1.4The Phylogeny and Phylogenetic Tree of Living Organisms

Figure 1-3 shows the phylogenetic tree of all living organisms known until now. This phylogenetic tree categorizes organisms mostly according to the differences in the bases of their DNA. The tree divides organisms into three large categories called "domains": bacteria, archaea, and eukarya (eukaryotes). Organisms in the first two categories are called prokaryotes because they do not have definite nuclei. Bacteria and archaea have not only different lipid compositions in their cell membranes but also clearly different genetic compositions. Plants and humans are classified as eukaryotes. Eukaryotes diverged not from bacteria but from the archaea branch.
The subcellular organelles (see Chapter 2) of eukaryotes usually comprise mitochondria, but there are also organisms that have lost their mitochondria, namely the protists (protista). Flagellates, which are protists, have no mitochondria. Furthermore, since mitochondria are surrounded by a double membrane and have circular DNA, they are thought to have evolved from a bacterium. According to this hypothesis, a bacterium undergoing aerobic respiration invaded a primitive eukaryote, became symbiotic with it, and consequently, became a subcellular organelle with its own genes (Endosymbiotic Theory, Figure 2-7). Similarly, the chloroplasts that are observed in higher plants are thought to have originated from a cell that was symbiotically invaded by a photosynthetic cyanobacterium.

Fig. 1-3. Phylogenetic Tree of Living Organisms

Fig. 1-4. Genealogy of Humans

This figure is a conceptual diagram.
See the main text for accurate information

The most primitive eukaryotic organisms are the protists. The protists include the above-mentioned flagellates, the malaria parasites, and the dinoflagellates, which cause red tide. The protists also include euglenophytes, which can photosynthesize, and slime molds, which can differentiate and change shape even though they are unicellular organisms.
At this point in evolution, the group of organisms called "plants" diverged. Plants are photosynthetic multicellular organisms whose cells are surrounded by cell walls. Plants are called "autotrophs" because they can synthesize organic compounds using carbon dioxide and water as raw materials. Plants are producers—they provide nutrition to all other living organisms on the earth.
The next to diverge were the fungi, also called "mold," "mushrooms," or in terms of nutrition, "decomposers." Although their cells are surrounded by cell walls, the fungi live as heterotrophs and do not photosynthesize. Finally, the animals emerged. Animals are also heterotrophs, since they lack cell walls and the ability to photosynthesize. In terms of nutrition, animals are called "consumers."
The ancestors of mammals appeared during the Mesozoic era 150 million years ago, the monotremes and marsupials emerged thereafter, and modern mammals adaptively radiated throughout the world 80 million years ago. The divergence between monkeys and humans occurred 6 million years ago, and was followed by the appearance of Australopithecus, Homo habilis, Homo erectus, and finally Homo sapiens (Fig. 1-4). It is now believed that Homo neanderthalensis (neanderthal man) was not the ancestor of modern humans, but was a separate member of the genus Homo (see Column in Section 5 of Chapter 1).

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