Bidirectional Introgression between Mus musculus domesticus and Mus spretus

Abstract

Introgressed variants from other species can be an important source of genetic variation because they may arise rapidly, can include multiple mutations on a single haplotype, and have often been pre-tested by selection in the species of origin. While introgressed alleles are generally deleterious, several studies have reported introgression as the source of adaptive alleles—including the rodenticide resistant variant of Vkorc1 that introgressed from Mus spretus into European populations of Mus musculus domesticus. Here, we conducted bidirectional genome scans to characterize introgressed regions into one wild population of Mus spretus from Spain and three wild populations of Mus musculus domesticus from France, Germany and Iran. Despite the fact that these species show considerable intrinsic postzygotic reproductive isolation, introgression was observed in all individuals, including in the M. musculus reference genome (GRCm38). M. spretus individuals had a greater proportion of introgression compared to M. m. domesticus, and within M. m. domesticus the proportion of introgression decreased with geographic distance from the area of sympatry. Introgression was observed on all autosomes for both species, but not on the X-chromosome in M. m. domesticus, consistent with known X-linked hybrid sterility and inviability genes that have been mapped to the M. spretus X-chromosome. Tract lengths were generally short with a few outliers of up to 2.7 Mb. Interestingly, the longest introgressed tracts were in olfactory receptor regions, and introgressed tracts were significantly enriched for olfactory receptor genes in both species, suggesting that introgression may be a source of functional novelty even between species with high barriers to gene flow.

Genome polarisation for detecting barriers to geneflow

“…We compare diem to two methods inspired by phylogenetics (Banker et al . 2022) and population genetics (Falush et al .…”

“…(2022) study involves distances measured relative to two different references: GRCm38 (aka mm10, short reads, proxy for domesticus ) and GCA 001624865.1 (short reads, proxy for spretus ). Direct comparison of the approaches’ output is made possible by NCBI Genome Remapping Service (https://www.ncbi.nlm.nih.gov/genome/tools/remap), which allows us to exchange Banker et al . (2022) introgression locations in their Supplementary Table 3 very precisely between reference accessions.…”

“…Comparison of diem genome polarization with a sequence-divergence based method to detect introgression (Banker et al . 2022).…”

“…This dataset was chosen for two reasons. First, high divergence between the taxa (∼ 5%) allows diem to be benchmarked for large n. Second, previous studies suggested geneflow between these taxa (Orth et al 2002; Banker et al 2022), and in particular capture of M. spretus warfarin-resistance genes by M. musculus domesticus (Song et al 2011). In Fig.…”

Estimation of Cross-Species Introgression Rates Using Genomic Data Despite Model Unidentifiability

“…In the Anopheles gambiae group of African mosquitoes, introgression between A. gambiae and A. arabiensis in both directions was suspected, but detailed analyses detected gene flow from A. arabiensis to A. gambiae only but not in the opposite direction ( Thawornwattana et al, 2018 ). In another example, Banker et al (2022) detected bidirectional introgression (with different rates) between Mus spretus and wild populations of M. m. domesticus from Europe, despite considerable postzygotic reproductive isolation between the species. At any rate, BDI is one of the most plausible introgression models and appears to be one of the most common forms of cross-species gene flow.…”