Complex pattern of coalescence and fast evolution of a mitochondrial rRNA pseudogene in a recent radiation of tiger beetles
Complex pattern of coalescence and fast evolution of a mitochondrial rRNA pseudogene in a recent radiation of tiger beetles
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DOI：
10.1093/molbev/msi085
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发表时间：
2005-04-01
影响因子：
10.7
通讯作者：
Vogler, AP
中科院分区：
文献类型：
--
作者：
Pons, J;Vogler, AP
线粒体DNA的转位拷贝进入细胞核（numts）很普遍，但迄今为止还没有从鞘翅目（甲虫）中描述过。在这里，我们报告了澳大利亚虎甲虫（属Rivacindela）线粒体核糖体RNA基因衍生的numt的发现。nnumt的功能丧失由高比例的反译、大量的茎区非代偿性替换和功能重要序列的大量缺失证实。对同源numt序列和相应的mtDNA谱系进行系统发育分析，以研究其转置拷贝在近缘种群和物种中的起源和建立。所有的numt序列都是单系的，这表明该元素的起源是单一的。然而，由于numt的存在，种群呈现多态性，基于numt序列的系统发育树与相应的mtDNA系统发育不一致，表明与mtDNA序列相比，固定过程较慢。在与它们的mtDNA姊妹谱系的并排比较中，numts的核苷酸取代率为1.66 X 10（-8）个/位点/年，与该组mtDNA的平均取代率大致相等，但大大高于先前对脊椎动物中性核率的估计。numt进化枝受到几个缺失的影响，但没有插入，估计核苷酸丢失的速度超过核苷酸取代的速度约5倍。Rivacindela numt进化支的年龄很小，在一个狭窄的相关个体谱系之外的物种中没有它们的存在，以及高缺失率表明插入不会在这个群体中持续存在，这与鞘翅目相对较小的基因组含有较少的线粒体和其他核假基因的观点是一致的。
Transposed copies of mitochondrial DNA into the nucleus (numts) are widespread, but to date they have not been described from the Coleoptera (beetles). Here we report the discovery of a numt derived from a mitochondrial ribosomal RNA gene in Australian tiger beetles (genus Rivacindela). The loss of function of the numt was confirmed by high proportion of trans-versions, numerous noncompensatory substitutions in stem regions, and large deletions in functionally important sequences. Phylogenetic analysis of orthologous numt sequences was performed together with the corresponding mtDNA lineage for a study of origination and establishment of the transposed copies in closely related populations and species. All numt sequences were strongly supported to be monophyletic, indicating a single origin of this element. However, populations were polymorphic for the presence of the numt, and phylogenetic trees based on the numt sequences showed inconsistencies with the corresponding mtDNA phylogeny, suggesting slower processes of fixation compared to the mtDNA sequences. In a side-by-side comparison with their mtDNA sister lineage, the nucleotide substitution rate of 1.66 X 10(-8) substitutions/site/year in the numts was approximately equal to the average rate of mtDNA in this group but substantially higher than previous estimates of neutral nuclear rates in vertebrates. The numt clade was affected by several deletions but no insertions, with estimates of nucleotide loss exceeding the rate of nucleotide substitutions by approximately five times. The young age of the Rivacindela numt clade, their absence in species outside of a narrow lineage of related individuals, and the high rate of deletions suggest that insertions do not persist in this group, which is consistent with the view that comparatively small genomes as those of Coleoptera harbor fewer mitochondrial and other nuclear pseudogenes.