Exploring data processing strategies in NGS target enrichment to disentangle radiations in the tribe Cardueae (Compositae)
Exploring data processing strategies in NGS target enrichment to disentangle radiations in the tribe Cardueae (Compositae)
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DOI：
10.1016/j.ympev.2018.07.012
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发表时间：
2018-11-01
影响因子：
4.1
通讯作者：
Vilatersana, Roser
中科院分区：
文献类型：
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作者：
Herrando-Moraira, Sonia;Antonio Calleja, Juan;Vilatersana, Roser
目标富集是一种具有成本效益的测序技术，有望阐明快速进化谱系中的进化关系。然而，生物信息学序列处理在系统发育推断中的潜在偏差和影响尚未得到彻底探讨。在这里，我们调查这个问题的最终目标是揭示到一个高度多样化的菊科（菊科）由四个主要属：牛蒡属，紫菀属，风毛菊属，和侏罗纪。具体来说，我们比较了在两个易于使用的工作流程中实现的序列数据提取方法，PHYLUCE和HybPiper，并评估了旨在减少系统发育噪声的两种过滤方法的影响。此外，我们比较了两种系统发育推断方法：（1）连接方法，其中所有位点连接在一个超矩阵中;（2）合并方法，其中基因树独立产生，然后在合并假设下用于构建物种树。在这里，我们确认的有用性的1061 COS目标（一个核保守的直系同源基因座组开发的菊科）在各种分类水平。属间关系完全解决：有两个姐妹组，牛蒡，紫金牛和风毛菊，这是在与形态假设。牛蒡属、Cousinia和风毛菊属物种之间的属内关系也得到了很好的定义。相反，在侏罗纪，物种关系仍然存在冲突。方法的选择显着影响的拓扑结构，分支长度，和支持的遗传。在所有的分析中，使用HybPiper和去除快速进化位点的最严格方案获得的遗传学估计为最佳。关于方法的选择，我们得出结论：（1）在合并方法下得到的树在拓扑上比使用连接方法推断的树更一致;（2）在连接方法下，细化处理只提高了支持值;以及（3）当在级联方法中去除快速演变的位点时分支支持值被最大化，以及当在聚结方法中分析更高数量的基因座时。
Target enrichment is a cost-effective sequencing technique that holds promise for elucidating evolutionary relationships in fast-evolving lineages. However, potential biases and impact of bioinformatic sequence treatments in phylogenetic inference have not been thoroughly explored yet. Here, we investigate this issue with an ultimate goal to shed light into a highly diversified group of Compositae (Asteraceae) constituted by four main genera: Arctium, Cousinia, Saussurea, and Jurinea. Specifically, we compared sequence data extraction methods implemented in two easy-to-use workflows, PHYLUCE and HybPiper, and assessed the impact of two filtering practices intended to reduce phylogenetic noise. In addition, we compared two phylogenetic inference methods: (1) the concatenation approach, in which all loci were concatenated in a supermatrix; and (2) the coalescence approach, in which gene trees were produced independently and then used to construct a species tree under coalescence assumptions. Here we confirm the usefulness of the set of 1061 COS targets (a nuclear conserved orthology loci set developed for the Compositae) across a variety of taxonomic levels. Intergeneric relationships were completely resolved: there are two sister groups, Arctium-Cousinia and Saussurea-Jurinea, which are in agreement with a morphological hypothesis. Intrageneric relationships among species of Arctium, Cousinia, and Saussurea are also well defined. Conversely, conflicting species relationships remain for Jurinea. Methodological choices significantly affected phylogenies in terms of topology, branch length, and support. Across all analyses, the phylogeny obtained using HybPiper and the strictest scheme of removing fast-evolving sites was estimated as the optimal. Regarding methodological choices, we conclude that (1) trees obtained under the coalescence approach are topologically more congruent between them than those inferred using the concatenation approach; (2) refining treatments only improved support values under the concatenation approach; and (3) branch support values are maximized when fast-evolving sites are removed in the concatenation approach, and when a higher number of loci is analyzed in the coalescence approach.