Recent Evolution in Rattus norvegicus Is Shaped by Declining Effective Population Size.
Recent Evolution in Rattus norvegicus Is Shaped by Declining Effective Population Size.
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褐家鼠最近的进化是由有效种群规模的下降造成的。
DOI：
10.1093/molbev/msv126
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发表时间：
2015-10
影响因子：
10.7
通讯作者：
Keightley PD
中科院分区：
文献类型：
--
作者：
Deinum EE;Halligan DL;Ness RW;Zhang YH;Cong L;Zhang JX;Keightley PD
褐家鼠是一种臭名昭著的害虫，也是生物医学研究中经常使用的模型。通过分析中国东北地区12只野生棕色大鼠的基因组序列，以及沿着一只黑色大鼠的基因组序列，我们研究了选择和人口因素对基因组变异的影响。我们估计，最近的有效人口规模（Ne）的这个物种=，基于沉默的网站多样性。我们比较了这些基因组的多样性模式与家鼠（小家鼠）的多个基因组序列中的模式，它具有更大的Ne。这揭示了哺乳动物基因组进化中遗传漂变强度变化的重要作用。通过对人口统计历史的成对序贯马尔可夫结合分析，我们推断，最近在野生大鼠中出现了人口规模瓶颈，我们可以追溯到大约20，000年前。与此一致，野生大鼠种群经历了轻度有害突变的增加，在蛋白质编码基因和保守的非编码元件中以更高的频率分离。这导致了蛋白质和保守非编码元件的适应性进化速率（α）的负估计，我们讨论了与野生家鼠中观察到的强阳性估计有关的结果。由于种群瓶颈的存在，野生大鼠的连锁不平衡随物理距离的变化比野生家鼠慢得多。
The brown rat, Rattus norvegicus, is both a notorious pest and a frequently used model in biomedical research. By analyzing genome sequences of 12 wild-caught brown rats from their presumed ancestral range in NE China, along with the sequence of a black rat, Rattus rattus, we investigate the selective and demographic forces shaping variation in the genome. We estimate that the recent effective population size (Ne) of this species = , based on silent site diversity. We compare patterns of diversity in these genomes with patterns in multiple genome sequences of the house mouse (Mus musculus castaneus), which has a much larger Ne. This reveals an important role for variation in the strength of genetic drift in mammalian genome evolution. By a Pairwise Sequentially Markovian Coalescent analysis of demographic history, we infer that there has been a recent population size bottleneck in wild rats, which we date to approximately 20,000 years ago. Consistent with this, wild rat populations have experienced an increased flux of mildly deleterious mutations, which segregate at higher frequencies in protein-coding genes and conserved noncoding elements. This leads to negative estimates of the rate of adaptive evolution (α) in proteins and conserved noncoding elements, a result which we discuss in relation to the strongly positive estimates observed in wild house mice. As a consequence of the population bottleneck, wild rats also show a markedly slower decay of linkage disequilibrium with physical distance than wild house mice.
影响因子：
3.4
作者：
Gaffney DJ;Keightley PD
通讯作者：
Keightley PD