Mitochondrial DNA (mtDNA) sequences are comonly used for inferring phylogenetic relationships. However, the strand-specific bias in the nucleotide composition of the mtDNA, which is thought to reflect assymetric mutational constraints, combined with the important compositional heterogeneity among taxa, are known to be highly problematic for phylogenetic analyses. Here, nucleotide composition was compared across 49 species of Metazoa (34 arthropods, 2 annelids, 2 molluscs, and 11 deuterosomes), and analyzed for a mtDNA fragment including six protein-coding genes, i.e., atp6, atp8, cox1, cox2, cox3, and nad2. The analyses show that most metazoan species present a clear strand assymetry, where one strand is biased in favor of A and C, whereas the other strand has reverse bias, i.e. in favor of T and G. the origin of this strand bias can be related to assymetric mutational constraints involving deaminations of A and C nucleotides during the replication and/or transcription processes. The analyses reveal that six unrelated genera are characterized by a reversal of the usual strand bias, i.e., Argiope (Araneae), Euscorpius (Scorpiones), Tigrioupus (Maxillopoda), Branchiostoma (Cephalochordata) Florometra (Echinodermata), and Katharina (Mollusca). It is proposed that assymetric mutational constraints have been independantly reversed in these six genera, through an inversion of the control region, i.e., the region that contains most regulatory elements for replication and transcription of the mtDNA. We show that reversals of assymetric mutational constraints have dramatic consequences on the phylogenetic analyses, as taxa characterized by reverse strand bias tend to group together due to long-branch attraction artifacts. We propose a new method for limiting this specific problem in tree reconstruction under the Bayesian approach. We apply our method to deal with the question of phylogenetic relationships of the major lineages of Arthropoda, This new approach provides a better congruence with nuclear analyses based on mtDNA sequences, our data suggest that Chelicerata, Crustacea, Myriapoda, Pancrustacea, and Paradoxopoda are monophyletic.

中文翻译：

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后生动物线粒体基因组进化过程中不对称突变约束多次逆转的证据，以及系统发育推断的后果

线粒体 DNA (mtDNA) 序列通常用于推断系统发育关系。然而，已知 mtDNA 核苷酸组成中的链特异性偏差，这被认为反映了不对称突变约束，加上分类群之间重要的组成异质性，已知对于系统发育分析来说是一个很大的问题。在这里，比较了 49 种后生动物（34 种节肢动物、2 种环节动物、2 种软体动物和 11 种氘体）的核苷酸组成，并分析了一个 mtDNA 片段，其中包括六个蛋白质编码基因，即 atp6、atp8、cox1、cox2、cox3 , 和 nad2。分析表明，大多数后生动物物种呈现出明显的链不对称性，其中一条链偏向于 A 和 C，而另一条链具有反向偏向性，即偏向于 T 和 G。这种链偏向性的起源可能与不对称突变约束有关，包括在复制和/或转录过程中 A 和 C 核苷酸的脱氨基。分析表明，六个不相关的属的特征是通常链偏差的逆转，即 Argiope (Araneae)、Euscorpius (Scorpiones)、Tigrioupus (Maxillopoda)、Branchiostoma (Cephalochordata) Florometra (Echinodermata) 和 Katharina (Mollusca)。建议通过控制区域的反转，即包含大多数用于 mtDNA 复制和转录的调控元件的区域，在这六个属中不对称突变约束已被独立逆转。我们表明，不对称突变约束的逆转对系统发育分析产生了巨大的影响，由于以反向链偏向为特征的分类群由于长分支吸引伪影而倾向于聚集在一起。我们提出了一种新方法来限制贝叶斯方法下树重建中的这个特定问题。我们应用我们的方法来处理节肢动物主要谱系的系统发育关系问题，这种新方法提供了与基于 mtDNA 序列的核分析更好的一致性，我们的数据表明螯肢、甲壳纲、多足纲、全足纲和副足纲是单系的.