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Gene duplication and loss are major sources of genetic polymorphism in populations, and are important forces shaping the evolution of genome content and organization. We have reconstructed the origin and history of a 127 kbp segmental duplication,R2d, in the house mouse (Mus musculus). R2dcontains a single protein-coding gene,Cwc22. De novoassembly of both the ancestral (R2d1) and the derived (R2d2) copies reveals that they have been subject to non-allelic gene conversion events spanning tens of kilobases.R2d2is also a hotspot for structural variation: its diploid copy number ranges from zero in the mouse reference genome to more than 80 in wild mice sampled from around the globe. Hemizgyosity for high-copy-number alleles ofR2d2is associated inciswith meiotic drive, suppression of meiotic crossovers, and copy-number instability, with a mutation rate in excess of 1 per 100 transmissions in laboratory populations. We identify an additional 57 loci covering 0.8% of the mouse genome with patterns of sequence variation similar to those atR2d1andR2d2. Our results provide a striking example of allelic diversity generated by duplication and demonstrate the value ofde novoassembly in a phylogenetic context for understanding the mutational processes affecting duplicate genes.

Cell-cell signaling in microorganisms is still poorly characterized. In this Methods paper, we describe a genetic procedure for detecting cell-nonautonomous genetic effects, and in particular cell-cell signaling, termed the chimeric colony assay (CCA). The CCA measures the effect of a gene on a biological response in a neighboring cell. This assay can measure cell autonomy for range of biological activities including transcript or protein accumulation, subcellular localization, and cell differentiation. To date, the CCA has been used exclusively to investigate colony patterning in the budding yeast Saccharomyces cerevisiae. To demonstrate the wider potential of the assay, we applied this assay to two other systems: the effect of Grr1 on glucose repression of GAL1 transcription in yeast and the effect of rpsL on stop-codon translational readthrough in Escherichia coli. We also describe variations of the standard CCA that address specific aspects of cell-cell signaling, and we delineate essential controls for this assay. Finally, we discuss complementary approaches to the CCA. Taken together, this Methods paper demonstrates how genetic assays can reveal and explore the roles of cell-cell signaling in microbial processes.

Background Newly emerged mutations within the Plasmodium falciparum chloroquine resistance transporter (PfCRT) can confer piperaquine resistance in the absence of amplified plasmepsin II (pfpm2). In this study, we estimated the prevalence of co-circulating piperaquine resistance mutations in P. falciparum isolates collected in northern Cambodia from 2009 to 2017. Methods The sequence of pfcrt was determined for 410 P. falciparum isolates using PacBio amplicon sequencing or whole genome sequencing. Quantitative polymerase chain reaction was used to estimate pfpm2 and pfmdr1 copy number. Results Newly emerged PfCRT mutations increased in prevalence after the change to dihydroartemisinin-piperaquine in 2010, with >98% of parasites harboring these mutations by 2017. After 2014, the prevalence of PfCRT F145I declined, being outcompeted by parasites with less resistant, but more fit PfCRT alleles. After the change to artesunate-mefloquine, the prevalence of parasites with amplified pfpm2 decreased, with nearly half of piperaquine-resistant PfCRT mutants having single-copy pfpm2. Conclusions The large proportion of PfCRT mutants that lack pfpm2 amplification emphasizes the importance of including PfCRT mutations as part of molecular surveillance for piperaquine resistance in this region. Likewise, it is critical to monitor for amplified pfmdr1 in these PfCRT mutants, as increased mefloquine pressure could lead to mutants resistant to both drugs.

House mice (Mus musculus) have spread globally as a result of their commensal relationship with humans. In the form of laboratory strains, both inbred and outbred, they are also among the most widely used model organisms in biomedical research. Although the general outlines of house mouse dispersal and population structure are well known, details have been obscured by either limited sample size or small numbers of markers. Here we examine ancestry, population structure, and inbreeding using SNP microarray genotypes in a cohort of 814 wild mice spanning five continents and all major subspecies of Mus, with a focus on M. m. domesticus. We find that the major axis of genetic variation in M. m. domesticus is a south-to-north gradient within Europe and the Mediterranean. The dominant ancestry component in North America, Australia, New Zealand, and various small offshore islands are of northern European origin. Next we show that inbreeding is surprisingly pervasive and highly variable, even between nearby populations. By inspecting the length distribution of homozygous segments in individual genomes, we find that inbreeding in commensal populations is mostly due to consanguinity. Our results offer new insight into the natural history of an important model organism for medicine and evolutionary biology.

House mice (Mus musculus) have spread globally as a result of their commensal relationship with humans. In the form of laboratory strains, both inbred and outbred, they are also among the most widely-used model organisms in biomedical research. Although the general outlines of house mouse dispersal and population structure are well known, details have been obscured by either limited sample size or small numbers of markers. Here we examine ancestry, population structure and inbreeding using SNP microarray genotypes in a cohort of 814 wild mice spanning five continents and all major subspecies of Mus, with a focus on M. m. domesticus. We find that the major axis of genetic variation in M. m. domesticus is a south-to-north gradient within Europe and the Mediterranean. The dominant ancestry component in North America, Australia, New Zealand and various small offshore islands is of northern European origin. Next we show that inbreeding is surprisingly pervasive and highly variable, even between nearby populations. By inspecting the length distribution of homozygous segments in individual genomes, we find that inbreeding in commensal populations is mostly due to consanguinity. Our results offer new insight into the natural history of an important model organism for medicine and evolutionary biology.

Background Tanzania’s Zanzibar archipelago has made significant gains in malaria control over the last decade and is a target for malaria elimination. Despite consistent implementation of effective tools since 2002, elimination has not been achieved. Importation of parasites from outside of the archipelago is thought to be an important cause of malaria’s persistence, but this paradigm has not been studied using modern genetic tools. Methods Whole-genome sequencing (WGS) was used to investigate the impact of importation, employing population genetic analyses of Plasmodium falciparum isolates from both the archipelago and mainland Tanzania. Ancestry, levels of genetic diversity and differentiation, patterns of relatedness, and patterns of selection between these two populations were assessed by leveraging recent advances in deconvolution of genomes from polyclonal malaria infections. Results Significant decreases in the effective population sizes were inferred in both populations that coincide with a period of decreasing malaria transmission in Tanzania. Identity by descent analysis showed that parasites in the two populations shared long segments of their genomes, on the order of 5 cM, suggesting shared ancestry within the last 10 generations. Even with limited sampling, two of isolates between the mainland and Zanzibar were identified that are related at the expected level of half-siblings, consistent with recent importation. Conclusions These findings suggest that importation plays an important role for malaria incidence on Zanzibar and demonstrate the value of genomic approaches for identifying corridors of parasite movement to the island.

Over the 180 million years since their origin, the Y chromosomes of mammals have evolved a gene repertoire highly specialized for function in the male germline. The mouse Y chromosome is unique among mammal Y chromosomes studied to date in that it is large, gene-rich and almost entirely euchromatic. Yet little is known about its diversity in natural populations. Because the Y chromosome is passed only through the male germline and is obligately transmitted from fathers to sons without recombination, it provides a rich view into male-specific mutational, selective and demographic processes. We therefore took advantage of a recent high-quality assembly of the mouse Y to perform a systematic survey of a diverse sample of Y chromosomes using published whole-genome sequencing datasets. Sequence diversity in non-repetitive regions of Y chromosomes is

Host genetic variation is known to contribute to differential pathogenesis following infection. Mouse models allow direct assessment of host genetic factors responsible for susceptibility to Severe Acute Respiratory Syndrome coronavirus (SARS-CoV). Based on an assessment of early stage lines from the Collaborative Cross mouse multi-parent population, we identified two lines showing highly divergent susceptibilities to SARS-CoV: the resistant CC003/Unc and the susceptible CC053/Unc. We generated 264 F2 mice between these strains, and infected them with SARS-CoV. Weight loss, pulmonary hemorrhage, and viral load were all highly correlated disease phenotypes. We identified a quantitative trait locus of major effect on chromosome 18 (27.1–58.6 Mb) which affected weight loss, viral titer and hemorrhage. Additionally, each of these three phenotypes had distinct quantitative trait loci [Chr 9 (weight loss), Chrs 7 and 12 (virus titer), and Chr 15 (hemorrhage)]. We identified Ticam2, an adaptor protein in the TLR signaling pathways, as a candidate driving differential disease at the Chr 18 locus. Ticam2−/− mice were highly susceptible to SARS-CoV infection, exhibiting increased weight loss and more pulmonary hemorrhage than control mice. These results indicate a critical role for Ticam2 in SARS-CoV disease, and highlight the importance of host genetic variation in disease responses.

Meiotic recombination ensures the faithful segregation of chromosomes and influences patterns of genetic diversity. Morgan et al. used genotype data.. Meiotic recombination is an essential feature of sexual reproduction that ensures faithful segregation of chromosomes and redistributes genetic variants in populations. Multiparent populations such as the Diversity Outbred (DO) mouse stock accumulate large numbers of crossover (CO) events between founder haplotypes, and thus present a unique opportunity to study the role of genetic variation in shaping the recombination landscape. We obtained high-density genotype data from 6886 DO mice, and localized 2.2 million CO events to intervals with a median size of 28 kb. The resulting sex-averaged genetic map of the DO population is highly concordant with large-scale (order 10 Mb) features of previously reported genetic maps for mouse. To examine fine-scale (order 10 kb) patterns of recombination in the DO, we overlaid putative recombination hotspots onto our CO intervals. We found that CO intervals are enriched in hotspots compared to the genomic background. However, as many as 26% of CO intervals do not overlap any putative hotspots, suggesting that our understanding of hotspots is incomplete. We also identified coldspots encompassing 329 Mb, or 12% of observable genome, in which there is little or no recombination. In contrast to hotspots, which are a few kilobases in size, and widely scattered throughout the genome, coldspots have a median size of 2.1 Mb and are spatially clustered. Coldspots are strongly associated with copy-number variant (CNV) regions, especially multi-allelic clusters, identified from whole-genome sequencing of 228 DO mice. Genes in these regions have reduced expression, and epigenetic features of closed chromatin in male germ cells, which suggests that CNVs may repress recombination by altering chromatin structure in meiosis. Our findings demonstrate how multiparent populations, by bridging the gap between large-scale and fine-scale genetic mapping, can reveal new features of the recombination landscape.

The goal of the Collaborative Cross (CC) project was to generate and distribute over 1000 independent mouse recombinant inbred strains derived from eight inbred founders. With inbreeding nearly complete, we estimated the extinction rate among CC lines at a remarkable 95%, which is substantially higher than in the derivation of other mouse recombinant inbred populations. Here, we report genome-wide allele frequencies in 347 extinct CC lines. Contrary to expectations, autosomes had equal allelic contributions from the eight founders, but chromosome X had significantly lower allelic contributions from the two inbred founders with underrepresented subspecific origins (PWK/PhJ and CAST/EiJ). By comparing extinct CC lines to living CC strains, we conclude that a complex genetic architecture is driving extinction, and selection pressures are different on the autosomes and chromosome X. Male infertility played a large role in extinction as 47% of extinct lines had males that were infertile. Males from extinct lines had high variability in reproductive organ size, low sperm counts, low sperm motility, and a high rate of vacuolization of seminiferous tubules. We performed QTL mapping and identified nine genomic regions associated with male fertility and reproductive phenotypes. Many of the allelic effects in the QTL were driven by the two founders with underrepresented subspecific origins, including a QTL on chromosome X for infertility that was driven by the PWK/PhJ haplotype. We also performed the first example of cross validation using complementary CC resources to verify the effect of sperm curvilinear velocity from the PWK/PhJ haplotype on chromosome 2 in an independent population across multiple generations. While selection typically constrains the examination of reproductive traits toward the more fertile alleles, the CC extinct lines provided a unique opportunity to study the genetic architecture of fertility in a widely genetically variable population. We hypothesize that incompatibilities between alleles with different subspecific origins is a key driver of infertility. These results help clarify the factors that drove strain extinction in the CC, reveal the genetic regions associated with poor fertility in the CC, and serve as a resource to further study mammalian infertility.

Wild-derived mouse inbred strains are becoming increasingly popular for complex traits analysis, evolutionary studies, and systems genetics. Here, we report the whole-genome sequencing of two wild-derived mouse inbred strains, LEWES/EiJ and ZALENDE/EiJ, of Mus musculus domesticus origin. These two inbred strains were selected based on their geographic origin, karyotype, and use in ongoing research. We generated 14× and 18× coverage sequence, respectively, and discovered over 1.1 million novel variants, most of which are private to one of these strains. This report expands the number of wild-derived inbred genomes in the Mus genus from six to eight. The sequence variation can be accessed via an online query tool; variant calls (VCF format) and alignments (BAM format) are available for download from a dedicated ftp site. Finally, the sequencing data have also been stored in a lossless, compressed, and indexed format using the multi-string Burrows-Wheeler transform. All data can be used without restriction.

The Democratic Republic of the Congo (DRC) harbors 11% of global malaria cases, yet little is known about the spatial and genetic structure of the parasite population in that country. We sequence 2537 Plasmodium falciparum infections, including a nationally representative population sample from DRC and samples from surrounding countries, using molecular inversion probes - a high-throughput genotyping tool. We identify an east-west divide in haplotypes known to confer resistance to chloroquine and sulfadoxine-pyrimethamine. Furthermore, we identify highly related parasites over large geographic distances, indicative of gene flow and migration. Our results are consistent with a background of isolation by distance combined with the effects of selection for antimalarial drug resistance. This study provides a high-resolution view of parasite genetic structure across a large country in Africa and provides a baseline to study how implementation programs may impact parasite populations., The genome of the malaria parasite Plasmodium falciparum contains a record of past evolutionary forces. Here, using 2537 parasite sequences from the Democratic Republic of the Congo, the authors demonstrate how drug pressure and human movement have shaped the present-day parasite population.

Faithful segregation of mammalian X and Y chromosomes in male meiosis depends on pairing and recombination in a short interval of residual sequence homology known as the pseudoautosomal region (PAR)... Faithful segregation of homologous chromosomes at meiosis requires pairing and recombination. In taxa with dimorphic sex chromosomes, pairing between them in the heterogametic sex is limited to a narrow interval of residual sequence homology known as the pseudoautosomal region (PAR). Failure to form the obligate crossover in the PAR is associated with male infertility in house mice (Mus musculus) and humans. Yet despite this apparent functional constraint, the boundary and organization of the PAR is highly variable in mammals, and even between subspecies of mice. Here, we estimate the genetic map in a previously documented expansion of the PAR in the M. musculus castaneus subspecies and show that the local recombination rate is 100-fold higher than the autosomal background. We identify an independent shift in the PAR boundary in the M. musculus musculus subspecies and show that it involves a complex rearrangement, but still recombines in heterozygous males. Finally, we demonstrate pervasive copy-number variation at the PAR boundary in wild populations of M. m. domesticus, M. m. musculus, and M. m. castaneus. Our results suggest that the intensity of recombination activity in the PAR, coupled with relatively weak constraints on its sequence, permit the generation and maintenance of unusual levels of polymorphism in the population of unknown functional significance.

Gene duplication and loss are major sources of genetic polymorphism in populations, and are important forces shaping the evolution of genome content and organization. We have reconstructed the origin and history of a 127-kbp segmental duplication, R2d, in the house mouse (Mus musculus). R2d contains a single protein-coding gene, Cwc22. De novo assembly of both the ancestral (R2d1) and the derived (R2d2) copies reveals that they have been subject to nonallelic gene conversion events spanning tens of kilobases. R2d2 is also a hotspot for structural variation: its diploid copy number ranges from zero in the mouse reference genome to >80 in wild mice sampled from around the globe. Hemizygosity for high copy-number alleles of R2d2 is associated in cis with meiotic drive; suppression of meiotic crossovers; and copy-number instability, with a mutation rate in excess of 1 per 100 transmissions in some laboratory populations. Our results provide a striking example of allelic diversity generated by duplication and demonstrate the value of de novo assembly in a phylogenetic context for understanding the mutational processes affecting duplicate genes.

Genotyping microarrays are an important resource for genetic mapping, population genetics, and monitoring of the genetic integrity of laboratory stocks. We have developed the third generation of the Mouse Universal Genotyping Array (MUGA) series, GigaMUGA, a 143,259-probe Illumina Infinium II array for the house mouse (Mus musculus). The bulk of the content of GigaMUGA is optimized for genetic mapping in the Collaborative Cross and Diversity Outbred populations, and for substrain-level identification of laboratory mice. In addition to 141,090 single nucleotide polymorphism probes, GigaMUGA contains 2006 probes for copy number concentrated in structurally polymorphic regions of the mouse genome. The performance of the array is characterized in a set of 500 high-quality reference samples spanning laboratory inbred strains, recombinant inbred lines, outbred stocks, and wild-caught mice. GigaMUGA is highly informative across a wide range of genetically diverse samples, from laboratory substrains to other Mus species. In addition to describing the content and performance of the array, we provide detailed probe-level annotation and recommendations for quality control.

RelatednessRelatedness in the genetic sense refers to the proportion of alleles shared between two individuals. The degree to which two individuals are genetically related depends on the number of common ancestors they share and the number of generations which have elapsed since they shared them. A pedigree describes the expected relatedness between individuals: first-degree relatives (parents or siblings) share, on average, half of their alleles; second-degree relatives (grandparents) one-fourth; and so on. With dense genotype data, we can instead compute realized relatedness as the proportion of shared, unlinked alleles. Using dense genotypes, we can define relatedness both at the genome-wide and at the local scale. In the presence of admixture or introgression (see below), local relatedness in different regions of the genome may deviate from the genome-wide average. Population structure A population is “structured” when it has experienced deviations from random mating, or equivalently, when it is divided into subpopulations with restricted genetic exchange between them. In a structured population, some groups of individuals are more closely related to (share more alleles with) each other than with other groups. Geography and mating behavior generate at least some degree of structure in most natural populations. Population structure in laboratory mouse strains is widespread: for instance, the 129 and C57BL strain groups form a genetic cluster distinct from so-called “Swiss mice” including FVB/NJ, the NOD substrains, and ICR outbred stock (Beck et al. 2000). Failure to account for population structure can lead to false-positive QTL in genetic mapping of complex traits. Linkage disequilibrium (LD) Two loci are said to be in LD if the frequencies of pairwise genotypes depart from those expected if alleles were sampled randomly at each locus. LD is decreased by recombination, and therefore generally decreases with time and with physical distance between loci. Unlinked markers are expected to be in linkage equilibrium, but non-random mating can produce “long-range” LD between unlinked loci in structured populations. Haplotype block A haplotype block is a chromosomal segment in which there is no evidence for recombination during the history of a sample of individuals. Within a block, individuals in a population can be collapsed into one of a small (relative to the population size) number of ancestral haplotypes (Wall et al. 2003). LD is relatively high between loci within a block, but relatively low between loci in adjacent blocks. Although many schemes have been proposed for defining haplotype blocks, the one discussed in this review is the four-gamete test (Hudson et al. 1985). Consider two loci A and B with alleles A,a and B,b, respectively. There are four possible haploid genotypes (gametes)—AB, aB, Ab, and ab—and if all four are observed in a sample, recombination between A and B must have occurred at least once in the past. Haplotype blocks are a useful means of investigating patterns of genetic diversity at intermediate timescales since a common ancestor, such as among classical inbred strains of mice (Yang et al. 2011). But because recombination events accumulate and LD decreases with time, haplotype blocks shared between two individuals with a common ancestor far in the past—for example, a wild-derived inbred strain and a classical laboratory strain—will be very short. For this reason, haplotype blocks were not inferred for the wild mice and wild-derived strains in Yang et al. (2011). Identity by descent (IBD) A chromosomal segment is shared identical-by-descent between two individuals if it was inherited from their common ancestor without recombination. The notion of IBD is closely related to the haplotype block. Admixture Admixture refers to inter-breeding between individuals from populations which were previously genetically isolated from one another. Admixture facilitates gene flow between populations, and in the process creates heterogeneity of relatedness across the genome. IntrogressionIntrogression refers to the introduction of a chromosomal segment from one population into a separate, genetically distinct population. It is often used to describe gene flow between species or subspecies which can still form fertile hybrids. Unlike admixture, which describes ongoing inter-breeding, introgression describes events which are episodic in nature. In this review, we refer to genetic exchange between mouse subspecies, which do not interbreed in the wild except at narrow hybrid zones (Ursin 1952), as introgression. Ancestry inference Broadly speaking, an ancestry-inference procedure steps along the genome of an individual and attempts to assign each segment to one of a few ancestral clusters. These clusters may represent ancestral population groups, for samples from natural populations, or founder haplotypes in laboratory populations. Examples of ancestry inference discussed in this review include assignment of subspecific origin in wild mice (Yang et al. 2011), which labels genomic regions with one of three subspecies; and haplotype reconstruction on the CC and DO (Fu et al. 2012), which assigns genomic regions to one of those populations’ 8 founder strains. Hidden Markov model (HMM) A hidden Markov model is a probabilistic model which describes how an observed sequence can be generated from an underlying, unknown sequence of “hidden states” (Baum and Petrie 1966; Rabiner 1989). Efficient algorithms can be used to “decode” the sequence of hidden states given an observed sequence. In this review, we discuss HMMs in which the observed sequences are genotypes along a chromosome, and the hidden states are founder haplotypes.

Host genetic variation is known to contribute to differential pathogenesis following infection. Mouse models allow direct assessment of host genetic factors responsible for susceptibility to Severe Acute Respiratory Syndrome coronavirus (SARS-CoV). Based on an assessment of early stage lines from the Collaborative Cross mouse multi-parent population, we identified two lines showing highly divergent susceptibilities to SARS-CoV: the resistant CC003/Unc and the susceptible CC053/Unc. We generated 264 F2 mice between these strains, and infected them with SARS-CoV. Weight loss, pulmonary hemorrhage, and viral load were all highly correlated disease phenotypes. We identified a quantitative trait locus of major effect on chromosome 18 (27.1–58.6 Mb) which affected weight loss, viral titer and hemorrhage. Additionally, each of these three phenotypes had distinct quantitative trait loci [Chr 9 (weight loss), Chrs 7 and 12 (virus titer), and Chr 15 (hemorrhage)]. We identified Ticam2, an adaptor protein in the TLR signaling pathways, as a candidate driving differential disease at the Chr 18 locus. Ticam2−/− mice were highly susceptible to SARS-CoV infection, exhibiting increased weight loss and more pulmonary hemorrhage than control mice. These results indicate a critical role for Ticam2 in SARS-CoV disease, and highlight the importance of host genetic variation in disease responses.

The Collaborative Cross (CC) is a multiparent panel of recombinant inbred (RI) mouse strains derived from eight founder laboratory strains. RI panels are popular because of their long-term genetic stability, which enhances reproducibility and integration of data collected across time and conditions. Characterization of their genomes can be a community effort, reducing the burden on individual users. Here we present the genomes of the CC strains using two complementary approaches as a resource to improve power and interpretation of genetic experiments. Our study also provides a cautionary tale regarding the limitations imposed by such basic biological processes as mutation and selection. A distinct advantage of inbred panels is that genotyping only needs to be performed on the panel, not on each individual mouse. The initial CC genome data were haplotype reconstructions based on dense genotyping of the most recent common ancestors (MRCAs) of each strain followed by imputation from the genome sequence of the corresponding founder inbred strain. The MRCA resource captured segregating regions in strains that were not fully inbred, but it had limited resolution in the transition regions between founder haplotypes, and there was uncertainty about founder assignment in regions of limited diversity. Here we report the whole genome sequence of 69 CC strains generated by paired-end short reads at 30× coverage of a single male per strain. Sequencing leads to a substantial improvement in the fine structure and completeness of the genomes of the CC. Both MRCAs and sequenced samples show a significant reduction in the genome-wide haplotype frequencies from two wild-derived strains, CAST/EiJ and PWK/PhJ. In addition, analysis of the evolution of the patterns of heterozygosity indicates that selection against three wild-derived founder strains played a significant role in shaping the genomes of the CC. The sequencing resource provides the first description of tens of thousands of new genetic variants introduced by mutation and drift in the CC genomes. We estimate that new SNP mutations are accumulating in each CC strain at a rate of 2.4 ± 0.4 per gigabase per generation. The fixation of new mutations by genetic drift has introduced thousands of new variants into the CC strains. The majority of these mutations are novel compared to currently sequenced laboratory stocks and wild mice, and some are predicted to alter gene function. Approximately one-third of the CC inbred strains have acquired large deletions (>10 kb) many of which overlap known coding genes and functional elements. The sequence of these mice is a critical resource to CC users, increases threefold the number of mouse inbred strain genomes available publicly, and provides insight into the effect of mutation and drift on common resources.

Summary Laboratory mice, while paramount for understanding basic biological phenomena, are limited in modeling complex diseases of humans and other free-living mammals. Because the microbiome is a major factor in mammalian physiology, we aimed to identify a naturally evolved reference microbiome to better recapitulate physiological phenomena relevant in the natural world outside the laboratory. Among 21 distinct mouse populations worldwide, we identified a closely related wild relative to standard laboratory mouse strains. Its bacterial gut microbiome differed significantly from its laboratory mouse counterpart and was transferred to and maintained in laboratory mice over several generations. Laboratory mice reconstituted with natural microbiota exhibited reduced inflammation and increased survival following influenza virus infection and improved resistance against mutagen/inflammation-induced colorectal tumorigenesis. By demonstrating the host fitness-promoting traits of natural microbiota, our findings should enable the discovery of protective mechanisms relevant in the natural world and improve the modeling of complex diseases of free-living mammals. Video Abstract

Complex human traits are influenced by variation in regulatory DNA through mechanisms that are not fully understood. Because regulatory elements are conserved between humans and mice, a thorough annotation of cis regulatory variants in mice could aid in further characterizing these mechanisms. Here we provide a detailed portrait of mouse gene expression across multiple tissues in a three-way diallel. Greater than 80% of mouse genes have cis regulatory variation. Effects from these variants influence complex traits and usually extend to the human ortholog. Further, we estimate that at least one in every thousand SNPs creates a cis regulatory effect. We also observe two types of parent-of-origin effects, including classical imprinting and a new global allelic imbalance in expression favoring the paternal allele. We conclude that, as with humans, pervasive regulatory variation influences complex genetic traits in mice and provide a new resource toward understanding the genetic control of transcription in mammals.

The 28th International Mammalian Genome Conference (IMGC) was held October 26–29th, 2014 in scenic Bar Harbor, Maine. In addition to being the home of The Jackson Laboratory, Mount Desert Island is a popular summer vacation destination. More than 200 attendees of the conference enjoyed the last few days of the tourist season as the autumn leaves fell and the local residents prepared for winter. Darla Miller and Dasha Li Kappe organized the meeting, with the help of local organizers Ron Korstanje, Karen Svenson, Erin McDevitt, and Nancy Place. Scientists presented cutting-edge research in the fields of mammalian genetics and genomics that highlighted the importance of mammalian models for human genetics and disease research. The plenary presentations demonstrated the broad applicability of mammalian models to study a range of topics from gene evolution to rare human diseases. Meanwhile, the Verne Chapman lecture provided a historical account of mouse genetics research and encouraged a new, automated approach to forward genetics. Bioinformatics and Systems Genetics Workshops gave participants hands-on opportunities to become familiar with genetic and genomic tools. A student satellite symposium afforded budding scientists the chance to share their work and two poster sessions encouraged interaction among researchers. The meeting program and abstracts are available online at www.imgs.org/Archive/abstracts/2014Abstracts/IMGS2014Program.pdfwww.imgs.org. Online resources presented at the meeting are listed in Table 1. Table 1 Databases, resources, and tools Bioinformatics workshops Several workshops provided conference attendees with opportunities for hands-on guided tours of publicly available informatics resources relevant to IMGS members. The pre-conference Bioinformatics Workshop offered three mini-sessions: (1) a guide to genome annotations produced by the GENCODE consortium, and differences between annotation sets provided by popular databases (Laurens Wilming, Wellcome Trust Sanger Institute); (2) an overview of the International Knockout Mouse Consortium's pipeline and progress (Mark Thomas, Wellcome Trust Sanger Institute); and (3) a tour of the International Mouse Phenotyping Consortium's database of mutant mouse phenotypes (www.mousephenotype.org). An online link to these workshop powerpoint presentations can be found under the “History” tab on the IMGS home page (www.imgs.org). The System Genetics Workshops, led by Dan Gatti (The Jackson Laboratory), Marty Ferris (University of North Carolina at Chapel Hill), Gary Churchill (The Jackson Laboratory) along with Andrew Morgan and Fernando Pardo-Manuel de Villena (University of North Carolina at Chapel Hill) featured talks on the design and status of two important multiparental genetic reference populations, the Collaborative Cross (CC) and the Diversity Outbred (DO) mice. Didactic sessions were supplemented with small-group discussions on rational experimental designs using these populations and available online tools for analyses (www.csbio.unc.edu/CCstatus/index.py) were described by Leonard McMillan, Chen-Ping Fu, and Chia-yu Kao (University of North Carolina at Chapel Hill). This year's Mouse Genome Informatics(MGI) Workshops (www.informatics.jax.org) were led by Joanne Berghout and David Shaw (The Jackson Laboratory). The hands-on workshops included seminar-style demonstrations followed by the opportunity to navigate MGI using self-guided exercises. Participants were instructed on how to locate biological information by performing a variety of searches, and were also introduced to new tools such as the Human-Mouse: Disease Connection portal (www.informatics.jax.org/humanDisease.shtml), the Recombinase (Cre) Activity portal (www.informatics.jax.org/recombinase.shtml), and the MouseMine computational access platform (www.mousemine.org/mousemine/begin.do). In celebration of the 25th birthday of the MGI database, Janan Eppig (The Jackson Laboratory; O-30) tracked the history of the MGI from a pre-web version distributed on floppy disks to the MGI website (www.informatics.jax.org) that we know today. Janan emphasized the continued commitment of MGI to provide integrated genetic, genomic, and biological data for mouse and to provide increased access to translational data views to support discovery and hypothesis building for studies of human disease. Janan also recognized the contributions of many individuals who worked to develop MGI over the years and described future plans as MGI evolves to meet the growing needs of the scientific community.

Quantitative trait locus (QTL) analyses of intercross populations between widely used mouse inbred strains provide a powerful approach for uncovering genetic factors that influence susceptibility to atherosclerosis. Epistatic interactions are common in complex phenotypes and depend on genetic backgrounds. To dissect genetic architecture of atherosclerosis, we analyzed F2 progeny from a cross between apolipoprotein E-null mice on DBA/2J (DBA-apoE) and C57BL/6J (B6-apoE) genetic backgrounds and compared the results with those from two previous F2 crosses of apolipoprotein E-null mice on 129S6/SvEvTac (129-apoE) and DBA-apoE backgrounds, and B6-apoE and 129-apoE backgrounds. In these round-robin crosses, in which each parental strain was crossed with two others, large-effect QTLs are expected to be detectable at least in two crosses. On the other hand, observation of QTLs in one cross only may indicate epistasis and/or absence of statistical power. For atherosclerosis at the aortic arch, Aath4 on chromosome (Chr)2:66 cM follows the first pattern, with significant QTL peaks in (DBAx129)F2 and (B6xDBA)F2 mice but not in (B6x129)F2 mice. We conclude that genetic variants unique to DBA/2J at Aath4 confer susceptibility to atherosclerosis at the aortic arch. A similar pattern was observed for Aath5 on chr10:35 cM, verifying that the variants unique to DBA/2J at this locus protect against arch plaque development. However, multiple loci, including Aath1 (Chr1:49 cM), and Aath2 (Chr1:70 cM) follow the second type of pattern, showing significant peaks in only one of the three crosses (B6-apoE x 129-apoE). As for atherosclerosis at aortic root, the majority of QTLs, including Ath29 (Chr9:33 cM), Ath44 (Chr1:68 cM) and Ath45 (Chr2:83 cM), was also inconsistent, being significant in only one of the three crosses. Only the QTL on Chr7:37 cM was consistently suggestive in two of the three crosses. Thus QTL analysis of round-robin crosses revealed the genetic architecture of atherosclerosis.

Mouse models are paramount for understanding basic immunological mechanisms, but can be limited in recapitulating human diseases. The microbiome has been identified as a main factor influencing host physiology as illustrated by many studies that disrupt or modify host-microbe interactions in laboratory mice. Differences in the gut microbiome contribute to the variability of research results obtained with genetically identical animals from different vendors. In an effort to identify an external reference that better recapitulates physiologically important interactions found in a natural habitat, we asked how far removed the gut microbiome of laboratory mice is from that of their outbred, wild-living relative. Through genetic analysis we identify the closest wild relatives to classical laboratory strains among 21 distinct populations from Europe, Asia and the Americas. We establish that their gut microbiome differs significantly from that of C57BL/6 mice from the leading breeders worldwide, and that it can be transferred and maintained over several generations under vivarium conditions. Offspring of pregnant germ-free C57BL/6 mice reconstituted with the gut microbiome of wild mice exhibit a significantly reduced inflammatory response and increased survival following influenza A virus infection. This restoration of the natural ‘microbial identity’ of laboratory mice also improved their resistance against mutagen- and inflammation-induced colorectal cancer. Collectively, these data show the beneficial effects of the wild mouse microbiome in two diseases of global relevance. They also illustrate a novel approach towards developing animal models of greater biological relevance and translational research value.

Since the publication of the first comprehensive linkage map for the laboratory mouse, the architecture of recombination as a basic biological process has become amenable to investigation in mammalian model organisms. Here we take advantage of high-density genotyping and the unique pedigree structure of the incipient Collaborative Cross to investigate the roles of sex and genetic background in mammalian recombination. Our results confirm the observation that map length is longer when measured through female meiosis than through male meiosis, but we find that this difference is modified by genotype at loci on both the X chromosome and the autosomes. In addition, we report a striking concentration of crossovers in the distal ends of autosomes in male meiosis that is absent in female meiosis. The presence of this pattern in both single- and double-recombinant chromosomes, combined with the absence of a corresponding asymmetry in the distribution of double-strand breaks, indicates a regulated sequence of events specific to male meiosis that is anchored by chromosome ends. This pattern is consistent with the timing of chromosome pairing and evolutionary constraints on male recombination. Finally, we identify large regions of reduced crossover frequency that together encompass 5% of the genome. Many of these “cold regions” are enriched for segmental duplications, suggesting an inverse local correlation between recombination rate and mutation rate for large copy number variants.

Nat. Genet. 47, 353–360 (2015); published online 2 March 2015; corrected after print 16 April 2015 In the version of this article initially published, an accession number was not provided for RNA-seq data sets. The RNA-seq data sets that passed quality control are available at the Sequence Read Archive (SRA) under accession SRP056236.