Phylogenetic inference from conserved sites alignments

Molecular sequences provide a rich source of data for inferring the phyloge netic relationships among species. However, recent work indicates that even an accurate multiple alignment of a large sequence set may yield an incorr ect phylogeny and that the quality of the phylogenetic tree improves when t he input consists only of the highly conserved, motif regions of the alignm ent. This work introduces two methods of producing multiple alignments that include only the conserved regions of the initial alignment. The first met hod retains conserved motifs, whereas the second retains individual conserv ed sites in the initial alignment. Using parsimony analysis on a mitochondr ial data set containing 19 species among which the phylogentetic relationsh ips are widely accepted, both conserved alignment methods produce better ph ylogenetic trees than the complete alignment. Unlike any of the 19 inferenc e methods used before to analyze this data, both methods produce trees that are completely consistent with the known phylogeny. The motif-based method employs far fewer alignment sites for comparable error rates. For a larger data set containing mitochondrial sequences from 39 species, the site-base d method produces a phylogenetic tree that is largely consistent with known phylogenetic relationships and suggests several novel placements. (C) 1999 Wiley-Liss, Inc.