Alignment-ambiguous nucleotide sites and the exclusion of systematic data.
Molecular systematists generally rely on computer algorithms to establish the alignment of DNA sequences. However, when alignment regions are characterized by multiple insertions and deletions, these gap-filled stretches of DNA are often excised before phylogenetic reconstruction. This exclusion of systematic data is generally determined by subjective criteria. We explore a replicable methodology in which the comparison of several multiple sequence alignments can be used to eliminate regions of unstable sequence alignment. Using crocodilian and insect mitochondrial (mt) ribosomal (r) DNA as examples, we caution against the removal of sequence data prior to phylogenetic reconstruction.
Department of Invertebrates, American Museum of Natural History, New York, New York 10024.
J
J
Gatesy
R
R
DeSalle
W
W
Wheeler
D000465:Algorithms; D000489:Alligators and Crocodiles / Q000145:classification / Q000235:genetics; D000818:Animals; D001483:Base Sequence; D004272:DNA, Mitochondrial / Q000235:genetics; D007313:Insecta / Q000145:classification / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment
D004272:DNA, Mitochondrial