弗兰格尔岛上一只长毛猛犸象的基因组缺陷过多
Excess of genomic defects in a woolly mammoth on Wrangel island
摘要：
长毛猛犸象（Mammuthus mammgenius）在更新世和全新世早期居住在西伯利亚、白令海和北美。最近在古代DNA测序方面取得的突破使得两个长毛猛犸标本的完整基因组测序成为可能（Palkopoulou et al. 2015）。一个猛犸象标本来自45,000年前的大陆种群，当时猛犸象数量很多。第二，4300岁的标本，来自弗兰格尔岛上的一个孤立的人口猛犸象生存的小有效种群大小比以前的人口低43倍以上。这些有效种群大小的极端差异提供了一个难得的机会来测试单个物种内基因组架构进化的近乎中性的模型。使用这些先前发表的猛犸序列，我们确定缺失，逆转录酶，和非功能点突变。在弗兰格尔岛猛犸象中，我们发现了更多的缺失，更大比例的影响基因序列的缺失，更多的候选逆转录基因，以及更多的提前终止密码子。这种有害突变的积累与弗兰格尔岛上日益减少的猛犸象种群中的低有效种群大小引起的基因组崩溃是一致的。此外，我们观察到嗅觉受体和尿蛋白的损失率很高，因为这些位点是非必需的，或者因为它们在岛屿环境中受到不同选择压力的青睐。最后，在FOXQ 1基因座，我们观察到两个独立的功能丧失突变，这将赋予缎大衣表型在这个岛猛犸象。
英文摘要：
Woolly mammoths (Mammuthus primigenius) populated Siberia, Beringia, and North America during the Pleistocene and early Holocene. Recent breakthroughs in ancient DNA sequencing have allowed for complete genome sequencing for two specimens of woolly mammoths (Palkopoulou et al. 2015). One mammoth specimen is from a mainland population ~45,000 years ago when mammoths were plentiful. The second, a 4300 yr old specimen, is derived from an isolated population on Wrangel island where mammoths subsisted with small effective population size more than 43-fold lower than previous populations. These extreme differences in effective population size offer a rare opportunity to test nearly neutral models of genome architecture evolution within a single species. Using these previously published mammoth sequences, we identify deletions, retrogenes, and non-functionalizing point mutations. In the Wrangel island mammoth, we identify a greater number of deletions, a larger proportion of deletions affecting gene sequences, a greater number of candidate retrogenes, and an increased number of premature stop codons. This accumulation of detrimental mutations is consistent with genomic meltdown in response to low effective population sizes in the dwindling mammoth population on Wrangel island. In addition, we observe high rates of loss of olfactory receptors and urinary proteins, either because these loci are non-essential or because they were favored by divergent selective pressures in island environments. Finally, at the locus of FOXQ1 we observe two independent loss-of-function mutations, which would confer a satin coat phenotype in this island woolly mammoth.
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