Phylogeny of the cycads based on multiple single-copy nuclear genes: congruence of concatenated parsimony, likelihood and species tree inference methods
Phylogeny of the cycads based on multiple single-copy nuclear genes: congruence of concatenated parsimony, likelihood and species tree inference methods
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DOI：
10.1093/aob/mct192
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发表时间：
2013-11-01
期刊：
影响因子：
4.2
通讯作者：
Namoff, Sandra
中科院分区：
文献类型：
--
作者：
Salas-Leiva, Dayana E.;Meerow, Alan W.;Namoff, Sandra
尽管最近有了新的分类，苏铁类的稳定的亲缘关系一直是难以捉摸的，特别是关于Bowenia，Stangeria和Dioon的分辨率。在这项研究中，五个单拷贝核基因（SCNGs）被应用于苏铁目植物的生殖。具体的目的是评估几个基因treespecies树和解的方法，以发展一个准确的系统发育的顺序，将它们与级联简约分析，并解决以前的问题，这三个genes.DNA序列的系统发育位置的苏铁20种苏铁代表所有10个属苏铁。这些分析与简约，最大似然（ML）和三个贝叶斯方法的基因树种树和解，苏铁作为外群。利用贝叶斯方法建立了一个校准的数据估计模型，并进行了树图分析，级联简约法、ML和三物种树推理方法在大多数节点上都能精确地解决高支持度的相同树拓扑。Dioon和Bowenia分别是苏铁目中苏铁属的第一和第二分支，其次是一个脑状分支（MacrozamiaLepidozamiaEncephalartos），该分支与一个zamioid分支姐妹，其中Ceratozamia是第一分支，Stangeria是Microcycas和Zamia的姐妹。然而，从化石记录中推断出的大规模灭绝事件消除了Zamiaceae内更广泛的祖先分布，这一假设损害了祖先地理区域的准确优化。虽然苏铁目的主要谱系是古老的，但所有现代属的冠龄都不超过1200万年，这支持了最近的一个假设，即大多数是中新世辐射。该系统发育关系有助于对泽米科进行准确的科下分类。
Despite a recent new classification, a stable phylogeny for the cycads has been elusive, particularly regarding resolution of Bowenia, Stangeria and Dioon. In this study, five single-copy nuclear genes (SCNGs) are applied to the phylogeny of the order Cycadales. The specific aim is to evaluate several gene treespecies tree reconciliation approaches for developing an accurate phylogeny of the order, to contrast them with concatenated parsimony analysis and to resolve the erstwhile problematic phylogenetic position of these three genera.DNA sequences of five SCNGs were obtained for 20 cycad species representing all ten genera of Cycadales. These were analysed with parsimony, maximum likelihood (ML) and three Bayesian methods of gene treespecies tree reconciliation, using Cycas as the outgroup. A calibrated date estimation was developed with Bayesian methods, and biogeographic analysis was also conducted.Concatenated parsimony, ML and three species tree inference methods resolve exactly the same tree topology with high support at most nodes. Dioon and Bowenia are the first and second branches of Cycadales after Cycas, respectively, followed by an encephalartoid clade (MacrozamiaLepidozamiaEncephalartos), which is sister to a zamioid clade, of which Ceratozamia is the first branch, and in which Stangeria is sister to Microcycas and Zamia.A single, well-supported phylogenetic hypothesis of the generic relationships of the Cycadales is presented. However, massive extinction events inferred from the fossil record that eliminated broader ancestral distributions within Zamiaceae compromise accurate optimization of ancestral biogeographical areas for that hypothesis. While major lineages of Cycadales are ancient, crown ages of all modern genera are no older than 12 million years, supporting a recent hypothesis of mostly Miocene radiations. This phylogeny can contribute to an accurate infrafamilial classification of Zamiaceae.