Partitional Classification: A Complement to Phylogeny

Abstract

The tree of life is currently an active object of research, though next to vertical gene transmission non vertical gene transfers proved to play a significant role in the evolutionary process. To overcome this difficulty, trees of life are now constructed from genes hypothesized vital, on the assumption that these are all transmitted vertically. This view has been challenged. As a frame for this discussion, we developed a partitional taxonomical system clustering taxa at a high taxonomical rank. Our analysis (1) selects RNase P RNA sequences of bacterial, archaeal, and eucaryal genera from genetic databases, (2) submits the sequences, aligned, to k-medoid analysis to obtain clusters, (3) establishes the correspondence between clusters and taxa, (4) constructs from the taxa a new type of taxon, the genetic community (GC), and (5) classifies the GCs: Archaea-Eukaryotes contrastingly different from the six others, all bacterial. The GCs would be the broadest frame to carry out the phylogenies.

Keywords: RNase P RNA; bioinformatics; classification; cluster analysis; evolution; k-medoid analysis.

Figure 1

Plot diagrams inferred by CA. Inertia rates in brackets next to the factorial axes (FAs). Squares with C_n in gray are clusters. Dots with abbreviated names in black are taxa. Factorial planes generated by two factorial axes: (A) F1 and F2; (B) F1 and F3; (C) F3 and F4; (D) F4 and F5; (E) F5 and F6; (F) F5 and F7.

Figure 2

HCA dendrogram. Distance = DI = Manhattan; aggregation method = Ward. Cut at distance ca. 3200. ${\mathcal{A}}_i$ = cluster families: ${\mathcal{A}}_1$ = {C₁, C₁₃, C₁₇}; ${\mathcal{A}}_2$ = {C₂, C₅, C₁₀}; ${\mathcal{A}}_3$ = {C₄, C₆, C₁₄}; ${\mathcal{A}}_4$ = {C₁₁}; ${\mathcal{A}}_5$ = {C₁₂}; ${\mathcal{A}}_6$ = {C₁₅}; and ${\mathcal{A}}_7$ = {C₁₆}.