DOI: 10.5061/dryad.9p8cz8wnb
title: Data from: Inference of selective force on house mice genomes during secondary contact in East Asia

description: The house mouse (Mus musculus), commensal to humans, has spread globally
 via human activities, leading to secondary contact between genetically
 divergent subspecies. This pattern of genetic admixture can provide
 insights into the selective forces at play in this well-studied model
 organism. Our analysis of 163 house mouse genomes, mainly from East Asia,
 revealed substantial admixture between the subspecies castaneus and
 musculus, particularly in Japan and southern China. We revealed, despite
 the admixture, that all Y chromosomes in the East Asian samples belonged
 to the musculus-type haplogroup, potentially explained by genomic
 conflict under sex ratio distortion due to varying copy numbers of
 ampliconic genes on sex chromosomes. We also investigated the influence of
 natural selection on the post-hybridization of the subspecies castaneus
 and musculus in Japan. Even though the genetic background of most Japanese
 samples closely resembles the subspecies musculus, certain genomic regions
 overrepresented the castaneus-like genetic components, particularly in
 immune-related genes. Furthermore, a large genomic block containing a
 vomeronasal/olfactory receptor gene cluster predominantly harbored
 castaneus-type haplotypes in the Japanese samples, highlighting the
 possible role of olfaction-based recognition in shaping hybrid genomes.
description: # Title of Dataset --- Inference of Selective Force on House Mice Genomes
 during Secondary Contact in East Asia Analysis of 163 house mouse genomes,
 mainly from East Asia, revealed considerable admixture between the
 castaneus and musculus subspecies, especially in Japan and southern China.
 Despite the admixture, all Y chromosomes in the East Asian samples
 belonged to the musculus haplogroup, which could be explained by genomic
 alleles under sex ratio distortion due to different copy numbers of
 amplified genes on sex chromosomes. This dataset contains configuration
 and script files for the simulation of X-chromosome, Y-chromosome, and
 mitochondrial genome introgression under sex ratio distortion, as well as
 for the demographic inference and admixture simulation of Mus musculus.
 First Author Information Name: Kazumichi Fujiwara Institution: (1)
 Graduate School of Information Science and Technology, Hokkaido
 University/(2) Mouse Genomics Resource Laboratory, National Institute of
 Genetics Address: (1) Kita 14, Nishi 9, Kita-ku, Sapporo, Hokkaido,
 060-0814, Japan/(2) 1111 Yata, Mishima, Shizuoka, 411-8540, Japan ORCID:
 [https://orcid.org/0000-0002-7840-4676](https://orcid.org/0000-0002-7840-4676) Email: [kazumichi.m.fujiwara@gmail.com](mailto:kazumichi.m.fujiwara@gmail.com) Corresponding author Information/Principal Investigator Name: Naoki Osada Institution: Graduate School of Information Science and Technology, Hokkaido University Address: Kita 14, Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0814, Japan ORCID: [https://orcid.org/0000-0003-0180-5372](https://orcid.org/0000-0003-0180-5372) Email: [nosada@ist.hokudai.ac.jp](mailto:nosada@ist.hokudai.ac.jp) Information about funding sources that supported our research The Ministry of Education,Culture,Sports,Science and Technology (MEXT) KAKENHI grant 18H05511, 23H04846, 18H05508 ## Description of the data and file structure /alpha_simulation/5pop_gf.est estimation file defining the parameters used in fastsimcoal2. /alpha_simulation/5pop_gf.tpl template file defining the demographic model of house mouse subspecies used in fastsimcoal2 /alpha_simulation/5pop_gf_MSFS.obs observed minor site frequency spectrum (MSFS) file of house mouse subspecies used in fastsimcoal2 /alpha_simulation/alpha_simulation.py python script to generate 20-kbp-length genomic fragments from samples using the maximum-likelihood estimators and estimate alpha 100,000 times /sex_ratio_distortion_simulation/XYsimulation.py python script to be used as module in simulation_main.py and perform sex-ratio distortion simulation with gene flow /sex_ratio_distortion_simulation/simulation_main.py main wrapper python script to simulate sex-ratio distortion using 7 parameters from command line. The paramters are, RAA, RXA, RMA, RXY, alpha, Nm, r. /sex_ratio_distortion_simulation/simulation_repeat.py\ sub wrapper python script to simulate sex-ratio distortion using 7 parameters from command line. The paramters are, RAA, RXA, RMA, RXY, alpha, Nm, r. /sex_ratio_distortion_simulation/results\ contains result files used in the manuscript. ## Sharing/Access information --- Links to other publicly accessible locations of the data: * to be updated Data was derived from the following sources: * PRJDB11969, PRJDB11027, PRJEB9450, PRJEB11742, PRJEB14167, PRJEB2176, PRJDB16017 ## Code/Software The scripts were written in python3. Dependency packages are follows: matplotlib numpy msprime tskit pandas IPython allel ([https://github.com/cggh/scikit-allel](https://github.com/cggh/scikit-allel))