True Homoplasy of Retrotransposon Insertions in Primates
True Homoplasy of Retrotransposon Insertions in Primates
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DOI：
10.1093/sysbio/syy076
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发表时间：
2019-05-01
影响因子：
6.5
通讯作者：
Schmitz, Juergen
中科院分区：
文献类型：
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作者：
Doronina, Liliya;Reising, Olga;Schmitz, Juergen
在准无限基因组空间中随机插入的所谓无同质反转录转座子的存在/缺失插入模式有多可靠？为了在最新的多基因组比较中系统地研究这个问题，我们筛选了数百万个灵长类转位的Alu正弦元件，以寻找同型精确插入和缺失的发生率。在全基因组分析中，我们鉴定并手动验证了两个类人猿谱系中9个明显相同的元素在直系位置上的精确平行Alu插入案例，以及12个先前建立的Sine精确缺失的案例。相应地，在一项跨越灵长类多样性范围的旅猴灵长类和人类插入的比较中，检测到8个精确的平行插入，没有精确的缺失。由于人类-黑猩猩-恒河猴Alu插入的总频率仅为0.01%(对于人-黑猩猩-恒河猴)和0.02-0.04%(对于人-丛林狐猴)和精确的Alu缺失(对于人-黑猩猩-恒河猴)0.001-0.002%，真正的同质性被认为不是进化噪音的量化相关来源。因此，Alu反转录转座子的存在/缺失模式以及所有LINE1动员的元件实际上代表了它们被认为是几乎无同质性的标记。因此，祖先不完全的谱系分类和杂交仍然是反转录转座子插入存在/缺失模式冲突的唯一严重来源，因此是可以检测和量化的。
How reliable are the presence/absence insertion patterns of the supposedly homoplasy-free retrotransposons, which were randomly inserted in the quasi infinite genomic space? To systematically examine this question in an up-to-date, multigenome comparison, we screened millions of primate transposed Alu SINE elements for incidences of homoplasious precise insertions and deletions. In genome-wide analyses, we identified and manually verified nine cases of precise parallel Alu insertions of apparently identical elements at orthologous positions in two ape lineages and twelve incidences of precise deletions of previously established SINEs. Correspondingly, eight precise parallel insertions and no exact deletions were detected in a comparison of lemuriform primate and human insertions spanning the range of primate diversity. With an overall frequency of homoplasious Alu insertions of only 0.01% (for human-chimpanzee-rhesus macaque) and 0.02-0.04% (for human-bushbaby-lemurs) and precise Alu deletions of 0.001-0.002% (for human-chimpanzee-rhesus macaque), real homoplasy is not considered to be a quantitatively relevant source of evolutionary noise. Thus, presence/absence patterns of Alu retrotransposons and, presumably, all LINE1-mobilized elements represent indeed the virtually homoplasy-free markers they are considered to be. Therefore, ancestral incomplete lineage sorting and hybridization remain the only serious sources of conflicting presence/absence patterns of retrotransposon insertions, and as such are detectable and quantifiable.