Bridging two scholarly islands enriches both: COI DNA barcodes for species identification versus human mitochondrial variation for the study of migrations and pathologies

Abstract

DNA barcodes for species identification and the analysis of human mitochondrial variation have developed as independent fields even though both are based on sequences from animal mitochondria. This study finds questions within each field that can be addressed by reference to the other. DNA barcodes are based on a 648‐bp segment of the mitochondrially encoded cytochrome oxidase I. From most species, this segment is the only sequence available. It is impossible to know whether it fairly represents overall mitochondrial variation. For modern humans, the entire mitochondrial genome is available from thousands of healthy individuals. SNPs in the human mitochondrial genome are evenly distributed across all protein‐encoding regions arguing that COI DNA barcode is representative. Barcode variation among related species is largely based on synonymous codons. Data on human mitochondrial variation support the interpretation that most – possibly all – synonymous substitutions in mitochondria are selectively neutral. DNA barcodes confirm reports of a low variance in modern humans compared to nonhuman primates. In addition, DNA barcodes allow the comparison of modern human variance to many other extant animal species. Birds are a well‐curated group in which DNA barcodes are coupled with census and geographic data. Putting modern human variation in the context of intraspecies variation among birds shows humans to be a single breeding population of average variance.

Why should mitochondria define species?

“…Modern humans are a low-average animal species in terms of the APD. The molecular clock as a heuristic marks 1% sequence divergence per million years which is consistent with evidence for a clonal stage of human mitochondria between 100,000-200,000 years ago and the 0.1% APD found in the modern human population [34,155,156]. A conjunction of factors could bring about the same result.…”

“…The most data are available for modern humans, who have an APD of 0.1% calculated in the same way as for other animals (See Fig. 2 in [34] and Fig. 7 in this paper).…”

“…The best documented mechanism for altering the efficiency of translation is when the changed codon(s) are near to the first-translated end of the gene [54]. The approximately even distribution of synonymous variation among mitochondrial genes in modern humans [34] is most compatible with neutrality [63].…”

Indication of ongoing amphipod speciation in Lake Baikal by genetic structures within endemic species

“…The evolutionary rates of mtDNA in different animal taxa were indicated by studies e.g. on the Drosophila obscura group [18] and on humans and chimpanzees [19] examining COI sequence differences. Based on those studies it may be assumed that a separation of E. verrucosus from the west coast and from Bolshoy Ushkaniy Island for 150,000 years should result in a genetic divergence of < 1%, which would be in agreement with our observation.…”

COI and ND1 as DNA barcodes to identify Taenia hydatigena (Cestoda: Taeniidae) from canine small intestine on Hainan Island in China

“…There are approximately 4.5 million COI gene barcodes in GenBank and BOLD (Barcode of Life Data Systems), including different individuals across 250,000 species. It has become a common phenomenon to identify different animals by using the barcode of the COI gene (Thaler et al 2016). In the identification of some species, the COI gene is more suitable for identifying individuals (Laopichienpong et al 2016).…”