4.4 The choice of mtDNA.
Surprisingly, despite the popularity of mtDNA as a marker in
evolutionary studies, this assumption only relies on a handful of
comparisons involving mostly vertebrate’s species (Nabholz et al.,
2009). Depending on species, mtDNA mutation rate was much higher or
lower than nuclear DNA (nuDNA) rate. For example, it is not always
clonal, far from neutrally evolving and certainly not clock-like, and
the ratio of mitochondrial to nuclear mutation rate varies widely among
animals (Allio et al., 2017; Galtier et al., 2009). Despite these
long-acknowledged concerns, similar results were obtained in several
studies that have employed mtDNA and nuDNA to investigate genetic
structuring and demographic history in populations of marine fishes
(Machado-Schiaffino et al., 2009; Vinas et al., 2010; Adams et al.,
2006; Mccusker & Bentzen, 2010; Yang et al., 2022).