1.7Major Classification of Organisms

Although many classification systems have been proposed for organisms, the most representative are the five-kingdom and three-domain theories (Fig. 1-4). The five-kingdom theory classifies organisms into animals, plants, fungi, protists, and monera (bacteria), which is based on species and relatively fits to our senses. Based on homology in ribosomal RNA (see Chapters 8 and 9) base sequences, the three-domain theory proposes the domains of Eukarya, Bacteria, and Archaea. While prokaryotes (bacteria) are divided into two groups, eukaryotes belong to one group. In this model, animals and plants are classified as closely related groups after quantitative assessment of phylogenetic relationships. However, Thomas Cavalier-Smith proposed a new classification system on the basis of detailed analysis of gene sequence information. As per his classification, eukaryotes are divided into three groups (Fig. 1-4C). In this model, animals and fungi form one group and protists, plants, and algae form another. One of the group characteristics is the location and number of flagella, with the former group including organisms with one flagellum located at the posterior position and the latter group including organisms with two flagella located at the anterior position. There is no overlap between the two groups. All eukaryotic photosynthetic organisms are included in the latter group, which is a unique point of this model. While primary symbiotic algae emerged through symbiosis with cyanobacteria, secondary symbiotic algae emerged through symbiosis with other algae and are dispersed through the range of protists. Based on latest molecular phylogenetic analysis (see Chapter 24), this new classification system integrates the five-kingdom and three-domain theories in terms of the placement of eukaryotes within the system. A notable point is that fungi, which were once believed to be plants, are now considered to be closer to animals.

Over the years, there has been much debate over the major classification of organisms, and the main issue has been whether taxonomy indicates evolution. At present, taxonomy is based on evolution through phylogenetic analysis, but the debate continues because taxonomy and evolution cannot be easily confirmed through experiments. However, despite these arguments, taxonomy can still aid in our understanding of biological phenomena if our viewpoint is changed. Whether we can learn something by classifying organisms in a certain manner is more important than whether a classification method is correct.

Figure 1-4 Phylogenetic systematics of representative organisms

(A) Five-kingdom theory based on morphological features. (B) Three-domain theory based on ribosomal RNA sequences (Woese et al., modified in 1990). (C) Taxonomy based on gene sequences. The text is also a reference. Refer to in Chapter 24 for principles underlying the construction of phylogenetic trees and phylogenetic evolution. *Organisms that have chloroplasts and perform photosynthesis. +Organisms that do not perform photosynthesis but have vestigial chloroplasts (plastids). Secondary symbiotic algae are algae that emerged through symbiosis with primary symbiotic algae. Metazoa are equivalent to “animals” in the five-kingdom theory and include porifers, mesozoans, arthropods, and vertebrates.

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