Reduced nucleotide variability at an androgen-binding protein locus (Abpa) in house mice: evidence for positive natural selection.

Previous work has shown that the gene for the alpha subunit of androgen-binding protein, Abpa, may be involved in premating isolation between different subspecies of the house mouse, Mus musculus. We investigated patterns of DNA sequence variation at Abpa within and between species of mice to test several predictions of a model of neutral molecular evolution. Intraspecific variation among 10 Mus musculus domesticus alleles was compared with divergence between M. m. domesticus and M. caroli for Abpa and two X-linked genes, Glra2 and Amg. No variation was observed at Abpa within M. m. domesticus. The ratio of polymorphism to divergence was significantly lower at Abpa than at Glra2 and Amg, despite the fact that all three genes experience similar rates of recombination. Interspecific comparisons among M. m. domesticus, Mus musculus musculus, Mus musculus castaneus, Mus spretus, Mus spicilegus, and Mus caroli revealed that the ratio of nonsynonymous substitutions to synonymous substitutions on a per-site basis (Ka/Ks) was generally greater than one. The combined observations of no variation at Abpa within M. m: domesticus and uniformly high Ka/Ks values between species suggest that positive directional selection has acted recently at this locus.     

Testing for selection on the androgen-binding protein in the Danish mouse hybrid zone

The three peripheral subspecies of the house mouse Mus musculus have fixed specific variants of the androgen-binding protein (ABP) that have been proposed to be part of a recognition mechanism that could participate in sexual isolation between the subspecies. We tested for selection on Abpa by characterizing the pattern of Abpa introgression across a transect of the hybrid zone between M. m. musculus and M. m. domesticus in Jutland. On the musculus side, the cline for Abpa resembled that of a nearly neutral allozyme more than that of strongly selected X and Y chromosome markers. However, the high central step which displaces the tail of introgression of Abpa to higher frequencies was best accounted for by linkage to a locus under strong selection against hybrids. Still, we cannot exclude that this pattern results from weak selection against Abpa in the tail of introgression, which would be compatible with an assortative choice mechanism. On the domesticus side there was little introgression close to the hybrid zone, presumably due to a geographical barrier to migration. However, substantial frequencies of musculus alleles occurred further away, suggesting mixed colonization patterns as well as flow across the hybrid zone.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 447–459.     

The house mouse progression in Eurasia: a palaeontological and archaeozoological approach

A palaeontological and archaeozoological survey has allowed us to establish the different steps in the colonization of western Eurasia and northern Africa by the house mouse Mus musculus . After successive immigration waves of the genus Mus into this zone from the late Pliocene to the upper Pleistocene, the house mouse appeared and remained confined to the easternmost Mediterranean Basin at the uppermost Pleistocene. The first progression of this species into the Mediterranean Basin occurred in the Middle East from the Epipaleolithic to the Neolithic. Subsequently, this species was found in the western Mediterranean Basin during the Bronze Age and in north-west Europe during the Iron Age. In comparison to this latter zone, north central Europe was colonized relatively early, from the Neolithic to the Bronze Age which may, in fact, not only correspond to a much earlier invasion of Europe by M. musculus musculus but also suggest that the distribution of this subspecies extended much further west than it does nowadays, at a time when M. musculus domesticus was restricted to the Mediterranean zone. This archaeological survey is in agreement with genetic data which provide indications as to the speed, steps and pathways of progression of house mouse populations in western Eurasia.     

Patterns of morphological evolution in the mandible of the house mouse Mus musculus (Rodentia: Muridae)

The worldwide distributed house mouse, Mus musculus, is subdivided into at least three lineages, Mus musculus musculus, Mus musculus domesticus, and Mus musculus castaneus. The subspecies occur parapatrically in a region considered to be the cradle of the species in Southern Asia (‘central region’), as well as in the rest of the world (‘peripheral region’). The morphological evolution of this species in a phylogeographical context is studied using a landmark‐based approach on mandible morphology of different populations of the three lineages. The morphological variation increases from central to peripheral regions at the population and subspecific levels, confirming a centrifugal sub‐speciation within this species. Furthermore, the outgroup comparison with sister species suggests that M. musculus musculus and populations of all subspecies inhabiting the Iranian plateau have retained a more ancestral mandible morphology, suggesting that this region may represent one of the relevant places of the origin of the species. Mus musculus castaneus, both from central and peripheral regions, is morphologically the most variable and divergent subspecies. Finally, the results obtained in the present study suggest that the independent evolution to commensalism in the three lineages is not accompanied by a convergence detectable on jaw morphology. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 635–647.     

Evidence for Pervasive Adaptive Protein Evolution in Wild Mice

The relative contributions of neutral and adaptive substitutions to molecular evolution has been one of the most controversial issues in evolutionary biology for more than 40 years. The analysis of within-species nucleotide polymorphism and between-species divergence data supports a widespread role for adaptive protein evolution in certain taxa. For example, estimates of the proportion of adaptive amino acid substitutions (α) are 50% or more in enteric bacteria and Drosophila. In contrast, recent estimates of α for hominids have been at most 13%. Here, we estimate α for protein sequences of murid rodents based on nucleotide polymorphism data from multiple genes in a population of the house mouse subspecies Mus musculus castaneus, which inhabits the ancestral range of the Mus species complex and nucleotide divergence between M. m. castaneus and M. famulus or the rat. We estimate that 57% of amino acid substitutions in murids have been driven by positive selection. Hominids, therefore, are exceptional in having low apparent levels of adaptive protein evolution. The high frequency of adaptive amino acid substitutions in wild mice is consistent with their large effective population size, leading to effective natural selection at the molecular level. Effective natural selection also manifests itself as a paucity of effectively neutral nonsynonymous mutations in M. m. castaneus compared to humans.     

Positive and negative selection on noncoding DNA close to protein-coding genes in wild house mice

During the past two decades, evidence has accumulated of adaptive evolution within protein-coding genes in a variety of species. However, with the exception of Drosophila and humans, little is known about the extent of adaptive evolution in noncoding DNA. Here, we study regions upstream and downstream of protein-coding genes in the house mouse Mus musculus castaneus, a species that has a much larger effective population size (N(e)) than humans. We analyze polymorphism data for 78 genes from 15 wild-caught M. m. castaneus individuals and divergence to a closely related species, Mus famulus. We find high levels of nucleotide diversity and moderate levels of selective constraint in upstream and downstream regions compared with nonsynonymous sites of protein-coding genes. From the polymorphism data, we estimate the distribution of fitness effects (DFE) of new mutations and infer that most new mutations in upstream and downstream regions behave as effectively neutral and that only a small fraction is strongly negatively selected. We also estimate the fraction of substitutions that have been driven to fixation by positive selection (α) and the ratio of adaptive to neutral divergence (ω(α)). We find that α for upstream and downstream regions (～ 10%) is much lower than α for nonsynonymous sites (～ 50%). However, ω(α) estimates are very similar for nonsynonymous sites (～ 10%) and upstream and downstream regions (～ 5%). We conclude that negative selection operating in upstream and downstream regions of M. m. castaneus is weak and that the low values of α for upstream and downstream regions relative to nonsynonymous sites are most likely due to the presence of a higher proportion of neutrally evolving sites and not due to lower absolute rates of adaptive substitution.     

Female preference for male saliva: implications for sexual isolation of Mus musculus subspecies

We studied the effects of a single genetic change on a complex mammalian behavior using animals congenic for two variants of Abpa, the gene for the alpha subunit of mouse salivary androgen-binding protein (ABP), in two-way preference tests. Females exhibited a preference for investigating salivas of males of their own genetic type of ABP but not for urines of either type of male. This preference behavior is consistent for samples of mice from geographically diverse populations of Mus musculus domesticus and M. m. musculus. These findings provide an explanation for the observation that this gene is evolving under strong selection.     

SALIVARY ANDROGEN-BINDING PROTEIN (ABP) MEDIATES SEXUAL ISOLATION IN MUS MUSCULUS

We wanted to determine whether the microevolution of the mouse salivary androgen-binding protein (ABP) Alpha subunit gene (Abpa) could mediate sexual selection and thereby have a potential role in maintaining gene pool integrity where radiating mouse subspecies make secondary contact. This hypothesis is based upon previous work in this laboratory, which has shown that each subspecies apparently has its own allele and that these alleles have a 25-fold excess of nonsynonymous/synonymous base substitutions compared to an average protein under purifying selection. We provide direct evidence for ABP-assortative mate selection in a laboratory setting: Mus musculus domesticus and M. m. musculus female mice recognize and discriminate between the territories of male mice that essentially differ solely in their Abpa genotype and, when the males are present, the female prefers to mate with the one of her own ABP type. The observation that females could differentiate between the territories of the two males when those mice were absent suggests that the males marked their territories with ABP. In this study, we also detected ABP on the pelts of male mice and in their environment. It is likely that the animals apply the protein to their pelts by licking and that it is then deposited in their surroundings. We suggest that females of the two subspecies are able to discriminate between males of those subspecies on the basis of this protein molecule. Mouse salivary ABP might present a worthwhile system with which to study a prezygotic isolation mechanism in a mammal.     

A Candidate Subspecies Discrimination System Involving a Vomeronasal Receptor Gene with Different Alleles Fixed in M. m. domesticus and M. m. musculus

Assortative mating, a potentially efficient prezygotic reproductive barrier, may prevent loss of genetic potential by avoiding the production of unfit hybrids (i.e., because of hybrid infertility or hybrid breakdown) that occur at regions of secondary contact between incipient species. In the case of the mouse hybrid zone, where two subspecies of Mus musculus (M. m. domesticus and M. m. musculus) meet and exchange genes to a limited extent, assortative mating requires a means of subspecies recognition. We based the work reported here on the hypothesis that, if there is a pheromone sufficiently diverged between M. m. domesticus and M. m. musculus to mediate subspecies recognition, then that process must also require a specific receptor(s), also sufficiently diverged between the subspecies, to receive the signal and elicit an assortative mating response. We studied the mouse V1R genes, which encode a large family of receptors in the vomeronasal organ (VNO), by screening Perlegen SNP data and identified one, Vmn1r67, with 24 fixed SNP differences most of which (15/24) are nonsynonymous nucleotide substitutions between M. m. domesticus and M. m. musculus. We observed substantial linkage disequilibrium (LD) between Vmn1r67 and Abpa27, a mouse salivary androgen-binding protein gene that encodes a proteinaceous pheromone (ABP) capable of mediating assortative mating, perhaps in conjunction with its bound small lipophilic ligand. The LD we observed is likely a case of association rather than residual physical linkage from a very recent selective sweep, because an intervening gene, Vmn1r71, shows significant intra(sub)specific polymorphism but no inter(sub)specific divergence in its nucleotide sequence. We discuss alternative explanations of these observations, for example that Abpa27 and Vmn1r67 are coevolving as signal and receptor to reinforce subspecies hybridization barriers or that the unusually divergent Vmn1r67 allele was not a product of fast positive selection, but was derived from an introgressed allele, possibly from Mus spretus.     

Characterization of two forms of mouse salivary androgen-binding protein (ABP): implications for evolutionary relationships and ligand-binding function

Mouse salivary androgen-binding protein (ABP) is a member of the secretoglobin family produced in the submaxillary glands of house mice (Mus musculus). We report the cDNA sequences and amino acid sequences of the beta and gamma subunits of ABP from a mouse cDNA library, identifying the two subunits by their pIs and molecular weights. An anomalously high molecular weight of the alpha subunit is likely due to glycosylation at a single site. A phylogenetic comparison of the three subunits of ABP with the chains of other mammalian secretoglobins shows that ABP is most closely related to mouse lachrymal protein and to the major cat allergen Fel dI. An evaluation of the most conserved residues in ABP and the other secretoglobins, in light of structural data reported by others [Callebaut, I., Poupon, A., Bally, R., Demaret, J.-P., Housset, D., Delettre, J., Hossenlopp, P., and Mornon, J.-P. (2000) Ann. N.Y. Acad. Sci. 923, 90-112; Pattabiraman, N., Matthews, J., Ward, K., Mantile-Selvaggi, G., Miele, L., and Mukherjee, A. (2000) Ann. N.Y. Acad. Sci. 923, 113-127], allows us to draw conclusions about the critical residues important in ligand binding by the two different ABP dimers and to assess the importance of ligand binding in the function of the molecule. In addition to the cDNAs, which represent those of the musculus subspecies of Mus musculus, we also report the coding regions of the beta and gamma subunit cDNAs from two other mouse inbred strains which represent the other two subspecies: M. musculus domesticus and M. musculus castaneus. The high nonsynonymous/synonymous substitution rate ratios (K(a)/K(s)) for both the beta and gamma subunits suggest that these two proteins are evolving under strong directional selection, as has been reported for the alpha subunit [Hwang, J., Hofstetter, J., Bonhomme, F., and Karn, R. (1997) J. Hered. 88, 93-97; Karn, R., and Clements, M. (1999) Biochem. Genet. 37, 187-199].     

Salivary androgen-binding protein variation in Mus and other rodents.

We have searched for genetic variation in the expression of salivary androgen-binding protein (ABP) in a wide variety of mice and other rodents. ABP was present in the salivas of mice of all species and subspecies studied. Genetic studies have identified three common variants of the ABP Alpha subunit (Abpaa, Abpab, and Abpac) in Mus musculus populations with distributions that correspond roughly to those of the subspecies studied (domesticus, musculus, and castaneus, respectively). It appears that the ABP a and b polymorphisms conform to the hybrid zone between the domesticus and musculus subspecies characterized by others. Our studies suggest that the presence of Abpab in inbred strains may be due to a M. m. musculus contribution, perhaps via oriental fancy mice bred to European mice in the early lines leading to the common inbred strains. The relatively common occurrence of the ABP a type in other Mus species leads us to conclude that it is the ancestral type in mice. Further, the observation of what amounts to unique alleles in the three different subspecies indicates that microevolution of the protein has occurred. In a broader survey, ABP was also found in the salivas of Murid and Cricetid rodents generally. These findings suggest that ABP has an important functional role in rodent salivas.     

The role of salivary androgen-binding protein in reproductive isolation between two subspecies of house mouse: Mus musculus musculus and Mus musculus domesticus

Previous behavioural studies using inbred lines have suggested that the gene ( Abpa ) for the alpha subunit of salivary androgen-binding protein (ABP) plays a role in prezygotic isolation between house mouse Mus musculus subspecies. We tested this hypothesis in animals from wild allopatric (121 individuals from four samples) and parapatric (320 animals from 15 samples) populations sampled on the Czech–Bavarian transect across the hybrid zone between M. m. domesticus and M. m. musculus . The study did not reveal a consistent statistically significant trend of homosubspecific preferences in individual allopatric and parapatric populations. Nonetheless, the whole pattern of preference was skewed toward homosubspecific preference mostly on the M. m. musculus side of the hybrid zone. The pattern of homosubspecific preferences was stronger for the time spent sniffing than it was for the first choice of the signal (the ratio of homosubspecific vs. heterosubspecific preferences for both sexes was 6 : 2 in allopatric and 21 : 9 in parapatric populations, while the same rates were 4 : 4 and 16 : 14 for the first choice). To the extent that Y-maze tests reflect preference under wild conditions, we suggest that this slight preference may not in itself be sufficient to impede gene flow between the two subspecies and thus act as a reproductive barrier. ABP most probably participates in a complex system of subspecies-specific recognition in the hybrid zone, but the picture is far too complex at this time to allow a conclusive evaluation of the importance of this role.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 349–361.     

Subspecies recognition in the house mouse: a study of two populations from the border of a hybrid zone

Mate choice is the outcome of sexual preference for partnerscarrying specific signals. Thus, mating among conspecifics(homogamy) depends on the occurrence of species recognitionsystems. We asked what happens if populations diverge, andwe investigated female sexual preference between two subspeciesof the house mouse in populations from the borders of a hybridzone (Jutland, Denmark). We used choice tests to analyze theoccurrence of recognition signals and to locate these signalsin soiled bedding and urine. Our results show that populationsof the two subspecies can be discriminated on the basis ofurinary signals, suggesting that the latter have diverged. Additionally, these signals seem to have similar features inpopulations of different geographical origins, suggesting thatsubspecific differentiation occurs. This is the first demonstrationthat subspecific recognition through urinary signals occursin the house mouse. However, while Mus musculus domesticusdoes not display a preference, we show that Mus musculus musculusfemales tend to mate with males of the same subspecies. We discuss the different factors that could explain these discrepanciesbetween females of the two taxa: differences in signal perception,evolution at a different pace, or evolution under differentselective pressures in their area of contact. Further, we proposethat the divergence in male signal was at least partly initiatedin allopatry and discuss different evolutionary scenario thatmay explain the patterns observed in Denmark and their relevance to isolation between the two taxa.     

Sperm Morphology in Two House Mouse Subspecies: Do Wild-Derived Strains and Wild Mice Tell the Same Story?

Being subject to intense post-copulatory selection, sperm size is a principal determining component of male fitness. Although previous studies have presented comparative sperm size data at higher taxonomic levels, information on the evolution of sperm size within species is generally lacking. Here, we studied two house mouse subspecies, Mus musculus musculus and Mus musculus domesticus, which undergo incipient speciation. We measured four sperm dimensions from cauda epididymis smears of 28 wild-caught mice of both subspecies. As inbred mouse strains are frequently used as proxies for exploring evolutionary processes, we further studied four wild-derived inbred strains from each subspecies. The subspecies differed significantly in terms of sperm head length and midpiece length, and these differences were consistent for wild mice and wild-derived strains pooled over genomes. When the inbred strains were analyzed individually, however, their strain-specific values were in some cases significantly shifted from subspecies-specific values derived from wild mice. We conclude that: (1) the size of sperm components differ in the two house mouse subspecies studied, and that (2) wild-derived strains reflect this natural polymorphism, serving as a potential tool to identify the genetic variation driving these evolutionary processes. Nevertheless, we suggest that more strains should be used in future experiments to account for natural variation and to avoid confounding results due to reduced variability and/or founder effect in the individual strains.     

Genetics and evolution of hybrid male sterility in house mice

Comparative genetic mapping provides insights into the evolution of the reproductive barriers that separate closely related species. This approach has been used to document the accumulation of reproductive incompatibilities over time, but has only been applied to a few taxa. House mice offer a powerful system to reconstruct the evolution of reproductive isolation between multiple subspecies pairs. However, studies of the primary reproductive barrier in house mice-hybrid male sterility-have been restricted to a single subspecies pair: Mus musculus musculus and Mus musculus domesticus. To provide a more complete characterization of reproductive isolation in house mice, we conducted an F(2) intercross between wild-derived inbred strains from Mus musculus castaneus and M. m. domesticus. We identified autosomal and X-linked QTL associated with a range of hybrid male sterility phenotypes, including testis weight, sperm density, and sperm morphology. The pseudoautosomal region (PAR) was strongly associated with hybrid sterility phenotypes when heterozygous. We compared QTL found in this cross with QTL identified in a previous F(2) intercross between M. m. musculus and M. m. domesticus and found three shared autosomal QTL. Most QTL were not shared, demonstrating that the genetic basis of hybrid male sterility largely differs between these closely related subspecies pairs. These results lay the groundwork for identifying genes responsible for the early stages of speciation in house mice.     

A pronounced evolutionary shift of the pseudoautosomal region boundary in house mice

The pseudoautosomal region (PAR) is essential for the accurate pairing and segregation of the X and Y chromosomes during meiosis. Despite its functional significance, the PAR shows substantial evolutionary divergence in structure and sequence between mammalian species. An instructive example of PAR evolution is the house mouse Mus musculus domesticus (represented by the C57BL/6J strain), which has the smallest PAR among those that have been mapped. In C57BL/6J, the PAR boundary is located just ~700 kb from the distal end of the X chromosome, whereas the boundary is found at a more proximal position in Mus spretus, a species that diverged from house mice 2-4 million years ago. In this study we used a combination of genetic and physical mapping to document a pronounced shift in the PAR boundary in a second house mouse subspecies, Mus musculus castaneus (represented by the CAST/EiJ strain), ~430 kb proximal of the M. m. domesticus boundary. We demonstrate molecular evolutionary consequences of this shift, including a marked lineage-specific increase in sequence divergence within Mid1, a gene that resides entirely within the M. m. castaneus PAR but straddles the boundary in other subspecies. Our results extend observations of structural divergence in the PAR to closely related subspecies, pointing to major evolutionary changes in this functionally important genomic region over a short time period.     

Congenic strain analysis reveals genes that are rapidly evolving components of a prezygotic isolation mechanism mediating incipient reinforcement

Two decades ago, we developed a congenic strain of Mus musculus, called b-congenic, by replacing the androgen-binding protein Abpa27(a) allele in the C3H/HeJ genome with the Abpa27(b) allele from DBA/2J. We and other researchers used this b-congenic strain and its C3H counterpart, the a-congenic strain, to test the hypothesis that, given the choice between signals from two strains with different a27 alleles on the same genetic background, test subjects would prefer the homosubspecific one. It was our purpose in undertaking this study to characterize the segment transferred from DBA to the C3H background in producing the b-congenic strain on which a role for ABPA27 in behavior has been predicated. We determined the size of the chromosome 7 segment transferred from DBA and the genes it contains that might influence preference. We found that the "functional" DBA segment is about 1% the size of the mouse haploid genome and contains at least 29 genes expressed in salivary glands, however, only three of these encode proteins identified in the mouse salivary proteome. At least two of the three genes Abpa27, Abpbg26 and Abpbg27 encoding the subunits of androgen-binding protein ABP dimers evolved under positive selection and the third one may have also. In the sense that they are subunits of the same two functional entities, the ABP dimers, we propose that their evolutionary histories might not be independent of each other.     

Mouse biodiversity in the genomic era

Comparative genomics has developed by comparison of distantly related genomes, for which the link between the reported evolutionary changes and species development/physiology/ecology is not obvious. It is argued that the mouse (genus Mus) is an optimal model for microevolutionary genomics in vertebrates. This is because the mouse genome sequence, physical and genetic map have been completed, because mouse genetics, morpho-anatomy, pathology, behavior and ecology are well-studied, and because the Mus genus is a diverse, well- documented taxon, allowing comparative studies at the level of individual, population, subspecies, and species. The potential of the interaction between mouse genome and mouse biodiversity is illustrated by recent studies of speciation in the house mouse Mus musculus, and studies about the evolution of isochores, the peculiar pattern of GC-content variation across mammalian genomes.     

Prdm9 Polymorphism Unveils Mouse Evolutionary Tracks

PR/SET domain containing 9 (Prdm9) mediates histone modifications such as H3K4me3 and marks hotspots of meiotic recombination. In many mammalian species, the Prdm9 gene is highly polymorphic. Prdm9 polymorphism is assumed to play two critical roles in evolution: to diversify the spectrum of meiotic recombination hotspots and to cause male hybrid sterility, leading to reproductive isolation and speciation. Nevertheless, information about Prdm9 sequences in natural populations is very limited. In this study, we conducted a comprehensive population survey on Prdm9 polymorphism in the house mouse, Mus musculus. Overall M. musculus Prdm9 displays an extraordinarily high level of polymorphism, particularly in regions encoding zinc finger repeats, which recognize recombination hotspots. Prdm9 alleles specific to various M. musculus subspecies dominate in subspecies territories. Moreover, introgression into other subspecies territories was found for highly divergent Prdm9 alleles associated with t-haplotype. The results of our phylogeographical analysis suggest that the requirement for hotspot diversity depends on geographical range and time span in mouse evolution, and that Prdm9 polymorphism has not been maintained by a simple balanced selection in the population of each subspecies.