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Chapter 35. Biodiversity

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1. Biological Classification

2. Domain

3. Eukaryota Domain

4. Kingdom Protista

5. Evolution of Animals

1. Biological Classification

⑴ Purpose: A classification of organisms to reveal their relationships with each other.

⑵ Methods

① Natural Classification: Classifying organisms according to their evolutionary processes or relationships.

② Artificial Classification: Classifying organisms based on arbitrary criteria.

○ Example: Terrestrial animals, aquatic plants, medicinal plants, edible fungi, herbivores, etc.

⑶ Methodologies in Systematics

① Method 1. Structural similarity (morphology)

○ Used mainly when classifying extinct organisms known only from fossils.

○ The geologic time scale subdivides the history of life, so it is used as a reference in classification.

○ On the basis of such classifications, fossil assemblages are determined and used to refine subdivisions of geologic time.

② Method 2. Modern phylogenetic classification (evolutionary systematics)

○ In DNA sequence comparisons, organisms that are evolutionarily close have more similar DNA.

○ Comparisons often use the small-subunit ribosomal rRNA gene, cytochrome c amino-acid sequences, etc.

○ Because these encode essential proteins, they are highly conserved over evolution.

③ Modern species are divided—based on structural similarity and evolutionary relationships—into domains and, within them, biological kingdoms.

⑷ Biological Classification System

① Hierarchical taxonomic ranks: reflect degrees of relatedness; grouping species within the same taxon implies a shared recent common ancestor.

② Taxonomic ranks: Domain – Kingdom – Phylum – Class – Order – Family – Genus – Species (eight levels total).

○ Domains: Bacteria, Archaea, Eukarya.

○ Kingdoms: Within Eukarya, Protista, Plantae, Fungi, Animalia.

○ Current framework: three domains and six kingdoms.

③ History of classification

○ Aristotle: classified 540 animal species.

○ Two-kingdom system: plants (non-motile) vs. animals (motile).

○ Three-kingdom system: with microscopy, unicellular organisms were placed in Protista.

○ Four-kingdom system: among protists, organisms lacking a nucleus were placed in Monera (Prokaryota).

○ Five-kingdom system: Fungi, which do not perform photosynthesis, were separated from plants.

○ Three-domain/six-kingdom system: discovery that Archaea are more similar to eukaryotes than to true bacteria.

④ When finer resolution is needed, insert intermediate ranks between the main ones: subphylum, subclass, suborder, subfamily, subgenus, subspecies.

○ Subspecies: a morphologically and/or geographically distinct population; no reproductive barrier.

○ Variety: a group that differs in two or three traits or in distribution due to natural mutation.

○ Form/cultivar: a group within a species produced by artificial improvement (breeding).

⑸ Scientific Names

① Need: to ensure uniformity in scholarly research.

○ Latin is no longer used in daily life, so names do not change with place or time.

② Binomial nomenclature: list the genus name and the specific epithet in Latin.

○ Devised by Linnaeus (Sweden) in the 18th century.

○ Genus – specific epithet – author.

③ Trinomial nomenclature

○ Used to indicate infraspecific ranks below species: subspecies, variety, form.

○ Genus – specific epithet – (subspecies/variety/form) – author.

④ How to write scientific names

○ Genus: capitalized, italic.

○ Specific epithet: lowercase, italic.

○ Subspecies/variety/form: lowercase, italic.

○ Variety is indicated by inserting “var.”

○ Form is indicated by inserting “for.”

○ Author: capitalized, roman (upright) type; may be omitted or abbreviated to initials.

○ Example 1. tiger: Felis tiger Linne

○ Example 2. Korean tiger (subspecies): Felis tiger coreansis Brass

2. Domain

⑴ Prokaryotes (Bacteria Domain + Archaea Domain) vs. Eukaryotes

① Nucleus, Mitochondria, Chloroplasts: Absent vs. Present

② Unicellular vs. Unicellular, Multicellular

⑵ Domain Bacteria

① Most bacteria are harmless, but the ones most familiar to us are usually pathogens.

② Many bacteria act as decomposers, obtaining nutrients by breaking down the bodies of dead organisms.

③ Features unique to Bacteria

○ Cell structure: peptidoglycan (cell-wall component), LPS, teichoic acids.

④ RNA polymerase: α₂ββ’

⑤ Useful substances of bacterial origin

○ Antibiotics: over 50% of antibiotics are derived from bacteria.

○ Restriction enzymes: proteins that cut DNA at specific sequences; used in biotechnology.

⑥ Initiator amino acid: fMet (formyl-methionine); a hallmark of bacteria; translation is faster than in Archaea and eukaryotes.

○ fMet is associated with faster translation.

⑶ Domain Archaea

① Types

○ Thermophilic archaea (hyperthermophiles): inhabit high-temperature volcanic hot springs and deep-sea hydrothermal vents.

○ Halophilic archaea (extreme halophiles): inhabit high-salinity environments such as the Dead Sea and salt pans; maintain high intracellular K⁺ to balance osmotic pressure.

○ Acidophilic archaea (extreme acidophiles): inhabit highly acidic environments.

○ Methanogens: inhabit oxygen-poor environments such as swamps and marshes.

② Features unique to Archaea: related to cell structures such as phospholipids, cell wall, and S-layer.

○ Ether linkages in phospholipids: an adaptation to extreme environments.

○ Archaeal phospholipids = phosphate head + ether linkage to fatty acid + fatty acid × 2 + ether linkage to fatty acid + phosphate head.

○ Bacterial and eukaryotic phospholipids = phosphate head + ester linkage to fatty acid + fatty acid × 2.

Figure 1. Differences between archaeal phospholipids and bacterial/eukaryotic phospholipids.

○ As a note, bacterial and eukaryotic phospholipids differ at the hydrophilic end (e.g., ethanolamine).

○ Phospholipid monolayer: organized by tetraethers.

○ Many fatty acids show isoprenes: branched hydrocarbons (polyisoprenoid alcohol).

○ Cell wall: pseudomurein with β 1→3 linkages.

○ Peptidoglycan: unbranched.

○ Pseudomurein: branched; β 1→3 linkages.

○ Peptidoglycan contains muramic acid, whereas pseudomurein contains N-acetyltalosaminuronic acid.

○ S-layer: analogous to LPS (Gram-negative bacteria) or teichoic acids (Gram-positive bacteria).

○ Some archaea even have unusual shapes such as rectangles.

③ Similarities between Archaea and Bacteria

○ Transcriptional regulation.

○ A single type of RNA polymerase (Archaea also recently corrected to one type).

○ No nuclear envelope; no membrane-bound organelles; unicellular.

○ Circular DNA; plasmids (can move via pili); operons; 70S ribosomes.

○ Restriction enzymes present.

○ Note that Eukaryotes have three RNA polymerases: RNA pol I, II, III.

○ Note that the eukaryote Caenorhabditis elegans possesses operons.

④ Similarities between Archaea and Eukaryotes: related to genome composition and regulation

○ Transcription mechanism.

○ Initiator amino acid is Met.

○ Histone proteins and introns present.

○ TATA box sequence present.

○ HU: a histone-like protein in prokaryotes.

○ Branched hydrocarbon chains in membrane lipids.

○ Not susceptible to penicillin, ampicillin, or lysozyme (these target peptidoglycan).

○ Not susceptible to streptomycin, chloramphenicol, or tetracycline (these specifically target bacterial ribosomes).

⑤ Note that even in eukaryotic cells, histone protein genes lack introns.

⑥ Archaea inhabit extreme environments (high temperature, high pressure, high salinity, etc.).

○ Because they are less competitive than aerobic bacteria, they colonize environments where ordinary life cannot survive.

○ Taq polymerase is derived from the archaeon Thermus aquaticus.

⑦ rRNA base sequences are more similar to those of the Eukarya than to those of Bacteria → Archaea are more closely related to Eukarya.

⑷ Density and Total Amount of Prokaryotes

Table. 1. Density and Total Amount of Prokaryotes

⑸ Domain Eukarya: Divided into 4 kingdoms

① RNA Polymerase: RNA pol Ⅰ, Ⅱ, Ⅲ

② Presence of nuclear envelope and membrane-bound organelles

3. Eukaryota Domain

⑴ Kingdom Monera: Eubacteria, Archaea

⑵ Kingdom Protista: Mostly unknown; estimated 8–80 phyla

① Animal-like protists: parasitic pathogens

○ Examples: malaria parasite, sleeping sickness parasite, Trichomonas vaginalis

② Fungus-like protists

○ Example: crop pest (potato late blight pathogen)

③ Plant-like protists: photosynthetic autotrophs that serve as a food source for other organisms

○ Examples: diatoms, green algae, brown algae

⑶ Kingdom Animalia: 25 phyla

① Multicellular, heterotrophic organisms with motility

② The Cambrian explosion (~530 million years ago) gave rise to modern animal groups.

③ Development of intercellular signaling systems and of organs and organ systems

④ Invertebrates (6–30 million species) comprise about 96% of Animalia.

⑤ Humans belong to phylum Chordata.

⑷ Kingdom Fungi

① Heterotrophs; absorb nutrients via hyphae; can spread across wide areas.

② DNA sequence analyses show fungi are more closely related to animals than to plants.

③ As decomposers, fungi compete with bacteria and produce antibiotics (about one-third of all antibiotics).

○ Example: penicillin

⑸ Kingdom Plantae

① Characteristics

○ Photoautotrophic: chlorophyll a, chlorophyll b, carotenoids

○ Multicellular eukaryotes with differentiated cells and tissues

○ Cell walls composed mainly of cellulose

○ Rosette-type cellulose synthase complexes: a trait shared only by charophyte green algae and land plants

○ No motility

○ Adapted to life on land.

○ Terrestrial dryness: a waxy cuticle develops on surfaces.

○ Differentiated and developed into roots, stems, and leaves

○ Vascular tissues such as xylem and phloem are developed (exception: bryophytes).

② Evolution

○ Present on land for more than 400 million years.

○ Earliest land plants: small and lacking vascular tissue

○ Evolution of vascular tissue enabled the rise of large trees and growth in arid regions.

○ Seeds: an adaptation to dry terrestrial environments

○ Evolution of flowers: most modern plants are flowering plants that appeared about 140 million years ago.

○ Adaptive radiation of flowering plants into ~150 families; over 90% of modern plants: evolution of double fertilization

○ Double fertilization: the pollen tube carries two sperm; one fertilizes the egg to form the embryo (2n), the other fuses with two polar nuclei to form the endosperm (3n).

○ No allocation of nutrients until the egg is fertilized.

○ Fertilization aided by animals, wind, and water.

③ Classification of Plant Kingdom

④ Uses

○ Chemical defense: secondary metabolites (by-products of primary metabolism) produce toxins → e.g., morphine from opium poppy, caffeine from coffee

○ Primary source of natural medicines; the second source is bacteria, the third is fungi.

4. Kingdom Protista

⑴ Characteristics

① Eukaryotic; possess a nuclear envelope and membrane-bound organelles.

② Unicellular or multicellular.

③ In multicellular forms, tissues/organs are not as fully differentiated as in other eukaryotic kingdoms.

⑵ Classification 1. Protozoa: heterotrophs, classified by type of locomotory organelle.

① Type 1. Flagellates (e.g., Trypanosoma): flagella

② Type 2. Ciliates (e.g., Paramecium): cilia

③ Type 3. Amoeboids (e.g., Amoeba): amoeboid movement (pseudopodia)

④ Type 4. Sporozoans (e.g., the malarial parasite Plasmodium): no locomotory organelles

⑶ Classification 2. Algae: photosynthetic; classified by photosynthetic pigments.

① Green algae: tissue level; chlorophylls a and b

○ Among algae, they are most closely related to land plants.

○ Pigments: chlorophyll a, chlorophyll b, carotenoids (e.g., xanthophylls, carotenes)

○ Similar cell-wall component: cellulose

○ Examples: Spirogyra; green laver (Ulva)

② Diatoms: unicellular level; chlorophylls a and c

③ Brown algae: tissue level; chlorophylls a and c

○ Contain iodine

○ Examples: wakame (Undaria), kelp (Laminaria/Saccharina)

④ Red algae: tissue level; chlorophylls a and d

○ Among algae, most closely related to cyanobacteria.

○ Both red algae and cyanobacteria possess phycobilisomes.

○ Examples: laver (Porphyra/Pyropia), agarophytes such as Gelidium

⑤ Euglena: unicellular level; chlorophylls a and b

○ Flagellum: locomotion

○ Eyespot: light reception

○ Contractile vacuole: osmoregulation

○ Chloroplasts: photosynthesis; capable of both autotrophy and heterotrophy, but tends to prefer heterotrophy.

⑷ Classification 3. Slime molds

① Heterotrophic, feeding on organic matter from dead organisms.

② Form spores.

③ Multinucleate stage

⑸ Summary of Protista

① Tissue level: red algae, green algae, brown algae

② Multinucleate stage: dinoflagellates, slime molds

③ Unicellular level: euglenoids, diatoms, sporozoans, ciliates, flagellates, amoeboids

④ Chlorophyll a + d: red algae

⑤ Chlorophyll a + b: green algae, euglenoids

⑥ Chlorophyll a + c: brown algae, dinoflagellates, diatoms

⑦ Spore formation: slime molds, sporozoans

⑧ No spore formation: ciliates, flagellates, amoeboids

5. Evolution of Animals

⑴ Overview

① Homology analysis: presence of shared traits.

② Analogy (convergent evolution) analysis: the coelom is a representative example.

⑵ 1^st. Colonial choanoflagellates are the oldest animal form.

⑶ 2^nd. From colonial choanoflagellates, Parazoa and Eumetazoa diverged.

① Parazoa: animals that have only a blastula stage.

○ Examples: sponges (e.g., bath sponge, “volcano” sponge).

② Eumetazoa: animals that have a gastrula stage.

○ Examples: all others except ①.

⑷ 3^rd. From Eumetazoa, diploblastic and triploblastic animals diverged.

① Sponges: no germ-layer differentiation.

② Diploblastic animals: the radially symmetrical groups.

○ Examples: cnidarians (= Coelenterata), ctenophores, placozoans.

○ Cnidaria (e.g., sea anemones, hydra, jellyfish): diffuse nerve net; digestion occurs in the coelenteron.

③ Triploblastic animals: the bilaterally symmetrical groups, i.e., everything except ① and ②.

⑸ 4^th. From triploblastic animals, protostomes and deuterostomes diverged.

① Protostomes: the blastopore at the gastrula stage becomes the mouth; i.e., everything except ②.

○ Additional feature: the solid mesoderm splits to form the coelom.

○ Examples: Platyhelminthes, Rotifera, Nematoda, Mollusca, Annelida, Arthropoda.

② Deuterostomes: the blastopore at the gastrula stage becomes the anus; radial cleavage.

○ Additional feature: the coelom forms from wrinkles of the archenteron.

○ Examples: Echinodermata, Chordata, Hemichordata.

⑹ Protostomes: during development the blastopore at the gastrula stage becomes the mouth.

① 5^th—1^st. Within protostomes, Ecdysozoa and Lophotrochozoa diverged.

② Lophotrochozoa: pass through a trochophore larval stage.

○ Trochophore larva (trochophora): a planktonic larval form.

○ Type 1. Platyhelminthes (e.g., planaria): first excretory system (flame cells); body flattened; bilateral symmetry.

○ Type 2. Rotifera (rotifers)

○ Type 3. Bryozoa (Ectoprocta), Brachiopoda, Phoronida: characterized by a lophophore (tentacle crown).

○ Type 4. Nemertea, Mollusca, Annelida: characterized by spiral cleavage.

○ Mollusca (e.g., snails, squid, clams): characterized by trochophore larva with a true coelom; segmentation reduced.

○ Annelida (e.g., earthworms, polychaetes): characterized by trochophore larva with a true coelom; segmentation developed.

○ Annelida: segmentation is characteristic.

③ Ecdysozoa

○ Type 1. Nematoda

○ Examples: Caenorhabditis elegans, Ascaris (roundworms).

○ Type 2. Arthropoda: segmentation and a chitinous exoskeleton.

○ Segment: a repeated structural unit with very similar appearance and organization.

○ Examples: insects, arachnids.

⑺ Deuterostomes: during development the blastopore at the gastrula stage becomes the anus.

① 5^th—2^nd. Chordates diverged.

② Echinodermata: larvae are bilaterally symmetrical; adults are radially symmetrical.

○ Examples: starfish, sea urchins, sea cucumbers.

③ Chordata

○ Autapomorphy 1. Notochord: a flexible rod situated parallel between the gut and the nerve cord.

○ In adult humans the notochord is reduced to part of the intervertebral discs.

○ Autapomorphy 2. Dorsal, hollow nerve cord → develops into the brain and spinal cord.

○ Autapomorphy 3. Pharyngeal slits.

○ Autapomorphy 4. Post-anal muscular tail.

④ Major chordate groups

○ Cephalochordata (e.g., lancelets/amphioxus): retain the notochord throughout life.

○ Urochordata (e.g., sea squirts): notochord present only in the larval stage.

○ Vertebrata: notochord replaced by a vertebral column; closed circulatory system; kidneys; dioecious (separate sexes).

Table 2. Classification of Vertebrates

⑻ 6^th. Evolution of the Coelom: the coelom is an analogous trait that arose multiple times by convergent evolution.

① Coelom: the space between the body wall and the viscera (e.g., the human thoracic and abdominal cavities).

② Acoelomates: no space between the gut and the body wall.

○ Examples: Porifera (sponges), Platyhelminthes (flatworms)

③ Pseudocoelomates: during development, possess a body cavity bounded by endoderm and mesoderm.

○ Examples: Rotifera, Nematoda

③ Eucoelomates (true coelomates): animals whose coelom is completely lined by mesodermal tissue; i.e., all others except ② and ③ above.

○ Examples: Mollusca, Annelida, Arthropoda, Echinodermata, Chordata

○ Trochophore with true coelomates: Mollusca, Annelida

Input: 2015.07.09 15:50

Modified: 2019.02.05 12:57