The Gene and Gene Expression (GAGE) Species Concept: An Universal Approach for All Eukaryotic Organisms.

ABSTRACT

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.].