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 of rDNA in fungi and plants changes with increasing genetic distance by successive removal of sequences from each data set followed by realignment and phylogenetic analysis. Increasing genetic distance can negatively affect phylogenetic reconstruction in two ways. First, it may cause errors in the alignment and therefore the homology hypotheses of the sequence characters. Second, it may cause errors in the homology assessments of character states because of multiple hits on individual branches. 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 gaps at the wrong positions. Errors in tree resolution, topology, and/or branch-support values were more often caused by multiple hits than by misaligned positions. This suggests that increasing genetic distance negatively affects our primary homology assessments of character states more severely than our primary homology assessments of characters. We suggest that increasing taxon sampling with the aim of subdividing long branches is a strategy for obtaining reliable alignments.