SIMMONS, MARK P.* and JOHN V. FREUDENSTEIN. The Ohio State University Herbarium, Ohio State University, 1315 Kinnear Road, Columbus, Ohio 43212. - The effects of increasing genetic distance on alignment of, and tree construction from, rDNA internal transcribed spacer sequences.
We examined how alignment of internal transcribed spacers (ITS) of
rDNA changes with increasing genetic distance between sequences, using
four fungal and four plant datasets. Increasing genetic distance can
negatively affect the tree topology and branch-support values in two
ways. First, it may cause errors in the alignment and therefore the
homology of the characters that are based on the misaligned positions.
Second, it may cause errors in the homology assessments of positions
that underwent multiple hits as genetic distance increased, therefore
causing errors in homology assessments of the states for those
characters. These two causes of error in phylogenetic inference were
distinguished from one another in our analysis. The errors in
alignment caused by increasing genetic distance were primarily due to
inserting too few gaps and inserting them at the wrong positions. We
suggest that terminals on branches that represent genetic distances of
over 0.118 are likely to have negative effects on tree construction
caused by misaligned positions and multiple hits. Significant errors
in tree resolution, topology, and/or branch-support values were more
often caused by multiple hits (and/or absence of interaction of the
excluded terminals with the included terminals) than by misaligned
positions. This suggests that increasing genetic distance negatively
affects our primary homology assessments of character states (due to
multiple hits) more severely than our primary homology assessments of
characters (due to misaligned positions). We suggest that increasing
taxon sampling with the aim of subdividing long branches is the
preferred strategy for obtaining reliable alignments; manual
adjustment of alignments and/or eliminating ambiguously aligned
positions from the analysis are of lesser benefit.
Key words: alignment, genetic distance, internal transcribed spacer, multiple hits, rDNA, tree construction