S ribosomal DNA to illustrate how the new animal phylogeny (Aguinaldo AMA et al. 1997. Evidence for a clade of nematodes, arthropods, and other moulting animals. Nature 387:489-493; Lake JA. 1990. Origin of themetazoa. Proc Natl Acad Sci USA 87:763-766) may be rooted directly fromsequences, evenwhen they are short and paralogs are unavailable. These results are consistent with the current root (Philippe H et al. 2011. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature 470:255-260). © 2012 The Author(s).