Selective sweeps versus introgression - population genetic dynamics of the murine leukemia virus receptor Xpr1 in wild populations of the house mouse (Mus musculus)

The computational implementation of a platform of relative identity-by-descent scores algorithm for introgressive mapping

With the development of genotyping and sequencing technology, researchers working in the area of conservation genetics are able to obtain the genotypes or even the sequences of a representative sample of individuals from the population. It is of great importance to examine the genomic variants and genes that are highly preferred or pruned during the process of adaptive introgression or long-term hybridization. To the best of our knowledge, we are the first to develop a platform with computational integration of a relative identity-by-descent (rIBD) scores algorithm for introgressive mapping. The rIBD algorithm is designed for mapping the fine-scaled genomic regions under adaptive introgression between the source breeds and the admixed breed. Our rIBD calculation platform provides compact functions including reading input information and uploading of files, rIBD calculation, and presentation of the rIBD scores. We analyzed the simulated data using the rIBD calculation platform and calculated the average IBD score of 0.061 with a standard deviation of 0.124. The rIBD scores generally follow a normal distribution, and a cut-off of 0.432 and -0.310 for both positive and negative rIBD scores is derived to enable the identification of genomic regions showing significant introgression signals from the source breed to the admixed breed. A list of genomic regions with detailed calculated rIBD scores is reported, and all the rIBD scores for each of the considered windows are presented in plots on the rIBD calculation platform. Our rIBD calculation platform provides a user-friendly tool for the calculation of fine-scaled rIBD scores for each of the genomic regions to map possible functional genomic variants due to adaptive introgression or long-term hybridization.

Patterns of Coevolutionary Adaptations across Time and Space in Mouse Gammaretroviruses and Three Restrictive Host Factors

The classical laboratory mouse strains are genetic mosaics of three Mus musculus subspecies that occupy distinct regions of Eurasia. These strains and subspecies carry infectious and endogenous mouse leukemia viruses (MLVs) that can be pathogenic and mutagenic. MLVs evolved in concert with restrictive host factors with some under positive selection, including the XPR1 receptor for xenotropic/polytropic MLVs (X/P-MLVs) and the post-entry restriction factor Fv1. Since positive selection marks host-pathogen genetic conflicts, we examined MLVs for counter-adaptations at sites that interact with XPR1, Fv1, and the CAT1 receptor for ecotropic MLVs (E-MLVs). Results describe different co-adaptive evolutionary paths within the ranges occupied by these virus-infected subspecies. The interface of CAT1, and the otherwise variable E-MLV envelopes, is highly conserved; antiviral protection is afforded by the Fv4 restriction factor. XPR1 and X/P-MLVs variants show coordinate geographic distributions, with receptor critical sites in envelope, under positive selection but with little variation in envelope and XPR1 in mice carrying P-ERVs. The major Fv1 target in the viral capsid is under positive selection, and the distribution of Fv1 alleles is subspecies-correlated. These data document adaptive, spatial and temporal, co-evolutionary trajectories at the critical interfaces of MLVs and the host factors that restrict their replication.

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.

Population Genomics of the House Mouse and the Brown Rat

Mice (Mus musculus) and rats (Rattus norvegicus) have long served as model systems for biomedical research. However, they are also excellent models for studying the evolution of populations, subspecies, and species. Within the past million years, they have spread in various waves across large parts of the globe, with the most recent spread in the wake of human civilization. They have developed into commensal species, but have also been able to colonize extreme environments on islands free of human civilization. Given that ample genomic and genetic resources are available for these species, they have thus also become ideal mammalian systems for evolutionary studies on adaptation and speciation, particularly in the combination with the rapid developments in population genomics. The chapter provides an overview of the systems and their history, as well as of available resources.

The genomic impact of historical hybridization with massive mitochondrial DNA introgression

BACKGROUND

The extent to which selection determines interspecific patterns of genetic exchange enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be selection-driven, but also result from demographic processes, especially in cases of invasive species replacements, which can promote introgression at their invasion front. Because invasion and selective sweeps similarly mold variation, population genetics evidence for selection can only be gathered in an explicit demographic framework. The Iberian hare, Lepus granatensis, displays in its northern range extensive mitochondrial DNA introgression from L. timidus, an arctic/boreal species that it replaced locally after the last glacial maximum. We use whole-genome sequencing to infer geographic and genomic patterns of nuclear introgression and fit a neutral model of species replacement with hybridization, allowing us to evaluate how selection influenced introgression genome-wide, including for mtDNA.

RESULTS

Although the average nuclear and mtDNA introgression patterns contrast strongly, they fit a single demographic model of post-glacial invasive replacement of timidus by granatensis. Outliers of elevated introgression include several genes related to immunity, spermatogenesis, and mitochondrial metabolism. Introgression is reduced on the X chromosome and in low recombining regions.

CONCLUSIONS

General nuclear and mtDNA patterns of introgression can be explained by purely demographic processes. Hybrid incompatibilities and interplay between selection and recombination locally modulate levels of nuclear introgression. Selection promoted introgression of some genes involved in conflicts, either interspecific (parasites) or possibly cytonuclear. In the latter case, nuclear introgression could mitigate the potential negative effects of alien mtDNA on mitochondrial metabolism and male-specific traits.

Human-Mediated Introgression of Haplotypes in a Modern Dairy Cattle Breed

Domestic animals can serve as model systems of adaptive introgression and their genomic signatures. In part, their usefulness as model systems is due to their well-known histories. Different breeding strategies such as introgression and artificial selection have generated numerous desirable phenotypes and superior performance in domestic animals. The modern Danish Red Dairy Cattle is studied as an example of an introgressed population. It originates from crossing the traditional Danish Red Dairy Cattle with the Holstein and Brown Swiss breeds, both known for high milk production. This crossing happened, among other things due to changes in the production system, to raise milk production and overall performance. The genomes of modern Danish Red Dairy Cattle are heavily influenced by regions introgressed from the Holstein and Brown Swiss breeds and under subsequent selection in the admixed population. The introgressed proportion of the genome was found to be highly variable across the genome. Haplotypes introgressed from Holstein and Brown Swiss contained or overlapped known genes affecting milk production, as well as protein and fat content (CD14, ZNF215, BCL2L12, and THRSP for Holstein origin and ITPR2, BCAT1, LAP3, and MED28 for Brown Swiss origin). Genomic regions with high introgression signals also contained genes and enriched QTL associated with calving traits, body confirmation, feed efficiency, carcass, and fertility traits. These introgressed signals with relative identity-by-descent scores larger than the median showing Holstein or Brown Swiss introgression are mostly significantly correlated with the corresponding test statistics from signatures of selection analyses in modern Danish Red Dairy Cattle. Meanwhile, the putative significant introgressed signals have a significant dependency with the putative significant signals from signatures of selection analyses. Artificial selection has played an important role in the genomic footprints of introgression in the genome of modern Danish Red Dairy Cattle. Our study on a modern cattle breed contributes to an understanding of genomic consequences of selective introgression by demonstrating the extent to which adaptive effects contribute to shape the specific genomic consequences of introgression.

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.

Electronic supplementary material

The online version of this article (10.1186/s12983-018-0266-9) contains supplementary material, which is available to authorized users.