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.

中文翻译：

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使家鼠（小家鼠）中的淀粉酶基因簇反复渗入，包括拯救假基因。

背景技术淀粉酶基因簇与人类和哺乳动物饮食中淀粉量的适应性拷贝数变化有关。但是，对于人类和哺乳动物来说，这种解释受到了质疑。自然种群的信息很少。结果使用光学作图和基因组读取信息，我们在这里表明，天然家鼠种群中的淀粉酶簇确实是Amy2b旁系基因拷贝（称为Amy2a1-Amy2a5）的拷贝数变量，但与淀粉饮食的直接联系并不明显。然而，我们发现淀粉酶簇受到小家鼠亚种之间单倍型的渗入。可以追溯到西欧人群最近的基因渗入，这也导致了Amy2b假基因的抢救。源自西方家鼠（Mus musculus domesticus）的一些种群和近交系在第一个外显子中带有一个带有终止密码子的胰淀粉酶（Amy2b）副本，使其无功能。但是法国的人群中有一种由完整的阅读框组成的东部家鼠（小家鼠）的单倍型。沿着淀粉酶簇的系统发育模式的详细分析表明，以前有渗入的其他历史。结论我们的结果表明，淀粉酶基因簇是小鼠基因组中基因渗入的热点，使其成为超出先前观察到的拷贝数变化的进化活性区域。但是法国的人群中有一种由完整的阅读框组成的东部家鼠（小家鼠）的单倍型。沿着淀粉酶簇的系统发育模式的详细分析表明，以前有渗入的其他历史。结论我们的结果表明，淀粉酶基因簇是小鼠基因组中基因渗入的热点，使其成为超出先前观察到的拷贝数变化的进化活性区域。但是法国的人群拥有一种由完整的阅读框架从东部家鼠（小家鼠）中渗入的单倍型。沿着淀粉酶簇的系统发育模式的详细分析表明，以前有渗入的其他历史。结论我们的结果表明，淀粉酶基因簇是小鼠基因组中基因渗入的热点，使其成为超出先前观察到的拷贝数变化的进化活性区域。