Ultraconserved elements show utility in phylogenetic inference of Adephaga (Coleoptera) and suggest paraphyly of 'Hydradephaga'
Ultraconserved elements show utility in phylogenetic inference of Adephaga (Coleoptera) and suggest paraphyly of 'Hydradephaga'
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DOI：
10.1111/syen.12244
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发表时间：
2017-10-01
影响因子：
4.8
通讯作者：
Short, Andrew E. Z.
中科院分区：
文献类型：
--
作者：
Baca, Stephen M.;Alexander, Alana;Short, Andrew E. Z.
甲虫亚级Adephaga已成为利用各种数据源和推理方法的许多系统发育重建的主题。但是，在主要的Adephagan谱系之间的关系上尚无强烈共识。超级保守的元素（UCE）已被证明可用于推断脊椎动物，蛛网膜和膜翅目不同时间尺度上的困难或未解决的系统发育。最近，使用Polyphagan基因组为鞘翅目开发了一个UCE诱饵集，并且是链球菌的成员作为外组。在这里，我们在第一个体外应用中研究了UCES重建Adephagan家族的系统发育的实用性。我们的最终数据集包括305个UCE基因座，适用于所有Adephagan家族的18位代表，除Aspidytidae和两个Polyphagan Outgroups外，总串联长度为83 547 bp。我们使用串联的UCE比对和结合物种树方法的最大似然分析（Astral II，Astrid，SVDQuartets）推断了树木。尽管结合物种的树种方法的分辨率和支持较弱，但串联分析产生了良好的，高度支持的树木。 Hydradephaga被恢复为副业，Gyrinidae姐妹与Geadephaga和所有其他Adephagans。 Haliplidae被恢复为Dytiscoidea的姐妹，Hygrobiidae和Amphizoidae的姐妹与Dytiscidae的姐妹一起。最终，诺特里德（Noteridae）被恢复为单系和梅鲁伊德（Meruidae）的姐妹。鉴于UCE数据成功地解决了Adephaga内的系统发育关系，我们建议使用具有改进的分类单元采样的UCE并通过开发Adephaga特异性探针来进一步解决Adephaga之间的关系。
The beetle suborder Adephaga has been the subject of many phylogenetic reconstructions utilizing a variety of data sources and inference methods. However, no strong consensus has yet emerged on the relationships among major adephagan lineages. Ultraconserved elements (UCEs) have proved useful for inferring difficult or unresolved phylogenies at varying timescales in vertebrates, arachnids and Hymenoptera. Recently, a UCE bait set was developed for Coleoptera using polyphagan genomes and a member of the order Strepsiptera as an outgroup. Here, we examine the utility of UCEs for reconstructing the phylogeny of adephagan families, in the first in vitro application a UCE bait set in Coleoptera. Our final dataset included 305 UCE loci for 18 representatives of all adephagan families except Aspidytidae, and two polyphagan outgroups, with a total concatenated length of 83 547 bp. We inferred trees using maximum likelihood analyses of the concatenated UCE alignment and coalescent species tree methods (astral II, ASTRID, svdquartets). Although the coalescent species tree methods had poor resolution and weak support, concatenated analyses produced well-resolved, highly supported trees. Hydradephaga was recovered as paraphyletic, with Gyrinidae sister to Geadephaga and all other adephagans. Haliplidae was recovered as sister to Dytiscoidea, with Hygrobiidae and Amphizoidae successive sisters to Dytiscidae. Finally, Noteridae was recovered as monophyletic and sister to Meruidae. Given the success of UCE data for resolving phylogenetic relationships within Adephaga, we suggest the potential for further resolution of relationships within Adephaga using UCEs with improved taxon sampling, and by developing Adephaga-specific probes.