Data from: Nomenclature for the nameless: a proposal for an integrative molecular taxonomy of cryptic diversity exemplified by planktonic foraminifera

Investigations of biodiversity, biogeography and ecological processes rely on the identification of “species” as biologically significant, natural units of evolution. In this context, morpho-taxonomy 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 (MOTUs) 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、生物地理学及生态过程的研究，均以将“物种”认定为具有生物学意义的自然演化单元为基础。在此语境下，只有当生殖隔离与形态分化相匹配时，形态分类学（morpho-taxonomy）才能提供足够的分辨能力。在诸多生物类群中，基于形态界定的物种往往掩盖了可观的遗传多样性，这可能预示着隐存种（cryptic species）的存在。基于形态界定的物种所隐藏的多样性，可通过遗传调查得以解析；同时，遗传调查还能获取遗传界定单元（genetically circumscribed units）的生态分布数据。这类单元可通过独特的DNA序列基序（DNA sequence motifs）加以识别，进而支持不同分化层级下的演化与生态过程研究。然而，形态物种内遗传界定单元的命名规则尚未得到规范，且缺乏稳定性。这为多利益相关方整合与传播遗传多样性相关数据的工作，构成了重大阻碍。我们在浮游有孔虫（planktonic foraminifera）的相关研究中便遭遇了这一困境：该领域的利益相关群体构成极为多元，涵盖了地球化学家、古海洋学家、古生物学家与生物学家；而在正式形态种层级之上缺乏稳定命名规则的现状，阻碍了知识的有效传播。为解决这一问题，我们参考正式命名系统的原则，为遗传界定单元设计了一套稳定、可复现且具备灵活性的命名体系。本体系基于以下核心要素：对单个个体内共存的独特DNA序列基序进行界定、对其进行模式标定（类比正模标本（holotypes））、利用系统发育层级结构界定形态物种之下的分化层级，以及一套保障命名稳定性的规则集。由此产生的分子操作分类单元（molecular operational taxonomic units, MOTUs）虽未纳入现行命名法规的管辖范畴，却可与该法规规范下的正式形态物种建立关联。后续我们将展示，如何利用小亚基核糖体DNA（SSU rDNA）标记，将本体系应用于浮游有孔虫的遗传界定单元分类；同时还将阐明，该体系在其他可实现分子分类与正式分类间高度关联的生物类群中的应用潜力。