COI gene is widely used as a DNA marker for population study. Many textbooks for molecular ecology study I have read are always written that COI is neutral, but I don’t think so. As COI sequence can be translated into a subunit of cytochrome c oxidase, a functional protein in mitochondria, so this gene should be selected by natural selection.
No, its a functional gene. It's not neutral. However, synonymous mutations (those occuring in the 3rd codon position for each amino acid) will be selectively neutral. But its worth noting that selection can easily shape variation at this locus. More importantly, the whole mitochondria is essentially a single locus because it is essentially non-recombining. So strong selection on any other mitochondrial gene is likely to effect variation at COI.
" ... this gene is subject to strong purifying selection" (Ward R.D., Holmes B.H. 2007. An analysis of nucleotide and amino acid variability in the barcode region of cytochrome c oxidase I (cox1) in fishes // Molecular Ecology Notes. V. 7. P. 899–907).
So I'm seeing allot about purifying selection (selection that purges deleterious mutations) here, but what about strong positive selection favoring different haplotypes? Different haplotypes at this locus (or other linked mitochondrial genes) may be favored in different environments. In this way, a novel haplotype may rapidly sweep to fixation, potentially replacing all other haplotypes. A sweep of this kind would completely erase within population variation.
" ... multiple sites in all 13 mitochondrial proteins are inferred to have experienced positive selection early in snake evolution, with the highest number of sites occurring in COI and CytB ..." (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2376058/).
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