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).