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.