No homology means there can be no analyses; a comment on Jose & Harikrishnan (Letter)

Abstract

A recent paper (Jose & Harikrishnan 2016) considers some issues surrounding the use of mitochondrial (mt) cytochrome c oxidase subunit I (COI or COX1) sequences as DNA barcodes. They provide a particular example of how the presence of two commonly used fragments of the gene, that are largely non-homologous, could lead to confusion for taxonomy, in this case for decapod crustaceans. Jose and Harikrishnan (2016) show the divergence between two COI fragments (termed ‘Folmer’ and ‘Palumbi’) for some freshwater shrimp taxa (Family Palaemonidae, Genus Macrobrachium) through a number of analyses, including neighbor-joining phylograms, sequence distance calculations and pairwise