A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae)
A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae)
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DOI：
10.1016/j.ympev.2017.02.006
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发表时间：
2017-12-01
影响因子：
4.1
通讯作者：
Granados Mendoza, Carolina
中科院分区：
文献类型：
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作者：
Fragoso-Martinez, Itzi;Salazar, Gerardo A.;Granados Mendoza, Carolina
我们进行了一项试点研究，使用锚定杂交富集来解决可能经历了最近进化辐射的大部分新热带鼠类谱系之间的关系。传统的标记（ITS， trnL-trnF和trnH-psbA）不能解决物种之间的关系，也不能解决谱系主干部分的关系。我们采集了12种Calosphace亚属的代表性种，并将鼠尾草属（Salvia）的近亲Lepechinia作为外群。杂交富集和测序成功，得到448个单个位点，平均长度为704 bp。系统发育数据在系统发育重建中的表现优于传统标记，增加了支持度和分辨率。由于捕获的基因座在不同的系统发育深度上的系统发育信息量不同，因此这些数据对这一群体以及Lamiales中可能的其他谱系的系统发育重建很有希望。然而，应该特别注意数据可能包含的系统发育噪声的数量。先前的探索步骤是使用系统发育信息性配置文件来检测具有不成比例的高替代率（显示“幽灵”峰值）的位点，如果需要，建议对有问题的数据进行随后的过滤。在我们的数据集中，过滤导致最大似然系统发育树中浅节点的支持度和分辨率增加，这是由所有基因座的串联分析产生的。此外，预计采样（基因座和分类群）的增加将有助于解决弱支持，短深的内部分支。(C) 2017爱思唯尔公司版权所有。
We conducted a pilot study using Anchored Hybrid Enrichment to resolve relationships among a mostly Neotropical sage lineage that may have undergone a recent evolutionary radiation. Conventional markers (ITS, trnL-trnF and trnH-psbA) have not been able to resolve the relationships among species nor within portions of the backbone of the lineage. We sampled 12 representative species of subgenus Calosphace and included one species of Salvia's s.l. closest relative, Lepechinia, as outgroup. Hybrid enrichment and sequencing were successful, yielding 448 alignments of individual loci with an average length of 704 bp. The performance of the phylogenomic data in phylogenetic reconstruction was superior to that of conventional markers, increasing both support and resolution. Because the captured loci vary in the amount of net phylogenetic informativeness at different phylogenetic depths, these data are promising in phylogenetic reconstruction of this group and likely other lineages within Lamiales. However, special attention should be placed on the amount of phylogenetic noise that the data could potentially contain. A prior exploration step using phylogenetic informativeness profiles to detect loci with sites with disproportionately high substitution rates (showing "phantom" spikes) and, if required, the ensuing filtering of the problematic data is recommended. In our dataset, filtering resulted in increased support and resolution for the shallow nodes in maximum likelihood phylogenetic trees resulting from concatenated analyses of all the loci. Additionally, it is expected that an increase in sampling (loci and taxa) will aid in resolving weakly supported, short deep internal branches. (C) 2017 Elsevier Inc. All rights reserved.