Molecular signature characters complement taxonomic diagnoses: A bioinformatic approach exemplified by ciliated protists (Ciliophora, Oligotrichea)
Molecular signature characters complement taxonomic diagnoses: A bioinformatic approach exemplified by ciliated protists (Ciliophora, Oligotrichea)
复制标题
DOI：
10.1016/j.ympev.2022.107433
复制
发表时间：
2022-03-04
影响因子：
4.1
通讯作者：
Agatha，Sabine
中科院分区：
文献类型：
--
作者：
Ganser，Maximilian H.;Santoferrara，Luciana F.;Agatha，Sabine
传统上，遵循植物学或动物学命名代码的分类群主要通过形态特征进行诊断，尽管综合分类学主张包括额外的特征。虽然许多分类学研究包括DNA序列分析，但诊断分子特征（签名特征）的系统整合仍然很少见。在这里，我们提出了一个实用的指南，检测和评估的签名字符，提供必要的手段，以补充诊断和促进识别。该指南包括普遍适用的标准，例如对生态上重要的浮游原生生物群体寡毛藻的案例研究。最近开发的工具DeSignate有助于检测多序列比对中的签名字符及其离散状态。此外，我们引入了一种新的生物信息学方法来测试不同的比对程序对签名字符一致性的影响。我们的工作流程，使检测的共识签名字符的大多数测试类群和包括这些字符的诊断中的三个订单，八个家庭，和两个属的寡毛类。所建议的方法是一个综合分类学的一步，将可靠的分子序列数据与生物体的性状联系起来。
Traditionally, taxa following the botanical or zoological codes of nomenclature are diagnosed mainly by morphological characters, although integrative taxonomy advocates including additional features. While many taxonomic studies include DNA sequence analyses, a systematic integration of diagnostic molecular characters (signature characters) is still rare. Here, we suggest a practical guideline for the detection and evaluation of signature characters that provides the means necessary to complement diagnoses and facilitates identifications. The guideline comprises generally applicable criteria exemplified by a case study on an ecologically important group of planktonic protists, the Oligotrichea. The detection of signature characters and their discrete states in multiple sequence alignments is facilitated by the recently developed tool DeSignate. Moreover, we introduce a novel bioinformatic approach to test the influence of different alignment programs on the consistency of signature characters. Our workflow enabled detection of consensus signature characters for most tested taxa and inclusion of such characters in the diagnoses of three orders, eight families, and two genera in the Oligotrichea. The suggested approach is a step towards an integrative taxonomy linking reliable molecular sequence data to organisms’ traits.