1) Introduction
Taxonomy is often seen as a trivial and boring part of biology but a system of classification is desired due to the tremendous diversity of living organisms [1]. Taxonomy allows the classification of huge amount of knowledge into an easily accessible system. It also helps in developing and supporting hypothesis regarding evolution and comparative studies. Moreover, it allows biologist to work and communicate efficiently with precise information [1]. For many decades, classification of organisms was based on morphology, behaviour and distribution in the environment. For microbiologists, this system could not be used easily and it often could be misleading due to the simplicity or uninterpretable data of microbial morphology and characteristics [2]. With the advance of molecular biology and the sequencing era, a modern classification tool arose; the small-subunit of ribosomal ribonucleic acid (16S rRNA for bacteria and archea, and 18S rRNA for eucarya). Sequencing of 16/18S RNA revealed interesting data and gave rise to the natural universal phylogenetic tree (see fig.1 and reference 2). The 16/18S rRNA-based tree changed the perspective of evolution of the cell.
2) The Universal Phylogenetic Classification
2.1) Restructuring the Systematic Systems
The old systematic system started with the creation of two kingdoms, the plants and the animals. Many years after the invention of the microscope, a third kingdom was added by Haeckel in 1866, the protist. Later on, Copeland added a forth branch, the Monera (i.e. bacteria and later the archea), and Whittaker created a fifth group, the fungi. The five kingdoms scheme (Whittaker’s model) was and still is one of the most widely accepted model for the organization of life [2]. As the sequencing era advanced, Woese and co-workers [2] felt that the five kingdoms model was not phylogenetically correct and natural. For many, kingdom Prostista and Fungi were artificial and were probably paraphyletic (share a common ancestor but do not include all the descendants) at best to the plant and animals [2]. The Monera kingdom was also viewed by Woese et al. [2] as a primary division whereas plants and animals were viewed as secondary division.
According to Woese and co-workers [2], the famous eukaryote-prokaryote concept could be misinterpreted by many. Eukaryotes are defined as a cell possessing a nucleus and organelles and it is a meaningful phylogenetic unit. In the other hands, prokaryotes are defined as lacking a nucleus and complex cellular organization (i.e. not eukaryotes). The definition of prokaryotes is meaningless scientifically and as a phylogenetic unit because the group is based on lack of characteristics rather than on possession of specific characteristics. This problem became more apparent when archea(bacteria) and (eu)bacteria were compared. Archea(bacteria) were indeed prokaryotes (they possess none of the eukaryotic characteristics) but shared little resemblance with (eu)bacteria. Therefore, Monera could not be view as a valid taxon.
Based on these arguments and recent sequencing of 16/18S rRNA of numerous species, Woese and co-workers [2] proposed a new model for the organization of life. For practical reasons, they introduced a new taxon level higher than kingdom, the domains. The taxa kingdom was retained for dividing major secondary group among the domains. Three domains were created namely Bacteria, Archea and Eucarya. A new universal phylogenetic tree was born (see fig 1 on page 2 and ref. 2).
2.2) Interpreting the Universal Phylogenetic Tree
The universal phylogenetic tree was misinterpreted as soon after it came out and the supporters of older models defended their ideas. Many assume that the organisms represented at the root of the tree and the early branching were equivalent to the modern cell organization. According to Woese, these organisms were primitive cellular entities, which were simpler and had a modular design (compartmental cell organization and each compartment is independent). The tree also does not possess a root in the classic sense. Bifurcations in classic phylogeny represent a common ancestor with sister lineage. In the universal phylogentic tree, the root and early branching does not imply such a thing. It implies that one side has passed a Darwinian threshold. Darwinian threshold is defined by the moment when a cellular entity, which is simple, highly modular and loosely connected, becomes complex and idiosyntracratically connected. The Darwinian threshold represents a drastic event in term of cellular evolution. Prior to the Darwinian threshold, species as we know them cannot exit. The threshold represents the true origin of the species, in other word speciation. The first cell type to pass the Darwinian threshold was the bacteria. Archaeal type cell probably pass the threshold before eukaryotes at second branching because the archaeal system for translation, transcription and genome replication are simpler in structure than the eukaryotic version . Therefore, three different cellular organizations have evolved independently.
Analysis of other conserved genes also demonstrated that different phylogenetic tree could be obtained. The problem with these analysis is that the genes are more associated with the evolutionary history rather than with the organism genealogy and they also give dissimilar phylogenetic tree (a horizontal gene transfer (HGT) hallmark). HGT is defined as transfer of genetic information between species and individuals rather than from parent to progeny (vertical transfer). HGT occurs at higher frequency prior to the Darwinian threshold and cellular entity cannot leave a stable record of their existence. Speciation brings stringency and allows genealogical information to be recorded within genes. In the other hand, analyses using several orthologous (having a similar function) protein support the 16/18S RNA phylogenetic tree .
The universal phylogenetic tree is a valid representation of the organism genealogy because it is not influence by HGT and the evolutionary history of the organism. The model also assumed that the primitive cell entities at the root and early branching were greatly different from the modern cell. This assumption takes us into the uncharted territory of the evolution.
