Exploring gene tree incongruence at the origin of ants and bees (Hymenoptera)
Exploring gene tree incongruence at the origin of ants and bees (Hymenoptera)
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探索蚂蚁和蜜蜂（膜翅目）起源的基因树不一致
DOI：
10.1111/zsc.12332
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发表时间：
2018
影响因子：
2.5
通讯作者：
Barbeitos, Marcos S.
中科院分区：
文献类型：
--
作者：
Camacho, Gabriela P.;Pie, Marcio R.;Feitosa, Rodrigo M.;Barbeitos, Marcos S.
不同的系统基因组数据集可能导致高度支持但不一致的结果，这一事实表明，真实数据集中基因树之间的冲突可能很严重。基于Johnson等人（Current Biology, 2013, 23,2058）的数据，我们对膜翅目昆虫的基因树空间进行了详细的探索，以研究它们之间的关系，其中蚂蚁和Apoidea（蜜蜂和圆形黄蜂）被恢复为姐妹类群，这与之前的研究相矛盾。我们在基因树中发现了高度的拓扑变异，其中一些与先前发表的假设不一致。为了在数据组合分析中分析新兴支持与冲突信号的动态，我们采用了一种基于随机数据增量添加到基于聚结的系统发育推断的新方法。虽然在308个可用的标记中，只有6.5%的标记可以恢复针叶虫科和蚁科的单一性，但只有在超过50%的位点被采样后，蚁科+足总科的信号才占主导地位。尽管如此，在所有基因被加入分析之前，对其他假设的不可忽略的支持仍然存在。我们的研究结果表明，系统发育冲突是相当普遍的，而不是分散在单个基因树中的噪声，因为替代拓扑不是从一个特定的子集中恢复的，而是从几个随机的位点组合中恢复的。因此，尽管从完整基因数据集中恢复的系统发育信号已经在更小的集合中占主导地位，但要克服系统发育冲突可能确实需要大量数据。
The fact that different phylogenomic data sets can lead to highly supported but inconsistent results suggest that conflict among gene trees in real data sets could be severe. We provide here a detailed exploration of gene tree space to investigate the relationships in Hymenoptera based on data obtained by Johnson et al. (Current Biology, 2013, 23, 2058), in which ants and Apoidea (bees and spheciform wasps) were recovered as sister groups, contradicting previous studies. We found high levels of topological variation among gene trees, several of them disagreeing with previously published hypotheses. To profile the dynamics of emerging support versus conflicting signal in combined analysis of data, we employed a novel method based on the incremental addition of randomized data to coalescence‐based phylogenetic inference. Although the monophyly of Aculeata and of Formicidae were consistently recovered using as little as 6.5% of the 308 available markers, signal for the Formicidae + Apoidea clade prevailed only after more than 50% of the loci were sampled. Still, non‐negligible support for alternative hypotheses remained until all genes were added to the analysis. Our results suggest that phylogenetic conflict is rather pervasive and not scattered as noise across individual gene trees because alternative topologies were recovered not from a specific subset, but from several random combinations of loci. Thus, even though phylogenetic signal recovered from full gene data sets was already dominant in much smaller ensembles, large amounts of data may be indeed necessary to overcome phylogenetic conflict.
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