PDF(Pubmed)
Abstract：
The mitochondrial genomes of Bilateria are relatively conserved in their protein-coding, rRNA, and tRNA gene complement, but the order of these genes can range from very conserved to very variable depending on the taxon. The supposedly conserved gene order of Annelida has been used to support the placement of some taxa within Annelida. Recently, authors have cast doubts on the conserved nature of the annelid gene order. Various factors may influence gene order variability including, among others, increased substitution rates, base composition differences, structure of noncoding regions, parasitism, living in extreme habitats, short generation times, and biomineralization. However, these analyses were neither done systematically nor based on well-established reference trees. Several focused on only a few of these factors and biological factors were usually explored ad-hoc without rigorous testing or correlation analyses. Herein, we investigated the variability and evolution of the annelid gene order and the factors that potentially influenced its evolution, using a comprehensive and systematic approach. The analyses were based on 170 genomes, including 33 previously unrepresented species. Our analyses included 706 different molecular properties, 20 life-history and ecological traits, and a reference tree corresponding to recent improvements concerning the annelid tree. The results showed that the gene order with and without tRNAs is generally conserved. However, individual taxa exhibit higher degrees of variability. None of the analyzed life-history and ecological traits explained the observed variability across mitochondrial gene orders. In contrast, the combination and interaction of the best-predicting factors for substitution rate and base composition explained up to 30% of the observed variability. Accordingly, correlation analyses of different molecular properties of the mitochondrial genomes showed an intricate network of direct and indirect correlations between the different molecular factors. Hence, gene order evolution seems to be driven by molecular evolutionary aspects rather than by life history or ecology. On the other hand, variability of the gene order does not predict if a taxon is difficult to place in molecular phylogenetic reconstructions using sequence data or not. We also discuss the molecular properties of annelid mitochondrial genomes considering canonical views on gene evolution and potential reasons why the canonical views do not always fit to the observed patterns without making some adjustments. [Annelida; compositional biases; ecology; gene order; life history; macroevolution; mitochondrial genomes; substitution rates.].
摘要：
Bilateria的线粒体基因组在蛋白质编码方面相对保守，rRNA和tRNA基因补体，但是这些基因的顺序可以从非常保守到非常可变，这取决于分类单元。Annelida的所谓保守基因顺序已用于支持Annelida中某些分类单元的放置。最近,作者对Annelid基因顺序的保守性表示怀疑。各种因素可能会影响基因顺序变异性，包括，其中,增加替代率，碱基组成差异，非编码区的结构，寄生，生活在极端的栖息地，短生成时间和生物矿化。然而,这些分析都没有系统地进行，也不是基于完善的参考树。一些只关注其中几个因素，通常在没有严格测试或相关分析的情况下对生物因素进行临时探索。在这里，我们研究了环形动物基因顺序的变异性和进化，以及潜在影响其进化的因素，采用全面系统的方法。分析基于170个基因组，包括33个以前没有代表的物种。我们的分析包括706种不同的分子性质,20个生活史和生态特征，以及对应于有关环节树的最新改进的参考树。结果表明，有和没有tRNA的基因顺序通常是保守的。然而,个体分类群表现出更高的变异性。所有分析的生活史和生态特征都不能解释线粒体基因序列中观察到的变异性。相比之下,替代率和碱基组成的最佳预测因素的组合和相互作用解释了多达30％的观察到的变异性。因此，对线粒体基因组不同分子特性的相关分析显示，不同分子因素之间存在复杂的直接和间接相关网络。因此，基因顺序进化似乎是由分子进化方面驱动的，而不是由生活史或生态学驱动的。另一方面,基因顺序的变异性无法预测分类单元是否难以使用序列数据进行分子系统发育重建。我们还讨论了环状线粒体基因组的分子特性，考虑了基因进化的规范观点，以及为什么规范观点不总是适合观察到的模式而不进行一些调整的潜在原因。
