Biodiversity and Classification

Five-kingdom system: In 1969, American ecologist Robert Whittaker proposed that all organisms be divided into five kingdoms: Monera, Protista, Fungi, Plantae and Animalia. In this system, kingdom Monera included all prokaryotes, while the other four kingdoms included eukaryotes.

Three-domain system: In 1990, American microbiologist Carl Woese suggested that there are two separate groups of prokaryotes — Archaea and Bacteria. On this basis he classified living organisms into three domains: Archaea, Bacteria and Eukarya.

Phylogeny: The evolutionary relationship among organisms is called phylogeny. A diagram that shows phylogeny is called a phylogenetic or evolutionary tree (Figure 1.1). Archaea and Bacteria evolved independently from a common ancestor. Molecular evidence suggests that archaea are more closely related to eukaryotes than to bacteria — in other words, Eukarya evolved from Archaea after archaea split off from Bacteria.

In the five-kingdom system, this domain was included in kingdom Monera. The name Archaea comes from the Greek word archaios (ancient). They are prokaryotes which diverged from bacteria in very ancient times. They were initially classified as a group of bacteria and were called archaebacteria.

Size and shape: Individual archaeans range from 0.1 µm to over 15 µm in diameter. Some form aggregates or filaments up to 200 µm in length. They occur in various shapes: 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.

How are Archaea unique?

Cell membrane: Their membrane lipids have an ether-linkage between glycerol and fatty acid chains, and the fatty acid chains are branched. That is why their membranes are more resistant to extreme conditions. Bacteria and Eukarya, by contrast, have fatty acids attached to glycerol by ester linkages, and their chains are unbranched (Figure 1.2).

Cell wall composition: Archaeal cell walls lack cellulose and peptidoglycan. Instead they contain distinct polysaccharides and proteins. Some archaea have pseudopeptidoglycan. Bacterial walls, by contrast, contain peptidoglycan (a polymer of sugars and amino acids that gives structural support). In Eukarya, cell walls — if present — are made of cellulose (plants) or chitin (fungi).

Genetic differences: Archaea share several genetic sequences and regulatory features with eukaryotes, highlighting their closer evolutionary relationship.

Metabolism: Archaea have unique metabolic processes like methanogenesis (production of methane), which is not found in bacteria or Eukarya. Bacteria show photosynthesis, nitrogen fixation and fermentation. In Eukarya, metabolism is often more complex: cellular respiration, photosynthesis (plants and algae) and various forms of fermentation.

Major groups of Archaea: Methanogens (produce methane as a metabolic by-product), Halobacteria (live in extremely saline environments), Thermococci (found in hot environments) and Thaumarchaeota (involved in the nitrogen cycle).

Significance of Archaea: Archaeans living in high acidity and alkalinity are a source of enzymes that function under harsh conditions. Enzymes of DNA replication extracted from such archaeans work best at high temperatures and allow rapid cloning of DNA in the laboratory. Methanogen archaeans are a vital part of sewage treatment — they carry out anaerobic digestion and produce biogas. Acidophilic archaea are used to extract metals such as gold, cobalt and copper from ores in mineral processing. In humans, intestinal gas is largely the result of the metabolism of methanogens.

In the five-kingdom system, this domain was also included in kingdom Monera. They are the true bacteria. Here are the general characteristics of domain Bacteria:

• 1. Cell structure: Like archaea, bacteria possess a prokaryotic cell — they lack a true nucleus and membrane-bound organelles.
• 2. Cell wall composition: Bacterial cell wall is composed of peptidoglycan, a unique polymer that provides structural support and shape.
• 3. Genetic material: Like archaea, bacteria possess a single, circular chromosome made of DNA, located in the nucleoid region.
• 4. Plasmids: Most bacteria have small, circular DNA molecules that can be transferred between bacteria, aiding genetic diversity and adaptation.
• 5. Reproduction: Bacteria primarily reproduce asexually through binary fission — a single cell divides into two identical daughter cells.
• 6. Nutritional modes: Autotrophs (self-feeding, e.g. photosynthetic bacteria) and heterotrophs (feeding on organic matter, e.g. decomposers).
• 7. Morphology (shapes): Cocci (spherical), bacilli (rod-shaped), spirilla (spiral-shaped) and vibrios (comma-shaped) — Figure 1.4.
• 8. Arrangement: Cells may be found singly, in pairs (diplococci), chains (streptococci), clusters (staphylococci) or other species-specific arrangements.
• 9. Flagella: Many bacteria have one or more flagella — whip-like structures that enable movement.
• 10. Pili and fimbriae: Hair-like structures in some bacteria. They help in attachment to surfaces and in exchange of genetic material with other bacteria.
• 11. Respiration: Bacteria can be obligate aerobes, obligate anaerobes, facultative anaerobes, microaerophiles or aerotolerant anaerobes. Some perform fermentation to produce energy without oxygen.
• 12. Extremophiles: Some bacteria thrive in extreme conditions — high temperature (thermophiles), high salinity (halophiles) and low pH (acidophiles).
• 13. Pathogenicity: Some bacteria cause diseases in humans, animals and plants, producing toxins or other virulence factors.
• 14. Symbiosis: Many bacteria live in symbiotic relationships — mutualism (both benefit) and commensalism (one benefits, the other is not harmed).

Major groups of Bacteria: Proteobacteria (e.g. Escherichia coli, Rhizobium, Helicobacter pylori); Firmicutes (e.g. Bacillus subtilis, Lactobacillus, Clostridium botulinum); Actinobacteria (e.g. Streptomyces, Mycobacterium tuberculosis); Cyanobacteria (e.g. Anabaena, Spirulina); Spirochaetes (e.g. Treponema pallidum); Acidobacteria (e.g. Acidobacterium); Aquificae (e.g. Aquifex pyrophilus).

Domain Eukarya encompasses all organisms with eukaryotic cells, which are fundamentally different from the prokaryotic cells of Bacteria and Archaea. Its general characteristics are:

• Cell structure: Eukaryotic cells with a true nucleus enclosed by a nuclear membrane. Cells have membrane-bound organelles — mitochondria, chloroplasts (in plants and algae), endoplasmic reticulum, Golgi apparatus, lysosomes and peroxisomes. Cells also have a cytoskeleton — a complex network of microtubules, microfilaments and intermediate filaments that provides structural support, enables cell movement and facilitates intracellular transport.
• Genetic material: DNA is organized into multiple linear chromosomes within the nucleus. DNA is associated with histone proteins, which help in the organization and regulation of genetic material.
• Reproduction: Most eukaryotes undergo sexual reproduction involving meiosis and fertilization, leading to genetic diversity. Some eukaryotes can also reproduce asexually through mitosis, producing genetically identical offspring.
• Complex cellular organization: In multicellular eukaryotes, cells differentiate into specialized types forming tissues and organs with specific functions.
• Evolutionary relationships: Eukaryotes are believed to have originated through endosymbiosis — certain prokaryotic cells (such as mitochondria and chloroplasts) were engulfed by a host cell, leading to a symbiotic relationship.

The classification of living organisms is organized into a hierarchical system that allows scientists to categorize and understand the relationships between different forms of life. This system includes several levels, known as taxa (singular: taxon), each representing a rank in the biological classification system. The primary levels are: kingdom, phylum, class, order, family, genus and species — with domain above them all.

• 1. Domain: The highest level of classification. Currently there are three domains: Archaea, Bacteria and Eukarya.
• 2. Kingdom: One of the highest taxonomic ranks, just below domain. It groups together all forms of life that share fundamental characteristics. Example: in domain Eukarya there are several kingdoms such as Animalia (animals), Plantae (plants), Fungi (fungi) and Protista (protists).
• 3. Phylum: The next level below kingdom. Organisms within a phylum share a basic body plan and significant structural features. Example: in kingdom Animalia, phylum Chordata includes all animals with a notochord, such as mammals, birds, reptiles, amphibians and fish.
• 4. Class: Further divides organisms within a phylum based on more specific common traits. Example: within phylum Chordata, class Mammalia includes all mammals, characterized by having hair and mammary glands.
• 5. Order: Categorizes organisms within a class based on additional shared characteristics and evolutionary history. Example: within class Mammalia, order Primates includes humans, monkeys and apes, characterized by their large brains and opposable thumbs.
• 6. Family: Groups organisms within an order that are even more closely related, sharing more precise common attributes. Example: within order Primates, family Hominidae includes great apes and humans.
• 7. Genus: A more specific rank within a family, grouping species that are very closely related and often visually similar. Example: within family Hominidae, genus Homo includes humans and our closest extinct relatives.
• 8. Species: The most specific level of classification, representing a single type of organism. Members of a species can interbreed and produce fertile offspring. Example: within genus Homo, species Homo sapiens refers to modern humans.

Remember the order (top → bottom): Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species. Domain is the largest group, species the smallest.

Note: this table is exactly as given in the book — the book lists "Angiosperms" as the onion's phylum and "Monocots" as its class.

Eukarya consists of the kingdoms Protista, Fungi, Plantae and Animalia. It includes all eukaryotes, which consist of complex eukaryotic cells containing a nucleus and other membrane-bound organelles.

1. Kingdom Protista: Kingdom Protista includes eukaryotes which are unicellular or colonial or filamentous or simple multicellular. Simple multicellular means that they do not have multicellular sex organs. There are three types of protists.

Major groups of protists:

• Protozoa — animal-like protists. They are unicellular and heterotrophic. Examples: Paramecium, Amoeba, Plasmodium and Trypanosoma.
• Algae — plant-like protists. They have cell walls made of cellulose. They have chlorophyll and are autotrophs. Examples: Euglena and diatoms.
• Myxomycota and Oomycota — fungi-like protists. They have hyphae-like structure and are saprophytic. Examples: slime molds and water molds.

Certain protists are parasitic and cause diseases like malaria (Plasmodium), amoebic dysentery (Entamoeba histolytica) and sleeping sickness (Trypanosoma).

2. Kingdom Fungi: Fungi are eukaryotic, heterotrophic organisms that are unicellular or multicellular. Their cells are covered by a cell wall made of chitin (a polysaccharide). Fungi get nutrients in a unique way — they do not ingest food like animals and some protists. They absorb food from their surroundings. Examples: mushrooms, rusts, smuts and molds.

Some fungi are used in the production of bread, cheese and beer. Others have medicinal properties, such as penicillin, an antibiotic derived from the fungus Penicillium.

Major groups of fungi:

• Zygomycota — fungi which lack septa in their hyphae. Examples: Rhizopus (bread molds), which grow on moist bread, fruits etc.
• Ascomycota — the largest group of fungi. They have septate hyphae. Examples: common molds, morels, truffles, cup fungi, Neurospora and yeasts.
• Basidiomycota — fungi with septate hyphae. Examples: mushrooms, toadstools, puffballs, jelly fungi, bracket/shelf fungi, rusts and smuts.

There are about 100,000 known species of fungi. Most of the Ascomycetes are found in lichens, and some are found in mycorrhizae.

3. Kingdom Plantae: It includes plants which are eukaryotic, multicellular organisms with cell walls made of cellulose. They are autotrophic and prepare food through photosynthesis. All plants develop from embryos. Examples: mosses, ferns, conifers and flowering plants.

Major groups of plants: Plants are divided into two major groups:

• Nonvascular plants or bryophytes lack conducting tissues (xylem and phloem). Examples: liverworts, hornworts and mosses.
• Vascular plants have conducting tissues. They are of two types: seedless plants (e.g. ferns) and seed plants (e.g. conifers and flowering plants). Seed-producing vascular plants are Gymnosperms (naked seeds) — cone-bearing, no flowers or fruits (e.g. Pine and Spruce) — whereas Angiosperms (flowering plants) are the most diverse plant group, producing seeds enclosed in fruits (Monocots e.g. grass, corn; Dicots e.g. rose, sunflower).

4. Kingdom Animalia: This kingdom of eukaryotes includes animals which are eukaryotic, multicellular and heterotrophic. They develop from embryos. They ingest food and digest it within their bodies.

Table: Distinguishing characteristics of the kingdoms of the three domains (as given in the book).

Kingdom Animalia is broadly divided into the following phyla. Study each phylum's body plan, symmetry, body cavity, digestive system and reproduction — examiners ask differences between them.

1. Phylum Porifera (sponges): This phylum contains sponges. Most of them are marine, while some live in freshwaters. Leucosolenia and Euplectella (Venus' flower basket) are marine sponges. Spongilla is a common freshwater sponge.

• Sponges do not have tissue-level organization. Most sponges are asymmetrical, but some have radial symmetry. They do not have a nervous system.
• There are numerous pores in the body wall called ostia. Through ostia, water enters the body. The larger pore through which water leaves the body is called the osculum.
• The outer layer of the body is made of thin, flat cells called pinacocytes. The second layer is jelly-like and is called mesohyl — it contains amoeboid cells. The third layer, which lines the spongocoel, is made of choanocytes or collar cells.
• They have a skeleton in the form of microscopic needles of calcium carbonate or silica.
• Most sponges reproduce asexually by budding or regeneration. Some sponges form resistant capsules called gemmules, containing masses of amoeboid cells. When the parent sponge dies, it releases its gemmules. In a favourable environment, amoeboid cells come out of the gemmules and form a new sponge.

A commercial sponge is prepared by drying, beating and washing a sponge until all cells are removed.

2. Phylum Cnidaria: Almost all cnidarians are marine, although a few are found in freshwater (e.g. jellyfish and hydra). Most cnidarians are colonial (e.g. obelia, corals, sea fans). Most of them are sessile (e.g. hydra, coral, obelia). Some cnidarians are motile (e.g. jellyfish).

• They are radially symmetrical animals and are diploblastic — the adult body contains two tissue layers: the epidermis (derived from ectoderm) and the gastrodermis (derived from endoderm). Between them, a jelly-like mesoglea is present, containing amoeboid cells that originated either from ectoderm or endoderm.
• They possess special cells called cnidocytes. A cnidocyte contains a special organelle called a nematocyst. Nematocysts defend the body and capture prey.
• Cnidarians have a blind-ending cavity called the gastrovascular cavity or enteron. It opens outside by a single opening, the mouth. The mouth also acts as an anus for the removal of undigested material. The mouth is surrounded by projections called tentacles. This type of digestive system, with a single opening for the entry of food and removal of undigested matter, is called a sac-like digestive system.
• The nervous system is in the form of a network of neurons in the body wall. There is no central nervous system (brain and spinal cord). They do not have respiratory, excretory and transport systems.
• There are two body forms: polyps (cylindrical, attached to a substrate at the aboral end, reproduce asexually) and medusae (umbrella-like, free-swimming, reproduce sexually).

Corals are colonial cnidarians. They produce a hard exoskeleton of calcium carbonate. The skeleton makes coral islands and coral reefs.

3. Phylum Platyhelminthes (flatworms): They are called "flatworms". They are mostly unsegmented and the body is soft and dorsoventrally compressed. Most of them are free-living (e.g. planaria). Some are endoparasites of humans and other animals (e.g. liver fluke, tapeworm and blood-fluke).

• They are triploblastic — the tissues of the body are derived from three embryonic layers: ectoderm, mesoderm and endoderm.
• They are acoelomates. A loose connective tissue called parenchyma fills the space between the body wall and body organs.
• They have bilateral symmetry, with distinct left and right sides as well as dorsal and ventral sides.
• They do not have respiratory and circulatory (transport) systems.
• They have a network of tubular protonephridia. These tubules have numerous branches. Each branch ends in a bulb-like cell called a flame cell. The cilia of flame cells beat to suck surrounding fluid into the tubules. The tubules filter waste materials from the fluid and release them out of the body wall through a small opening called a nephridiopore.
• They have a network of neurons. There are cerebral ganglia in the anterior end (head). These ganglia are attached to longitudinal nerve cords that are interconnected across the body by transverse branches.
• Most free-living flatworms have two simple eyespots at their anterior end.
• Flatworms reproduce asexually by "fission" — the animal constricts in the middle and divides into two pieces. Each piece then regenerates the missing part. Sexually reproducing flatworms are hermaphrodites (bisexual).

Tapeworms belonging to phylum Platyhelminthes are segmented.

4. Phylum Nematoda (roundworms): They are roundworms with an elongated, worm-like (round) body with pointed ends. Some roundworms are free-living (in water and soil), e.g. Caenorhabditis elegans. Many are parasites, e.g. ascaris, hookworm, pinworm and whipworm.

• They are triploblastic, bilaterally symmetrical and possess an unsegmented body.
• They are pseudocoelomates because they possess a false body cavity called a pseudocoelom filled with fluid.
• They possess a tube-like digestive system — an alimentary canal with two openings: mouth at the anterior end and anus at the posterior end. Parasitic roundworms have simplified digestive systems.
• Two main types of excretory systems exist: the glandular type (a single renette cell leading to a duct and pore) and the tubular type (an H-shaped structure of ducts).
• They possess a network of neurons. There is a nerve ring around the pharynx, attached to four longitudinal nerve cords.
• They have raised, hair-like sense organs called sensory papillae, present on the lips.
• They do not have defined respiratory and circulating systems.
• They are unisexual — male nematodes have testes and female nematodes have ovaries.

The pseudocoelomates are classified in seven phyla. These phyla are grouped as a unit called Aschelminths. Phylum Nematoda is the representative phylum of this group.

5. Phylum Mollusca: Molluscs have soft, unsegmented bodies. They are widely distributed in natural habitats. Some of them are exclusively aquatic (e.g. mussels, octopus and oyster). Others live in moist places (e.g. land snail).

• Molluscs are triploblastic and have bilateral symmetry. They possess a true coelom. Among coelomates, they are included in the group called protostomes.
• Their body can be divided into three parts: head, visceral mass (contains organs of digestion, excretion and reproduction) and foot (attached with the visceral mass).
• They have an epithelial envelope around the visceral mass called the mantle. The space between mantle and visceral mass is called the mantle cavity. In most molluscs, the outer surface of the mantle secretes a calcareous shell.
• All molluscs (except bivalvia) have a rasping, tongue-like organ called the radula.
• All of them (except cephalopods) have an open blood circulatory system. Their heart consists of a single ventricle and two auricles. In an open-type system, the blood does not remain in vessels — it directly bathes cells in tissue spaces (sinuses).
• They possess a tube-like digestive system in which the gut has two openings: mouth and anus.
• Their excretory system consists of paired tubular structures called nephridia. Wastes are gathered from sinuses and discharged into the coelom around the heart. The nephridia open in this coelom. Tiny cilia around their openings move the fluid from the coelom into the nephridia. Nephridia discharge waste materials into the mantle cavity, from where they are expelled out.
• In molluscs, gills work for the exchange of gases.
• They have three pairs of interconnected ganglia present in the head, visceral mass and foot. The ganglia are interconnected by means of a nerve cord.
• They move with the help of a muscular foot. Most molluscs are motile, while some are sessile. Most molluscs are unisexual.

Classes of molluscs: Gastropoda (slug, garden snail), Bivalvia (freshwater mussel, oyster) and Cephalopoda (cuttlefish, octopus).

6. Phylum Annelida (segmented worms): Annelids are commonly called segmented worms. They are found in marine water (e.g. nereis), freshwater (e.g. leech) and in damp soil (e.g. earthworm). Some annelids are ectoparasites (e.g. leeches).

• Their body is divided transversely into a number of similar parts called segments. Internally, the segments are separated from each other by cross walls called septa. Each segment is provided with its own circulatory, excretory and neural elements. This type of segmentation in the body is called metameric segmentation.
• Annelids are bilaterally symmetrical and triploblastic. They are protostome coelomates.
• Annelids have special parts called setae. Setae are chitinous bristles which are absent in leeches.
• Their body wall is surrounded by a moist, acellular cuticle secreted by the epidermis.
• They possess a tube-like digestive system. The digestive tube is divided into distinct parts, each performing a specific function. Parasitic annelids have a simplified digestive system.
• Their excretory system consists of ciliated, funnel-shaped metanephridia. Each segment has one pair of metanephridia.
• They possess a closed-type circulatory system — blood always flows in blood vessels. They have specialized pulsating blood vessels (pseudohearts). Blood of most annelids has the respiratory pigment haemoglobin, dissolved in blood plasma.
• Gaseous exchange occurs through the skin.
• There is a cerebral ganglion or brain in the anterior segment. A double, longitudinal ventral nerve cord arises from the brain and gives nerves in each segment. Ganglia are also present in each segment.
• They have tactile receptors, chemoreceptors, balance receptors and photoreceptors. Some annelids also have well-developed eyes with lenses.
• Most annelids are hermaphrodite (e.g. earthworm, leech) and some are unisexual (e.g. nereis).

The segments are indicated externally by constrictions of the body surface in the form of little rings — "Annelid" means "little ring".

7. Phylum Arthropoda: Arthropods are the most successful of all invertebrates. They are found in every type of habitat. Many of the terrestrial members can also fly.

• They are triploblastic, bilaterally symmetrical, protostome coelomates. The coelom is reduced and is present only around the reproductive and excretory systems.
• They have jointed appendages which are modified for specialized functions — running, crawling, swimming, capturing prey, respiration, reproduction etc. In different arthropods, the jointed appendages around the mouth are modified in different ways and form mouth parts.
• The body is segmented. Some segments are fused to form specialized body regions called tagmata — head, thorax and abdomen.
• They have an exoskeleton or cuticle, secreted by the epidermis of the body wall. It is made chiefly of chitin. In young arthropods, the exoskeleton is shed from time to time. After shedding, the animal grows at a fast rate and then re-secretes a new exoskeleton. This process is called ecdysis or molting.
• They possess an open-type circulatory system. Most of the time, blood flows in the haemocoel, which is derived from an embryonic cavity called the blastocoel. Their blood is colourless as it is without haemoglobin and is known as haemolymph.
• Most arthropods possess a respiratory system of air tubes called tracheae. Main tracheal tubes open through openings called spiracles. Aquatic arthropods respire through gills.
• Arthropods have a tube-like digestive system. The alimentary canal is divided into different parts.
• Their excretory system comprises Malpighian tubules — narrow tubules projected from the alimentary canal, attached at the junction of midgut and hindgut. Nitrogenous wastes are excreted in the form of solid uric acid crystals.
• They have a well-developed central nervous system with three fused pairs of cerebral ganglia (brain) in the head. There is a double ventral nerve cord which has ventral ganglia in each segment. Smaller nerves arise from ventral ganglia in each segment.
• They have well-developed compound eyes and antennae. They can swim, crawl or fly depending on their habitat. They are unisexual.

Important arthropods include insects (e.g. mosquito, butterfly, moth, wasp, beetle, grasshopper), crabs, lobsters, prawn, shrimps, crayfishes, spider, tick, mite, scorpion, centipedes and millipedes. Classes: Crustacea (crayfish, crab), Insecta (wasp, grasshopper), Arachnida (spider, mite) and Myriapoda (centipede, millipede).

8. Phylum Echinodermata: They are exclusively marine animals. Some are flattened like a biscuit (e.g. cake urchin), some are star-shaped with short arms (e.g. sea star or starfish), some are globular (e.g. sea urchin), some are star-shaped with long arms (e.g. brittle star) and some are elongated (e.g. sea cucumber).

• They are triploblastic and deuterostome coelomates. Their larvae are bilaterally symmetrical, but the adults show radial symmetry. In their radial symmetry, the body parts are arranged in five, or multiples of five, around an oral-aboral axis.
• They possess a calcareous endoskeleton in the form of plates called ossicles. These plates are derived from mesoderm but come out of the skin also and make spines on the skin.
• They have a water-vascular system consisting of tubes and spaces present in the coelom. A ring canal surrounds the mouth. It opens outside through a sieve-like plate called the madreporite. Five (or a multiple of five) radial canals branch from the ring canal. Many lateral canals emerge from each radial canal, and each lateral canal ends at a tube foot. Tube feet are extensions of the water vascular system. The tube feet extend and attach with some substrate. When water is drawn back from the sucked tube feet, the body is pulled.
• Echinoderms possess a tube-like digestive system. The mouth leads to oesophagus, stomach, intestine and rectum. The rectum opens out through the anus.
• There are no specialized organs for respiration and excretion.
• They possess a poorly developed nervous system made of a nerve net, a nerve ring, and five (or multiples of five) radial nerves. Most sensory receptors are distributed over the surface of the body and tube feet.
• Asexual reproduction involves division of the body, followed by regeneration of each half. Echinoderms are unisexual.

Many echinoderms are able to regenerate lost parts, and some — especially sea stars and brittle stars — drop various parts when they are under attack and then regenerate the lost parts.

9. Phylum Hemichordata — note: The book's Animalia list jumps from Echinodermata (8) to Chordata (10). Phylum 9 in the standard sequence (Hemichordata) is not given a separate section in this chapter of the book, so it is not added here — the book's own numbering is kept.

10. Phylum Chordata: Chordates are bilaterally symmetrical, triploblastic, deuterostome coelomates. The following four characteristics are unique to chordates, present at some stage in development:

• 1. Notochord: All chordates develop a notochord during embryonic life. It is a rod-like, semi-rigid body of vacuolated cells. It extends throughout the length of the body between the gut and the dorsal nerve cord. The lower chordates retain this notochord throughout life, while in vertebrates it is partly or entirely replaced by the vertebral column during development.
• 2. Pharyngeal slits: These are a series of openings in the lateral walls of the pharynx. All chordates develop paired gill slits in the embryonic stage. In some chordates (e.g. Amphioxus and fishes), these develop into gills. In some (e.g. most amphibians), these are functional for some period in their life history. In others (e.g. reptiles, birds and mammals), these are modified for various purposes.
• 3. Tubular nerve cord: In all chordates, a tubular nerve cord runs through the longitudinal axis of the body, just dorsal to the notochord. It expands anteriorly as a brain.
• 4. Post-anal tail: All chordates develop a tail, posteriorly beyond the anal opening. Some chordates retain it throughout life, while others degenerate it during embryonic life.

Phylum Chordata includes two major groups: invertebrate chordates and vertebrates.

• Subphylum Urochordata includes the invertebrate chordates in which the notochord and nerve cord are present only in their free-swimming larvae. Sea squirts are examples of urochordates.
• Subphylum Cephalochordata includes the invertebrate chordates in which the notochord persists throughout life. Amphioxus is a common cephalochordate.
• Vertebrates: They have a vertebral column and cranium. Vertebrates are divided into seven classes which are placed into two groups (the five groups are detailed in section 1.5 below).

Vertebrates are divided into five groups. Learn each group's body covering, skeleton, heart, respiration and reproduction — these are the favourite comparison questions.

1. Group Pisces (fishes): Members of class Pisces are aquatic vertebrates, meaning they live exclusively in freshwater or marine environments.

• Their bodies are streamlined or fusiform (spindle-shaped), which helps in reducing water resistance during swimming.
• The body is covered with scales (dermal in origin), such as placoid, cycloid or ctenoid scales, depending on the type of fish.
• Skeleton can be cartilaginous (as in sharks and rays) or bony (as in most modern fish).
• Respiration takes place through gills. Gills are usually covered by an operculum in bony fishes.
• They have a closed circulatory system. The heart is two-chambered (one auricle and one ventricle). Blood circulation is single and incomplete.
• Locomotion is achieved with the help of paired and unpaired fins. Fins also provide balance and direction during swimming.
• Mostly oviparous (egg-laying), but some are viviparous (give birth to young ones). Fertilisation may be external (common in bony fishes) or internal (common in cartilaginous fishes).
• Pisces are ectothermic (cold-blooded), meaning their body temperature varies with the environment.

Representative fishes: lungfish, seahorse, rohu, trout.

2. Class Amphibia: They have a bony endoskeleton. Unlike fishes, amphibians have a neck. The first vertebra (cervical vertebra) moves against the back of the skull and allows the skull to nod vertically.

• Their skin is smooth (without scales) and moist. It helps in gas exchange, temperature regulation, and absorption and storage of water.
• Their heart is double-circuit. It is three-chambered, with two atria and one ventricle.
• They respire by gills in the larval stage and by lungs and skin in the adult stage.
• They depend on an external heat source and so are ectotherms. They cannot regulate their body temperature and cannot maintain it constant. So they are poikilothermic animals and hibernate in winter.
• Salamander, newts and mud puppies are tailed amphibians. Frogs and toads are tail-less amphibians, and caecilians are leg-less amphibians.
• Amphibians are unisexual. Fertilization is usually external.

3. Class Reptilia: Reptiles are the first animal group that possess amniotic eggs. Amniotic eggs make protective extra-embryonic membranes: amnion, allantois and chorion. These membranes protect the embryo from drying out, nourish it and enable it to develop on land. The amniotic eggs also contain a large amount of yolk, the primary food supply for the embryo. Such eggs have abundant albumin, which provides additional nutrients and water. The amniotic eggs are also covered with a leathery calcareous shell which is partly permeable to gases but not to water.

• Reptiles have dry, scaly skin.
• The bony endoskeleton of reptiles is harder than amphibians. The skull is longer than amphibians.
• In reptiles, the first two cervical vertebrae (atlas and axis) allow more movements of the head.
• In their heart, the ventricle is incompletely partitioned into left and right ventricles.
• Reptiles, like amphibians, are ectothermic and use an external heat source for thermoregulation. They cannot keep their body temperature constant, and are poikilotherms.
• Fertilization is internal. They are oviparous (egg-laying).
• The present-day reptiles are lizards, snakes, tuatara and crocodiles (examples: turtle, cobra, tuatara, crocodile).

4. Class Aves (birds): Birds have a covering of feathers on the body. Feathers form the flight surfaces that provide lift and aid in steering. Feathers also prevent heat and water loss.

• Birds are endotherms — they can obtain heat from cellular processes. A source of internal heat allows them to maintain a nearly constant core temperature. Animals who can maintain their core temperature are known as homeotherms.
• The body of birds is streamlined and spindle-shaped. The forelimbs are modified into wings. Their bones are light due to large air spaces.
• A lighter sheath called a bill replaces the teeth. The sternum (chest bone) bears a large bone called the keel for the attachment of flight muscles.
• Bills and tongues are modified for a variety of feeding habits and food sources.
• In many birds, a diverticulum of the oesophagus called the crop is a storage structure that allows birds to quickly ingest large quantities of food.
• A region of the stomach called the gizzard has muscular walls to crush food.
• Their heart is four-chambered, with complete separation of atria and ventricles.
• Birds have a much-developed nervous system. Vision and hearing are important senses for most birds.
• Their external nares open in the pharynx through nasal passageways. The pharynx leads to the trachea and then bronchi. The organ of voice, called the syrinx, is situated at the lower end of the trachea. The bronchi lead to a complex system of air sacs that occupy much of the body and even extend to some of the bones. The air sacs connect to lungs, which are made of small air tubes called parabronchi.
• Like reptiles and mammals, birds have amniotic eggs with large amounts of yolk and albumin. Such eggs are also covered with a leathery shell. In birds, fertilization is internal and development is external — they are oviparous.
• Some birds have secondarily lost the power of flight and are called running birds (e.g. ostrich, kiwi, rhea, cassowary and emu). The flying birds include pigeon, parrot, crow, eagle, robin etc.

Representative birds: emu, kiwi, pigeon.

5. Class Mammalia: Mammalia includes the group of vertebrates which are nourished by milk from the mammary glands of the mother, and have hair on their body.

• Mammals have skin glands, developed from the epidermis. Sebaceous (oil) glands secrete an oily secretion. Sudoriferous (sweat) glands release watery secretions used in evaporative cooling. Mammary glands are functional in female mammals.
• Most mammals have two sets of teeth during their lives: milk teeth and permanent teeth.
• External ear or pinna is present. The middle ear has a chain of three bones: incus, malleus and stapes.
• Mammals are endothermic and homoeothermic animals. They possess a four-chambered heart.
• They have a muscular diaphragm that separates the coelom into thoracic and abdominal cavities.
• They have a well-developed voice apparatus in the form of the larynx (with vocal cords) and epiglottis.
• In mammals, fertilization is internal.

Three groups of mammals: Mammals are monotremes, marsupials and placentals.

• 1. Monotremes are egg-laying mammals that lay eggs in which the whole development of their embryo proceeds. They are oviparous — e.g. duckbill platypus and echidna (spiny anteater).
• 2. Marsupials have a pouch (marsupium) on the abdomen of the female. These mammals give birth to immature young ones which complete their development in the mother's pouch. Opossum, kangaroo and quoll are examples.
• 3. Placental mammals are the most advanced mammals. During development, a structure called the placenta is formed between the mother's uterus wall and the foetus body. The foetus is nourished and wastes from the foetus are removed through this placenta. They give birth to young ones — they are viviparous. Dolphin, rat, monkey, bat, elephant and human are examples; also squirrel, musk deer, walrus, wild boar and leopard.

Viruses are not considered organisms because they are acellular — not made of cells. They lack any of the characteristics of the three domains of life and are not classified in any domain and kingdom.

A virus consists of nucleic acid (DNA or RNA) surrounded by a protein coat. They cannot run any metabolism and depend upon the host cell (including plants, animals and bacteria) to replicate and synthesize their proteins.

Viruses are classified based on several characteristics, including their genetic material, replication strategy, morphology and the hosts they infect. The classification of viruses follows guidelines established by the International Committee on Taxonomy of Viruses (ICTV).

Classification on the basis of host range:

1. Animal viruses: Infect animals, including humans. Examples: Influenza virus, Rabies virus.
2. Plant viruses: Infect plants. Examples: Tobacco mosaic virus, Potato virus X.
3. Bacteriophages: Infect bacteria. Examples: T4 phage, Lambda phage.
4. Archaea viruses: Infect archaea. Examples: Sulfolobus spindle-shaped virus.

Classification on the basis of morphology:

1. Helical viruses: These have a capsid with a helical structure surrounding the nucleic acid. Examples: Tobacco mosaic virus, Rabies virus.
2. Icosahedral viruses: These have a capsid with a symmetrical icosahedral shape. Examples: Adenoviruses, Herpesviruses.
3. Complex viruses: These have a complex structure, often with a combination of icosahedral and helical features, and sometimes additional structures like tails. Examples: Bacteriophages (viruses that infect bacteria).
4. Enveloped viruses: These have an outer lipid envelope derived from the host cell membrane, surrounding their capsid. Examples: Influenza virus, HIV.
5. Non-enveloped (naked) viruses: These lack an outer lipid envelope and consist only of a capsid enclosing the nucleic acid. Examples: Poliovirus, Adenovirus.

Classification on the basis of genetic material:

1. DNA viruses: Viruses with DNA as their genetic material. This DNA can be single-stranded (ssDNA) or double-stranded (dsDNA). Examples: dsDNA viruses — Adenoviruses (cause respiratory infections), Herpesviruses (cause herpes, chickenpox); ssDNA viruses — Parvoviruses (cause gastroenteritis).
2. RNA viruses: Viruses with RNA as their genetic material. This RNA can be single-stranded (ssRNA) or double-stranded (dsRNA). Examples: ssRNA viruses — Coronaviruses (cause COVID-19), Influenza viruses (cause flu); dsRNA viruses — Rotaviruses (cause gastroenteritis).

Classification on the basis of replication strategy:

1. Positive-sense RNA viruses: The RNA genome is directly translated into proteins by the host cell's ribosomes. Examples: Poliovirus, Hepatitis C virus.
2. Negative-sense RNA viruses: The RNA genome is transcribed into mRNA by a viral RNA polymerase before translation. Examples: Rabies virus, Ebola virus.
3. Reverse transcribing viruses: These viruses replicate through a DNA intermediate using the enzyme reverse transcriptase. They can have RNA or DNA genomes. Examples: RNA genome — Retroviruses like HIV (cause AIDS); DNA genome — Hepadnaviruses like Hepatitis B virus.

Prions and viroids are also acellular. They are also not considered living organisms. Prions are composed of protein only and viroids are composed of circular RNA only. Both these particles cause infectious diseases.

Biodiversity, a term derived from "biological diversity", refers to the variety of life forms present in different ecosystems, encompassing the diversity of species, genes and ecosystems. It represents the richness and variability of living organisms and their interactions with each other and their environments.

Bio (life) + Diversity (variety) = all the different kinds of life on Earth — plants, animals, bacteria, fungi — all together.

Ecosystem: An ecosystem is a dynamic and interactive system composed of living organisms and their physical environment. It includes all the biotic factors as well as the abiotic factors.

Niche: A niche refers to the role or function of an organism or species within an ecosystem. It includes its habitat, its interactions with other organisms (predation, competition and symbiosis), and its role in energy flow within the ecosystem.

Biodiversity assessment levels: The assessment of biodiversity involves multiple levels, each providing unique insights into the complexity of life.

• Species level: At the species level, biodiversity is assessed by identifying and counting the different species present within a given area. Species diversity includes not only the number of species but also their relative abundance and distribution.
• Genetic level: At the genetic level, biodiversity refers to the variety of genetic information contained within all individual organisms of a species. This genetic diversity is crucial for the adaptability and survival of species, enabling them to cope with environmental changes and challenges.
• Ecosystem level: At this level, biodiversity assessment includes the range of habitats, from forests and wetlands to grasslands and deserts. It involves understanding how different ecosystems function and how they contribute to overall ecological health.

Importance of random sampling in determining biodiversity: Random sampling is a fundamental technique in ecological studies for assessing biodiversity within a specific area. This method is crucial for several reasons:

1. Minimizes bias: It ensures that every part of the study area has an equal chance of being sampled, which provides a more accurate representation of the overall biodiversity.
2. Provides reliable estimates: Random sampling allows for the collection of data that can be statistically analyzed to estimate species richness, abundance and distribution.
3. Facilitates comparisons: It enables comparisons between different areas or habitats by providing standardized methods of data collection.
4. Enhances representativeness: By covering different parts of the study area, random sampling ensures that the sample represents the diversity of the entire area.
5. Supports conservation efforts: Accurate biodiversity assessments through random sampling are essential for identifying areas of high conservation value and for monitoring changes in biodiversity over time.

Methods to assess biodiversity: Various methods are employed for assessing the distribution and abundance of organisms in an area.

Methods to assess distribution:

1. Quadrat sampling: It involves dividing the study area into a grid and sampling within randomly selected squares (quadrats). This method is particularly useful for studying plant populations or sessile organisms. For example, in a forest, a researcher might lay out quadrats of a fixed size and record the presence or absence of each plant species within these quadrats.
2. Transect sampling: It involves laying out a line or strip (transect) across the study area and recording species at regular intervals along this line. This method is effective for studying the distribution of species across environments. For example, in a coastal zone, a transect can be laid from the high tide line to the low tide line, to record the types and abundance of intertidal organisms.
3. Aerial surveys: Aerial surveys use aircraft or drones to observe and record the distribution of organisms over large areas. For example, it can be used to track the distribution of bird species across a large wetland area or to monitor large mammal populations in savannas.

Methods to assess abundance:

1. Point counts: Point counts involve observing and recording the number of individuals of a species from a fixed point over a specified period. This method is commonly used for birds and other mobile animals.
2. Mark-recapture: It involves capturing, marking and releasing individuals of a species, then recapturing them later to estimate population size and density. This method is useful for animals that are difficult to count directly.
3. Quadrat counts: In this method, researchers use quadrats to count the number of individuals of a species within each quadrat and then infer these counts to estimate overall abundance.
4. Capture-recapture methods: These models account for variables such as varying capture probabilities and movement between areas.
5. Remote sensing: Remote sensing uses satellite or drone imagery to assess the abundance and distribution of species, particularly for large-scale or inaccessible areas.

Species: The term "species" is a fundamental concept in biology. A species is generally defined as a group of individuals that can interbreed and produce fertile offspring under natural conditions. Members of the same species share common characteristics and genetic makeup, which distinguishes them from individuals of other species.

Identification of species by using physical traits and similarities can sometimes be problematic due to the existence of cryptic species — organisms that appear similar but are genetically distinct. To address this, German-American biologist Ernst Mayr emphasized reproductive isolation as the key criterion. According to this concept, species are groups of interbreeding natural populations. Members of different species do not typically mate or produce viable, fertile offspring.

Speciation: Speciation is the evolutionary process by which new species arise from a common ancestor. It involves the accumulation of genetic changes that lead to reproductive isolation between populations. There are several mechanisms of speciation:

• 1. Allopatric speciation: It occurs when a population is geographically separated into two or more isolated groups. These groups experience different environments and evolve independently. Over time, the accumulated differences can become significant enough to prevent interbreeding, even if the geographical barrier is removed. An example is the speciation observed in Darwin's finches on the Galápagos Islands, where different populations adapted to diverse environments.
• 2. Peripatric speciation: It involves a small, isolated population at the edge of a larger population. The small population undergoes rapid evolutionary changes, leading to divergence from the original population. An example can be seen in island species that evolve from a small founding population.
• 3. Parapatric speciation: This occurs when populations are adjacent to each other but occupy different environments along a gradient. Gene flow between the populations is limited, and they evolve adaptations to their specific environments. Over time, this can lead to reproductive isolation. An example is the grass species Anthoxanthum odoratum, which exhibits different adaptations to varying soil conditions across a gradient, leading to reproductive isolation in different soil types.
• 4. Sympatric speciation: In this form, new species arise within the same geographical area without physical barriers. Sympatric speciation often occurs through mechanisms such as polyploidy (where an organism has multiple sets of chromosomes) or niche differentiation (where different subpopulations exploit different resources). For instance, certain plants can undergo polyploidy, leading to immediate reproductive isolation and the formation of new species.

Figure 1.30 (Modes of speciation) shows all four modes starting from an original population, passing through an initial step and reproductive isolation, and ending in the evolution of new species.