Change in mt DNA Genotype via Selection
An alternative hypothesis to both neutral drift and demographic
bottlenecks for the generation of mt DNA barcode gaps between species is
directional selection on mt genotypes. Natural selection has the
potential to shape the mt genome in response to two distinct
environments: the external environment (both biotic and abiotic) and the
internal genomic environment created by the N genome (Rand et al. 2004;
Zhu et al. 2014; Barreto et al. 2018; Sloan et al. 2018; Hill 2019a).
There is now overwhelming evidence that the mt genome of at least some
animal lineages—and likely all animal lineages—are subject to
periods of directional selection as adaptive responses to the external
environment (Dowling et al. 2008; Ballard and Pichaud 2014; Kazancioǧlu
and Arnqvist 2014). In particular, thermal and chemical environments,
oxygen pressure, diet, salinity, and UV exposure can all exert natural
selection on the mt genome and lead to adaptive changes in
protein-coding genes (Ballard and Pichaud 2014; Hill 2019a). The
adaptive evolution of mt genomes in response to external environments is
now a major research topic in evolutionary biology (Sunnucks et al.
2017; Hill et al. 2019), and such changes to the nucleotide sequence of
mitochondria in response to directional selection pose a serious
challenge to core arguments for why mt DNA sequences will often fail as
a tool for diagnosing species (Hickerson et al. 2006). Adaptive
divergence of mt genotype in response to external environment is a key
reason why mt DNA is predicted to rapidly diverge between allopatric
populations (Gershoni et al. 2009; Tobler et al. 2019).
Perhaps even more important, and certainly more pervasive, than changes
to mt DNA gene sequence in response to external environment is the
potential for perpetual evolutionary change in the mt DNA in response to
changes in the internal genomic environment (Chou and Leu 2010; Burton
and Barreto 2012; Barreto et al. 2018; Sloan et al. 2018; Hill 2020).
The coadaptation of gene complexes is a foundational concept in
evolutionary biology (Dobzhansky 1937; Wright 1942). In a discussion of
the evolution of mt genomes, however, it is essential to grasp that
there are unique features to the co-evolution and coadaptation between
mt gene products and the products of a small list of N genes that code
for products that function in intimate interaction with mt gene products
(N-mt genes) (Hill 2019a; Shtolz and Mishmar 2019). First, the system
that depends on coadaptation of mt and N-mt genes—the electron
transport system—is the most critical biochemical system in the bodies
of eukaryotes that depend on energy from aerobic respiration (Wallace
2010; Lane 2014). Second, because of the complexity of the ETS in
controlling the flow of electrons and pumping of protons, very small
changes to interacting components can have huge fitness effects (Lane
2011; Sloan et al. 2018; Hill 2019a; Hill et al. 2019). Third,
mitonuclear coadaptation involves two genomes that can potentially
undergo independent evolution (Rand et al. 2004; Gershoni et al. 2014;
Wolff et al. 2014). Fourth and finally, the mt genome of animals does
not generally engage in recombination (Barr et al. 2005) and so
mitochondrial genes form one linkage group such that selection on one mt
gene can affect the frequencies of other mt genes (Meiklejohn et al.
2007; Oliveira et al. 2008). Functional divergence in mt DNA will be
particularly effective in creating Dobzhansky-Muller incompatibilities
in hybrid offspring and hence in establishing barriers to gene flow
because the mt DNA must maintain tight coadaptation with the N genome
(Burton and Barreto 2012; Hill 2017).
If changes in mt genotype between species were entirely neutral, then
matching the N genes of one species with the mt genes of a closely
related species—either through hybridization or in cell culture by
directly manipulating genomes—should result in no change in
mitochondrial function in the resulting cells or organisms. Indeed, this
logical extension of the neutral theory of mitochondrial evolution led
to a failed research program to propagate endangered species by pairing
mitochondria of donor species to the N genome of the species to be saved
(Lanza et al. 2000). Observations from cybrid and hybrid studies,
however, clearly established that, once sets of mt and N-mt genes
diverge in nucleotide sequences to the extent seen in sister species,
incompatibilities in non-coadapted gene sets cause a reduction in
mitochondrial function when they are forced to work together (reviewed
in Hill (2019a)). Mitonuclear incompatibilities in cybrid cells and
hybrid organisms is strong evidence that the evolution of mt genotypes
is not neutral with respect to the genomic environment (Barrientos et
al. 1998; Ellison and Burton 2008b; Lee et al. 2008; Garvin et al. 2011;
Latorre-Pellicer et al. 2016).
The evolution of uniquely coadapted mt and N-mt genotypes is a critical
concept because it potentially explains both how the mt genotypes of
sister species rapidly diverge and why there is so little introgression
of divergent mt genotypes between species within most clades of
bilaterian animals (Burton and Barreto 2012; Hill 2016). The evolution
of a clean mt DNA barcode gap requires that the propagation of
population-specific mitochondrial genotypes are constrained to remain
within species boundaries across generations (Hebert et al. 2003b). Even
a small amount of introgressive flow of mitochondrial genotypes, which
would be inevitable under neutral models of mitochondrial evolution if
species lived in sympatry, would add unacceptable ambiguity into
barcoding efforts (Papadopoulou et al. 2008). In the rare cases in which
mitochondria do introgress across species boundaries, the introgression
tends to be rampant, with complete replacement of one mitochondrial
genotype by another (Hill 2019b). All of these patterns are consistent
with a process whereby coevolution of mt and N-mt genotypes leads to
loss of fitness (at the level of the individual organism) when mt
genotypes are paired to N-mt genes to which they are not coadapted. The
barcode gap is more than an arbitrary marker of species boundaries—it
is the functional boundary that reinforces the uniqueness of a species’
mitonuclear genotype (Lane 2009a; Chou and Leu 2010; Burton and Barreto
2012; Hill 2016, 2017).