Ancient onset of geographical divergence, interpopulation genetic exchange, and natural selection on the Mc1r coat-colour gene in the house mouse (Mus musculus)

We examined genetic variation in house mice from India and Pakistan, a predominant part of the predicted homeland of this species and also the territory of the subspecies Mus musculus castaneus (CAS), using a nuclear marker for seven tandemly arranged genes (Fanca-Spire2-Tcf25-Mc1r-Def8-Afg3l1-Dbndd1) and compared them with those previously determined for mice from other parts of Eurasia. Construction of a network with the concatenate sequences yielded three distinct clusters representing the three major subspecies groups: CAS, Mus musculus domesticus (DOM) and Mus musculus musculus (MUS). STRUCTURE analysis provided evidence for further subdivision of CAS into two main haplogroups within the Indian subcontinent. Single-gene networks revealed not only gene-specific architecture for subgrouping in CAS, but also allelic exchange among subspecies. These results suggest the earlier onset of allopatric divergence in the predicted homeland (the Middle East and Indian subcontinent) and subsequent intermittent admixing via gene flow across the CAS haplogroups and among the three subspecies groups. A comparison of the levels of nucleotide diversity among the gene regions revealed a less divergent state in the chromosome region containing Mc1r and its adjacent genes, indicative of a selective sweep, suggesting the involvement of natural selection in the Mc1r allelic variation.(c) 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114, 778-794

Evolutionary Dynamics of Copy Number and Meiotic Recombination in Murine 5S rDNA: Possible Involvement of Natural Selection

We investigated evolutionary trends of the 5S ribosomal RNA gene in the house mouse, Mus musculus. First, we assessed the 5S cluster and copy numbers in eight laboratory strains by pulsed-field gel electrophoresis. The copy numbers in seven lines were estimated to be around 130-170 copies per cluster, with 63 copies in the remaining strain, implying that the copy number can change drastically and has been maintained under certain evolutionary constraints at similar to 140 copies. Second, we addressed the frequency of meiotic recombination mediated by the 5S cluster by performing a mating experiment with laboratory strains, and found that the 5S cluster did not accelerate recombination events. Third, we surveyed recombination events of the 5S-containing chromosome region in wild mice from the Japanese Islands, where the two subspecies lineages, M. m. castaneus and M. m. musculus, are historically mingled, and found that the influence of the 5S cluster on meiotic recombination was limited. Finally, we examined the nucleotide diversity of six genes in the neighboring regions of the 5S cluster and found reduced genetic diversity in the regions on both sides of the cluster, suggesting the involvement of either positive or background selection in the population-level sequence similarity of the 5S clusters. Therefore, the mouse 5S genes are considered to be evolving toward sequence similarity within a given cluster by certain intrachromosomal mechanisms and toward sharing of a specific 5S cluster within a population by certain selective processes

Heterogeneous genetic make-up of Japanese house mice (Mus musculus) created by multiple independent introductions and spatio-temporally diverse hybridization processes

In this study, phylogenetic analysis of relatively long sequences of mitochondrial DNA (4225 bp) in the Japanese house mouse Mus musculus provides the first evidence that both southern Asian subspecies of Mus musculus castaneus (CAS) and northern Asian subspecies of Mus musculus musculus (MUS) arrived in Japan through rapid population expansion events, from Southern China similar to 4000 years ago and the Korean Peninsula similar to 2000 years ago, respectively. Nuclear DNA haplotype structure analyses targeting a chromosome region with two different tract sizes, 1 and 5 Mb, consisting of nine and six tandemly arranged markers, respectively, yielded a possible average fragment length of 170 kb of CAS haplotypes in the MUS background genome in northern Japan, providing a rough estimate of its elapsed time of 815 generations under an assumption of continued backcrossing. Less frequent and shortened CAS-like haplotypes specific to Japan were detected, suggesting ancient introduction prior to the appearance of the South Chinese CAS in Japan. Our analyses also showed sporadic appearance of long fragments (2-5 Mb) from the west European subspecies Mus musculus domesticus, indicating contemporary stowaway introduction. Overall, multiple overseas introductions, and the time-lagged inter-subspecies genetic admixture, probably resulted in the heterogeneous state of Japanese wild mice

Historical Introduction of Japanese Wild Mice, Mus musculus, from South China and the Korean Peninsula

In Japan, the wild house mouse Mus musculus consists of two lineages, one from Southeast Asia (Mus musculus castaneus; CAS) and one from northern Eurasia (Mus musculus musculus; MUS). However, the exact origins of the parental lineages are unclear. A recent work using mitochondrial sequences revealed that Japanese CAS and MUS are closely related to haplotypes from South China and the Korean Peninsula, respectively. Recent phylogeographic analyses using nuclear gene sequences have also confirmed a close relationship between Japan and Korea in the MUS component. However, the Japanese CAS components in the nuclear genome are likely to be unique and to differ from those of other CAS territories, including South China. Although the origins are still unresolved, these results allow us to conclude that two areas of the continent, South China and the Korean Peninsula, are the primary source areas of Japanese wild mice and suggest pre-historical introductions associated with certain historical agricultural developments in East Asia

Data from: Ancient onset of geographic divergence, interpopulation genetic exchange, and natural selection on the Mc1r coat-color gene in the house mouse (Mus musculus) inferred from tandemly arranged nuclear gene markers

We examined genetic variation in house mice from India and Pakistan, a predominant part of the predicted homeland of this species and also the territory of the subspecies Mus musculus castaneus (CAS), using a nuclear marker for seven tandemly arranged genes (Fanca–Spire2–Tcf25–Mc1r–Def8–Afg3l1–Dbndd1) and compared them with those previously determined for mice from other parts of Eurasia. Construction of a network with the concatenate sequences yielded three distinct clusters representing the three major subspecies groups: CAS, Mus musculus domesticus (DOM) and Mus musculus musculus (MUS). STRUCTURE analysis provided evidence for further subdivision of CAS into two main haplogroups within the Indian subcontinent. Single-gene networks revealed not only gene-specific architecture for subgrouping in CAS, but also allelic exchange among subspecies. These results suggest the earlier onset of allopatric divergence in the predicted homeland (the Middle East and Indian subcontinent) and subsequent intermittent admixing via gene flow across the CAS haplogroups and among the three subspecies groups. A comparison of the levels of nucleotide diversity among the gene regions revealed a less divergent state in the chromosome region containing Mc1r and its adjacent genes, indicative of a selective sweep, suggesting the involvement of natural selection in the Mc1r allelic variatio

Data from: Heterogeneous genetic makeup of the Japanese house mouse (Mus musculus) created by multiple independent introductions and spatio-temporally diverse hybridization processes

In this study, phylogenetic analysis of relatively long sequences of mitochondrial DNA (4225 bp) in the Japanese house mouse Mus musculus provides the first evidence that both southern Asian subspecies of Mus musculus castaneus (CAS) and northern Asian subspecies of Mus musculus musculus (MUS) arrived in Japan through rapid population expansion events, from Southern China ~4000 years ago and the Korean Peninsula ~2000 years ago, respectively. Nuclear DNA haplotype structure analyses targeting a chromosome region with two different tract sizes, 1 and 5 Mb, consisting of nine and six tandemly arranged markers, respectively, yielded a possible average fragment length of 170 kb of CAS haplotypes in the MUS background genome in northern Japan, providing a rough estimate of its elapsed time of 815 generations under an assumption of continued backcrossing. Less frequent and shortened CAS-like haplotypes specific to Japan were detected, suggesting ancient introduction prior to the appearance of the South Chinese CAS in Japan. Our analyses also showed sporadic appearance of long fragments (2–5 Mb) from the west European subspecies Mus musculus domesticus, indicating contemporary stowaway introduction. Overall, multiple overseas introductions, and the time-lagged inter-subspecies genetic admixture, probably resulted in the heterogeneous state of Japanese wild mice

Haplotype sequences of the nuclear gene Cdk10.

Sequence file in Fasta format

7_Afg3l1_all

The Afg3lI sequence data used for the construction of the Neighbor Net network shown in Fig. 2A (Kodama et al., 2015)