Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment
Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment
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DOI：
10.1186/s12862-015-0415-0
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发表时间：
2015-06-14
影响因子：
3.4
通讯作者：
Near, Thomas J.
中科院分区：
文献类型：
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作者：
Eytan, Ron I.;Evans, Benjamin R.;Near, Thomas J.
背景：过去十年在解决生命之树问题方面取得了显著进展。然而，尽管基因组规模数据集的使用越来越多，一些系统发育关系仍然难以解决。在这里，我们采用锚定系统基因组学捕获了29种棘形硬骨鱼的107个核位点，其中25种来自最近划分的硬骨鱼枝。以往使用多位点核外显子数据集的研究无法确定Ovalentaria树底部的节点。在这里，我们测试系统基因组方法是否会为这些节点提供更好的支持，如果不是，为什么会这样。结果：在使用一种新的方法来解释同源位点后，我们使用最大似然和物种树方法来估计系统发育，使用超过80,000个碱基对的DNA序列比对。鱼科中几个关键的关系已经很好地解决了，包括1)慈鱼科和Pholidichthys之间的姐妹分类群关系，2)一个包含blenies， gramma，粘鱼和颚鱼的分支，以及3)Atherinomorpha（顶鲦鱼，飞鱼和银鱼）的单系关系。然而，在一些分析中，许多与缬草早期多样化相关的系统发育节点都没有得到很好的解决。通过使用稀疏曲线，我们表明，在Ovalentaria系统发育的最早节点中，有限的系统发育分辨率似乎不是由于数据不足，因为当只有1/3的采样位点被用于分析时，平均全局节点支持度停止增加。相反，由于氨基酸数据集的贝叶斯混合模型分析为Ovalentaria树的部分碱基提供了良好的支持，因此这种分辨率的缺乏可能是由模型错误规范驱动的。结论：尽管在Ovalentaria系统发育的最早节点之间有限的系统发育分辨率似乎不是由于数据的缺乏，但可能是由于模型错误规范导致的随机和系统误差在Ovalentaria树基础的低分辨率中起作用，因为贝叶斯方法能够解决一些更深的节点，而其他方法则无法解决。
Background: The past decade has witnessed remarkable progress towards resolution of the Tree of Life. However, despite the increased use of genomic scale datasets, some phylogenetic relationships remain difficult to resolve. Here we employ anchored phylogenomics to capture 107 nuclear loci in 29 species of acanthomorph teleost fishes, with 25 of these species sampled from the recently delimited clade Ovalentaria. Previous studies employing multilocus nuclear exon datasets have not been able to resolve the nodes at the base of the Ovalentaria tree with confidence. Here we test whether a phylogenomic approach will provide better support for these nodes, and if not, why this may be.Results: After using a novel method to account for paralogous loci, we estimated phylogenies with maximum likelihood and species tree methods using DNA sequence alignments of over 80,000 base pairs. Several key relationships within Ovalentaria are well resolved, including 1) the sister taxon relationship between Cichlidae and Pholidichthys, 2) a clade containing blennies, grammas, clingfishes, and jawfishes, and 3) monophyly of Atherinomorpha (topminnows, flyingfishes, and silversides). However, many nodes in the phylogeny associated with the early diversification of Ovalentaria are poorly resolved in several analyses. Through the use of rarefaction curves we show that limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny does not appear to be due to a deficiency of data, as average global node support ceases to increase when only 1/3rd of the sampled loci are used in analyses. Instead this lack of resolution may be driven by model misspecification as a Bayesian mixed model analysis of the amino acid dataset provided good support for parts of the base of the Ovalentaria tree.Conclusions: Although it does not appear that the limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny is due to a deficiency of data, it may be that both stochastic and systematic error resulting from model misspecification play a role in the poor resolution at the base of the Ovalentaria tree as a Bayesian approach was able to resolve some of the deeper nodes, where the other methods failed.