Data from: Routine mitochondrial recombination drives rapid concerted evolution of duplicated control regions in a wild fish

Duplications and concerted evolution of control regions (CRs) in animal
mitogenomes have been reported across diverse taxa, yet the tempo and
mechanism of gene conversion remain poorly understood. Here, we assembled
the complete mitochondrial genome of the western Indian ricefish Oryzias
setnai and found that the CR is duplicated. Comparative analysis of CR1
and CR2 sequences across individuals sampled throughout the species’ range
revealed that they are identical in most individuals, and differ by only
one or two mutations in the rest—indicating recent and ongoing concerted
evolution. We estimated that gene conversion events occur at a rapid pace,
on the order of once every <1,000 years or less. Using both short-
and long-read amplicon sequencing, we directly detected a substantial
number of recombinant mitogenome molecules resulting from homologous
recombination between CR paralogues. This provides the first clear
evidence that homologous recombination is the mechanism driving
mitochondrial gene conversion. Our findings challenge the prevailing view
that recombination in animal mitochondria is exceedingly rare, and
demonstrate that mitogenome recombination can occur routinely in natural
populations.