Diagnosing species with mitochondrial genes
There is a widely held view that the use of mt DNA to diagnose species is a certain-to-be-flawed approximation that evolutionary biologists must endure until advances in sequencing technology allow us to do the job correctly with N genes. Because the mitochondrial genome is a single linkage group (at least for bilaterian animals), it is proposed that sequences from multiple N genes will reveal species boundaries with fundamentally better accuracy than the mt genes (Pazhenkova and Lukhtanov 2019). For instance, Chase et al. (2005) wrote that we will advance from mt gene sequences to “more sophisticated barcoding tools, which would be multiple, low-copy nuclear markers with sufficient genetic variability and PCR-reliability” to “identify the ‘genetic gaps’ that are useful in assessing species limits”. Along the same lines, Edwards et al. (2005) commented that ‘in our view, maternally inherited mtDNA can never capture enough of a species’ history to delimit species on its own’ and that ‘mtDNA should not have priority over N genes in avian species delimitation.’ Furthermore, it is sometimes stated that mt genomes introgress across species boundaries more readily than N alleles (Bonnet et al. 2017). The success of DNA barcoding across the majority bilaterian animals is conspicuous evidence that introgression of mt genomes across species boundaries is a rare rather than a common event. As evolutionary biologists compare N genes and mt genes between closely related species of bilaterian animals, the typical pattern that emerges is that the boundaries revealed by N genes are fuzzy while the boundaries between mitochondrial genotypes are discrete (Barrowclough and Zink 2009; Petit and Excoffier 2009; Toews et al. 2016; Hill 2019a). This pattern, of course, is why mt genes are used as DNA barcode genes. If mitonuclear interactions underlie the process of speciation, species limits are best defined by coadapted sets of co-functioning mt and N-mt genes, and a close proxy to this true species diagnosis is simply mt genotype (Hill 2017).