Data from: Population genomic analysis in wild medaka populations: Identifying candidate loci for balancing selection
Data files
Sep 25, 2026 version files 19.55 GB
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 sweeps in the northern medaka, Oryzias sakaizumii, in Japan by performing whole-genome resequencing of wild individuals. In addition, we re-evaluated 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 Fd 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 an outlier for the Fd statistics, indicating that 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.
Dataset DOI: 10.5061/dryad.xpnvx0kth
Description of the data and file structure
Files and variables
File: medakaWGS_sak40samples_snpsQC_exIndelMultialleic_snps.vcf.gz
Description: bgzip compressed VCF file format
Single-nucleotide variant and invariant sites dataset based on whole-genome re-sequencing of wild medaka populations (Oryzias latipes and Oryzias sakaizumii) in the Japanese archipelago. Wild individuals were collected from 26 locations between 2019 and 2021. Population structure and introgressive region between O. latipes and O. sakaizumii were examined.
Wild individuals were collected from four locations, including Aomori (N = 8), Kitatsugaru (N = 8), Niigata (N = 8), and Tsuruga (N= 16). An equal number of Males and females were sequenced in each location.
File: medakaWGS_sak_lat_45samples_snpsQC_invariant.vcf.gz
Description: bgzip compressed VCF file format
To explore the signature of selection in Oryzias sakaizumii, genome scans were performed using nucleotide diversity,Tajima's D, Intersexual-FST, and Integrated haplotype score. Wild individuals were collected from four locations of O. sakaizumii, including Aomori (N = 8), Kitatsugaru (N = 8), Niiga
Single-nucleotide variant and invariant sites based on whole-genome re-sequencing of wild medaka populations (Oryzias latipes and Oryzias sakaizumii) in the Japanese archipelago. 44 wild individuals were collected from 26 locations between 2019 and 2021. Genotype data of one individual of the HSOK strain (from the East Korean population) was excluded from this publicly available dataset because the individual was sequenced by another researcher (Spivakov et al. 2014, G3; Genes|Genomes|Genetics, https://doi.org/10.1534/g3.113.008722).
Code/software
Bgzip-compressed VCF files can be opened using BCFtools.
Twelve years of SAMtools and BCFtools
Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li
GigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008
Access information
Other publicly accessible locations of the data:
- Sequences of wild individuals (Oryzias latipes and Oryzias sakaizumii) were deposited in the DDBJ Sequence Read Archive (DRA) database under the accession number (BioProject: PRJDB20255).
Data was derived from the following sources:
- Ichikawa, K., Tomioka, S., Suzuki, Y., Nakamura, R., Doi, K., Yoshimura, J., ... & Morishita, S. (2017). Centromere evolution and CpG methylation during vertebrate speciation. Nature communications, 8(1), 1833.