MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany,
Université de Lyon; UMR5023 Ecologie des Hydrosystémes Naturels et Anthropisés; Universiteì Lyon 1; ENTPE; CNRS; 6 rue Raphaël Dubois, 69622 Villeurbanne, France.
Syst Biol. 2016 Sep;65(5):925-40. doi: 10.1093/sysbio/syw031. Epub 2016 Apr 12.
Investigations of biodiversity, biogeography, and ecological processes rely on the identification of "species" as biologically significant, natural units of evolution. In this context, morphotaxonomy only provides an adequate level of resolution if reproductive isolation matches morphological divergence. In many groups of organisms, morphologically defined species often disguise considerable genetic diversity, which may be indicative of the existence of cryptic species. The diversity hidden by morphological species can be disentangled through genetic surveys, which also provide access to data on the ecological distribution of genetically circumscribed units. These units can be identified by unique DNA sequence motifs and allow studies of evolutionary and ecological processes at different levels of divergence. However, the nomenclature of genetically circumscribed units within morphological species is not regulated and lacks stability. This represents a major obstacle to efforts to synthesize and communicate data on genetic diversity for multiple stakeholders. We have been confronted with such an obstacle in our work on planktonic foraminifera, where the stakeholder community is particularly diverse, involving geochemists, paleoceanographers, paleontologists, and biologists, and the lack of stable nomenclature beyond the level of formal morphospecies prevents effective transfer of knowledge. To circumvent this problem, we have designed a stable, reproducible, and flexible nomenclature system for genetically circumscribed units, analogous to the principles of a formal nomenclature system. Our system is based on the definition of unique DNA sequence motifs collocated within an individual, their typification (in analogy with holotypes), utilization of their hierarchical phylogenetic structure to define levels of divergence below that of the morphospecies, and a set of nomenclature rules assuring stability. The resulting molecular operational taxonomic units remain outside the domain of current nomenclature codes, but are linked to formal morphospecies as regulated by the codes. Subsequently, we show how this system can be applied to classify genetically defined units using the SSU rDNA marker in planktonic foraminifera and we highlight its potential use for other groups of organisms where similarly high levels of connectivity between molecular and formal taxonomies can be achieved.
生物多样性、生物地理学和生态过程的研究依赖于将“物种”鉴定为具有生物学意义的、进化的自然单位。在这种情况下，如果生殖隔离与形态分歧相匹配，形态分类学才提供了足够的分辨率。在许多生物体群体中，形态定义的物种经常掩盖了相当大的遗传多样性，这可能表明存在隐种。通过遗传调查可以解开隐藏在形态物种中的多样性，遗传调查还提供了有关遗传上界定的单位生态分布的数据。这些单位可以通过独特的 DNA 序列模式来识别，并允许在不同的分歧水平上研究进化和生态过程。然而，形态物种内遗传界定单位的命名法不受监管，缺乏稳定性。这是综合和交流遗传多样性数据的努力的主要障碍，多个利益相关者都需要这些数据。在我们对浮游有孔虫的工作中，我们就遇到了这样一个障碍，在这项工作中，利益相关者群体特别多样化，涉及地球化学家、古海洋学家、古生物学家和生物学家，而且超出正式形态物种水平的稳定命名法缺乏，这阻碍了知识的有效传递。为了规避这个问题，我们设计了一个稳定、可重复和灵活的遗传界定单位命名法系统，类似于正式命名法系统的原则。我们的系统基于独特的 DNA 序列模式的定义，这些模式在个体内共定位，对它们进行典型化（类似于模式标本），利用它们的层次系统发育结构来定义低于形态物种的分歧水平，以及一套命名规则以确保稳定性。由此产生的分子操作分类单位仍然不在当前命名法代码的范围内，但与代码所规定的正式形态物种相关联。随后，我们展示了如何使用浮游有孔虫的 SSU rDNA 标记应用该系统对遗传定义的单位进行分类，并强调了它在其他可以实现分子和正式分类学之间高度连接的生物体群体中的潜在用途。
