Universal species concept: pipe dream or a step toward unifying  biology?
The Universal Tree of Life, which is based on phylogenetic analysis of the RNA sequence from the small ribosomal subunit, was a breakthrough in understanding the relatedness among all living organisms. The result has had a major impact on taxonomy by separating life into three domains: Eukarya, Bacteria, and Archaea. Indeed, microbiologists have used the 16S ribosomal RNA (rRNA) of the small ribosomal subunit to construct the hierarchical classification of Bacteria and Archaea from the level of domain to genus. However, the 16S rRNA of the Bacteria and Archaea and the corresponding 18S rRNA of the Eukarya are too highly conserved to be useful phylogenetically at the species level. For this reason, I propose that biologists adopt a phylogenomic species concept that utilizes both phylogenetic analyses of less highly conserved genes and proteins as well as genomic analyses for the circumscription of species. If biologists adopt a phylogenomic concept for species, the classification of all living organisms from domain to species could be completed. Furthermore, this universal species concept could help provide a more equitable circumscription among all species, as well as aid in the unification of biologists and biology.
Department of Microbiology, University of Washington, Seattle, WA 98195, USA. jtstaley@u.washington.edu
James T
JT
Staley
D001105:Archaea / Q000145:classification*; D001419:Bacteria / Q000145:classification*; D049810:Genetic Speciation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D012341:RNA, Ribosomal, 5S / Q000737:chemistry / Q000235:genetics; D013045:Species Specificity
D012341:RNA, Ribosomal, 5S