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The concept of ‘species’ is a persistent biological problem. In discussions about the species phenomenon, the ‘cryptic species’ concept currently prevails. We propose that the ‘cryptic species’ concept as it is currently understood strongly emphasizes the distinctions between morphological and molecular levels and obscures multiple other biological levels and the organism itself. Therefore we suggest, instead of the term ‘species’, a multilevel organismal diversity concept (MOD) as an alternative that is well-supported by numerous data. We also highlight the central role of ontogeny in a broad sense (one that encompasses all major properties and traits of an organism as well as both genetic and epigenetic traits) for the future development of taxonomy and phylogenetics. Potential consequences of a new understanding of the species phenomenon for biological nomenclature are outlined. A general scheme for the future development of organism studies within the framework of MOD is presented.
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