Biological Classification and Taxonomy

Taxonomy and Biological Classification Principles

Definition of Taxonomy: Taxonomy is the broader science involving the identification, naming, and classification of organisms based on shared characteristics. It encompasses the principles, rules, and procedures used for categorizing life.
Biological Classification: This is the systematic grouping of organisms into a structured hierarchy (e.g., kingdom, phylum, class) based on specific characteristics, including:
- Anatomy.
- Developmental patterns.
- Modes of nutrition.
- Levels of biological organization.
- Biochemical composition.
The Linnaean System: Introduced by the Swedish botanist Car Von Linne ( $1707\text{--}1778$ ), also known by his Latin name, Carolus Linnaeus.
- Linnaeus is regarded as the Father of Taxonomy.
- Hierarchical Order: He classified organisms into seven major divisions:
  1. Kingdom
  2. Phylum
  3. Class
  4. Order
  5. Family
  6. Genus
  7. Species
- Species Definition: Species represent organisms with highly similar features that are capable of interbreeding among themselves.
- Binomial Nomenclature: A system of giving organisms two Names (Genus and Species). An example is human beings, named $Homo\ sapiens$ .

Domains of Life

Introduction: Classification into domains was introduced by Carl Woese in $1990$ .
The Three Major Domains:
1. Archaebacteria: Comprised of prokaryotes.
2. Eubacteria: Comprised of prokaryotes.
3. Eukarya: Comprised of eukaryotes.

Cellular Organizations: Prokaryotes and Eukaryotes

Prokaryotic Organisms (Prokaryotes):
- Contain prokaryotic cells which lack a nucleus and membrane-bound organelles.
- DNA Location: Found in the central part of the cell known as the Nucleoid region.
- Unicellularity: All prokaryotic organisms are unicellular.
Eukaryotic Organisms (Eukaryotes):
- Contain eukaryotic cells with a definite nucleus.
- Possess membrane-bound organelles.
Organelle Classification by Membrane:
- Double Membraned: Nucleus, Mitochondria, and Chloroplast.
- Single Membraned: Vacuole, Lysosome, Golgi Apparatus, and Endoplasmic Reticulum.
- Non-Membraned: Ribosomes, Centrioles, Cytoskeleton, and Cell Wall.

The Five Kingdoms of Life

Biologists widely recognize five distinct kingdoms:
1. Monera
2. Protista
3. Fungi
4. Plantae
5. Animalia

Kingdom Monera

Overview: The simplest group of organisms, consisting of all unicellular prokaryotes. All bacteria belong to this kingdom.
Examples: Cyanobacteria (blue-green algae), Anabaena, and Oscillatoria.
Nutrition: Bacteria can be autotrophic (photosynthetic or chemosynthetic) or heterotrophic (parasitic or saprophytic).
Major Divisions:
- A. Schizophyta: Bacteria.
- B. Cyanophyta: Cyanobacteria.
General Characteristics of Bacteria:
1. Prokaryotic cell structure lacking a definite nucleus and membrane-bound organelles.
2. Cell Wall Structure: Made of Peptidoglycan (also known as Murein).
  - Comparison: Plant cell walls are Cellulose; Fungal cell walls are Cellulose or Chitin; Bacterial cell walls are Peptidoglycan.
3. Lack a nuclear envelope; DNA is a long strand suspended in the nucleoid.
4. Exclusively unicellular.
5. Can be aerobic or anaerobic.
6. Shapes: Spherical, rod-like, or spiral.
7. Motility: May be motile (possess flagella) or non-motile.
8. Reproduction: Primarily via binary fission.
9. Primarily saprophytes, though some are parasites.
Cyanophyta (Cyanobacteria/Blue-green Algae):
- Distinguished from other bacteria by the presence of chlorophyll, allowing for photosynthesis.
- Note: They contain chlorophyll but lack chloroplasts; chlorophyll is stored in thylakoids within the cytoplasm.
Gram Staining Technique Classification:
1. Gram Positive: Possess a thick peptidoglycan layer and lack an outer lipid membrane. They stain Violet or Purple (e.g., $Staphylococcus$ , $Bacillus$ , and $Lactobacillus$ ).
2. Gram Negative: Possess a thin peptidoglycan layer and an outer lipid membrane. The lipid layer provides resistance to antibodies. They retain a Pink colour after staining (e.g., $Salmonella$ , $Escherichia\ coli$ ).

Kingdom Protista

Characteristics: Single-celled eukaryotes with well-defined nuclei. They inhabit moist environments, water, and body fluids.
Movement: Utilize pseudopodia, flagella, or cilia.
Reproduction: Asexual or sexual (via spores).
Diversity: Classified into approximately $18$ phyla.
Major Phyla:
- A. Phylum Protophyta: Plant-like protists with chloroplasts and cellulose cell walls (e.g., $Chlamydomonas$ , $Chlorella$ , Diatoms).
- B. Phylum Protozoa: Animal-like protists lacking chloroplasts and cellulose cell walls (e.g., $Amoeba$ , $Paramecium$ ).
Classes of Protozoans (by Locomotion):
1. Rhizopoda: Use pseudopodia (e.g., $Amoeba$ ).
2. Ciliophora: Use cilia (e.g., $Paramecium$ ).
3. Mastigophora: Use flagellum (e.g., $Trichomonas$ ).
4. Sporozoa: No specialized organelles for movement; rely on gliding, twisting, and bending (e.g., $Plasmodium$ ).
Trophic Modes:
1. Autotrophic: Photosynthetic plant-like protists (e.g., Diatoms, Dinoflagellates).
2. Heterotrophic: Animal-like protists (e.g., Foraminiferans, Ciliates, Amoebae).
3. Saprotrophic: Fungal-like protists feeding on decaying organic matter (e.g., Slime moulds, Slime nets, Water molds).
4. Mixotrophic: Combine different modes.
Specific Organisms:
- Euglena viridis: Belonging to Euglenozoa ( $1800$ species). Size: $15\text{--}500\,\mu\text{m}$ . Displays both plant and animal characteristics.
  - Animal Traits: Flagellum, Gullet, Contractile vacuole (osmoregulation/excretion), Eyespot (light detection), Pellicle (flexibility/shape).
  - Plant Traits: Chloroplasts, Pyrenoids (starch storage), stores food as paramylum and starch granules.
- Paramecium caudatum: A ciliate with a slipper-like shape.
  - Pellicle: Protects cell contents and provides shape.
  - Nuclei: Meganucleus (normal function) and Micronucleus (reproduction).
  - Vacuoles: Food vacuole (digestion) and Contractile vacuole (osmoregulation/excretion).
  - Cilia: Movement and food gathering.
  - Trichocysts: Defensive structures against predators.

Kingdom Fungi

Basic Biology: Eukaryotic organisms, can be multicellular (mushrooms, moulds) or unicellular (yeast such as $Saccharomyces\ cerevisiae$ ).
Structure: Composed of thread-like filaments called hyphae.
- Hypha: A single filament or branch.
- Mycelium: A mass or bunch of hyphae constituting the vegetative body of the fungus.
- Septa: Internal cross-walls dividing hyphae into cells. Hyphae with septa are "septate"; those without are "coenocytic".
Cellular Details: Cells can be uninucleate, binucleate, or multinucleate. Most fungi are multinucleate; yeast is uninucleated.
Nutrition: Lack chlorophyll; primarily saprophytes (feeding on dead matter) or parasites.
Chemical Components:
- Cell Wall: Made of Chitin.
- Food Storage: Store food as Glycogen. They absorb carbohydrates as glucose but store them as starch.
Reproduction: Sexual and asexual via spore formation.
Examples: $Rhizopus$ , mushrooms, yeast, and $Penicillium$ (source of penicillin).
Fungal Anatomy:
- Substrate: The substance on which the fungus grows (e.g., bread).
- Sporangiophore: Vertical hyphae.
- Sporangium: Capsule structure where reproductive spores are produced and stored.
- Stolon: Horizontal hyphae connecting sporangiophores.
- Rhizoid: Root-like structures for anchoring and nutrient absorption.
Classification:
1. Phycomycetes (Conjugated Fungi): Divided into Zygomycetes (e.g., $Rhizopus\ stolonifera$ ) and Oomycetes (e.g., $Phytophthora$ , $Albugo$ ).
2. Ascomycetes (Sac Fungi): e.g., Yeasts, $Penicillium$ , $Aspergillus$ .
3. Basidiomycetes (Club Fungi): e.g., Mushrooms, shelf fungi, puffballs.
4. Deuteromycetes (Fungi Imperfecti): e.g., $Alternaria$ , $Colletotrichum$ , $Trichoderma$ . Produce conidia.
Note on Reproductive Bodies:
- Holocarpic: Entire body (thallus) converts into a reproductive structure.
- Eucarpic: Only a specific part of the thallus is used for reproduction.

Kingdom Plantae

Description: Eukaryotic multicellular organisms with cellulose cell walls and autotrophic nutrition.
Three Major Divisions:
1. Thallophyta.
2. Bryophyta.
3. Tracheophyta (Vascular plants), further split into Pteridophyta and Spermatophyta.
Key Terminologies:
- Cryptogam: Non-flowering plants (Thallophyta, Bryophyta, Pteridophyta).
- Phanerogams: Flowering plants (Spermatophytes).
- Vascular Plants: Possess xylem and phloem (Pteridophyta, Spermatophyta).
- Non-Vascular Plants: Lack or have poorly developed vascular bundles (Thallophyta, Bryophyta).
Alternation of Generation: The phenomenon where a plant exhibits two phases in its life cycle:
- Gametophyte: Multicellular haploid $(n)$ phase producing gametes via mitosis.
  - Antheridium: Male structure producing sperm.
  - Archegonium: Female structure producing eggs.
- Sporophyte: Multicellular diploid $(2n)$ phase producing spores via meiosis.
- Spore Types:
  - Homosporous: Spores are indistinguishable in size.
  - Heterosporous: Differing sizes. Megaspores produce megagametophytes (eggs); Microspores produce microgametophytes (sperms).

Plant Divisions Detail

Thallophyta (Algae):
- Plant-like organisms with a thallus (lack differentiated roots, stems, leaves, or vascular systems).
- Found in water or moist surfaces. Largest group of terrestrial plants.
- Categories:
  - Chlorophyta (Green Algae): e.g., $Spirogyra$ , $Ulothrix$ , $Volvox$ (unicellular colonial).
  - Phaeophyta (Brown Algae): e.g., $Fucus$ , $Sargassum$ , $Laminaria$ (Kelp).
  - Rhodophyta (Red Algae): e.g., $Polysiphonia$ , $Batrachospermum$ .
- Lifecycle: Gametophyte is the dominant stage; sporophyte is dependent. All spores are homosporous.
Bryophyta:
- Known as "plant amphibians" because they live on land but require water for sexual reproduction (fertilization).
- Non-vascular, seedless. Possess rhizoids instead of roots and leaf-like scales with chloroplasts.
- Lifecycle: Gametophyte is dominant; sporophyte depends on it.
- Classes: Musci (Mosses), Hepaticae (Liverworts), Anthocerotae (Hornworts).
Pteridophyta (Ferns):
- First land plants to evolve. Vascular cryptogams (no seeds, but sporous).
- Possess true roots, stems, and leaves (fronds/pinnae).
- Structure: Sporangia grouped in sori, sometimes protected by indusium. Gametophyte is a heart-shaped prothallus.
- Lifecycle: Sporophyte is dominant and independent of the gametophyte.
- Examples: $Selaginella$ , $Pteris$ , $Dryopteris$ , $Adiantum$ .
Spermatophyta (Seed Plants):
1. Gymnosperms: Produce naked seeds (not enclosed in ovary). Produce cones. Evergreen woody plants (e.g., Pines, Cycads, Ginkgo).
2. Angiosperms (Flowering Plants): Seeds enclosed in an ovary/fruit. Possess flowers and endosperm.
  - Monocotyledonous: One cotyledon, adventitious roots, parallel venation, trimerous flowers. Most advanced (e.g., Cereals, Banana).
  - Dicotyledonous: Two cotyledons, tap root system, reticulate venation, vascular bundles in a ring (e.g., Grapes, Sunflower, Tomatoes).

Kingdom Animalia

General Features: Multicellular heterotrophic eukaryotes lacking chlorophyll and cell walls.
Analytical Framework:
- Coelom: Acoelomate, pseudocoelomate, or coelomate.
- Body layers: Diploblastic (two) or Triploblastic (three).
- Symmetry: Asymmetrical, radial, or bilateral.
- Cephalization: Localization of sensory organs and nerves at the front.

Animal Phyla Survey

Porifera (Sponges):
- "Pore-bearing", simplest animals. Cellular level organization.
- Acoelomate, diploblastic, asymmetrical.
- Anatomy: Osculum (water exit), skeleton of Spongin or spicules ( $CaCO_3$ or silica).
- Classes: Calcarea (calcareous spicules), Hexactinellida (glass sponges), Demospongiae (spongin).
Coelenterata (Cnidarians):
- Acoelomate, diploblastic, radial symmetry. Carnivorous.
- Specialized Cells: Cnidocytes containing nematocysts (stinging structures).
- Body Forms: Polyp (sessile) and Medusa (motile).
- Classes: Hydrozoa ( $Hydra$ ), Scyphozoa (Jellyfish), Anthozoa (Sea anemones, corals).
Platyhelminthes (Flatworms):
- Dorsoventrally flattened, triploblastic, bilateral symmetry, acoelomate.
- First phylum to show cephalization.
- Classes: Turbellaria ( $Planaria$ ), Trematoda (Flukes like $Fasciola\ hepatica$ ), Cestoda (Tapeworms like $Taenia\ solium$ ).
Nematoda (Roundworms):
- Cylindrical body, triploblastic, bilateral, pseudocoelomate.
- Dioecious (separate sexes); males are smaller.
- Examples: $Ascaris\ lumbricoides$ , $Wuchereria\ bancrofti$ (causes elephantiasis).
Annelida (Segmented Worms):
- Metamerically segmented, coelomate, triploblastic.
- Excretion: Nephridia. Circulation: Contains hemoglobin (red color).
- Classes: Polychaeta ( $Nereis$ ), Oligochaeta (Earthworms), Hirudinea (Leeches).
Mollusca:
- Unsegmented body divided into head, visceral mass, muscular foot, and mantle.
- Possess a radula (rasping organ). Coelomates.
- Classes: Gastropoda (Snails), Pelecypoda (Clams), Cephalopoda (Squids).
Arthropoda:
- Largest phylum. Segmented bodies, jointed appendages, chitinous exoskeleton.
- Growth: Through ecdysis (molting).
- Excretion: Malpighian tubules (terrestrial) or green/coaxal glands (aquatic).
- Subgroups:
  - Crustacea: Cephalothorax, $5$ pairs of legs, $2$ pairs of antennae, green glands.
  - Insecta: Head/thorax/abdomen, $3$ pairs of legs, $1$ pair of antennae, wings usually present.
  - Arachnida: Cephalothorax/abdomen, $4$ pairs of legs, no antennae, book lungs/tracheae.
  - Myriapoda: Chilopoda (centipedes, $1$ pair leg/segment); Diplopoda (millipedes, $2$ pairs legs/segment).
Echinodermata:
- Exclusively marine, spiny-skinned, triploblastic coelomates.
- Symmetry: Bilateral as larvae, penta-radial as adults.
- Feature: Water vascular system with tube feet. Power of regeneration.
Chordata:
- Core Traits: Notochord, dorsal hollow nerve cord, pharyngeal slits, muscular post-anal tail.
- Subphyla: Urochordata (Tunicates), Cephalochordata (Lancelets), Vertebrata.

Subphylum Vertebrata

Definition: Chordates where the notochord is replaced by a vertebral column in adults.
Class Pisces (Fishes):
- Agnatha: Jawless fishes.
- Chondrichthyes: Cartilaginous (sharks, rays). Placoid scales (dermal denticles). Internal fertilization.
- Osteichthyes: Bony (tilapia). Cycloid/ctenoid scales. External fertilization.
- Traits: Two-chambered heart, poikilothermic, lateral line system for vibration detection.
Class Amphibia:
- Larvae aquatic (gills), adults terrestrial (lungs/skin/mouth). Poikilothermic.
- Three-chambered heart ( $2$ auricles, $1$ ventricle).
Class Reptilia:
- First fully terrestrial chordates. Dry skin with scales. Poikilothermic.
- Internal fertilization; oviparous; no aquatic larval stage.
Class Aves (Birds):
- Homoeothermic (warm-blooded). Four-chambered heart.
- Hollow bones with air sacs. Feathers. Oviparous with parental care.
Class Mammalia:
- Homoeothermic. Possess hair, mammary glands, sebaceous/sweat glands, and diaphragm.
- Heterodont dentition (incisors, canines, premolars, molars). Pinnae (external ears).
- Groups:
  1. Monotremes: Egg-laying (e.g., Platypus).
  2. Marsupials: Give birth to partially formed young; development in pouch (e.g., Kangaroo).
  3. Placental: Long internal development via placenta and umbilical cord (e.g., Humans).

Viruses

Nature: Infectious agents containing living and non-living characteristics.
Living Traits: Reproduction inside host, possess DNA or RNA, capable of mutation and response to stimuli.
Non-living Traits: Non-cellular (no cytoplasm/organelles), no independent metabolism, cannot produce own energy, can be crystallized.
Analogy: Described as being more like "androids" than real living organisms.