More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy
More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy
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DOI：
10.1093/molbev/msi121
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发表时间：
2005-05-01
影响因子：
10.7
通讯作者：
Carroll, SB
中科院分区：
文献类型：
--
作者：
Rokas, A;Carroll, SB
分类群数量和基因数量对系统发育推断准确性的相对贡献是系统发育学的一个主要问题，对成功重建生命之树大致草图的实验策略的选择至关重要。尽管其必要性仍然是争论的主题，但取样分类群数量的最大化是大多数系统发育学家青睐的策略。由于基因组学的进步，基因数量的大量增加现在是可能的，但是大量的基因将只能用于有限数量的分类群，这就提出了这样一个问题：这种基因组规模的系统发育是否对分类群的增加是稳健的。为了检验增加分类群数量或基因数量对系统发育准确性的相对好处，我们开发了一种利用对称差异树距离作为系统发育准确性的测量方法。我们已经将该试验应用于包含来自14种酵母的106个基因的基因组规模数据矩阵。我们的研究结果表明，分类群数量的增加与系统发育准确性的轻微下降相关。相反，增加基因数量对系统发育准确性有显著的正向影响。对同一酵母支系的另一个分类群丰富数据矩阵的分析表明，分类群数量对系统发育准确性没有显著影响。通过对哺乳动物和被子植物两个数据矩阵的分析，证实了基因数量对系统发育准确性的正影响和分类群数量对系统发育准确性的不影响。我们的结论是，对于典型的数据集，使用的基因数量可能比分类群数量更重要的决定系统发育准确性。
The relative contribution of taxon number and gene number to accuracy in phylogenetic inference is a major issue in phylogenetics and of central importance to the choice of experimental strategies for the successful reconstruction of a broad sketch of the tree of life. Maximization of the number of taxa sampled is the strategy favored by most phylogeneticists, although its necessity remains the subject of debate. Vast increases in gene number are now possible due to advances in genomics, but large numbers of genes will be available for only modest numbers of taxa, raising the question of whether such genome-scale phylogenies will be robust to the addition of taxa. To examine the relative benefit of increasing taxon number or gene number to phylogenetic accuracy, we have developed an assay that utilizes the symmetric difference tree distance as a measure of phylogenetic accuracy. We have applied this assay to a genome-scale data matrix containing 106 genes from 14 yeast species. Our results show that increasing taxon number correlates with a slight decrease in phylogenetic accuracy. In contrast, increasing gene number has a significant positive effect on phylogenetic accuracy. Analyses of an additional taxon-rich data matrix from the same yeast clade show that taxon number does not have a significant effect on phylogenetic accuracy. The positive effect of gene number and the lack of effect of taxon number on phylogenetic accuracy are also corroborated by analyses of two data matrices from mammals and angiosperm plants, respectively. We conclude that, for typical data sets, the number of genes utilized may be a more important determinant of phylogenetic accuracy than taxon number.