Unit 1: Biodiversity & Classification — Interactive Notes
In the five-kingdom system, this domain was included in kingdom Monera. The name Archaea comes from the Greek archaios ("ancient"). They are prokaryotes which diverged from bacteria in very ancient times.
★ Archaebacteria: Archaea were initially classified as a group of bacteria, and were called archaebacteria.
Size: Individual archaeans range from 0.1 μm to over 15 μm in diameter, some form aggregates or filaments up to 200 μm in length.
Morphology: They occur in various shapes, such as spherical, rod-shape, spiral, lobed, or rectangular.
Reproduction: Archaea reproduce asexually by binary or multiple fission, fragmentation, or budding. Mitosis and meiosis do not occur in archaea.
1. Cell Membrane — Archaean cell membrane contains lipids with ether-linkage between glycerol and fatty acid chains. The fatty acid chains are branched, making their membranes more resistant to extreme conditions. Bacteria and Eukarya have membrane lipids with fatty acids attached to glycerol by ester linkages, with unbranched fatty acid chains.
2. Cell Wall Composition — Archaea cell walls lack cellulose and peptidoglycan; instead they contain distinct polysaccharides and proteins (some archaea have pseudopeptidoglycan). Bacterial cell walls contain peptidoglycan, a polymer of sugars and amino acids. In Eukarya, cell walls (if present) are cellulose in plants or chitin in fungi.
3. Genetic Differences — Archaea share several genetic sequences and regulatory features with eukaryotes, highlighting their closer evolutionary relationship.
4. Metabolism — Archaea have unique metabolic processes like methanogenesis (production of methane), not found in bacteria or Eukarya. Bacteria exhibit photosynthesis, nitrogen fixation and fermentation. Eukarya metabolism is often more complex, including cellular respiration, photosynthesis, and fermentation.
Methanogens (produce methane), Halobacteria (extremely saline environments), Thermococci (hot environments), Thaumarchaeota (nitrogen cycle).
In the five-kingdom system, this domain was included in kingdom Monera. They are the true bacteria, with several distinct characteristics differentiating them from Archaea and Eukarya.
Proteobacteria (E. coli, Rhizobium, H. pylori), Firmicutes (Bacillus subtilis, Lactobacillus, Clostridium botulinum), Actinobacteria (Streptomyces, M. tuberculosis), Cyanobacteria (Anabaena, Spirulina), Spirochaetes (Treponema pallidum), Acidobacteria (Acidobacterium), Aquificae (Aquifex pyrophilus).
The domain Eukarya encompasses all organisms with eukaryotic cells, fundamentally different from the prokaryotic cells of Bacteria and Archaea.
Classification is organized into a hierarchical system of taxa (singular: taxon), from Domain down to Species:
1. Domain — highest level; three domains: Archaea, Bacteria, Eukarya.
2. Kingdom — groups life sharing fundamental characteristics e.g. Animalia, Plantae, Fungi, Protista within Eukarya.
3. Phylum — organisms share a basic body plan e.g. phylum Chordata (notochord).
4. Class — more specific common traits e.g. class Mammalia (hair, mammary glands).
5. Order — shared characteristics and evolutionary history e.g. order Primates (large brains, opposable thumbs).
6. Family — even more closely related e.g. family Hominidae.
7. Genus — very closely related, visually similar species e.g. genus Homo.
8. Species — most specific; single interbreeding type e.g. Homo sapiens.
| Rank | Human | Sparrow | Onion |
|---|---|---|---|
| Domain | Eukarya | Eukarya | Eukarya |
| Kingdom | Animalia | Animalia | Plantae |
| Phylum | Chordata | Chordata | Angiosperms |
| Class | Mammalia | Aves | Monocots |
| Order | Primates | Passeriformes | Asparagales |
| Family | Hominidae | Passeridae | Amaryllidaceae |
| Genus | Homo | Passer | Allium |
| Species | Homo sapiens | Passer domesticus | Allium cepa |
Eukarya consists of kingdoms Protista, Fungi, Plantae and Animalia — all with complex eukaryotic cells containing a nucleus and other membrane-bound organelles.
Eukaryotes which are unicellular, colonial, filamentous or simple multicellular (no specialized multicellular sex organs).
Major Groups: Protozoa (animal-like, unicellular, heterotrophic — Paramecium, Amoeba, Plasmodium, Trypanosoma); Algae (plant-like, cellulose walls, chlorophyll, autotrophs — Euglena, diatoms, dinoflagellates, red/green/brown algae); Fungi-like protists (Myxomycota — slime molds, Oomycota — water molds, saprophytic, hyphae-like structure).
Eukaryotic, heterotrophic, uni/multicellular; cell wall of chitin; absorb food rather than ingest.
Major Groups: Zygomycota (aseptate hyphae e.g. Rhizopus), Ascomycota (largest group — molds, morels, truffles, yeasts), Basidiomycota (septate hyphae — mushrooms, toadstools, puffballs, rusts, smuts). ~100,000 known species; most Ascomycetes found in lichens, some in mycorrhizae.
Eukaryotic, multicellular, cellulose cell walls, autotrophic (photosynthesis), develop from embryos.
Major Groups: Non-vascular (bryophytes — liverworts, hornworts, mosses); Vascular (tracheophytes) — seedless (ferns) and seed plants: Gymnosperms (naked seeds e.g. Pine, Spruce) and Angiosperms (flowering, most diverse — 235,000 species; Monocots e.g. grass, corn and Dicots e.g. rose, sunflower).
Eukaryotic, multicellular, heterotrophic; develop from embryos; ingest food and digest it within their bodies e.g. mammals, birds, reptiles.
| Feature | Bacteria | Archaea | Protista | Fungi | Plantae | Animalia |
|---|---|---|---|---|---|---|
| Cell type | Prokaryotic | Prokaryotic | Eukaryotic | Eukaryotic | Eukaryotic | Eukaryotic |
| Nuclear envelope | Absent | Absent | Present | Present | Present | Present |
| Cell wall | In all | In all | In some | In all | In all | Absent |
| Wall composition | Peptidoglycan | Various chemicals | Polysaccharides & proteins | Chitin | Cellulose | No cell wall |
| Nutrition | Auto/heterotroph | Auto/heterotroph | Photo/heterotroph or combo | Absorptive heterotroph | Photosynthetic autotroph | Ingestive heterotroph |
| Multicellularity | Absent | Absent | Absent in most forms | Present in most forms | Present in all forms | Present in all forms |
Animals (metazoa) are subclassified into: Parazoa (phylum Porifera — lack tissues organized into organs, indeterminate/asymmetrical shape) and Eumetazoa (tissues organized into organs/organ systems — includes radially symmetrical Grade Radiata (phylum Cnidaria) and bilaterally symmetrical Grade Bilateria).
Diploblastic animals: body of two cell layers (ectoderm, endoderm); lesser specialization, sac-like digestive system, no CNS. Triploblastic animals: body of three layers (ectoderm, mesoderm, endoderm); greater specialization, specialized organ systems, blood vascular system present in most.
Triploblastic animals may be acoelomate, pseudocoelomate or coelomate:
Coelomates are further divided into: Protostomes (blastopore becomes mouth; coelom via schizocoely — Aschelminthes, Annelida, Mollusca, Arthropoda) and Deuterostomes (mouth forms away from blastopore, which becomes anus; coelom via enterocoely — Echinodermata, Hemichordata, Chordata).
Phylum Porifera (literal meaning: pore bearing) contains sponges.
1. Habitat: Mostly marine (Leucosolenia, Euplectella - Venus flower basket); Spongilla is a common freshwater sponge.
2. Level of Organization: No tissue-level organization; mostly asymmetrical, some radially symmetrical.
3. Nervous System: Absent.
4. Water Flow System: Numerous pores (ostia) let water in; a larger osculum lets water out.
5. Body Structure: Outer pinacoderm (pinacocytes); middle jelly-like mesohyle (amoeboid cells); inner choanoderm (choanocytes/collar cells) lining the spongocoel. Skeleton of calcium carbonate or silica needles (spicules).
6. Reproduction: Mostly asexual (budding, regeneration); some form gemmules (resistant capsules) — released on parent's death, amoeboid cells emerge to form a new sponge in favourable conditions.
1. Habitat: Almost all marine (few freshwater e.g. hydra, jellyfish); most colonial (obelia, corals) and sessile (hydra, coral); some motile (jellyfish).
2. Symmetry: Radially symmetrical, diploblastic.
3. Body Structure: Epidermis (ectoderm) + gastrodermis (endoderm), with jelly-like mesoglea between containing amoeboid cells.
4. Defense System: Cnidocytes contain nematocysts for defense and prey capture.
5. Digestive System: Sac-type — single opening (mouth = anus), gastrovascular cavity, mouth surrounded by tentacles.
6. Nervous System: Nerve net; no CNS, respiratory, excretory or transport systems.
7. Body Forms: Polyps (cylindrical, attached at aboral end, asexual) and Medusae (umbrella-like, free-swimming, sexual).
"Flatworms" — unsegmented, soft, dorsoventrally compressed.
1. Habitat: Free-living (planaria) or endoparasitic (liver fluke, tapeworm, blood-fluke).
2. Body Organization: Triploblastic. Tapeworms are segmented.
3. Body Cavity: Acoelomate — parenchyma fills space between body wall and organs.
4. Symmetry: Bilateral.
5. Excretory System: Protonephridia with flame cells; waste exits via nephridiopore.
6–7. Respiratory/Circulatory/Nervous: No respiratory/circulatory systems; nerve net with cerebral ganglia and longitudinal cords.
8. Eyespots: Most free-living flatworms have two simple eyespots anteriorly.
9. Reproduction: Asexual fission; sexual reproducers are hermaphrodites.
"Thread-like" roundworms. ★ Aschelminthes — pseudocoelomates classified in seven phyla, of which Nematoda is representative.
1. Habitat: Free-living (Caenorhabditis elegans) or parasitic (ascaris, hookworm, pinworm, whipworm).
2. Body Organization: Triploblastic, bilateral, unsegmented; pseudocoelomate (false cavity filled with fluid).
3. Digestive System: Tube-like, mouth (anterior) and anus (posterior).
4. Excretory System: Protonephridia + two excretory canals uniting anteriorly into a single canal opening via nephridiopore (ventral).
5. Nervous System: Nerve ring around pharynx attached to four longitudinal nerve cords.
6. Sense Organ: Sensory papillae (hair-like) on lips.
7–8. Respiratory/Circulatory/Reproduction: No defined respiratory/circulatory systems; unisexual (separate testes/ovaries).
"Soft bodied" molluscs, un-segmented.
1. Habitat: Widely distributed; aquatic (mussels, octopus, oyster) or moist places (land snail).
2. Body Organization: Triploblastic, bilateral, true coelom; protostomes.
3. Body Structure: Head, visceral mass (digestion/excretion/reproduction organs), foot.
4. Mantle Cavity: Epithelial envelope (mantle) around visceral mass; secretes calcareous shell in most.
5. Radula: Rasping tongue-like organ (absent in bivalves).
6. Circulatory: Open type (except cephalopods) — single ventricle, two auricles.
7–8. Digestive/Excretory: Tube-like gut (mouth+anus); paired nephridia discharge into mantle cavity.
9. Respiratory: Gills.
10. Nervous: Three pairs of ganglia (head, visceral mass, foot).
11–12. Locomotion/Classes: Muscular foot; Class Gastropoda (slug, garden snail), Class Bivalvia (mussel, oyster), Class Cephalopoda (octopus, cuttlefish).
"Little rings" — segmented worms.
1. Habitat: Marine (nereis), freshwater (leech), damp soil (earthworm); some ectoparasitic (leeches).
2. Body organization: Bilateral, triploblastic, protostome coelomates.
3. Metameric Segmentation: Body divided into similar segments separated by septa, each with its own circulatory, excretory, neural elements.
4. Setae: Chitinous bristles for anchoring during movement (absent in leeches).
5. Digestive System: Tube-like, divided into distinct parts (simplified in parasitic forms).
6. Excretory System: Ciliated, funnel-shaped metanephridia, one pair per segment.
7. Circulatory System: Closed type; pulsating blood vessels (pseudohearts); haemoglobin dissolved in plasma.
8. Respiratory: Through skin.
9. Nervous System: Cerebral ganglion (brain), double ventral nerve cord, ganglia per segment.
10. Receptors: Tactile, chemoreceptors, balance, photoreceptors; some have well-developed eyes.
11. Reproduction: Mostly hermaphrodite (earthworm, leech); some unisexual (nereis).
"Jointed legs" — insects, crustaceans, spiders, scorpions, centipedes; found in every habitat.
1–2. Habitat/Symmetry: Triploblastic, bilateral, protostome coelomates; coelom reduced to reproductive/excretory systems.
3. Jointed Appendages: Modified for running, swimming, capturing prey, respiration, reproduction, mouthparts.
4. Body Structure: Segmented; fused into tagmata — head, thorax, abdomen.
5. Exoskeleton & Ecdysis: Chitin exoskeleton, shed periodically (ecdysis/molting, driven by hormone ecdysone) to allow growth.
6. Circulatory: Open type; blood (haemolymph) in hemocoel, colourless (no haemoglobin).
7. Respiratory: Tracheal tubes opening via spiracles; aquatic forms use gills.
8. Digestive: Tube-like, with mouth, esophagus, crop, gizzard, mesenteron, ileum, colon, rectum, anus.
9. Excretory: Malpighian tubules; excrete solid uric acid crystals.
10. Nervous: Well-developed CNS, three fused cerebral ganglia, double ventral nerve cord; compound eyes, antennae.
11. Reproductive: Unisexual, egg-laying.
12. Classes: Crustacea (crayfish, crab), Insecta (fly, butterfly), Arachnida (spider, mite, scorpion), Myriapoda (centipede, millipede).
"Spiny skinned" — exclusively marine (cake urchin, sea star, sea urchin, brittle star, sea cucumber).
1–2. Organization: Triploblastic, deuterostome coelomates; larvae bilateral, adults radially symmetrical (5 or multiples of 5 around oral-aboral axis).
3. Skeleton: Calcareous endoskeleton (ossicles) from mesoderm; forms spines.
4–5. Water-Vascular System & Tube Feet: Ring canal around mouth ↔ madreporite; radial canals → lateral canals → tube feet (locomotion via water pressure).
6. Digestive: Tube-like — mouth, oesophagus, stomach, intestine, rectum, anus.
7. Respiratory/Excretory: No specialized organs.
8. Nervous: Poorly developed — nerve net, nerve ring, radial nerves.
9. Reproduction: Asexual (body division + regeneration) and unisexual. ★ Many echinoderms (especially sea stars, brittle stars) can drop and regenerate body parts.
Chordates are bilateral, triploblastic, deuterostome coelomates, with four unique characteristics present at some developmental stage:
1. Notochord — rod-like semi-rigid body of vacuolated cells; extends between gut and dorsal nerve cord; retained throughout life in lower chordates, replaced by vertebral column in vertebrates.
2. Pharyngeal slits — series of openings in pharynx wall; develop into gills (Amphioxus, fishes), functional temporarily (amphibians), or modified (reptiles/birds/mammals — e.g. Eustachian tube).
3. Tubular nerve cord — dorsal to notochord, expands anteriorly as brain.
4. Post-anal tail — posterior to anus; retained in some, degenerates in others during development.
Phylum Chordata includes: Invertebrate Chordates — Subphylum Urochordata (notochord/nerve cord only in free-swimming larvae e.g. sea squirts) and Subphylum Cephalochordata (notochord persists throughout life e.g. Amphioxus); and Vertebrates — possess vertebral column and cranium, divided into seven classes in two groups (Pisces & Tetrapoda).
| Group | Class | Key Characteristics | Examples |
|---|---|---|---|
| Agnathans (jawless) | Myxini | 4 pairs tentacles; 5–15 pairs pharyngeal slits | Hagfish |
| Cephalaspidomorphi | Sucking mouth, 7 pairs pharyngeal slits | Lamprey | |
| Gnathostomes (jawed) | Chondrichthyes | Cartilaginous skeleton, no swim bladder/lungs | Sharks, skates, ratfish |
| Osteichthyes | Bony skeleton, pneumatic sac (swim bladder/lungs) | Lungfish, Coelacanths |
First class of tetrapods.
i. Monotremes — egg-laying (oviparous) e.g. Duckbill platypus, echidna (spiny anteater).
ii. Marsupials — pouch (marsupium); immature young complete development in pouch e.g. opossum, kangaroo, Tasmanian wolf.
iii. Placental mammals — most advanced; placenta nourishes foetus & removes waste; viviparous e.g. dolphin, rat, monkey, bat, elephant, human.
Acellularity: Viruses are acellular (not made of cells); lack characteristics of the three domains; not classified in any domain/kingdom.
Structure: Nucleic acid (DNA or RNA) surrounded by a protein coat.
Reproduction: No independent metabolism; depend on host cell (plants, animals, bacteria) to replicate and synthesize proteins.
Classification: Based on genetic material, replication strategy, morphology, and hosts infected — per International Committee on Taxonomy of Viruses (ICTV) guidelines.
Animal viruses (Influenza, Rabies), Plant viruses (Tobacco mosaic virus, Potato virus X), Bacteriophages (T4 phage, Lambda phage), Archaea viruses (Sulfolobus spindle-shaped virus).
Helical (Tobacco mosaic virus, Rabies virus); Icosahedral (Adenoviruses, Herpesviruses); Complex (Bacteriophages); Enveloped (Influenza virus, HIV); Non-enveloped/Naked (Poliovirus, Adenovirus).
DNA viruses — dsDNA (Adenoviruses, Herpes viruses), ssDNA (Parvoviruses); RNA viruses — ssRNA (Coronaviruses, Influenza), dsRNA (Rotaviruses).
Positive-sense RNA viruses (Poliovirus, Hepatitis C virus); Negative-sense RNA viruses (Rabies virus, Ebola virus); Reverse transcribing viruses — RNA genome e.g. HIV (AIDS), DNA genome e.g. Hepatitis B virus.
Ecosystem: A dynamic, interactive system of living organisms and their physical environment — includes biotic and abiotic factors.
i. Biotic Components: All living organisms supported by the biosphere (extends ~8–10 km into atmosphere and ocean depths).
ii. Abiotic Components: Atmosphere (air), hydrosphere (water), lithosphere (earth/soil).
Niche: The role or function of a species within an ecosystem — its habitat, interactions (predation, competition, symbiosis), and role in energy flow. Includes physical factors necessary for survival (temperature range, humidity, pH).
Biodiversity refers to the variety of life forms present in different ecosystems — species, genes, and ecosystems.
i. Species Level: Identifying/counting species — number, abundance, distribution; helps identify threatened/endangered species for conservation.
ii. Genetic Level: Variety of genetic information within a species; crucial for adaptability and survival; helps conserve species with low genetic variety (higher extinction risk).
iii. Ecosystem Level: Range of habitats (forests, wetlands, grasslands, deserts); helps protect and restore degraded ecosystems.
Sampling investigates abundance/distribution of species in a given time and area — random or systematic. In random sampling, location is selected by chance.
Importance: 1. Minimizes bias 2. Provides reliable estimates 3. Facilitates comparisons 4. Enhances representativeness 5. Supports conservation efforts.
1. Quadrat Sampling — dividing area into a grid, sampling randomly selected squares; useful for plant populations/sessile organisms.
2. Transect Sampling — line/strip across study area, recording species at intervals; effective for studying distribution across environmental gradients (e.g. coastal high-to-low tide line).
3. Aerial Surveys — aircraft/drones observe organism distribution over large areas.
Point counts, Mark-recapture, Quadrat counts, Capture-recapture methods, Remote sensing (satellite/drone imagery).
Species: A group of individuals that can interbreed and produce fertile offspring under natural conditions, sharing common characteristics and genetic makeup that distinguish them from other species. Identification by physical traits alone can be problematic due to cryptic species (similar-looking but genetically distinct).
German-American biologist Ernst Mayr emphasized reproductive isolation as the key criterion — species are groups of interbreeding natural populations; members of different species do not typically mate or produce viable, fertile offspring.
Speciation: The evolutionary process by which new species arise from a common ancestor, through accumulation of genetic changes leading to reproductive isolation.
1. Allopatric Speciation — geographic separation into isolated groups; different environments → independent evolution → reproductive isolation even if barrier removed. Example: Darwin's finches, Galápagos Islands.
2. Peripatric Speciation — small isolated population at edge of larger population; rapid evolutionary change → divergence. Example: island species from a small founding population.
3. Parapatric Speciation — adjacent populations, different environments along a gradient; limited gene flow → reproductive isolation. Example: grass species Anthoxanthum odoratum, adapted to varying soil conditions across a gradient.
4. Sympatric Speciation — new species arise within same geographic area, no physical barriers; via polyploidy or niche differentiation. Example: certain plants undergoing polyploidy → immediate reproductive isolation.
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Click a domain, then a kingdom (for Eukarya), to explore its characteristics — built from the classification hierarchy in this chapter.