PAST WORK
Data Analysis - Sequence Alignments and Indels
DNA sequence analyses are critically reliant upon the ability to identify and compare homologous nucleotide positions. This task is greatly complicated by insertion and deletion events because, unless they are recognized, sequence comparisons downstream of their occurrence will involve sites that are not homologous. The analysis of ribosomal DNA is particularly difficult because indels are relatively common since the excision or insertion of a few nucleotides often has little impact on rRNA function. Moreover, there are no clear structural cues to signal their precise position. By contrast, indels are much less common in protein-coding genes because they ordinarily lead to a shift in the reading frame, savaging the gene product. Because of the rarity of indels, protein-coding genes are easier to align. Moreover, when an indel is present, it invariably involves the addition of a multiple of 3 nucleotides to enable preservation of the reading frame.

Indels in COI
Complete COI sequences are now available for 70 mammals, 66 bony fishes, 30 arthropods and 26 members of other phyla. The shortest reported COI gene product is 510 amino acids long (in the silkworm, Bombyx mori), while the largest is 534 amino acids long (in the colubrid snake, Dinodon semicorinatus).

Although further work is required to provide a detailed view of their occurrence, past studies have indicated that most of the indels responsible for these length variations occur in the COI-3' section. However, indels are not unknown in the COI-5' segment. In some cases, all members of a major taxonomic group share an indel, suggesting its occurrence early in evolution of the lineage. For example, members of the phylum Aschelminthes possess a 3bp insert at nucleotide position 78. In other cases, indels have a much narrower taxonomic distribution, suggesting their recent origin. These indels tend to recur in certain regions of COI-5'. For example, almost all of the indels detected in gastropod molluscs occur in E2, the second external loop.