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Chapter 35. Biodiversity

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1. Biological Classification

2. Domain

3. Eukaryota Domain

4. Prokaryota Domain

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 Phylogenetic Classification Methods

Method 1: Structural similarity

○ Mainly used to classify extinct species; based on geological age.

○ Used for subdividing the history of extinct organisms, determining geological epochs.

Method 2: Modern phylogenetic classification

○ DNA sequences of closely related organisms are more similar in evolution.

○ Comparison using small subunit rRNA genes (ribosomal RNA), cytochrome c amino acid sequences, etc.

○ These encode important proteins, thus evolutionarily conserved.

③ Modern species are divided into domains and their subdomains based on structural similarity and phylogenetic history.

⑷ Biological Classification System

① Comprehensive Taxonomic Ranks : Implying recent shared ancestry within the same rank.

② Taxonomic Ranks : Domain – Kingdom – Phylum – Class – Order – Family – Genus – Species, total of 8 levels.

○ Domain : Bacteria domain, Archaea domain, Eukarya domain

○ Kingdom : Eukarya domain subdivided into Protista, Plantae, Fungi, Animalia

○ Current classification system : 3 domains, 6 kingdoms

③ History of Classification

○ Aristotle : Classified 540 animal species.

○ 2-kingdom classification : Divided into non-motile plants and motile animals.

○ 3-kingdom classification : Classified unicellular organisms as Protista.

○ 4-kingdom classification : Divided non-nucleated organisms into Prokaryota.

○ 5-kingdom classification : Separated non-photosynthetic bacteria from Plantae.

○ 3-domain, 6-kingdom classification : Archaea found to be more similar to Eukarya than Bacteria.

④ When finer classification is needed, terms like Domain, Division, Phylum, Class, Order, Family, Genus, and Subspecies are added between each rank.

○ Subspecies : Geographically or morphologically distinct group, no reproductive barriers.

○ Variety : Group with 2-3 differing traits or distributions due to natural mutations.

○ Cultivar : Cultivated group of a species with artificial selection.

⑸ Scientific Nomenclature

① Necessity : For the uniformity of academic research.

○ Latin remains unchanged over time and location.

② Binomial Nomenclature : Genus and species names combined in Latin.

○ Invented by Linnaeus in the 18th century.

○ Genus - Species - Namer

③ Trinomial Nomenclature

○ Used for subspecies, varieties, and cultivars.

○ Genus - Species - (Subspecies, Variety, Cultivar) - Namer

④ Writing scientific names

○ Genus : Capitalized, italicized

○ Species : Lowercase, italicized

○ Subspecies, Variety, Cultivar : Lowercase, italicized

○ Variety indicated by “var.”

○ Cultivar indicated by “for.”

○ Namer : Capitalized, regular font; can be omitted or only the first letter of the namer’s name can be used.

○ Example, Tiger : Felis tiger Linne

○ Example, 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

Archaea Domain

① Most archaea are harmless, but familiar ones are often pathogens.

② Many archaea decompose organic matter as decomposers.

③ Characteristics of Pure Archaea

○ Cell structure : Peptidoglycan (cell wall composition), LPS, Teichoic acid

④ RNA Polymerase : α2ββ’

⑤ Useful Compounds from Archaea

○ Antibiotics : Over 50% of antibiotics are derived from archaea.

○ Restriction enzymes : Proteins cutting DNA at specific sequences, used in biotechnology.

⑥ Initiator Amino Acid : fMet (formyl methionine), unique to archaea, faster translation than Eukarya

○ fMet leads to faster translation

Archaea Domain

① Types

○ Thermophilic Archaea : Inhabit high-temperature environments like hot springs, deep-sea hydrothermal vents.

○ Halophilic Archaea : Thrive in high salinity environments like salt pans, salt flats. Maintain high intracellular K+ concentration for osmotic balance.

○ Acidophilic Archaea : Live in highly acidic environments.

○ Methanogenic Archaea : Inhabit oxygen-depleted environments like swamps, marshes.

Archaea-Specific Characteristics : Related to cell structure, such as lipids, cell wall, S-layer.

○ Ether binding in archaeal lipids: for extreme environmental adaptation

○ Archaeal lipids of Crenarchaeota = Phosphate head + Ether linkage of fatty acids + Fatty acid × 2 + Ether linkage of fatty acids + Phosphate head

○ Lipids of Euryarchaeota and Thaumarchaeota = Phosphate head + Ester linkage of fatty acids + Fatty acid × 2


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Figure. 1. Difference between lipids of Crenarchaeota and lipids of Euryarchaeota and Thaumarchaeota


○ Note that the difference in lipids of Euryarchaeota and Thaumarchaeota lies in the hydrophilic end (e.g., ethanolamine).

○ Monolayer of lipids: Organized by tetraether

○ Isoprene frequently observed in fatty acids: Attached hydrocarbon (polyisoprenoid alcohol)

○ Cell wall : Pseudopeptidoglycan (similar to murein), β 1→3 linkage

○ Peptidoglycan: Absence of branches

○ Pseudopeptidoglycan: Presence of branches. Beta 1,3 linkage

○ Peptidoglycan has muramic acid, while N-Acetyltalosaminuronic acid is present in pseudopeptidoglycan.

○ S-layer (Surface layer): Similar to the LPS of Gram-negative bacteria or teichoic acid of Gram-positive bacteria in Euryarchaeota.

○ Archaea with unique shapes such as rectangles also exist.

Similarities between Archaea and Eukarya

○ Transcription regulation

○ RNA Polymerase only one type in Archaea, recently corrected

○ Lack of nuclear envelope, lack of membrane-bound organelles, unicellular

○ Circular DNA, plasmids (transferred by conjugation), operons, 70S ribosome

○ Presence of restriction enzymes

○ Eukaryotes have three types of RNA Polymerase: RNA pol Ⅰ, Ⅱ, Ⅲ

○ Eukaryotic organism Trypanosoma has operons

Similarities between Archaea and Eukarya : Pertaining to genome composition and regulation

○ Transcription mechanism

○ Initiation amino acid is Met

○ Histone proteins and introns present

○ TATA box sequence present

○ HU : Similar to eukaryotic histone proteins

○ Presence of branches in isoprene chains of membrane lipids

○ Resistant to penicillin, ampicillin, lysosome : These enzymes degrade peptidoglycan

○ Resistant to streptomycin, chloramphenicol, tetracycline : Only target prokaryotic ribosomes

⑤ Histone proteins are absent in eukaryotic cells too.

⑥ Archaea thrive in extreme conditions (high temperature, pressure, salinity).

○ Less competitive compared to mesophiles, so they inhabit environments where typical organisms cannot survive.

○ Taq polymerase is derived from the thermophilic archaeon Thermus aquaticus.

⑦ rRNA sequences are more similar between Archaea and Eukarya than between Archaea and Bacteria → Eukarya and Archaea have a closer relationship.

⑷ Density and Total Amount of Prokaryotes


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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. Eukarya Domain

⑴ Monera Kingdom : Archaea, Bacteria

⑵ Protista Kingdom : Mostly unknown, estimated 8-80 phyla

① Animal-like Protists : Parasites, pathogens

○ Examples : Malaria parasite, sleeping sickness parasite, vaginal trichomonad

② Algae-like Protists

○ Examples : Plant pests (potato blight pathogen)

③ Plant-like Protists : Photosynthetic autotrophic organisms, primary producers

○ Examples : Diatoms, green algae, brown algae

⑶ Animal Kingdom : 25 phyla

① Multicellular, heterotrophic, motile

② Emerged around 530 million years ago in the Cambrian Explosion

③ Development of intercellular communication, organ systems, and organizations

④ Invertebrates (6-30 million species) comprise around 96% of the animal kingdom

⑤ Humans belong to the Chordata phylum

⑷ Fungi Kingdom

① Dependent nutrition organisms, obtaining nutrition through mycorrhizae, capable of spreading over wide areas.

② DNA sequence analysis shows that algae are more closely related to animals than to plants.

③ Algae are decomposers, competing with bacteria and producing antibiotics (1/3 of antibiotics).

○ Example: Penicillin

⑸ Plant Kingdom

① Characteristics

○ Autotrophic nutrition: Chlorophyll a, b, carotenoids

○ Multicellular eukaryotes with differentiated cells and tissues

○ Main component of cell walls: Cellulose

○ Rosette-forming cellulose synthesis enzymes: Shared only with brown algae (Phaeophyceae) and land plants

○ Non-motile

○ Adapted to terrestrial life

○ Adapted to dry environments: Thick cuticle layer with high water repellency on the surface

○ Differentiation from roots, stems, and leaves

○ Development of water-conducting and vascular tissues (exception: bryophytes)

② Evolution

○ Exist on land for over 400 million years

○ First land plants: Small size, no vascular tissue

○ Evolution of vascular tissue allowed the emergence of large trees and growth in dry areas

○ Seeds: Adaptation to dry terrestrial environments

○ Evolution of flowers: Most modern plants evolved around 140 million years ago

○ Diversification of angiosperms led to 150 families, over 90% of modern plants: Duplicated modifications

○ Double fertilization: Two sperm cells, one fertilizes the egg to form a diploid embryo (2n), the other fuses with two polar nuclei to form a triploid endosperm (3n)

○ Lack of nutrient provisioning until egg is fertilized

○ Assisted by animals, wind, water for fertilization

Classification of Plant Kingdom

④ Uses

○ Chemical defense: Secondary metabolites produce toxins as byproducts of primary metabolic processes → Examples: morphine in poppies, caffeine in coffee

○ Primary source of natural medicine: Bacteria as secondary source, algae as tertiary source



4. Prokaryota Domain

⑴ Characteristics

① Eukaryotes; nuclear membrane and membrane-bound organelles present

② Unicellular or multicellular

③ In multicellular forms, organs not fully differentiated compared to other eukaryotes

Classification 1. Protozoa : Heterotrophic, classified based on types of locomotion

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

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

Type 3. Amoebas (e.g., Amoeba): Amoeboid movement

Type 4. Sporozoans (e.g., Plasmodium): Non-motile

Classification 2. Algae : Perform photosynthesis, classified based on photosynthetic pigments

① Chlorophyta (Green algae): Tissue-level organization, chlorophyll a, b

○ Closest relationship with terrestrial plants

○ Shared chlorophyll a, b, carotenoids (e.g., chlorophytes, carotenes)

○ Similar cell wall composition: Cellulose

○ Examples: Ulva, kelp

② Rhodophyta (Red algae): Unicellular stage, chlorophyll a, c

③ Phaeophyceae (Brown algae): Tissue-level organization, chlorophyll a, c

○ Contains iodine

○ Examples: Kelp, wakame

④ Rhodophyta (Red algae): Tissue-level organization, chlorophyll a, d

○ Closest relationship with cyanobacteria

○ Both possess phycobilins

○ Examples: Nori, dulse

⑤ Euglenids: Unicellular stage, chlorophyll a, b

○ Flagella: Mode of movement

○ Eyespot: Light reception

○ Contractile vacuole: Maintains osmotic pressure

○ Chloroplasts: Photosynthesis, can be both autotrophic and heterotrophic, but prefer heterotrophy

Classification 3. Protozoa

① Depend on organic matter from dead organisms for nutrition

② Form spores

③ Multinucleate stage

⑸ Summary of Protista Kingdom

① Tissue-level organization: Red algae, green algae, brown algae

② Multinucleate stage: Ciliates, sporozoans

③ Unicellular stage: Euglenids, dinoflagellates, diatoms, ciliates, flagellates, amoebas

④ Chlorophyll a + d: Red algae

⑤ Chlorophyll a + b: Green algae, euglenids

⑥ Chlorophyll a + c: Brown algae, ciliates, diatoms

⑦ Spore formation: Sporozoans, dinoflagellates

⑧ No spore formation: Ciliates, flagellates, amoebas



5. Evolution of Animals

⑴ Overview

① Homology analysis: Shared traits exist

② Convergence analysis (convergent evolution): Example is body shape

⑵ 1st. Choanoflagellates are the oldest animal form

⑶ 2nd. From choanoflagellates, branching to sponges and cnidarians

① Cnidarians: Animals with only a gastrovascular cavity

○ Examples: Bathypelagic animals (e.g., bathysal, volcanoan)

② Ctenophores: Animals with tentacles

○ Examples: Excluding ①

⑷ 3rd. From cnidarians, branching to bilaterians and triploblasts

① Cnidarians: No distinction between body layers

○ Example: Sponges

② Bilaterians: Bilateral symmetry animal group

○ Examples: Bilateria (= coelomate animals), Ecdysozoa, Lophotrochozoa

○ Bilateria (e.g., tapeworm, hydra): Nervous system, digestion in coelom

③ Triploblasts: Radial symmetry animal group, excluding ① and ②

⑸ 4th. From triploblasts, branching to protostomes and deuterostomes

① Protostomes: Embryonic blastopore becomes mouth, excluding ②

Additional feature: Tough mesodermal blocks form muscles between the gut and nerve cords

○ Examples: Platyhelminthes, Rotifera, Annelida, Mollusca, Arthropoda, Echinodermata

② Deuterostomes: Embryonic blastopore becomes anus, radial cleavage occurs

Additional feature: Hollow dorsal nerve cord → develops into brain or spinal cord

Additional feature: Gill slits

Additional feature: Muscular tail posterior to anus

⑹ Protostomes: Embryonic blastopore becomes mouth

① 5th - 1st. Branching to molting animals and lophotrochozoans

② Lophotrochozoans: Larvae pass through trochophore stage

○ Trochophore: Free-swimming larva

Type 1: Flatworms (e.g., planarians): First excretory system (flame cells), flat and bilaterally symmetrical body

Type 2: Rotifers (e.g., rotifers)

Type 3: Trochozoa, Bilateria, Brachiopoda: Presence of lophophore

Type 4: Annelida, Mollusca, Echiura: Presence of spiral cleavage

○ Annelida (e.g., snails, squids, clams): Presence of trochophore larva, segmentation reduction

○ Mollusca (e.g., snails, squids, clams): Presence of trochophore larva, development of foot

○ Echiura (e.g., spoonworms): Presence of trochophore larva, development of segmented body

○ Echiura: Presence of segmented body

③ Ecdysozoans

Type 1: Ecdysozoans

○ Examples: C. elegans, nematodes

Type 2: Arthropods

Defining trait 1: Ecdysis: Flexible, chitinous exoskeleton between digestive tract and body wall

○ Arthropods (e.g., insects, spiders): Ecdysis throughout life

Type 3: Lophophorates: Possess lophophore within mesodermally derived cells

Defining trait 1: Lophophore: Circular, ciliated or tentacled structure between digestive tract and body wall

○ Lophophorates (e.g., brachiopods, phoronids, bryozoans): Unique feeding structure

⑺ Deuterostomes: Embryonic blastopore becomes anus

① 5th - 2nd. Branching to chordates

② Echinoderms: Bilaterally symmetrical in larval stage, radial in adult

○ Examples: Jellyfish, sea urchins, sea cucumbers

③ Chordates

○ Defining trait 1: Notochord: A flexible rod located between the digestive tube and nerve cord

○ Defining trait 2: Hollow dorsal nerve cord: Develops into the brain and spinal cord

○ Defining trait 3: Pharyngeal slits: Develop into gills or other respiratory structures

○ Defining trait 4: Muscular, post-anal tail

④ Classification of Chordates

○ Urochordates (e.g., tunicates): Retain notochord only in larval stage

○ Cephalochordates (e.g., amphioxus): Retain notochord throughout life

○ Vertebrates: Notochord replaced by vertebral column, closed circulatory system, kidneys, cranium


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Table 2. Classification of Vertebrates


⑻ 6th. Evolution of Coelom: Coelom evolved independently through convergent evolution, shared trait

① Coelom: Cavity between animal body wall and inner organs (e.g., human thoracic and abdominal cavities)

② Acoelomates: No space between digestive tract and body wall

○ Examples: Bathypelagic animals, flatworms

③ Pseudocoelomates: Coelom enclosed by mesoderm and endoderm during development

○ Examples: Rotifers, Ctenophores

④ Eucoelomates: Coelom fully enclosed by mesoderm-derived tissues, excluding ② and ③

○ Examples: Annelida, Mollusca, Brachiopoda, Cnidaria, Echinodermata

○ Deuterostome eucoelom: Annelida, Echinodermata



Input: 2015.07.09 15:50

Modified: 2019.02.05 12:57

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