scholarly journals Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions

2015 ◽  
Vol 25 (8) ◽  
pp. 1114-1124 ◽  
Author(s):  
Željka Pezer ◽  
Bettina Harr ◽  
Meike Teschke ◽  
Hiba Babiker ◽  
Diethard Tautz
Keyword(s):  
Copy Number Variation ◽  
House Mouse ◽  
Mus Musculus ◽  
Copy Number ◽  
Natural Populations ◽  
Mus Musculus Domesticus ◽  
Conserved Genes ◽  
Number Variation

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

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Miriam Linnenbrink ◽  
Kristian K. Ullrich ◽  
Ellen McConnell ◽  
Diethard Tautz
Keyword(s):  
Gene Cluster ◽  
House Mouse ◽  
Mus Musculus ◽  
Copy Number ◽  
Stop Codon ◽  
Natural Populations ◽  
Gene Clusters ◽  
Mus Musculus Domesticus ◽  
Amylase Gene ◽  
Copy Number Changes

Abstract 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.

scholarly journals The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse

2020 ◽  
Vol 375 (1806) ◽  
pp. 20190540 ◽  
Author(s):  
Henry L. North ◽  
Pierre Caminade ◽  
Dany Severac ◽  
Khalid Belkhir ◽  
Carole M. Smadja
Keyword(s):  
Mate Choice ◽  
Copy Number Variation ◽  
Reproductive Isolation ◽  
House Mouse ◽  
Copy Number ◽  
Structural Changes ◽  
Sexual Isolation ◽  
Number Variation ◽  
Tandem Duplications

Reinforcement has the potential to generate strong reproductive isolation through the evolution of barrier traits as a response to selection against maladaptive hybridization, but the genetic changes associated with this process remain largely unexplored. Building upon the increasing evidence for a role of structural variants in adaptation and speciation, we addressed the role of copy-number variation in the reinforcement of sexual isolation evidenced between the two European subspecies of the house mouse. We characterized copy-number divergence between populations of Mus musculus musculus that display assortative mate choice, and those that do not, using whole-genome resequencing data. Updating methods to detect deletions and tandem duplications (collectively: copy-number variants, CNVs) in Pool-Seq data, we developed an analytical pipeline dedicated to identifying genomic regions showing the expected pattern of copy-number displacement under a reinforcement scenario. This strategy allowed us to detect 1824 deletions and seven tandem duplications that showed extreme differences in frequency between behavioural classes across replicate comparisons. A subset of 480 deletions and four tandem duplications were specifically associated with the derived trait of assortative mate choice. These ‘Choosiness-associated’ CNVs occur in hundreds of genes. Consistent with our hypothesis, such genes included olfactory receptors potentially involved in the olfactory-based assortative mate choice in this system as well as one gene, Sp110 , that is known to show patterns of differential expression between behavioural classes in an organ used in mate choice—the vomeronasal organ. These results demonstrate that fine-scale structural changes are common and highly variable within species, despite being under-studied, and may be important targets of reinforcing selection in this system and others. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.

scholarly journals Genomic copy number variation in Mus musculus

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
M Elizabeth O Locke ◽  
Maja Milojevic ◽  
Susan T Eitutis ◽  
Nisha Patel ◽  
Andrea E Wishart ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Mus Musculus ◽  
Copy Number ◽  
Genomic Copy Number ◽  
Genomic Copy ◽  
Number Variation ◽  
Genomic Copy Number Variation

scholarly journals Copy number variation of the putative speciation genes in the European house mouse hybrid zone

2021 ◽  
Author(s):  
Alexey Yanchukov ◽  
Zusana Hiadlovska ◽  
Zeljka Pezer ◽  
Milos Macholan ◽  
Jaroslav Pialek ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
House Mouse ◽  
Hybrid Zone ◽  
Copy Number ◽  
Digital Pcr ◽  
Gene Copy ◽  
Ancestral Population ◽  
Hybrid Zones ◽  
Interaction Sites ◽  
Number Variation

Hybrid zones have long been described as "windows on the evolutionary process", and studying them has become even more important since the advance in the genome analysis tools. The hybrid zone between two subspecies of the house mouse (Mus musculus musculus and Mus m. domesticus) is a unique model speciation system to study fine scale interactions of recently diverged genomes. Here, we explore the role of gene Copy Number Variation in shaping the barrier to introgression in the hybrid zone within a previously established transect in Central Europe. The CNV of seven pre-selected candidate genes was determined via droplet-digital PCR and analyzed in the context of ~500k SNPs, with the ancestral population (i.e. musculus or domesticus) of every SNP allele previously inferred in the admixed individuals (Baird et al., in prep.). The copy numbers of five genes were clearly associated with the prevalence of either musculus or domesticus genomes across the hybrid zone. In three cases, the highest and/or outlying levels of association were observed at or very close to the annotated positions of the respective gene amplicons, demonstrating the power of our approach in confirming the reference locations of copy number variants. Notably, several other reference locations were recognized as positive outliers in the association with particular CNV genes, possibly representing the extra gene copies and/or their epistatic interaction sites.

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