Topics to be Learn :

  • Systematics
  • Taxonomy
  • Classification
  • Three Domains of Life
  • Cladogram
  • Phylogeny
  • DNA Barcoding
  • Taxonomic Categories
  • Taxonomic Hierarchy
  • Units of Classification
  • Nomenclature
  • Salient Features of Five Kingdoms
  • Acellular Organisms
Systematics and Taxonomy: Key Concepts and Definitions

Systematics:

  • Definition (by G. Simpson, 1961): Study of kinds and diversity of organisms and their comparative and evolutionary relationships.
  • Focus: Considers evolutionary relationships between organisms.
  • Origin: Derived from the Latin word Systema, meaning systematic arrangement.

Taxonomy:

Definition: Classification following certain rules or principles.
Branch of biology dealing with:
  • Nomenclature: Naming of organisms.
  • Collection: Gathering specimens.
  • Identification: Determining the identity of organisms.
  • Description: Detailed account of organisms.
  • Classification: Organizing organisms into categories.
Term Introduction: By A. P. de Candolle (Swiss Botanist) [1778-1841].

Uses of Taxonomy

  • Systematic Framework: Assigns each organism an appropriate place in classification.
  • Grouping: Organizes animals and plants based on characteristics and relationships.
  • Classification: Based on similarities and differences among organisms.
  • Nomenclature: Essential for identification and avoiding confusion in the scientific community.
  • Identification Tool: Helps identify new or unknown organisms by comparison with known species.

Classification: Overview and Types
  • Definition: Arrangement of organisms or groups of organisms into distinct categories based on a particular, well-established plan.
  • Basis: Similarities and differences among organisms.

Types of Classification Systems

1. Artificial System:

  • Basis: Observable, non-evolutionary characters (e.g., habit, color, form).
  • Characteristics: Does not consider relationships among organisms.
  • Example: Linnaeus system of classification.

2. Natural System:

  • Basis: Objectively significant characters, considering affinities with other organisms.
  • Example: Bentham and Hooker's system of classification.

3. Phylogenetic System:

  • Basis: Phylogenetic relationships, common evolutionary descent.
  • Example: Engler and Prantl’s classification.

Visible Characters in Classification

  • Habit: General growth pattern or structure of the organism.
  • Color: Pigmentation and appearance.
  • Form: Physical shape and structure.
  • Mode of Respiration: How organisms take in oxygen and release carbon dioxide.
  • Growth: Development and life cycle patterns.
  • Reproduction: Methods and processes of producing offspring.

Evolution

  • Definition: Adaptation of an organism to its environment.
  • Life originated on Earth in a simple form.
  • Early organisms evolved through constant struggle, leading to more complex life forms.
  • Evolution results in diverse species through natural selection.
  • Involves changes in flora and fauna over generations.
  • The process is slow and occurs over long periods.

Three Domains of Life

  • Proposed by: Carl Woese in 1990.
  • Domains:
    1.Archaea: Prokaryotic cells; unique cell wall structure.
    2. Bacteria: Prokaryotic cells; distinct from Archaea in cell wall composition.
    3. Eukarya: Eukaryotic cells; includes all organisms with complex cell structures.
  • Note: A domain is a classification unit larger than a kingdom.

Chemotaxonomy

  • Definition: Biological classification based on chemical compound similarities and differences among organisms.
  • Chemical Constituents: Classification based on the presence of specific chemicals (e.g., cell wall components).
  • Examples:
  • Bacteria have cell walls with peptidoglycan.
  • Archaea lack peptidoglycan.
  • Fungi have chitinous cell walls, while plants have cellulosic cell walls.

Numerical Taxonomy

  • Definition: Classification based on the quantification of characters and the use of algorithms.
  • Groups organisms based on overall similarities or dissimilarities.
  • Developed using numeric algorithms like cluster analysis.
  • Proposed by: Sokel and Sneath in 1963.

Cladogram and Phylogeny

Cladogram

  • Definition: A diagram that represents hypothetical relationships among organisms and their common ancestors.
  • Depicts evolutionary relationships.
  • Has a branching pattern showing divergence from common ancestors.

Diagrammatic Representation of Three Domains of Life (Cladogram)

  • Archaea: Branches from a common ancestor distinct from Bacteria and Eukarya.
  • Bacteria: Shares a common ancestor with Archaea but on a separate branch.
  • Eukarya: Branches from a different common ancestor, representing organisms with eukaryotic cells.

Phylogeny

  • Definition: The study of the evolutionary relationships among organisms.
  • Importance:
  • Considers both morphological and genetic relationships.
  • Helps classify organisms based on their evolutionary history and metabolic functions.
  • Examples:
  • Woese’s Three Domain Concept: Classifies life into Archaea, Bacteria, and Eukarya based on genetic differences.
  • Whittaker’s Five Kingdom System: Divides life into five kingdoms based on cell structure, mode of nutrition, and other factors.

DNA Barcoding: Overview, Process, and Applications

DNA Barcoding

  • Definition: A method for identifying species based on a specific DNA sequence obtained from a small tissue sample.
  • Purpose: Identification and study of species using genetic information.

Use of DNA Barcoding

  • Study Newly Identified Species: Helps in the identification and classification of new species.
  • Understanding Relationships: Analyzes ecological and evolutionary relationships between organisms.

Process of DNA Barcoding

  1. Collecting DNA Barcode Data: Gather DNA sequences from known species to create a reference library.
  2. Matching Barcode Sequence: Compare the DNA sequence of an unknown sample with the reference library for identification.

Applications of DNA Barcoding

  • Protection of Endangered Species: Helps in conservation efforts by identifying species at risk.
  • Preservation of Natural Resources: Assists in maintaining biodiversity and natural habitats.
  • Pest Control in Agriculture: Identifies pest species to implement control measures.
  • Identification of Disease Vectors: Determines organisms responsible for spreading diseases.
  • Authentication of Natural Health Products: Verifies the ingredients in natural products.
  • Identification of Medicinal Plants: Confirms the identity of plants used in traditional medicine.

Additional Information

  • Genebank: A public database where DNA barcodes are recorded and compared.
  • Case Study: Demonstrated that a common butterfly from Central America was actually a group of closely related species with similar morphology, revealing hidden biodiversity.

Recent Approaches in Taxonomy

1. Morphological Approach:

  • Definition: Identification based on observable physical features.
  • Observation: Conducted with the naked eye or a microscope.

2. Embryological Approach:

  • Definition: Uses embryonic stages for identification.
  • Application: Useful when morphological features are unreliable.

3. Ecological Approach:

  • Definition: Based on the habits and ecological niches of organisms.

4. Behavioral Approach / Ethological Approach:

  • Definition: Identification based on behavioral traits.
  • Traits: Genetically determined characteristics like sound production and bioluminescence.
  • Use: Helpful for identifying closely related species.

5. Genetical Approach / Cytological Approach:

  • Definition: Identification at the cellular level, including structural, genetic, and biochemical aspects.
  • Techniques: Includes DNA hybridization and karyological studies.

6. Biochemical Approach:

  • Definition: Identification based on biochemical composition.
  • Techniques: Includes chromatography, electrophoresis, and immunology.

7. Numerical Taxonomy:

  • Definition: Data is numerically evaluated to compare organisms.
  • Process: Organisms are grouped based on overall similarities or differences.

Taxonomic Categories

  • Definition: Ranks or levels in the hierarchical classification of organisms. Each rank is a unit of classification, and together they form the taxonomic hierarchy.

Compulsory Categories:

  1. Kingdom
  2. Division (for plants) / Phylum (for animals)
  3. Class
  4. Order
  5. Family
  6. Genus
  7. Species

Facultative Taxonomic Categories:

  • Examples: Sub-order, Sub-family, etc.
  • Use: Applied when additional specificity is needed.

Classification of China-rose and Cobra

Organisms with Their Taxonomic Categories

 

Nomenclature: The art of giving names to organisms.

Vernacular Names: Local names given to organisms in a particular region and language.

Disadvantages:
  • Lack of Information: Do not provide necessary details about the organism.
  • No Relationship Indication: Do not indicate the organism's relationships with others.
  • Non-Universal: Different regions may have multiple names for the same organism. For example, Viola tricolor L. (Pansy) has about 50 common names.
  • Limited Usage: Names can be confusing and vary locally. For example, Mangifera indica L. (mango) has over 50 names in Sanskrit.

Binomial System of Nomenclature

  • Definition: A system where the scientific name of an organism consists of two parts or epithets.
  • Developed By: Carl Linnaeus in his book Species Plantarum.

Rules of Binomial Nomenclature

1. Two Words: The scientific name consists of two Latin or Greek words.
2. Generic Name: Position: Comes first, Capitalization: Begins with a capital letter, Type: A simple noun.
3. Specific Name: Position: Comes second, Capitalization: Begins with a small letter, Type: A descriptive adjective. 
4. Formatting: Handwritten: Underline both names separately, Printed: Italicize both names. 
5. Length: Each name should have no fewer than three letters and no more than thirteen letters.
6. Author's Name: The name of the author who named the organism may be included, either in full or abbreviated form (e.g., Mangifera indica L., where L stands for Linnaeus).

Importance of Binomial Nomenclature

  • Simplicity: Names are simple, meaningful, and precise.
  • Standardization: Names are consistent worldwide, avoiding confusion.
  • Universal Use: Organisms are known by the same name globally.
  • Ease of Understanding: Binomials are easier to remember and understand.
  • Indicates Phylogeny: Reflects the evolutionary history of organisms.
  • Shows Inter-relationships: Helps understand the relationships between different organisms.

Five Kingdom System

Background

  • Two Kingdom System:
  • Introduced by Carl Linnaeus.
  • Divided organisms into two kingdoms: Kingdom Plantae and Kingdom Animalia.
  • Drawbacks:
  • Inadequate for classifying certain organisms (e.g., bacteria, fungi, Euglena).
  • Did not distinguish between unicellular vs. multicellular organisms, eukaryotes vs. prokaryotes, or photosynthetic vs. non-photosynthetic organisms.
  • Five Kingdom System:
  • Proposed by R.H. Whittaker.
  • Shows phylogenetic relationships among organisms.

The Five Kingdoms

  1. Kingdom Monera
  2. Kingdom Protista
  3. Kingdom Plantae
  4. Kingdom Fungi
  5. Kingdom Animalia

Criteria Used by Whittaker

  1. Cell Organization: Prokaryotic or eukaryotic.
  2. Body Organization: Unicellular or multicellular.
  3. Mode of Nutrition: Autotrophic or heterotrophic.
  4. Life Style: Producer, consumer, or decomposer.

Kingdom Monera

Salient Features

  • Size: Microscopic, unicellular, and prokaryotic.
  • Occurrence: Found in all types of environments, including extreme ones.
  • Nucleus: Lacks a well-defined nucleus; DNA exists as a double-stranded circular chromosome (nucleoid). Often has extra-chromosomal DNA (plasmids).
  • Cell Wall: Made of peptidoglycan (murein), a polymer of sugars and amino acids.
  • Membrane-Bound Organelles: Absent. Ribosomes are present and are smaller (70S) compared to eukaryotic cells.
  • Nutrition:Majority are heterotrophic (parasitic or saprophytic), Some are autotrophic (photoautotrophs or chemoautotrophs).
  • Reproduction: Asexual, through binary fission or budding, Sexual reproduction is rare, occurs through conjugation.
  • Examples: Archaebacteria: Methanobacillus, Thiobacillus, Eubacteria: Chlorobium, Chromatium, Cyanobacteria: Nostoc, Azotobacter.

Bacteria Classification and Characteristics

Morphological Classification

  • Spherical: Coccus
  • Rod-shaped: Bacillus
  • Comma or Kidney-shaped: Vibrio
  • Spiral: Spirillum

 Locomotion in Kingdom Monera

  • Motile: Via flagella, Gliding movements.
  • Non-motile: Do not move.

Archaebacteria and Eubacteria

Archaebacteria:

  • Primitive: Most ancient bacteria.
  • Habitat: Extreme environments (e.g., volcanic craters, salty lakes, hot springs).
  • Types: Halophiles: Tolerate high salinity, Thermophiles: Tolerate extreme temperatures.
  • Methanogens: Produce methane in biogas plants (e.g., found in the guts of ruminants).

Eubacteria:

  • True Bacteria: More common bacteria.
  • Cell Wall: Made of peptidoglycan.
  • Nutrition: Heterotrophic (most), Autotrophic (few), including: Photosynthetic (e.g., Chlorobium, Chromatium), Chemosynthetic (e.g., sulfur bacteria).
  • Structure:
  • Filamentous forms, mucilaginous sheath.
  • Genetic Material: Typical prokaryotic.
  • Photosynthetic Pigments: Chl-a, Chl-b, carotenes, xanthophylls.
  • Role: Mainly decomposers, breaking down large molecules.

Useful Bacteria

  • Decomposers: Break down large molecules into simpler ones.
  • Examples:
  • Lactobacillus: Curdles milk.
  • Azotobacter: Fixes nitrogen for plants.
  • Streptomyces: Produces antibiotics (e.g., streptomycin).
  • Methanogens: Produce methane (biogas).
  • Pseudomonas spp. and Alcanovorax borkumensis: Clean up oil spills by breaking down chemicals.

Harmful Bacteria

  • Disease-causing: Various illnesses.
  • Examples:
  • Salmonella typhi: Causes typhoid.
  • Vibrio cholerae: Causes cholera.
  • Mycobacterium tuberculosis: Causes tuberculosis.
  • Clostridium tetani: Causes tetanus.
  • Clostridium spp.: Causes food poisoning.
  • Mycoplasma: Many forms are pathogenic.

Mycoplasma:

  • Size: Smallest known living cells.
  • Characteristics: Lack cell wall, Pathogenic, Antibiotic Resistance: Resistant to common antibiotics due to the absence of a cell wall, Oxygen: Can survive without oxygen.

Kingdom Protista

Kingdom Protista consists of unicellular eukaryotic organisms that link various eukaryotic kingdoms such as Plantae, Fungi, and Animalia.

Types of Protists

1. Plant-like Protists (Photosynthetic Protists)

  • Name: Phytoplanktons (Chrysophytes)
  • Nutrition: Autotrophic (photosynthetic)
  • Role: Major producers in the ocean ecosystem
  • Characteristics:
  • Diatoms: Body Structure: Two silica covers fitting like soap boxes
 2. Animal-like Protists (Consumer Protists)
  • Name: Protozoans
  • Nutrition: Heterotrophic
  • Characteristics:
  • Amoeboid Protozoans: Locomotion: Pseudopodia, Examples: Amoeba (free-living), Entamoeba (causes amoebic dysentery)
  • Flagellated Protozoans: Locomotion: Flagella, Example: Trypanosoma
  • Ciliated Protozoans: Locomotion: Cilia, Example: Paramecium
  • Sporozoans: Characteristics: Forms spores in one life stage, Example: Plasmodium (causes malaria).
 3. Dinoflagellates
  • Habitat: Mostly marine and aquatic
  • Nutrition: Autotrophic (photosynthetic)
  • Characteristics: Photosynthetic Pigments: Yellow, green, brown, blue, red, Cell Wall: Cellulosic stiff plates, Locomotion: Two flagella (motile), Phenomenon: Responsible for 'red tide', Example: Gonyaulax

4. Fungi-like Protists (Consumer Decomposer Protists)

  • Name: Myxomycetes
  • Nutrition: Saprophytic (decaying leaves)
  • Characteristics: Structure: Aggregate to form a large cell mass called plasmodium, Spores: Tough, can survive extreme conditions, Example: Slime molds

5. Euglenoids

  • Cell Wall: Lacks, has a tough proteinaceous pellicle
  • Pellicle: Provides flexibility and contractibility
  • Flagella: Two (one short, one long)
  • Nutrition: Heterotrophic in absence of light, photosynthetic in light
  • Example: Euglena

Kingdom Plantae

Characteristics of Kingdom Plantae:

  • Nutrition: Primarily autotrophic; includes some semiautotrophic (e.g., Venus flytrap, pitcher plant) and heterotrophic parasitic members (e.g., Cuscuta).
  • Cell Type: Eukaryotic, multicellular, with chlorophyll.
  • Cell Wall: Mostly composed of cellulose.
  • Life Cycle: Exhibits alternation of generations (two distinct phases).
  • Classification: Divided into two major groups: Cryptogams & Phanerogams
Kingdom Fungi

General Characteristics:

  • Type of Organisms: Eukaryotic, heterotrophic with extracellular digestion. Can be unicellular or multicellular.
  • Nucleus: Cells may be multinucleate or uninucleate.
  • Body Structure: Mycelium: Body consisting of thread-like structures called hyphae, Hyphae: Can be septate (with septa) or aseptate (without septa). Non-septate multinucleated hyphae are coenocytic.
  • Cell Wall: Composed of chitin or fungal cellulose.
  • Cell Organelles: Contains well-organized membrane-bound organelles, except chloroplasts.
  • Nutrition: Heterotrophic (cannot photosynthesize). Mostly saprophytes; some are parasitic or predators.
  • Reproduction: Both sexual and asexual. Asexual reproduction occurs by fragmentation, fission, and budding.
  • Symbiosis: Some form symbiotic relationships, like lichens (with algae) or mycorrhiza (with plant roots).

Types of Fungi:

Phycomycetes:

  • Common Name: Algal fungi
  • Hyphae: Aseptate coenocytic
  • Habitat: Moist, damp places, decaying organic matter, aquatic habitats, or as plant parasites
  • Examples: Mucor, Rhizopus (bread mold), Albugo (parasitic fungus on mustard)

Ascomycetes:

  • Common Name: Sac fungi
  • Hyphae: Branched and septate
  • Forms: Mostly multicellular, rarely unicellular (e.g., yeast)
  • Roles: Decomposers, parasites, coprophilous (dung-growing)
  • Examples: Aspergillus, Penicillium, Neurospora (genetic assays), Claviceps, Saccharomyces (unicellular)

Basidiomycetes:

  • Common Name: Club fungi
  • Hyphae: Branched and septate
  • Examples: Agaricus (mushrooms), Ganoderma (bracket fungi), Ustilago (smuts), Puccinia (rusts)

Deuteromycetes:

  • Common Name: Imperfect fungi
  • Reproduction: Only asexual (by conidia)
  • Roles: Mainly decomposers; some are parasitic
  • Examples: Alternaria
  • Note: If a sexual stage is discovered, they are reclassified based on that stage.

Reproduction in Fungi

Asexual Reproduction:

  • Phycomycetes: Motile zoospores: Produced endogenously in sporangium, Non-motile aplanospores: Also produced endogenously in sporangium.
  • Ascomycetes: Conidia: Produced exogenously on conidiophores. Germination of conidia produces mycelium.
  • Basidiomycetes: Generally Not Found: Asexual reproduction is uncommon or not observed.
  • Deuteromycetes: Conidia: Produced asexually.

Sexual Reproduction:

  • Phycomycetes: Zygospore Formation: Occurs through isogamy (similar gametes fuse), anisogamy (dissimilar gametes fuse), or oogamy (small flagellated male gamete and large non-flagellated female gamete fuse).
  • Ascomycetes: Ascospores: Produced endogenously in sac-like asci (sing. ascus). Asci are arranged in fruiting bodies called ascocarps.
  • Basidiomycetes: Plasmogamy: Fusion of two vegetative cells forms a basidium. Karyogamy and Meiosis: Occur in basidium to produce four basidiospores.
  • Deuteromycetes: Sexual Reproduction: Either absent or not well known.
Economic Importance of Fungi

Role of Fungi in Medicine:

  • Antibiotics: Penicillin obtained from Penicillium.
  • Drugs: Includes cyclosporine (immunosuppressant), precursors of steroid hormones, etc.

Role of Fungi in Industries:

  • Yeast: Used in bread making to rise dough; also used in breweries and wine making. Fermentation of sugars in grapes by yeast produces alcohol.
  • Lichen: Symbiotic association of algae and fungi used to prepare litmus paper for acid-base testing.

Role of Fungi in Food:

  • Mushrooms: Consumed as a high-protein food source.
  • Penicillium: Helps in the ripening of cheese.

Role of Fungi as Biocontrol Agents:

  • Weed Control: Fungi help manage weed growth.
  • Pathogenic Fungi: Includes Fusarium sp., Phytophthora palmivora, Alternaria crassa, etc., used as mycoherbicides.

Plant Diseases

Common Plant Diseases:

  • Leaf Rust Disease: Pathogen: Puccinia triticina (fungus), Effect: Most common rust disease of wheat.
  • Blight Disease in Rice: Pathogen: Xanthomonas oryzae (bacteria), Effect: Causes wilting of seedlings and yellowing/drying of leaves.
  • Early Blight of Potato: Pathogen: Alternaria solani (fungus), Effect: Causes 'bulls eye' patterned leaf spots and tuber blight on potato.
  • Crown Gall Disease: Pathogen: Agrobacterium tumefaciens (bacteria), Effect: Forms rough-surfaced galls on stem and roots.

Kingdom Animalia

General Characteristics:

  • Types of Organisms: Multicellular and eukaryotic.
  • Habitat: Aquatic, terrestrial, amphibious, or aerial.
  • Cell Organelles: Lack cell wall, plastids, and central vacuole.
  • Locomotion: Mostly motile; some like sponges are sedentary.
  • Sense Organs: Possess sense organs and a nervous system; respond to stimuli.
  • Reproduction: Mostly sexual; some asexual.
  • Nutrition: Heterotrophic, mostly holozoic, sometimes parasitic.
  • Growth: Determinate (follows a definite pattern).

Comparison: Plantae vs. Animalia

Acellular Organisms

Viruses:

  • Discovery: Name "virus" by M. J. Beijerinek, Originally termed 'contagium vivum fluidum' (infectious living fluid).
  • Acellular and ultramicroscopic.
  • Possess genetic material (either DNA or RNA, but never both).
  • Covered by a protein coat (capsid).
  • Do not show activity outside a host; replicate within host cells.
  • Lack their own metabolic machinery; use host cell's machinery for reproduction.
  • Known as infectious nucleoproteins. 
  • Structure:
  • Genetic material: single or double stranded RNA or double stranded DNA.
  • Capsid: Protein coat protecting genetic material.
  • Capsomeres: Smaller units of the capsid, arranged in polyhedral or helical forms.

Types of Viruses:

1. Plant Virus:

  • Shape: Rod-shaped or cylindrical with helical symmetry.
  • Genetic Material: Mostly RNA (Exception: Cauliflower Mosaic Virus with double stranded DNA).
  • Example: Tobacco Mosaic Virus (TMV).

2. Animal Virus:

  • Shape: Polyhedral with radial symmetry.
  • Genetic Material: DNA or RNA.
  • Example: Influenza Virus.

3. Bacteriophage:

  • Shape: Tadpole-like.
  • Infects bacteria.
  • Discovered by Twort.
  • Genetic Material: Double stranded DNA.
  • Structure: Head, collar, and tail.
Diseases Caused by Viruses:
  • In Plants: Leaf curling, yellowing, mosaic formation.
  • In Animals: Swine flu, smallpox, mumps, herpes, common cold, AIDS.

Viroids:

  • Discovery: Theodor Diener.
  • First Viroid: Potato Spindle Tuber Viroid (PSTV).
  • Characteristics:Plant pathogens, Circular, single stranded RNA without a protein coat, Smaller and simpler than viruses.

Difference Between Viruses and Viroids:

Lichens: Symbiotic association between algae and fungi.

Types:

  • Algal Component (Phycobiont): Cyanobacteria (blue-green algae) or green algae.
  • Fungal Component (Mycobiont): Provides shelter and absorbs water/minerals for the algae.

Characteristics:

  • Found in extreme environments (e.g., snow-clad poles).
  • Mutualistic relationship: Algae produces food, fungi provides shelter.
  • Sensitive to pollution; used as pollution indicators.
  • Important in soil formation through acid production.