Taxonomy: science of classifying organisms into categories based on shared characteristics. Three aspects: Identification (What is it?), Nomenclature (What is it called?), Classification (Where does it fit in the system?). Systematics: broader science that includes taxonomy + evolutionary relationships (phylogeny). Carolus Linnaeus (1707-1778): Father of Taxonomy. Published Systema Naturae (1758, 10th edition) — proposed binomial nomenclature and hierarchical classification. Hierarchical levels (Kingdom → Species): Kingdom → Phylum (Division in plants) → Class → Order → Family → Genus → Species. Mnemonic: "Kings Play Chess On Fine Green Silk." Or "Kamli Puri Chatni Omit Faro Gaya Suno."

The rules of binomial nomenclature are governed by: International Code of Zoological Nomenclature (ICZN) for animals. International Code of Nomenclature for algae, fungi, and plants (ICNafp). International Code of Nomenclature of Prokaryotes (ICNP). Universal rules: (1) Biological name = two-part Latin/Latinised name. (2) First word = Generic name (Genus) — starts with CAPITAL letter. (3) Second word = Specific epithet — starts with small letter. (4) Both words in italics when printed; underlined separately when handwritten. (5) When author's name is mentioned, it follows the name without italics (e.g., Mangifera indica Linnaeus). (6) Type specimen: the physical specimen on which the species description is based. (7) Priority principle: the earliest validly published name is the correct one.

Using humans as example: Kingdom: Animalia. Phylum: Chordata. Class: Mammalia. Order: Primates. Family: Hominidae. Genus: Homo. Species: sapiens. Full name: Homo sapiens Linnaeus, 1758. Using mango: Kingdom: Plantae. Division: Magnoliophyta. Class: Magnoliopsida. Order: Anacardiaceae (Sapindales). Family: Anacardiaceae. Genus: Mangifera. Species: indica. Full name: Mangifera indica. Tiger: Panthera tigris. Lion: Panthera leo (same genus → related). Leopard: Panthera pardus. Note: same genus → closely related, similar characteristics. Generic name (Panthera) can be abbreviated to P. after first use: P. tigris.

Species: most fundamental unit of classification. Biological species concept (Ernst Mayr, 1942): species = group of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups. Limitations: doesn't apply to asexual organisms, fossils, or allopatric populations (geographically separated). Morphological species concept: species defined by shared morphological features. Phylogenetic species concept: smallest monophyletic group (ancestors + all descendants). Ecological species concept: organisms with same ecological niche. Cohesion species concept: organisms connected by gene flow and/or developmental constraints. In practice: most species are identified by morphological characters + genetic data. Cryptic species: morphologically identical but genetically distinct. Ring species: populations connected by gene flow around a geographic barrier but terminal populations cannot interbreed.

Herbarium: collection of preserved (dried, pressed) plant specimens mounted on sheets with labels. Used for: identification, reference, taxonomy research. World's largest herbaria: Kew Royal Botanic Gardens (UK), Museum National d'Histoire Naturelle (Paris), New York Botanical Garden. India's largest: Central National Herbarium (CNH), Howrah, Kolkata. Botanical gardens: living collections of plants for scientific study, conservation, education. Kew Royal Botanical Gardens, London — most famous worldwide. India: Indian Botanical Garden (IBG), Howrah — largest in Asia (established 1787). National Botanical Research Institute (NBRI), Lucknow. Museums: zoological specimens preserved (taxidermy, pickled). Zoological parks: in-situ-like conservation, also education, research. National Zoological Park, Delhi. Keys: dichotomous keys for identification — pair of contrasting characters at each step → identify organism.

Woese and Fox (1977): proposed Three-Domain classification based on 16S/18S rRNA gene sequences. Three domains: Bacteria, Archaea, Eukarya. Archaea differ fundamentally from bacteria: ether-linked lipids, no peptidoglycan, different rRNA, some have histones. Archaea more closely related to Eukarya than to Bacteria. Versus Whittaker's Five Kingdoms (1969): Monera (prokaryotes), Protista, Fungi, Plantae, Animalia. Key differences: Three-domain splits Monera into Bacteria and Archaea. Five-kingdom groups all prokaryotes together as Monera. Three-domain based on molecular phylogeny. Five-kingdom based on morphological/nutritional criteria. For NEET: both systems must be known. Whittaker's (Five Kingdom) is used in NCERT curriculum. Three-domain is accepted in modern research.

Viruses: not classified in the five-kingdom system as they are acellular (no cell structure). Virus classification is under International Committee on Taxonomy of Viruses (ICTV). Virus names: often descriptive of disease or origin. Not always following Latin binomial strictly. Categories: Order, Family, Subfamily, Genus, Species. Examples: SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) — causes COVID-19. HIV (Human Immunodeficiency Virus) — causes AIDS. Influenza A virus — seasonal flu. TMV (Tobacco Mosaic Virus) — first virus discovered (Iwanowski, 1892; Beijerinck named it virus, 1898). Bacteriophage lambda (λ phage) — infects E. coli. Viruses have: protein coat (capsid), nucleic acid (DNA or RNA), may have envelope. They use host cell machinery for replication.

Molecular phylogenetics: determining evolutionary relationships using molecular data (DNA, RNA, protein sequences). Advantages over morphological: more objective, can compare distantly related species, can resolve ancient evolutionary events. Methods: sequence alignment (BLAST, CLUSTAL), phylogenetic tree construction (UPGMA, Neighbour-joining, Maximum Parsimony, Maximum Likelihood, Bayesian). Molecular clock: rate of mutation approximately constant → can estimate divergence times. Key molecular markers: 16S rRNA (bacteria identification and phylogeny — Woese's approach). 18S rRNA (eukaryotic phylogeny). rbcL, matK (plant barcoding). COX1 (cytochrome oxidase 1 — animal DNA barcoding, mitochondrial gene). ITS (internal transcribed spacer) of rRNA — fungi barcoding. DNA barcoding: use short standardised gene regions to identify species — like barcode scanner for species identification. BOLD (Barcode of Life Database).