Hassanin Alexandre, Léger Nelly, Deutsch Jean
Muséum National d'Histoire Naturelle, Départment Systématique et Evolution, Case Postale, Paris, France.
Syst Biol. 2005 Apr;54(2):277-98. doi: 10.1080/10635150590947843.
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.
线粒体DNA（mtDNA）序列通常用于推断系统发育关系。然而，mtDNA核苷酸组成中的链特异性偏差，被认为反映了不对称的突变限制，再加上不同分类群之间重要的组成异质性，已知对系统发育分析来说是非常有问题的。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种后口动物）的核苷酸组成，并对一个包含六个蛋白质编码基因（即atp6、atp8、cox1、cox2、cox3和nad2）的mtDNA片段进行了分析。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，而另一条链则有相反的偏向，即偏向于T和G。这种链偏向的起源可能与复制和/或转录过程中涉及A和C核苷酸脱氨基作用的不对称突变限制有关。分析揭示，有六个不相关的属具有通常链偏向的反转，即金蛛属（蜘蛛目）、真蝎属（蝎目）、虎斑猛水蚤属（颚足纲）、文昌鱼属（头索动物亚门）、海蛇尾属（棘皮动物门）和魁蚶属（软体动物门）。有人提出，在这六个属中，不对称的突变限制通过控制区（即包含mtDNA复制和转录的大多数调控元件的区域）的倒转而独立地发生了反转。我们表明，不对称突变限制的反转对系统发育分析有重大影响，因为具有反向链偏向的分类群由于长枝吸引假象往往聚集在一起。我们提出了一种在贝叶斯方法下限制树重建中这个特定问题的新方法。我们应用我们的方法来处理节肢动物主要类群的系统发育关系问题。这种新方法与基于mtDNA序列的核分析提供了更好的一致性，我们的数据表明螯肢亚门、甲壳亚门、多足亚门、泛甲壳亚门和奇异足亚门是单系的。
