Increased geographic sampling reveals considerable new genetic diversity in the morphologically conservative African Pygmy Mice (Genus Mus; Subgenus Nannomys)

African endemic pygmy mice (Genus Mus; sub-genus Nannomys) have considerable economic and public health significance, and some species exhibit novel sex determination systems, making accurate knowledge of their phylogenetics and distribution limits important. This phylogenetic study was based on the mitochondrial control region and cytochrome b gene, for which a substantial body of published data was available. Study specimens were sourced from eight previously unsampled or poorly sampled countries, and include samples morphologically identified as Mus bufo, M. indutus, M. callewaerti, M. triton and M. neavei. These analyses increase the known genetic diversity of Nannomys from 65 to 102 haplotypes; at least 5 unassigned haplotypes are distinguished by potentially species-level cytochrome b genetic distances. The monophyly of Nannomys is supported. Mus musculoides, M. callewaerti, M. indutus, M. bufo, M. haussa, M. mattheyi, M. baoulei and M. sorella are supported as discrete species. The range of M. indutus is extended to include Botswana. M. setulosus and M. minutoides appear to be species complexes. A south and east African M. minutoides clade was defined and includes 8 new haplotypes out of 15. M. setulosus sensu lato includes M. setulosus sensu stricto and a strongly-supported M. bufo clade. Two samples, morphologically identified as M. triton and M. neavei, fall within the M. minutoides clade.     

Multi‐scale habitat selection of Mus minutoides in the Lowveld of Swaziland

We investigated habitat selection of Mus minutoides in northeastern Swaziland. We used powder tracking to determine how M. minutoides selected habitat at a fine scale and a broader path scale. At the fine scale, we measured per cent cover of grass and shrubs, the number of forbs and visual obstruction (VO) at five evenly spaced points along a mouse's pathway and at a paired random location. At the path scale, we calculated the relative displacement (RD) of each path as the ratio of the distance from the start to the end point of the path to the total length of the path (values near one indicate less preference). We found that M. minutoides were positively associated with increases in visual obstruction, grass cover, and shrub cover at the fine scale, but not at the path scale. Our results indicate that M. minutoides selection of vegetative features at the path scale is not as important as their fine‐scale selection of vegetative structure. In addition, the shrub encroachment on our study site may be directly beneficial to M. minutoides at the fine scale. Our results provide us with an increased understanding of the basic ecology of M. minutoides and information on their response to a changing landscape.     

Phylogeography of Mus (Nannomys) minutoides (Rodentia,Muridae) in West Central African savannahs: singular vicariance in neighbouring populations

We studied the phylogeography of the strict savannah pygmy mice Mus (Nannomys) minutoides in West Central Africa. A total of 846 base pairs of the cytochrome b sequence were obtained for 66 individuals collected in Gabon, Cameroon, Republic of Congo and Central African Republic. These sequences were compared to those of M. minutoides from other African countries and to eight other species of the genus Mus. We performed maximum likelihood, Bayesian and nested clade analyses, as well as neutrality tests and time estimates. We show that M. minutoides is a well‐differentiated monophyletic species that separated from other pygmy mice 1.17 Myr ago. A distinct West Central African M. minutoides clade diverged early from the other African populations of the species, with a more recent common ancestor dating 0.14 Myr. West Central African populations are globally homogeneous, despite the present fragmentation of savannahs by the rain forest. However, our analyses show an unexpected vicariance between geographically close savannahs, embedded in the rain forest in Central Gabon. One of these populations is genetically more similar to very distant peripheral populations than to three closely neighbouring populations situated on both sides of the Ogooué River. A non‐river geographical barrier probably persisted in this area, durably isolating these local populations. This hypothesis about the history of the savannah landscape should be testable through the biogeographical analysis of other strict savannah small mammal species.     

Syphacia (Syphacia) ohtaorum n. sp. (Nematoda: Oxyuridae) from Mus caroli on Okinawa Island,Japan

Syphacia (Syphacia) ohtaorum n. sp. is described from Mus caroli on Okinawa Island, Japan. It is closest to Syphacia (Syphacia) megaloon Quentin, 1966 from Mus minutoides and M. setulosus of Africa, but is distinguished in having a slimmer body, distinct lateral alae in the male, many eggs in the female and a smaller egg-size.     

Population dynamics of Mus minutoides and Steatomys pratensis (Muridae: Rodentia) in a subtropical grasslandin Swaziland

The population dynamics of Mus minutoides and Steatomys pratensis are virtually unknown. These two species were live-trapped over a 12-month period in a subtropical grassland in Swaziland. Numbers of M. minutoides were relatively high in winter, declined in spring and the population disappeared in summer and autumn. By contrast, numbers of S. pratensis increased gradually from winter to summer and reached a peak in autumn. There were no differences between the mean weights of male and female M. minutoides and S. pratensis. There were, however, seasonal differences in the mean weight of male S. pratensis, with highest weights recorded in summer. Individuals of both species came into breeding condition in spring (October–November). Reproduction had ceased by the end of autumn (April–May). Monthly survival rates of M. minutoides were highest in winter, but did not vary seasonally in S. pratensis. Burning had a pronounced effect on the distribution of S. pratensis. Steatomys pratensis individuals selected recently burnt but revegetated areas over unburnt areas. The effect of burning on the M. minutoides population is difficult to assess, as this species disappeared shortly after the fire.     

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

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.     

Gene flow of unique sequences between Mus musculus domesticus and Mus spretus

Allelic diversity has been examined from a variety of Mus musculus subspecies and Mus spretus strains by sequencing at a 453-bp unique sequence locus. One M. m. domesticus classic inbred strain, C57BL/KsJ, contained a sequence identical to that in the M. spretus wild-derived inbred strain SEG, and other wild M. spretus isolates. Such a result should have been precluded by the expected divergence between the species unless there has been interspecies gene flow. Examination of C57BL/KsJ for M. spretus-specific repetitive sequences shows that it is neither a mis-identified spretus strain nor a domesticus/spretus hybrid. Thus, in addition to the previously reported presence of small amounts of Mus spretus-specific repetitive DNA in M. m. domesticus, there is a detectable flow of unique sequence between the two species. There was also ancestral polymorphism observed among the spretus alleles. The difficulty of distinguishing ancestral polymorphism from horizontal transfer is discussed. Received: 14 May 1999 / Accepted: 5 November 1999     

The telocentric tandem repeat at the p-arm is not conserved in Mus musculus subspecies

Mouse chromosomes, with the exception of the Y chromosome, are telocentric. The telomere at the p-arm is separated from the centromere by the tL1 sequence and TLC tandem repeats. A previous report showed that the TLC array was also conserved in other strains of the subgenus Mus. These results suggest that the TLC arrays promote the stable evolutionary maintenance of a telocentric karyotype in the subgenus Mus. In this study, we investigated the degree of conservation of TLC arrays among a variety of wild-derived inbred strains, all of which are descendants of wild mice captured in several areas of the world. Genomic PCR analysis indicates that the sequential order of telomere-tL1 is highly conserved in all strains, whereas tL1-TLC is not. Next, Southern blot analysis of DNAs isolated from a panel of mouse subspecies showed both Mus musculus domesticus and Mus musculus castaneus subspecies possess TLC arrays. Unexpectedly, this repeat appears to be lost in almost all Mus musculus musculus and Mus musculus molossinus subspecies, which show a clear geographic divide. These results indicate that either other unknown sequences were replaced by the TLC repeat or almost all M. m. musculus and M. m. molossinus subspecies do not have any sequence between the telomere and minor satellites. Our observation suggests that the TLC array might be evolutionarily unstable and not essential for murine chromosomal conformation. This is the first example of the subspecies-specific large genome alterations in mice.     

Cytological and molecular characterization of centromeres in Mus domesticus and Mus spretus

We have applied EM in situ hybridization (EMISH) and pulsed field gel electrophoresis (PFGE) to samples from diploid primary cell cultures and an established cell line to examine in detail the relative organization of the major and minor satellite DNAs and telomere sequences in the genomes of Mus domesticus and Mus spretus. EMISH localizes the Mus domesticus minor satellite to a single site at the centromere-proximal end of each chromosome. Double label hybridizations with both minor satellite and telomere probes show that they are in close proximity and possibly are linked. In fact, PFGE of M. domesticus DNA digested with Sal I and Sfi I reveals the presence of fragments which hybridize to both probes and is consistent with the physical linkage of these two sequences. The M. domesticus minor satellite is the more abundant satellite in Mus spretus. Its distribution in M. spretus is characterized by diffuse labeling with no obvious concentration near chromosome ends. In addition to this repeat the M. spretus genome contains a small amount of DNA that hybridizes to a M. domesticus major satellite probe. Unlike the M. domesticus minor satellite, it is not telomere proximal but is confined to a domain at the border of the centromere and the long arm. Thus, although both species possess all three sequences, except for the telomeres, their distribution relative to one another is not conserved. Based on the results presented, we propose preliminary molecular maps of the centromere regions of Mus domesticus and Mus spretus.     

Genomic copy number variation in Mus musculus

Background

Copy number variation is an important dimension of genetic diversity and has implications in development and disease. As an important model organism, the mouse is a prime candidate for copy number variant (CNV) characterization, but this has yet to be completed for a large sample size. Here we report CNV analysis of publicly available, high-density microarray data files for 351 mouse tail samples, including 290 mice that had not been characterized for CNVs previously.

Results

We found 9634 putative autosomal CNVs across the samples affecting 6.87 % of the mouse reference genome. We find significant differences in the degree of CNV uniqueness (single sample occurrence) and the nature of CNV-gene overlap between wild-caught mice and classical laboratory strains. CNV-gene overlap was associated with lipid metabolism, pheromone response and olfaction compared to immunity, carbohydrate metabolism and amino-acid metabolism for wild-caught mice and classical laboratory strains, respectively. Using two subspecies of wild-caught Mus musculus, we identified putative CNVs unique to those subspecies and show this diversity is better captured by wild-derived laboratory strains than by the classical laboratory strains. A total of 9 genic copy number variable regions (CNVRs) were selected for experimental confirmation by droplet digital PCR (ddPCR).

Conclusion

The analysis we present is a comprehensive, genome-wide analysis of CNVs in Mus musculus, which increases the number of known variants in the species and will accelerate the identification of novel variants in future studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1713-z) contains supplementary material, which is available to authorized users.     

Laboratory and field evidence of paternal care in the Algerian mouse (Mus spretus)

Paternal care is generally, although not exclusively, associated with monogamy in mammals. The Algerian mouse, Mus spretus, is a nocturnal murid living in xeric habitats in northern Africa, the Iberian peninsula and the south of France. We compared the amount of paternal care induced by removing young in Mus spretus and in the polygamous house mouse M. musculus domesticus in terms of the evolution of paternal care during the first 10-days post-partum and absolute (father alone) and relative (both parents) values. We then recovered indirect evidence of young being cared for by males from field data. The results were unambiguous in showing that the two species differed dramatically in paternal behaviour, with no variation being observed during the initial pup development. Mus spretus dedicated half of its time to caring from the young against less than 10% in M. m. domesticus. The former species showed the same number of retrieving acts and direct care bouts both in the presence and in the absence of the mother. Merging these results with field observations of spatial association “male-young” until subadult age, we drew conclusions on the likely occurrence of paternal care in M. spretus. Taken together with our previous results on socio-spatial organisation and pair bonding, we propose that social monogamy is advanced for this species.     

The uncharacterized gene 1700093K21Rik and flanking regions are correlated with reproductive isolation in the house mouse,Mus musculus

Reproductive barriers exist between the house mouse subspecies, Mus musculus musculus and M. m. domesticus, members of the Mus musculus species complex, primarily as a result of hybrid male infertility, and a hybrid zone exists where their ranges intersect in Europe. Using single nucleotide polymorphisms (SNPs) diagnostic for the two taxa, the extent of introgression across the genome was previously compared in these hybrid populations. Sixty-nine of 1316 autosomal SNPs exhibited reduced introgression in two hybrid zone transects suggesting maladaptive interactions among certain loci. One of these markers is within a region on chromosome 11 that, in other studies, has been associated with hybrid male sterility of these subspecies. We assessed sequence variation in a 20 Mb region on chromosome 11 flanking this marker, and observed its inclusion within a roughly 150 kb stretch of DNA showing elevated sequence differentiation between the two subspecies. Four genes are associated with this genomic subregion, with two entirely encompassed. One of the two genes, the uncharacterized 1700093K21Rik gene, displays distinguishing features consistent with a potential role in reproductive isolation between these subspecies. Along with its expression specifically within spermatogenic cells, we present various sequence analyses that demonstrate a high rate of molecular evolution of this gene, as well as identify a subspecies amino acid variant resulting in a structural difference. Taken together, the data suggest a role for this gene in reproductive isolation.     

Mitochondrial DNA restriction maps ofMus booduga,Mus terricolor andMus musculus tytleri

Restriction maps of milochondrial DNA of the Indian pygmy field miceMus booduga andM. terricolor, and the house mouseM. musculus tytleri were determined with seven six-cutter restriction enzymes. The restriction map of the mitochondrial DNA of the laboratory mouseM. m. domesticus was used as a reference. Pairwise comparison was made of the mitochondrial DNAs for the presence or absence of the restriction sites, and per cent sequence divergence was calculated. The results show that the sequence divergence betweenbooduga andterricolor is 8-7% while thedomesticus-tytleri andbooduga-terricolor groups are divergent by 16-3%. The mtDNA sequence divergences we have obtained suggest that thebooduga-terricolor lineage might not have diverged before the Southeast Asiancervicolor-cookii-caroli lineage during evolution of these lineages of the subgenusMus as inferred by others earlier. On the other hand, it seems likely that these lineages evolved in parallel.     

Role of Nematodes,Nematicides, and Crop Rotation on the Productivity and Quality of Potato,Sweet Potato,Peanut, and Grain Sorghum

The objective of this experiment was to determine the effects of fenamiphos 15G and short-cycle potato (PO)-sweet potato (SP) grown continuously and in rotation with peanut (PE)-grain sorghum (GS) on yield, crop quality, and mixed nematode population densities of Meloidogyne arenaria, M. hapla, M. incognita, and Mesocriconema ornatum. Greater root-gall indices and damage by M. hapla and M. incognita occurred on potato than other crops. Most crop yields were higher and root-gall indices lower from fenamiphos-treated plots than untreated plots. The total yield of potato in the PO-SP and PO-SP-PE-GS sequences increased from 1983 to 1985 in plots infested with M. hapla or M. arenaria and M. incognita in combination and decreased in 1986 to 1987 when root-knot nematode populations shifted to M. incognita. The total yields of sweet potato in the PO-SP-PE-GS sequence were similar in 1983 and 1985, and declined each year in the PO-SP sequence as a consequence of M. incognita population density increase in the soil. Yield of peanut from soil infested with M. hapla increased 82% in fenamiphos-treated plots compared to untreated plots. Fenamiphos treatment increased yield of grain sorghum from 5% to 45% over untreated controls. The declining yields of potato and sweet potato observed with both the PO-SP and PO-SP-PE-GS sequences indicate that these crop systems should not be used longer than 3 years in soil infested with M. incognita, M. arenaria, or M. hapla. Under these conditions, these two cropping systems promote a population shift in favor of M. incognita, which is more damaging to potato and sweet potato than M. arenaria and M. hapla.     

Population dynamics of small mammals at Mlawula, Swaziland

Population density, biomass and composition of a small mammal community in an Acacia nigrescens savanna were studied over 12 months from August 2000. The community consisted of Mus minutoides (A. Smith 1834), Mastomys natalensis (A. Smith 1834), Lemniscomys rosalia (Thomas 1904), Crocidura hirta (Peters 1952), Steatomys pratensis (Peters 1846); and on one occasion, Graphiurus murinus (Desmarest 1822) was caught. M. minutoides was the dominant species in the site. Species richness was found to vary significantly with the time of the year. The density of M. minutoides was significantly high in winter and low in the other seasons, the ratio of males to females was found to be equal, and pregnant females were caught from November to May. The biomass of small mammals in the area (also density and numbers) was generally low (mean biomass 212 g ha^?1). The occurrence of new individuals in catches remained high throughout the study, suggesting a high mortality or emigration rate or a combination of the two.     

Selection of Rodent Species Appropriate for mtDNA Transfer to Generate Transmitochondrial Mito-Mice Expressing Mitochondrial Respiration Defects

Previous reports have shown that transmitochondrial mito-mice with nuclear DNA from Mus musculus and mtDNA from M. spretus do not express respiration defects, whereas those with mtDNA from Rattus norvegicus cannot be generated from ES cybrids with mtDNA from R. norvegicus due to inducing significant respiration defects and resultant losing multipotency. Here, we isolated transmitochondrial cybrids with mtDNA from various rodent species classified between M. spretus and R. norvegicus, and compared the O₂ consumption rates. The results showed a strong negative correlation between phylogenetic distance and reduction of O₂ consumption rates, which would be due to the coevolution of nuclear and mitochondrial genomes and the resultant incompatibility between the nuclear genome from M. musculus and the mitochondrial genome from the other rodent species. These observations suggested that M. caroli was an appropriate mtDNA donor to generate transmitochondrial mito-mice with nuclear DNA from M. musculus. Then, we generated ES cybrids with M. caroli mtDNA, and found that these ES cybrids expressed respiration defects without losing multipotency and can be used to generate transmitochondrial mito-mice expressing mitochondrial disorders.     

Co-amplification of tail-to-tail copies of MuRVY and IAPE retroviral genomes on the Mus musculus Y Chromosome

We have isolated a clone from a C57BL/6 genomic library that contains both part of the Y Chromosome-specific 8.7 kbp MuRVY genome (Hutchinson and Eicher, J. Virol. 63, 4043, 1989) and a full-length 8.3 kbp Intracisternal A Particle genome (IAPE-Y), in a tail-to-tail organization. Although IAPs are encoded by a disperse multigene family (∼1000 copies per haploid genome), we present evidence that a significant proportion of the IAP-related sequences are present on the Y Chromosome (Chr) and that a >25 kbp genomic sequence, which contains the two proviral genomes, has been amplified on the Y Chr. Two discrete amplified families of MuRVY retroviral genomes distinguishable by a polymorphic restriction site were detected, suggestive that amplification occurred in incremental stages. The presence of MuRVY-related DNA sequences, but absence of IAPE-Y-related DNA sequences in Mus spretus suggests that the IAPE-Y retrotransposition event occurred after the evolutionary divergence of the lineages leading to Mus musculus and Mus spretus, and that the amplification of MuRVY occurred independently in the two lineages. Received: 28 July 1995 / Accepted: 1 September 1995     

PRDM9 Drives Evolutionary Erosion of Hotspots in Mus musculus through Haplotype-Specific Initiation of Meiotic Recombination

Meiotic recombination generates new genetic variation and assures the proper segregation of chromosomes in gametes. PRDM9, a zinc finger protein with histone methyltransferase activity, initiates meiotic recombination by binding DNA at recombination hotspots and directing the position of DNA double-strand breaks (DSB). The DSB repair mechanism suggests that hotspots should eventually self-destruct, yet genome-wide recombination levels remain constant, a conundrum known as the hotspot paradox. To test if PRDM9 drives this evolutionary erosion, we measured activity of the Prdm9 ^Cst allele in two Mus musculus subspecies, M.m. castaneus, in which Prdm9^Cst arose, and M.m. domesticus, into which Prdm9^Cst was introduced experimentally. Comparing these two strains, we find that haplotype differences at hotspots lead to qualitative and quantitative changes in PRDM9 binding and activity. Using Mus spretus as an outlier, we found most variants affecting PRDM9^Cst binding arose and were fixed in M.m. castaneus, suppressing hotspot activity. Furthermore, M.m. castaneus×M.m. domesticus F1 hybrids exhibit novel hotspots, with large haplotype biases in both PRDM9 binding and chromatin modification. These novel hotspots represent sites of historic evolutionary erosion that become activated in hybrids due to crosstalk between one parent''s Prdm9 allele and the opposite parent''s chromosome. Together these data support a model where haplotype-specific PRDM9 binding directs biased gene conversion at hotspots, ultimately leading to hotspot erosion.