Compositional heterogeneity and outgroup choice influence the internal phylogeny of the ants
Compositional heterogeneity and outgroup choice influence the internal phylogeny of the ants
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DOI：
10.1016/j.ympev.2019.01.024
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发表时间：
2019-05-01
影响因子：
4.1
通讯作者：
Ward, Philip S.
中科院分区：
文献类型：
--
作者：
Borowiec, Marek L.;Rabeling, Christian;Ward, Philip S.
蚂蚁（蚁科）是世界上物种最丰富的真社会性生物，自从分子遗传学出现以来，对蚂蚁的内部生殖和进化历史的了解已经大大提高。然而，在亚家族一级的一些关系仍然不确定。关键的未解决的问题包括蚂蚁生命树的根的位置和所谓的poneroid亚科之间的关系。在这里，我们收集了一个新的数据集，试图解决这两个问题，并进行分歧定年，重点是树冠蚁科的根节点的年龄。对于系统发育分析，我们包括110种蚂蚁的数据，包括关键物种Martialis heureka。我们把重点放在非蚁科谱系的蚂蚁，深入了解蚂蚁进化的深层节点的分类抽样。对于分歧定年，我们保留了一个子集的62个现存分类群和42个化石，以近似多样化的采样的背景下，生物的出生-死亡过程。我们对11个核基因片段进行了测序，共约7.5 kb，并研究了DNA序列数据中存在的α-分类群组成异质性，一种已知的误导系统发育推断的属性，以及其潜在的影响蚂蚁的生根。我们发现序列的Leptanillinae和几个外群类群是丰富的腺嘌呤和胸腺嘧啶（平均AT含量51%）相比，其余的蚂蚁（平均45%）。为了研究这种异质性是否会使系统发育推断产生偏差，我们进行了外群去除实验，成分均匀的网站分析和模拟研究。我们发现，成分的异质性确实出现影响蚂蚁树的根的位置，但最近的节点的影响有限。我们的研究结果有影响外群选择的遗传学，这不仅应该在密切关系的基础上，内组，但也应该考虑到序列的分歧和其他属性相对于内组。我们提出了一个假设，关于生根的蚂蚁的进化，其中Martialis和Leptanillinae一起构成了一个林间空地，是姐妹的所有其他蚂蚁。在校正了成分异质性之后，这成为蚂蚁树中深层节点关系的最佳支持假设。在此基础上，通过对冠层蚁科化石的生灭过程和多样性取样的分歧定年结果表明，冠层蚁科起源于早白垩世的阿尔比期或阿普梯期（103-124 Ma）。此外，我们发现支持单系poneroids包括亚科Agroecomyrmecinae，Amblyoponinae，Apomyrminae，Paraponerinae，Ponerinae和Proceratiinae，以及支持这些亚科之间的关系，除了Proceratiinae和（Amblyoponinae + Apomyrminae）的位置。我们的系统发育还强调了几个蚂蚁属的非单系性，包括Leptanillinae中的Protanilla和Leptanilla，Proceratiinae中的Proceratium，以及Ponerinae中的Cryptopone，Euponera和Mesoponera。
Knowledge of the internal phylogeny and evolutionary history of ants (Formicidae), the world's most species-rich Glade of eusocial organisms, has dramatically improved since the advent of molecular phylogenetics. A number of relationships at the subfamily level, however, remain uncertain. Key unresolved issues include placement of the root of the ant tree of life and the relationships among the so-called poneroid subfamilies. Here we assemble a new data set to attempt a resolution of these two problems and carry out divergence dating, focusing on the age of the root node of crown Formicidae. For the phylogenetic analyses we included data from 110 ant species, including the key species Martialis heureka. We focused taxon sampling on non-formicoid lineages of ants to gain insight about deep nodes in the ant phylogeny. For divergence dating we retained a subset of 62 extant taxa and 42 fossils in order to approximate diversified sampling in the context of the fossilized birth-death process. We sequenced 11 nuclear gene fragments for a total of similar to 7.5 kb and investigated the DNA sequence data for the presence of among-taxon compositional heterogeneity, a property known to mislead phylogenetic inference, and for its potential to affect the rooting of the ant phylogeny. We found sequences of the Leptanillinae and several outgroup taxa to be rich in adenine and thymine (51% average AT content) compared to the remaining ants (45% average). To investigate whether this heterogeneity could bias phylogenetic inference we performed outgroup removal experiments, analysis of compositionally homogeneous sites, and a simulation study. We found that compositional heterogeneity indeed appears to affect the placement of the root of the ant tree but has limited impact on more recent nodes. Our findings have implications for outgroup choice in phylogenetics, which should be made not only on the basis of close relationship to the ingroup, but should also take into account sequence divergence and other properties relative to the ingroup. We put forward a hypothesis regarding the rooting of the ant phylogeny, in which Martialis and the Leptanillinae together constitute a Glade that is sister to all other ants. After correcting for compositional heterogeneity this emerges as the best-supported hypothesis of relationships at deep nodes in the ant tree. The results of our divergence dating under the fossilized birth-death process and diversified sampling suggest that the crown Formicidae originated during the Albian or Aptian ages of the Lower Cretaceous (103-124 Ma). In addition, we found support for monophyletic poneroids comprising the subfamilies Agroecomyrmecinae, Amblyoponinae, Apomyrminae, Paraponerinae, Ponerinae, and Proceratiinae, and well-supported relationships among these subfamilies except for the placement of Proceratiinae and (Amblyoponinae + Apomyrminae). Our phylogeny also highlights the non-monophyly of several ant genera, including Protanilla and Leptanilla in the Leptanillinae, Proceratium in the Proceratiinae, and Cryptopone, Euponera, and Mesoponera within the Ponerinae.