Population Genomic Analysis in Wild Medaka Populations: Identifying Candidate Loci for Balancing Selection
9 affiliations
- 1Integrated Technology Center University of the Ryukyus Okinawa Japan
- 2Laboratory of Molecular Reproductive Biology, Institute for Environmental Sciences University of Shizuoka Shizuoka Japan
- 3Natural History Museum and Institute Chiba Chiba Japan
- 4Ryukyu University Museum Fujukan University of the Ryukyus Okinawa Japan
- 5School of Ocean and Earth Science University of Southampton Southampton UK
- 6Research Center for Conservation of Marine and Inland Water Resources National Research and Innovation Agency Jakarta Indonesia
- 7Graduate School of Fisheries and Environmental Sciences Nagasaki University Nagasaki Japan
- 8Faculty of Agriculture Setsunan University Hirakata Osaka Japan
- 9Graduate School of Medicine University of the Ryukyus Okinawa Japan
Abstract
Sexual selection, defined as individual differences in reproductive success, can contribute to the maintenance of genetic polymorphisms through pleiotropic trade‐offs between life history components. However, the extent to which sexual selection maintains genetic polymorphisms in wild populations remains unclear. Here, we explored genomic signatures of balancing selection and selective sweep in the northern medaka, Oryzias sakaizumii in Japan by performing whole‐genome resequencing of wild individuals. In addition, we reevaluated the population genetic structure and admixture of Oryzias latipes and O. sakaizumii across the Japanese archipelago and identified genomic regions largely affected by introgression between the two species using F d statistics to distinguish signatures of balancing selection from patterns potentially caused by introgression. Based on multiple population genetic statistics, we identified 18 candidate genomic regions showing signatures of selection. In particular, a 100‐kb region at 6.85–6.95 Mb on chromosome 18 showed high genetic diversity that did not show outlier for the F d statistics, indicating the extent of introgression in this region did not largely differ from the genome‐wide average. This pattern suggests that balancing selection maintains genetic polymorphisms of the locus in O. sakaizumii . The overlap with a QTL for female mating behavior and the known molecular function of a gene within this candidate region for balancing selection suggest that sexual selection through female mate choice may contribute to the maintenance of polymorphism at this locus.
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BibTeX
@article{fujimoto2026population,
title = {{Population Genomic Analysis in Wild Medaka Populations: Identifying Candidate Loci for Balancing Selection}},
author = {Shingo Fujimoto and Taijun Myosho and Hirozumi Kobayashi and Hiroaki Aoyama and Iki Murase and Bayu K. A. Sumarto and Mitsuharu Yagi and Taiga Kunishima and Masatoshi Matsunami and Ryosuke Kimura},
journal = {Ecology and Evolution},
year = {2026},
month = oct,
doi = {10.1002/ece3.74383},
url = {https://onlinelibrary.wiley.com/doi/10.1002/ece3.74383},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Population Genomic Analysis in Wild Medaka Populations: Identifying Candidate Loci for Balancing Selection
AU - Shingo Fujimoto
AU - Taijun Myosho
AU - Hirozumi Kobayashi
AU - Hiroaki Aoyama
AU - Iki Murase
AU - Bayu K. A. Sumarto
AU - Mitsuharu Yagi
AU - Taiga Kunishima
AU - Masatoshi Matsunami
AU - Ryosuke Kimura
PY - 2026
DA - 2026/10/21
JO - Ecology and Evolution
DO - 10.1002/ece3.74383
UR - https://onlinelibrary.wiley.com/doi/10.1002/ece3.74383
AB - Sexual selection, defined as individual differences in reproductive success, can contribute to the maintenance of genetic polymorphisms through pleiotropic trade‐offs between life history components. However, the extent to which sexual selection maintains genetic polymorphisms in wild populations remains unclear. Here, we explored genomic signatures of balancing selection and selective sweep in the northern medaka, Oryzias sakaizumii in Japan by performing whole‐genome resequencing of wild individuals. In addition, we reevaluated the population genetic structure and admixture of Oryzias latipes and O. sakaizumii across the Japanese archipelago and identified genomic regions largely affected by introgression between the two species using F d statistics to distinguish signatures of balancing selection from patterns potentially caused by introgression. Based on multiple population genetic statistics, we identified 18 candidate genomic regions showing signatures of selection. In particular, a 100‐kb region at 6.85–6.95 Mb on chromosome 18 showed high genetic diversity that did not show outlier for the F d statistics, indicating the extent of introgression in this region did not largely differ from the genome‐wide average. This pattern suggests that balancing selection maintains genetic polymorphisms of the locus in O. sakaizumii . The overlap with a QTL for female mating behavior and the known molecular function of a gene within this candidate region for balancing selection suggest that sexual selection through female mate choice may contribute to the maintenance of polymorphism at this locus.
SN - 2045-7758
SN - 2045-7758
ER -