Experimental Evaluation of a Direct Fitness Effect of the De Novo Evolved Mouse Gene Pldi.

De novo evolved genes emerge from random parts of noncoding sequences and have, therefore, no homologs from which a function could be inferred. While expression analysis and knockout experiments can provide insights into the function, they do not directly test whether the gene is beneficial for its carrier. Here, we have used a seminatural environment experiment to test the fitness of the previously identified de novo evolved mouse gene Pldi, which has been implicated to have a role in sperm differentiation. We used a knockout mouse strain for this gene and competed it against its parental wildtype strain for several generations of free reproduction. We found that the knockout (ko) allele frequency decreased consistently across three replicates of the experiment. Using an approximate Bayesian computation framework that simulated the data under a demographic scenario mimicking the experiment's demography, we could estimate a selection coefficient ranging between 0.21 and 0.61 for the wildtype allele compared to the ko allele in males, under various models. This implies a relatively strong selective advantage, which would fix the new gene in less than hundred generations after its emergence.

Reemergence of Lymphocytic Choriomeningitis Mammarenavirus, Germany.

Lymphocytic choriomeningitis mammarenavirus (LCMV) is a globally distributed zoonotic pathogen transmitted by house mice (Mus musculus). We report the reemergence of LCMV (lineages I and II) in wild house mice (Mus musculus domesticus) and LCMV lineage I in a diseased golden lion tamarin (Leontopithecus rosalia) from a zoo in Germany.

Fast adjustment of pace-of-life and risk-taking to changes in food quality by altered gene expression in house mice.

The pace-of-life syndrome hypothesis provides a framework for the adaptive integration of behaviour, physiology and life history between and within species. It suggests that behaviours involving a risk of death or injury should co-vary with a higher allocation to fast reproduction. Empirical support for this hypothesis is mixed, presumably because important influencing factors such as environmental variation, are usually neglected. By experimentally manipulating food quality of wild mice living under semi-natural conditions for three generations, we show that individuals adjust their life history strategies and risk-taking behaviours as well as trait covariation (Nindividuals  = 1442). These phenotypic differences are correlated to differences in transcriptomic gene expression of primary metabolic processes in the liver while no changes in gene frequencies occurred. Our discussion emphasises the need to integrate the role of environmental conditions and phenotypic plasticity in shaping relationships among behaviour, physiology and life history in response to changing environmental conditions.

Competitive ability is a fast-evolving trait between house mouse populations (Mus musculus domesticus).

BACKGROUND: House mice are commensal animals with a nearly global distribution, structured into well differentiated local populations. Besides genetic differences between the populations, they have also diverged behaviorally over time, whereby it remains open how fast general behavioral characteristics can change. Here we study the competitive potential of two very recently separated populations of the Western house mouse (Mus musculus domesticus) by using two different approaches-one under controlled cage conditions, the other under more natural conditions in enclosures mimicking a secondary encounter condition. RESULTS: We observe a clear bias in the competitive ability towards one of the populations for both tests. The measured behavioral bias is also reflected in the number of hybrid offspring produced in the enclosures. CONCLUSION: Our data suggest that key behavioral characteristics with a direct influence on relative fitness can quickly change during the evolution of populations. It seems possible that the colonization situation in Western Europe, with a rapid spread of the mice after their arrival, would have favored more competitive populations at the expansion front. The study shows the possible impact of behavioral changes on the evolution of populations.

The amylase gene cluster in house mice (Mus musculus) was subject to repeated introgression including the rescue of a pseudogene.

BACKGROUND: Amylase gene clusters have been implicated in adaptive copy number changes in response to the amount of starch in the diet of humans and mammals. However, this interpretation has been questioned for humans and for mammals there is a paucity of information from natural populations. RESULTS: Using optical mapping and genome read information, we show here that the amylase cluster in natural house mouse populations is indeed copy-number variable for Amy2b paralogous gene copies (called Amy2a1 - Amy2a5), but a direct connection to starch diet is not evident. However, we find that the amylase cluster was subject to introgression of haplotypes between Mus musculus sub-species. A very recent introgression can be traced in the Western European populations and this leads also to the rescue of an Amy2b pseudogene. Some populations and inbred lines derived from the Western house mouse (Mus musculus domesticus) harbor a copy of the pancreatic amylase (Amy2b) with a stop codon in the first exon, making it non-functional. But populations in France harbor a haplotype introgressed from the Eastern house mouse (M. m. musculus) with an intact reading frame. Detailed analysis of phylogenetic patterns along the amylase cluster suggest an additional history of previous introgressions. CONCLUSIONS: Our results show that the amylase gene cluster is a hotspot of introgression in the mouse genome, making it an evolutionary active region beyond the previously observed copy number changes.

Meta-populational demes constitute a reservoir for large MHC allele diversity in wild house mice (Mus musculus).

BACKGROUND: The MHC class I and II loci mediate the adaptive immune response and belong to the most polymorphic loci in vertebrate genomes. In fact, the number of different alleles in a given species is often so large that it remains a challenge to provide an evolutionary model that can fully account for this. RESULTS: We provide here a general survey of MHC allele numbers in house mouse populations and two sub-species (M. m. domesticus and M. m. musculus) for H2 class I D and K, as well as class II A and E loci. Between 50 and 90% of the detected different sequences constitute new alleles, confirming that the discovery of new alleles is indeed far from complete. House mice live in separate demes with small effective population sizes, factors that were proposed to reduce, rather than enhance the possibility for the maintenance of many different alleles. To specifically investigate the occurrence of alleles within demes, we focused on the class II H2-Aa and H2-Eb exon 2 alleles in nine demes of M. m. domesticus from two different geographic regions. We find on the one hand a group of alleles that occur in different sampling regions and three quarters of these are also found in both sub-species. On the other hand, the larger group of different alleles (56%) occurs only in one of the regions and most of these (89%) only in single demes. We show that most of these region-specific alleles have apparently arisen through recombination and/or partial gene conversion from already existing alleles. CONCLUSIONS: Demes can act as sources of alleles that outnumber the set of alleles that are shared across the species range. These findings support the reservoir model proposed for human MHC diversity, which states that large pools of rare MHC allele variants are continuously generated by neutral mutational mechanisms. Given that these can become important in the defense against newly emerging pathogens, the reservoir model complements the selection based models for MHC diversity and explains why the exceptional diversity exists.

Evaluating the maintenance of disease-associated variation at the blood group-related gene B4galnt2 in house mice.

BACKGROUND: B4galnt2 is a blood group-related glycosyltransferase that displays cis-regulatory variation for its tissue-specific expression patterns in house mice. The wild type allele, found e.g. in the C57BL/6 J strain, directs intestinal expression of B4galnt2, which is the pattern observed among vertebrates, including humans. An alternative allele class found in the RIIIS/J strain and other mice instead drives expression in blood vessels, which leads to a phenotype similar to type 1 von Willebrand disease (VWD), a common human bleeding disorder. We previously showed that alternative B4galnt2 alleles are subject to long-term balancing selection in mice and that variation in B4galnt2 expression influences host-microbe interactions in the intestine. This suggests that the costs of prolonged bleeding in RIIIS/J allele-bearing mice might be outweighed by benefits associated with resistance against gastrointestinal pathogens. However, the conditions under which such trade-offs could lead to the long-term maintenance of disease-associated variation at B4galnt2 are unclear. RESULTS: To explore the persistence of B4galnt2 alleles in wild populations of house mice, we combined B4galnt2 haplotype frequency data together with a mathematical model based on an evolutionary game framework with a modified Wright-Fisher process. In particular, given the potential for a heterozygote advantage as a possible explanation for balancing selection, we focused on heterozygous mice, which express B4galnt2 in both blood vessels and the gastrointestinal tract. We show that B4galnt2 displays an interesting spatial allelic distribution in Western Europe, likely due to the recent action of natural selection. Moreover, we found that the genotype frequencies observed in nature can be produced by pathogen-driven selection when both heterozygotes and RIIIS/J homozygotes are protected against infection and the fitness cost of bleeding is roughly half that of infection. CONCLUSION: By comparing the results of our models to the patterns of polymorphism at B4galnt2 in natural populations, we are able to recognize the long-term maintenance of the RIIIS/J allele through host-pathogen interactions as a viable hypothesis. Further, our models identify that a putative dominant-, yet unknown protective function of the RIIIS/J allele appears to be more likely than a protective loss of intestinal B4galnt2 expression in RIIIS/J homozygotes.

No speed dating please! Patterns of social preference in male and female house mice.

BACKGROUND: In many animal species, interactions between individuals of different sex often occur in the context of courtship and mating. During these interactions, a specific mating partner can be chosen. By discriminating potential mates according to specific characteristics, individuals can increase their evolutionary fitness in terms of reproduction and offspring survival. In this study, we monitored the partner preference behaviour of female and male wild house mice (Mus musculus domesticus) from populations in Germany (G) and France (F) in a controlled cage setup for 5 days and six nights. We analysed the effects of individual factors (e.g. population origin and sex) on the strength of preference (selectivity), as well as dyadic factors (e.g. neutral genetic distance and major histocompatibility complex (MHC) dissimilarity) that direct partner preferences. RESULTS: Selectivity was stronger in mice with a pure population background than mixed individuals. Furthermore, female mice with a father from the German population had stronger selectivity than other mice. In this group, we found a preference for partners with a larger dissimilarity of their father's and their partner's MHC, as assessed by sequencing the H2-Eß locus. In all mice, selectivity followed a clear temporal pattern: it was low in the beginning and reached its maximum only after a whole day in the experiment. After two days, mice seemed to have chosen their preferred partner, as this choice was stable for the remaining four days in the experiment. CONCLUSIONS: Our study supports earlier findings that mate choice behaviour in wild mice can be paternally influenced. In our study, preference seems to be potentially associated with paternal MHC distance. To explain this, we propose familial imprinting as the most probable process for information transfer from father to offspring during the offspring's early phase of life, which possibly influences its future partner preferences. Furthermore, our experiments show that preferences can change after the first day of encounter, which implies that extended observation times might be required to obtain results that allow a valid ecological interpretation.

Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus.

Wild populations of the house mouse (Mus musculus) represent the raw genetic material for the classical inbred strains in biomedical research and are a major model system for evolutionary biology. We provide whole genome sequencing data of individuals representing natural populations of M. m. domesticus (24 individuals from 3 populations), M. m. helgolandicus (3 individuals), M. m. musculus (22 individuals from 3 populations) and M. spretus (8 individuals from one population). We use a single pipeline to map and call variants for these individuals and also include 10 additional individuals of M. m. castaneus for which genomic data are publically available. In addition, RNAseq data were obtained from 10 tissues of up to eight adult individuals from each of the three M. m. domesticus populations for which genomic data were collected. Data and analyses are presented via tracks viewable in the UCSC or IGV genome browsers. We also provide information on available outbred stocks and instructions on how to keep them in the laboratory.

Communication at the Garden Fence--Context Dependent Vocalization in Female House Mice.

House mice (Mus musculus) live in social groups where they frequently interact with conspecifics, thus communication (e.g. chemical and/or auditory) is essential. It is commonly known that male and female mice produce complex vocalizations in the ultrasonic range (USV) that remind of high-pitched birdsong (so called mouse song) which is mainly used in social interactions. Earlier studies suggest that mice use their USVs for mate attraction and mate choice, but they could also be used as signal during hierarchy establishment and familiarization, or other communication purposes. In this study we elucidated the vocalization behaviour of interacting female mice over an extended period of time under semi-natural conditions. We asked, if the rate or structure of female vocalization differs between different social and non-social contexts. We found that female USV is mainly used in social contexts, driven by direct communication to an unknown individual, the rate of which is decreased over time by a familiarization process. In addition we could show that female mice use two distinct types of USVs, differing in their frequency, which they use differently depending on whether they directly or indirectly communicate with another female. This supports the notion that vocalization in mice is context dependent, driven by a reasonable and yet underestimated amount of complexity that also involves the interplay between different sensory signals, like chemical and auditory cues.

Environmentally determined differences in the murine lung microbiota and their relation to alveolar architecture.

Commensal bacteria control the micro-ecology of metazoan epithelial surfaces with pivotal effect on tissue homeostasis and host defense. In contrast to the upper respiratory tract, the lower respiratory tract of healthy individuals has largely been considered free of microorganisms. To understand airway micro-ecology we studied microbiota of sterilely excised lungs from mice of different origin including outbred wild mice caught in the natural environment or kept under non-specific-pathogen-free (SPF) conditions as well as inbred mice maintained in non-SPF, SPF or germ-free (GF) facilities. High-throughput pyrosequencing of reverse transcribed 16S rRNA revealed metabolically active murine lung microbiota in all but GF mice. The overall composition across samples was similar at the phylum and family level. However, species richness was significantly different between lung microbiota from SPF and non-SPF mice. Non-cultivatable Betaproteobacteria such as Ralstonia spp. made up the major constituents and were also confirmed by 16S rRNA gene cloning analysis. Additionally, Pasteurellaceae, Enterobacteria and Firmicutes were isolated from lungs of non-SPF mice. Bacterial communities were detectable by fluorescent in situ hybridization (FISH) at alveolar epithelia in the absence of inflammation. Notably, higher bacterial abundance in non-SPF mice correlated with more and smaller size alveolae, which was corroborated by transplanting Lactobacillus spp. lung isolates into GF mice. Our data indicate a common microbial composition of murine lungs, which is diversified through different environmental conditions and affects lung architecture. Identification of the microbiota of murine lungs will pave the path to study their influence on pulmonary immunity to infection and allergens using mouse models.

Genetic differentiation of hypothalamus parentally biased transcripts in populations of the house mouse implicate the Prader-Willi syndrome imprinted region as a possible source of behavioral divergence.

Parentally biased expression of transcripts (genomic imprinting) in adult tissues, including the brain, can influence and possibly drive the evolution of behavioral traits. We have previously found that paternally determined cues are involved in population-specific mate choice decisions between two populations of the Western house mouse (Mus musculus domesticus). Here, we ask whether this could be mediated by genomically imprinted transcripts that are subject to fast differentiation between these populations. We focus on three organs that are of special relevance for mate choice and behavior: The vomeronasal organ (VNO), the hypothalamus, and the liver. To first identify candidate transcripts at a genome-wide scale, we used reciprocal crosses between M. m. domesticus and M. m. musculus inbred strains and RNA sequencing of the respective tissues. Using a false discovery cutoff derived from mock reciprocal cross comparisons, we find a total of 66 imprinted transcripts, 13 of which have previously not been described as imprinted. The largest number of imprinted transcripts were found in the hypothalamus; fewer were found in the VNO, and the least were found in the liver. To assess molecular differentiation and imprinting in the wild-derived M. m. domesticus populations, we sequenced the RNA of the hypothalamus from individuals of these populations. This confirmed the presence of the above identified transcripts also in wild populations and allowed us to search for those that show a high genetic differentiation between these populations. Our results identify the Ube3a-Snrpn imprinted region on chromosome 7 as a region that encompasses the largest number of previously not described transcripts with paternal expression bias, several of which are at the same time highly differentiated. For four of these, we confirmed their imprinting status via single nucleotide polymorphism-specific pyrosequencing assays with RNA from reciprocal crosses. In addition, we find the paternally expressed Peg13 transcript within the Trappc9 gene region on chromosome 15 to be highly differentiated. Interestingly, both regions have been implicated in Prader-Willi nervous system disorder phenotypes in humans. We suggest that these genomically imprinted regions are candidates for influencing the population-specific mate-choice in mice.

Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice.

Understanding the origins of gut microbial community structure is critical for the identification and interpretation of potential fitness-related traits for the host. The presence of community clusters characterized by differences in the abundance of signature taxa, referred to as enterotypes, is a debated concept first reported in humans and later extended to other mammalian hosts. In this study, we provide a thorough assessment of their existence in wild house mice using a panel of evaluation criteria. We identify support for two clusters that are compositionally similar to clusters identified in humans, chimpanzees, and laboratory mice, characterized by differences in Bacteroides, Robinsoniella, and unclassified genera belonging to the family Lachnospiraceae. To further evaluate these clusters, we (i) monitored community changes associated with moving mice from the natural to a laboratory environment, (ii) performed functional metagenomic sequencing, and (iii) subjected wild-caught samples to stable isotope analysis to reconstruct dietary patterns. This process reveals differences in the proportions of genes involved in carbohydrate versus protein metabolism in the functional metagenome, as well as differences in plant- versus meat-derived food sources between clusters. In conjunction with wild-caught mice quickly changing their enterotype classification upon transfer to a standard laboratory chow diet, these results provide strong evidence that dietary history contributes to the presence of enterotype-like clustering in wild mice.

The role of biogeography in shaping diversity of the intestinal microbiota in house mice.

The microbial communities inhabiting the mammalian intestinal tract play an important role in diverse aspects of host biology. However, little is known regarding the forces shaping variation in these communities and their influence on host fitness. To shed light on the contributions of host genetics, transmission and geography to diversity in microbial communities between individuals, we performed a survey of intestinal microbial communities in a panel of 121 house mice derived from eight locations across Western Europe using pyrosequencing of the bacterial 16S rRNA gene. The host factors studied included population structure estimated by microsatellite loci and mitochondrial DNA, genetic distance and geography. To determine whether host tissue (mucosa)-associated communities display properties distinct from those of the lumen, both the caecal mucosa and contents were examined. We identified Bacteroides, Robinsoniella and Helicobacter as the most abundant genera in both the caecal content and mucosa-associated communities of wild house mice. Overall, we found geography to be the most significant factor explaining patterns of diversity in the intestinal microbiota, with a comparatively weaker influence of host population structure and genetic distance. Furthermore, the influence of host genetic distance was limited to the mucosa communities, consistent with this environment being more intimately coupled to the host.

Long-term balancing selection at the blood group-related gene B4galnt2 in the genus Mus (Rodentia; Muridae).

Recent surveys of the human genome have highlighted the significance of balancing selection in relation to understanding the evolutionary origins of disease-associated variation. Cis-regulatory variation at the blood group-related glycosyltransferase B4galnt2 is associated with a phenotype in mice that closely resembles a common human bleeding disorder, von Willebrand disease. In this study, we have performed a survey of the 5' flanking region of the B4galnt2 gene in several Mus musculus subspecies and Mus spretus. Our results reveal a clear pattern of trans-species polymorphism and indicate that allele classes conferring alternative tissue-specific expression patterns have been maintained for >2.8 My in the genus Mus. Furthermore, analysis of B4galnt2 expression patterns revealed the presence of an additional functional class of alleles, supporting a role for gastrointestinal phenotypes in the long-term maintenance of expression variation at this gene.

Different competitive potential in two coexisting mouse lemur species in northwestern Madagascar.

Interspecific competition has been suggested to influence the biogeographic distribution patterns of species. A high competitive potential could entail species-specific advantages during resource acquisition that could translate into a higher potential for range expansion. We investigated whether differences in the competitive potential of the morphologically similar and partially sympatric gray mouse lemur (Microcebus murinus) and golden-brown mouse lemur (Microcebus ravelobensis) may help to explain differences in their geographic range sizes. We carried out encounter experiments with 14 pairs of captured female mouse lemurs of both species. The experimental dyads were tested in a two-cage arrangement, with individuals being separated from each other outside the experiments. Two days of habituation and four subsequent days of 1-h encounter experiments were conducted, before releasing the animals again in the wild. In general, the M. murinus individuals won significantly more conflicts than their partners. In eight of 14 tested pairs, there was a significant species bias in winning conflicts, and in 87.5% of these dyads, M. murinus was the "dyad winner". A high competitive potential did not depend on body mass. Furthermore, "dyad winners" spent more time feeding (P < 0.05) and were less spatially restricted than "dyad losers". To conclude, our results suggest that the widely distributed M. murinus may indeed have a higher competitive potential than the regional endemic M. ravelobensis, which may, among other possible factors, have enabled this species to expand geographically, despite the presence of other competing congeners.