Temporal, spatial, and ecological modes of evolution of Eurasian Mus based on mitochondrial and nuclear gene sequences

Rodents represent around 43% of all mammalian species, are widely distributed, and are the natural reservoirs of a diverse group of zoonotic viruses, including hantaviruses, Lassa viruses, and tick-borne encephalitis viruses. Thus, analyzing the viral diversity harbored by rodents could assist efforts to predict and reduce the risk of future emergence of zoonotic viral diseases. We used next-generation sequencing metagenomic analysis to survey for a range of mammalian viral families in rodents and other small animals of the orders Rodentia, Lagomorpha, and Soricomorpha in China. We sampled 3,055 small animals from 20 provinces and then outlined the spectra of mammalian viruses within these individuals and the basic ecological and genetic characteristics of novel rodent and shrew viruses among the viral spectra. Further analysis revealed that host taxonomy plays a primary role and geographical location plays a secondary role in determining viral diversity. Many viruses were reported for the first time with distinct evolutionary lineages, and viruses related to known human or animal pathogens were identified. Phylogram comparison between viruses and hosts indicated that host shifts commonly happened in many different species during viral evolutionary history. These results expand our understanding of the viromes of rodents and insectivores in China and suggest that there is high diversity of viruses awaiting discovery in these species in Asia. These findings, combined with our previous bat virome data, greatly increase our knowledge of the viral community in wildlife in a densely populated country in an emerging disease hotspot.

/pdf/comparative-analysis-of-rodent-and-small-mammal-viromes-to-283r3f8pqf.pdf

Comparative analysis of rodent and small mammal viromes to better understand the wildlife origin of emerging infectious diseases

Differences in ATP Generation Via Glycolysis and Oxidative Phosphorylation and Relationships with Sperm Motility in Mouse Species

We examined the sequence variation of mitochondrial DNA control region and cytochrome b gene of the house mouse (Mus musculus sensu lato) drawn from ca. 200 localities, with 286 new samples drawn primarily from previously unsampled portions of their Eurasian distribution and with the objective of further clarifying evolutionary episodes of this species before and after the onset of human-mediated long-distance dispersals. Phylogenetic analysis of the expanded data detected five equally distinct clades, with geographic ranges of northern Eurasia (musculus, MUS), India and Southeast Asia (castaneus, CAS), Nepal (unspecified, NEP), western Europe (domesticus, DOM) and Yemen (gentilulus). Our results confirm previous suggestions of Southwestern Asia as the likely place of origin of M. musculus and the region of Iran, Afghanistan, Pakistan, and northern India, specifically as the ancestral homeland of CAS. The divergence of the subspecies lineages and of internal sublineage differentiation within CAS were estimated to be 0.37–0.47 and 0.14–0.23 million years ago (mya), respectively, assuming a split of M. musculus and Mus spretus at 1.7 mya. Of the four CAS sublineages detected, only one extends to eastern parts of India, Southeast Asia, Indonesia, Philippines, South China, Northeast China, Primorye, Sakhalin and Japan, implying a dramatic range expansion of CAS out of its homeland during an evolutionary short time, perhaps associated with the spread of agricultural practices. Multiple and non-coincident eastward dispersal events of MUS sublineages to distant geographic areas, such as northern China, Russia and Korea, are inferred, with the possibility of several different routes.

/pdf/evolutionary-and-dispersal-history-of-eurasian-house-mice-4tgc2d4sfh.pdf

Evolutionary and dispersal history of Eurasian house mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA

Deep sequencing analyses have shown that a large fraction of genomes is transcribed, but the significance of this transcription is much debated. Here, we characterize the phylogenetic turnover of poly-adenylated transcripts in a comprehensive sampling of taxa of the mouse (genus Mus), spanning a phylogenetic distance of 10 Myr. Using deep RNA sequencing we find that at a given sequencing depth transcriptome coverage becomes saturated within a taxon, but keeps extending when compared between taxa, even at this very shallow phylogenetic level. Our data show a high turnover of transcriptional states between taxa and that no major transcript-free islands exist across evolutionary time. This suggests that the entire genome can be transcribed into poly-adenylated RNA when viewed at an evolutionary time scale. We conclude that any part of the non-coding genome can potentially become subject to evolutionary functionalization via de novo gene evolution within relatively short evolutionary time spans.

/pdf/fast-turnover-of-genome-transcription-across-evolutionary-4oe8ytvwy0.pdf

Fast turnover of genome transcription across evolutionary time exposes entire non-coding DNA to de novo gene emergence

Serum samples from 337 wild house mice (Mus musculus) from 35 sites in China, collected in 1992 and 1993, were examined for antibodies against lymphocytic choriomeningitis virus (LCMV). Ten samples from eight sites were found to contain such antibodies. Six of the eight positive sites were located in the territory of M. m. gansuensis. One of the other two sites was located in the territory of M. m. castaneus in southern China and the other site was in a habitat of M. m. castaneus which had invaded into the western end of the territory of M. m. homourus. It seems likely that LCMV is distributed in the territories of M. m. gansuensis and M. m. castaneus in China. This is the first report of detection of these antibodies in wild house mice in China and specifically in the territories of M. m. gansuensis and M. m. castaneus.

Seroepidemiological Survey of Lymphocytic Choriomeningitis Virus in Wild House Mice in China with Particular Reference to Their Subspecies

Taxonomic Study of the Genus Mus in China, Korea, and Japan—Morphologic Identification

We examined intraspecific genetic variation in the mitochondrial cytochrome b gene (1140 bp) in the Okinawa mouse, Mus caroli (Rodentia, Muridae), from Okinawa, Taiwan, Hainan, Yunnan (southern China), Thailand, Vietnam and Java, to better understand their evolutionary history and human impact on dispersal and colonization by the mice. Populations from each of the seven localities had distinctive mitochondrial DNA sequences. The genetic distances, ranging from 0.015 to 0.045 (0.033 on average), were comparable with inter-subspecies differences in the house mouse Mus musculus (0.024). Assuming that nucleotide substitutions occur at a constant rate of 0.024/million years/lineage for mitochondrial DNA, the divergence of in M. caroli is estimated to have occurred 0.3-0.9 million years ago. The relatively great extent of intraspecific mitochondrial DNA variation in this taxon, and the spatial mode of variation suggest that M. caroli is genetically structured in space, to a considerable extent. Our data imply that local insular populations of M. caroli have been separated for long evolutionary periods, and that the scattered distribution patterns in the insular domains are due to historical shrinkage of appropriate areas of habitat, rather than to recent establishment of dispersed local populations by inadvertent human introductions.

Mei-Lei Jin

Papers

Evolutionary and dispersal history of Eurasian house mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA

Seroepidemiological Survey of Lymphocytic Choriomeningitis Virus in Wild House Mice in China with Particular Reference to Their Subspecies

Taxonomic Study of the Genus Mus in China, Korea, and Japan—Morphologic Identification

Geographic variation of Mus caroli from East and Southeast ASIA based on mitochondrial cytochrome b gene sequences

Genetic Polymorphisms of Hbb Haplotypes in Wild Mice