The impact of jumping alignments on mtDNA population analysis and database searching

Describing human mitochondrial DNA sequences by listing only those sites that differ from an aligned reference sequence is the standard practice for nomenclature. However this different-from-reference description can produce artificial alignments when comparing two non-reference sequences which in some situations may exaggerate the difference between the non-reference sequences-a problem called "jumping alignments." The impact of jumping alignments in database searching and population studies is evaluated. Alternative phylogenetic approaches for sequence alignment are also compared. The data show that a small percentage of jumping alignments occur with a standardized nomenclature system and with a phylogenetic approach, with a nominal impact on false exclusion database searching errors.