Gontcharov Andrey A, Marin Birger, Melkonian Michael
Botanisches Institut, Lehrstuhl I, Universität zu Köln, Köln, Germany.
Mol Biol Evol. 2004 Mar;21(3):612-24. doi: 10.1093/molbev/msh052. Epub 2004 Jan 22.
Although the combination of different genes in phylogenetic analyses is a promising approach, the methodology is not well established and analyses often suffer from inadequate, noncongruent taxon sampling, long-branch attraction, or conflicting evolutionary models of the genes analyzed. Conflicts or congruence between multigene and single-gene phylogenies, as well as the assumed superiority of the multigene approach, are often difficult to assess solely because of incongruent taxon sampling. In the present study, a data set of 43 nuclear-encoded SSU rDNA and plastid-encoded rbcL gene sequences was generated from the same strains of conjugating green algae (Zygnematophyceae, Streptophyta). Phylogenetic analyses used the genes individually and in combination, either as concatenated sequences or with the log-likelihood summation method. Single-gene analyses, although mostly congruent, revealed some conflicting nodes and showed different patterns of statistical support. Combined analyses confidently resolved the conflicts between the single-gene analyses, enhanced phylogenetic resolution, and were better supported by morphological information. Long-branch taxa were not the same for the two genes analyzed, and, thus, their effect on phylogenetic resolution was minimized in the combined analyses.
尽管在系统发育分析中组合不同基因是一种很有前景的方法，但该方法尚未完全确立，分析过程常常受到分类单元抽样不足、不一致、长枝吸引或所分析基因的进化模型相互冲突等问题的困扰。由于分类单元抽样不一致，多基因系统发育树和单基因系统发育树之间的冲突或一致性，以及多基因方法假定的优越性，往往很难单独评估。在本研究中，从同一组接合绿藻（双星藻纲，链形植物）菌株中生成了一个包含43个核编码小亚基核糖体DNA（SSU rDNA）和质体编码的核酮糖-1,5-二磷酸羧化酶/加氧酶大亚基基因（rbcL）序列的数据集。系统发育分析分别使用这些基因以及将它们组合起来进行，组合方式既可以是串联序列，也可以采用对数似然求和法。单基因分析虽然大多一致，但也揭示了一些相互冲突的节点，并显示出不同的统计支持模式。联合分析可靠地解决了单基因分析之间的冲突，提高了系统发育分辨率，并且得到了形态学信息更好的支持。对于所分析的两个基因而言，长枝分类单元并不相同，因此，在联合分析中它们对系统发育分辨率的影响被最小化。
