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首页> 外文期刊>International journal of plant sciences >A 567-TAXON DATA SET FOR ANGIOSPERMS: THE CHALLENGES POSED BY BAYESIAN ANALYSES OF LARGE DATA SETS
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A 567-TAXON DATA SET FOR ANGIOSPERMS: THE CHALLENGES POSED BY BAYESIAN ANALYSES OF LARGE DATA SETS

机译：567-TAXON的被子植物数据集：贝叶斯大型数据集分析带来的挑战

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Bayesian analyses of a three-gene, 567-taxon (560 angiosperms, seven outgroups) data set revealed the analytical challenges posed by such large data sets. Determining stationarity in Markov chains for such large data sets is difficult. In more than 30 analyses of up to 10 million generations each (with an average run time of 45 d), log-likelihood plots showed that runs can stabilize for several million generations before making jumps in likelihood scores. Simultaneous independent runs reached apparent stationarity as early as 2 million generations and as late as 9.7 million generations, suggesting that (a) 10 million generations are insufficient for data sets of this size and (b) periods of stationarity even as long as 6 million generations should not be taken as an indication that the tree is fully optimized. Our Bayesian analyses recovered a topology highly similar to that found previously with parsimony. However, a few topological differences were found between the Bayesian and shortest parsimony trees obtained for the same data set, the most noteworthy of which is that a clade (posterior probability [pp] = 0.99) of Amborellaceae + Nymphaeaceae is sister to all other extant angiosperms (pp = 1.0) in the Bayesian tree, whereas Amborellaceae alone are sister to all other extant angiosperms with parsimony. Additionally, the Bayesian analysis indicates that the magnoliids and Chloranthaceae are sister to Ceratophyllum and eudicots rather than to monocots, as indicated by the parsimony analyses. Many clades receiving moderate to low jackknife support in parsimony analyses received pp values of 1.0.
机译：贝叶斯对三基因，567个分类单元（560个被子植物，七个外群）的数据集进行的分析揭示了如此庞大的数据集所带来的分析挑战。对于如此大的数据集，很难确定马尔可夫链中的平稳性。在30多个分析中，每个分析多达1000万代（平均运行时间为45 d），对数似然图显示，运行可以稳定数百万代，然后才使可能性得分跃升。同时的独立运行早在200万代和970万代之前就达到了明显的平稳性，这表明（a）1000万代对于这种规模的数据集是不够的；（b）平稳时期甚至长达600万代不应将其视为树已完全优化的指示。我们的贝叶斯分析恢复了与先前使用简约方法高度相似的拓扑。但是，在同一数据集上获得的贝叶斯树和最短简约树之间发现了一些拓扑差异，其中最值得注意的是，伞形科+睡莲科的进化枝（后验概率[pp] = 0.99）是所有其他现存物种的姊妹贝叶斯树中的被子植物（pp = 1.0），而仅伞形科是所有其他现存的被子植物的同胞姐妹。此外，贝叶斯分析表明，木兰科和虎耳科是ae形目和双子叶植物的姐妹，而不是单子叶植物，如简约性分析所示。在简约分析中，许多接受中等至低折刀支持的进化枝的pp值为1.0。

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