Let us survey the phylogeny of all organisms. Understand the background behind the dominance of the three-domain system, the characteristics of each domain, and the phylogenetic positions of major groups of organisms.
Basic Knowledge
Three-domain system (Woese, 1977/1990): Based on comparisons of 16S rRNA sequences, all organisms can be divided into three domains.
① Bacteria domain: No nuclear membrane; cell wall made of peptidoglycan. Examples: Escherichia coli, lactic acid bacteria, cyanobacteria, and rhizobia.
② Archaea domain: No nuclear membrane; no peptidoglycan cell wall; membrane lipids are ether-linked (bacteria and eukaryotes have ester-linked lipids); related more closely to eukaryotes according to 16S rRNA. Habitats: extreme environments such as hot springs, strongly acidic environments, high-salt environments, and anaerobic environments (hyperthermophiles, halophiles, and methanogens).
③ Eukarya domain: Nuclear membrane present; membrane-bound organelles present. Plants, animals, fungi, and protists.
Phylogeny of major eukaryotes: Plants = green algae → bryophytes → ferns → gymnosperms → angiosperms (the largest number of species). Animals = sponges first, followed by cnidarians, flatworms, mollusks, annelids, arthropods, echinoderms, and chordates. Vertebrates: jawless fishes → fishes → amphibians → reptiles → (birds) and mammals.
Endosymbiotic theory: Mitochondria (originating from alphaproteobacteria) and chloroplasts (originating from cyanobacteria) were incorporated into ancestral eukaryotic cells and evolved.
Give two reasons, at the molecular level and based on cell membrane characteristics, why Archaea are considered a domain independent of Bacteria.
Answer: ① Molecular level: 16S rRNA sequences are closer to those of eukaryotes than to those of bacteria, and Archaea have eukaryote-like features such as histone-like proteins, introns, and splicing. ② Cell membrane: Archaeal membrane lipids have ether bonds between glycerol and isoprenoids, fundamentally differing from the ester-linked lipids of bacteria and eukaryotes.
- Three domains = Bacteria, Archaea, and Eukarya
- Archaea = molecularly more closely related to eukaryotes
- Archaeal membrane lipids = ether-linked (bacteria and eukaryotes have ester-linked lipids)
- Mitochondrial origin = alphaproteobacteria
- Chloroplast origin = cyanobacteria
- Angiosperms = plant group with the greatest species diversity
- Vertebrate phylogeny: fish → amphibians → reptiles → (birds) and mammals
Points to Note
① Archaea are not “ancient bacteria”; they are a separate lineage and, in many respects, are more closely related to eukaryotes. ② Fungi (mushrooms, molds, and yeasts) are not plants but eukaryotes more closely related to animals. ③ Viruses lack cellular structure and are not included in the three domains. ④ When reading branching patterns in a phylogenetic tree, the order of branching (topology), not branch length, is important.
Practice
- State all three domains and identify which is most closely related to eukaryotes.
- State the prokaryotic organisms that gave rise to mitochondria and chloroplasts, respectively, according to the endosymbiotic theory.
- Name at least three invertebrate phyla that diverged before the appearance of vertebrates in animal phylogeny.