Abstract
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 1000 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.
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Data availability
Raw sequences of the WGS and amplicon sequencing were registered in the DNA Data Bank of Japan (DDBJ) Sequence Read Archive under accession numbers DRR683959–DRR683961 and DRR685343–DRR685352, respectively. The complete mitogenome sequences and all CR sequences were also registered in DDBJ under accession numbers LC863176–LC863178 and LC870776–LC870877, respectively. All data used in the analyses are available from the Dryad Digital Repository: https://doi.org/10.5061/dryad.2547d7x3s.
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Acknowledgements
This study was conducted following the Regulation for Animal Experiments at the Kerala University of Fisheries and Ocean Studies (KUFOS), Kochi, India, and with permission from the National Biodiversity Authority (NBA) (permission number: INBAB202204012/22/22-23/2649). KUFOS provided basic facilities for laboratory experiments. We thank Suzanne Leech, PhD, from Edanz (http://jp.edanz.com/ac) for editing a draft of this manuscript.
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This study was supported by JSPS KAKENHI (grant no. 17H01675 and 21H04782) and JST CREST (grant no. JPMJCR20S2) to KY.
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KY conceived the study. VKA and RR conducted field collections, and HN performed laboratory molecular work. HN, JG, and KY performed analyses of PCR and WGS data, and RK and KY performed analyses of amplicon sequencing data. HN, RK, and KY wrote the first version of the manuscript, and all authors revised the manuscript.
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Nuryadi, H., Anoop, V.K., Kakioka, R. et al. Routine mitochondrial recombination drives rapid concerted evolution of duplicated control regions in a wild fish. Heredity 135, 46–54 (2026). https://doi.org/10.1038/s41437-025-00817-2
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DOI: https://doi.org/10.1038/s41437-025-00817-2
