Zardoya R, Meyer A
Department of Ecology and Evolution, State University of New York at Stony Brook 11794-5245, USA.
Mol Biol Evol. 1996 Sep;13(7):933-42. doi: 10.1093/oxfordjournals.molbev.a025661.
A large number of studies in evolutionary biology utilize phylogenetic information obtained from mitochondrial DNA. Researchers place trust in this molecule and expect it generally to be a reliable marker for addressing questions ranging from population genetics to phylogenies among distantly related lineages. Yet, regardless of the phylogenetic method and weighting treatment, individual mitochondrial genes might potentially produce misleading evolutionary inferences and hence might not constitute an adequate representation neither of the entire mitochondrial genome nor of the evolutionary history of the organisms from which they are derived. We investigated the performance of all mitochondrial protein-coding genes to recover two expected phylogenies of tetrapods and mammals. According to these tests, mitochondrial protein-coding genes can be roughly classified into three groups of good (ND4, ND5, ND2, cytb, and COI), medium (COII, COIII, ND1, and ND6), and poor (ATPase 6, ND3, ATPase 8, and ND4L) phylogenetic performers in recovering these expected trees among phylogenetically distant relatives. How general our findings are is unclear. Simple length differences and rate differences between these genes cannot account for their different phylogenetic performance. The phylogenetic performance of these mitochondrial genes might depend on various factors that play a role in determining the probability of discovering the correct phylogeny such as the density of lineage creation events in time, the phylogenetic "depth" of the question, lineage-specific rate heterogeneity, and the completeness of taxa representation.
进化生物学中的大量研究利用了从线粒体DNA获得的系统发育信息。研究人员信任这种分子，并期望它通常是一个可靠的标记，用于解决从种群遗传学到远缘谱系间系统发育等一系列问题。然而，无论采用何种系统发育方法和加权处理，单个线粒体基因都可能产生误导性的进化推断，因此可能既不能充分代表整个线粒体基因组，也不能代表其来源生物的进化历史。我们研究了所有线粒体蛋白质编码基因恢复四足动物和哺乳动物两个预期系统发育树的性能。根据这些测试，线粒体蛋白质编码基因在恢复远缘亲属间这些预期树时，大致可分为三类：系统发育性能良好的（ND4、ND5、ND2、细胞色素b和COI）、中等的（COII、COIII、ND1和ND6）以及较差的（ATPase 6、ND3、ATPase 8和ND4L）。我们的发现有多普遍尚不清楚。这些基因之间简单的长度差异和速率差异无法解释它们不同的系统发育性能。这些线粒体基因的系统发育性能可能取决于各种因素，这些因素在确定发现正确系统发育的概率中起作用，例如谱系形成事件在时间上的密度、问题的系统发育“深度”、谱系特异性速率异质性以及分类群代表性的完整性。
