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

README for data set from Nuryadi et al. 2025 Rapid concerted evolution of mitochondrial control regions by routine recombination. Proceedings of the Royal Society B. The data set accompanies one Dryad data file.

Uploaded: May 2025
Revised:
Contact: Kazunori Yamahira ([[e-mail]](mailto:[e-mail]))

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File_01_CR1_and_CR2_sequence.fas

The fasta file containing mitochondrial control region 1 and control region 2 sequences (634 bp) of Oryzias setnai, which was used for the ML phylogeny in figure 4.

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File_02_File_02_Short_read_amplicon_sequence_and_count.txt

The text file containing the data listed below.

*Amplicon group*: Short-read amplicon group
*Target region*: Target region (CR1 or CR2) amplified
*Sequence*: Sequences obtained
*Individual*: Individual ID of each sequence
*Read type*: Read type of each sequence (CR1 ...,