Department of Zoology, Senckenberg Museum of Natural History Görlitz, Am Museum 1, D-02826 Görlitz, Germany.
Syst Biol. 2020 Sep 1;69(5):1033-1038. doi: 10.1093/sysbio/syaa032.
The Gene and Gene Expression (GAGE) species concept, a new version of the Pragmatic Species Concept of Seifert (2014), is proposed as a concept applicable to any described recent or fossil eukaryotic organism independent from its mode of reproduction or evolutionary history. In addition to presenting the concept as such, the article also provides practical recommendations for taxonomists when delimiting species and describing taxa. The wording of the new concept contains a heading core sentence plus five attached sentences addressing essential conditions for its translation into a sound taxonomic practice: "Species are separable clusters that have passed a threshold of evolutionary divergence and are exclusively defined by nuclear DNA sequences and/or their expression products. Nuclear DNA sequences and their expression products are different character systems but have a highly correlated indicative function. Character systems with the least risk of epigenetic or ontogenetic modification have superior indicative value when conflicts between character systems of integrative studies arise. All character systems have to be described by an adequate numerics allowing cluster formation and determination of thresholds. Thresholds for each character system should be fixed by consensus among the experts under the principle of avoiding oversplitting or lumping. Clusters must not be the expression of intraspecific polymorphism." Recognizing the distortions and conflicts caused to taxonomy through barcoding or through assessment on the basis of association with other organisms, the GAGE species concept strongly downgrades the use of cytoplasmic DNA of endosymbiotic origin (mtDNA, cpDNA) or DNA of closely associated microbes (e.g., Wolbachia bacteria) for final taxonomic decision-making. Recognizing the distortion of phylogenies by the high frequency of reticulate evolution, it is argued that delimiting and naming species has to be separated from constructing bifurcating phylogenetic trees. [Cytoplasmic DNA; lumping; nuclear DNA; numeric taxonomy; oversplitting; reticulate evolution.].
基因和基因表达（GAGE）物种概念是 Seifert（2014 年）实用物种概念的新版本，它被提议作为一个适用于任何描述的最近或化石真核生物的概念，独立于其繁殖方式或进化历史。除了提出这样的概念外，本文还为分类学家在划定物种和描述分类群时提供了实用建议。新概念的措辞包含一个标题核心句，加上五个附加句，阐述了将其转化为健全分类实践的必要条件：“物种是可分离的聚类，已经通过进化分歧的阈值，并且仅由核 DNA 序列和/或其表达产物定义。核 DNA 序列和其表达产物是不同的特征系统，但具有高度相关的指示功能。当整合研究的特征系统之间发生冲突时，具有最低表观遗传或个体发生修饰风险的特征系统具有更高的指示价值。所有特征系统都必须通过允许聚类形成和确定阈值的充分数值来描述。每个特征系统的阈值应通过专家共识固定，遵循避免过度分割或合并的原则。聚类不得是种内多态性的表达。”通过条形码或基于与其他生物体的关联进行评估，GAGE 物种概念强烈贬低了内共生起源的细胞质 DNA（mtDNA、cpDNA）或密切相关微生物的 DNA（例如，沃尔巴克氏体细菌）在最终分类决策中的使用，认识到这对分类学造成的扭曲和冲突。认识到系统发育的扭曲是由高度频繁的网状进化引起的，因此，必须将物种的划定和命名与构建分叉系统发育树分开。[细胞质 DNA；合并；核 DNA；数值分类学；过度分割；网状进化。]。
