The amylase gene cluster in house mice ( Mus musculus ) was subject to repeated introgression including the rescue of a
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(2020) 20:56
RESEARCH ARTICLE
Open Access
The amylase gene cluster in house mice (Mus musculus) was subject to repeated introgression including the rescue of a pseudogene Miriam Linnenbrink†, Kristian K. Ullrich†, Ellen McConnell and Diethard Tautz*
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. Keywords: Amylase gene cluster, Copy number variation, Mus musculus, Natural populations, Introgression
Background The analysis of the evolution of the amylase locus in mammals has revealed different histories of duplication and specialization into salivary (Amy1) and pancreatic (Amy2b) amylases [1]. In the human lineage, gene copy number gains of Amy1 led to increased expression of the AMY1 enzyme in human saliva, correlated to starch-rich diet shifts [2]. In dogs, copy number variation at the * Correspondence: [email protected] † Miriam Linnenbrink and Kristian K. Ullrich contributed equally to this work. Max-Planck Institute for Evolutionary Biology, 24306 Plön, Germany
Amy2b gene has been linked to an increasing starch rich diet during domestication [3, 4] and analysis of amylase clusters across mammals has confirmed such a general tendency [1]. However, it has also been noted that diet correlation cannot fully explain copy number variation patterns in humans, especially since the AMY1 protein in the saliva has only a very limited role in starch digestion [5]. Physiological studies in humans have indeed yielded a more differentiated picture, including a possible role of amylase copy number in shaping the microbiome [6].
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