Chapter 2: Systematics of Living Organisms
For more than two hundred years, biologists were satisfied that they knew a certain small tropical butterfly. It had a proper scientific name, Astraptes fulgerator, a place in every reference book, and a familiar look — the same dark wings and blue-green sheen wherever it was found in Central and South America. As far as anyone could tell, it was one species.
Then, in the early 2000s, a team of biologists working in the forests of Costa Rica decided to check that assumption in a new way. Instead of comparing wings and colours, they compared a short stretch of DNA taken from tiny tissue samples of hundreds of these butterflies — a technique called DNA barcoding, developed by Paul Hebert and his colleagues at the University of Guelph in Canada. The result surprised everyone. What had been catalogued as a single species turned out to be a cluster of about ten different species, each with its own DNA signature, each feeding on its own set of food plants as caterpillars.
Nothing about the butterflies had changed. What changed was our ability to read the evidence. That is the story of systematics: a constant effort to sort the enormous variety of life on Earth into groups that are not merely convenient, but true to how organisms are actually related.
Diagram
Fig. 2.0 – Opening illustration: a forest scene with several near-identical butterflies, each linked by a fine line to a distinct DNA barcode strip, showing one apparent species resolving into several.
Keep these questions in mind as you read: this chapter will answer every one of them.
2.1 Systematics
The Need to Sort Living Things
Look around you and you will find an enormous variety of living organisms — trees, insects, birds, moulds on stale bread, bacteria you cannot even see. This variety is called biodiversity, and human beings have been making use of it since time immemorial for food, medicine, shelter and clothing.
To use this wealth, early humans first had to tell one organism from another — which fruit was safe, which root cured a fever, which animal was dangerous. This everyday need to distinguish and identify organisms slowly grew into a formal branch of biology called classification, and classification in turn gave rise to systematics.
This is not a modern habit. Indian, Greek and Roman philosophers all attempted to arrange living things into orderly groups thousands of years ago, and their efforts form the foundation on which modern systematics stands.
What Systematics Means
The word “systematics” comes from the idea of putting things into a system. It does not stop at sorting organisms into groups; it also asks how those groups came to exist, and how closely they are related to one another through evolution.
A widely accepted definition was given by the American palaeontologist G. Simpson in 1961.
Notice the two halves of that definition. “Kinds and diversity” covers the sorting work — recognising how many different types of organisms exist and what makes each distinct. “Comparative and evolutionary relationships” covers the deeper question — which groups share a recent common ancestor and which branched apart long ago.
Taxonomy: Classification With Rules
Taxonomy is the part of this work that follows definite rules and principles while arranging organisms. Without agreed rules, every biologist would group and name organisms differently, and the results could never be compared.
The word itself explains the idea. It is built from two Greek words: taxis, meaning arrangement, and nomos, meaning law or rule. So taxonomy literally means “the laws of arrangement.”
The term taxonomy was first introduced by A. P. de Candolle, a Swiss botanist who lived from 1778 to 1841.
How the Pieces Fit Together
It helps to see taxonomy and systematics as steps in one continuous process rather than as rival terms. Identification tells us what an organism is; nomenclature gives it a universally accepted name; classification places it in a group; and systematics adds the evolutionary story that explains why the groups look the way they do. This progression is shown in FC 2.1.
Flowchart
FC 2.1 – Scope of systematics: Identification (what is this organism?) → Nomenclature (giving it a valid scientific name) → Classification (placing it in ordered groups by fixed rules = taxonomy) → Systematics (adding comparative study and evolutionary relationships)
In NEET and board papers, this section is usually tested through short definition-based questions and assertion–reason items that check whether you can separate taxonomy from systematics, and whether you remember that the term taxonomy was coined by de Candolle while the quoted definition of systematics is credited to Simpson.
2.2 Classification
Classification is the practical heart of taxonomy. It means placing organisms, or groups of organisms, into distinct categories according to a particular and well-established scheme or plan.
The word “scheme” matters here. A classification is not a random sorting; it follows a plan that other biologists can understand and repeat. The plan itself is built on one simple foundation — the similarities and dissimilarities among organisms.
Everything then depends on which similarities a biologist chooses to trust. Choose colour and habit, and you get one arrangement. Choose flower structure, and you get another. Choose shared ancestry, and you get a third. This is why classification systems are grouped into three types — artificial, natural and phylogenetic — as compared in Fig. 2.2.
Diagram
Fig. 2.2 – The same set of plants sorted three ways: by an easily seen feature such as colour (artificial), by many structural features taken together (natural), and by branching descent from a common ancestor (phylogenetic).
Artificial Classification
An artificial system uses very few features, chosen because they are easy to observe rather than because they are biologically deep. Habit (whether a plant is a herb, shrub or tree), colour, and similar surface characters are typical choices.
Such features are non-evolutionary — they say nothing about ancestry. As a result, an artificial system often ignores the affinity, that is, the true relationship, between organisms, and may place unrelated organisms side by side simply because they look alike.
The classic example is the Linnaeus system of classification, in which flowering plants were grouped largely by the number and arrangement of their stamens and pistils. It was quick and workable, which is exactly why it spread — but plants with the same number of stamens are not necessarily relatives.
Natural Classification
A natural system is not built for convenience. It is based on characters that are objectively significant — features that genuinely reflect the overall nature of the organism, taken together in large numbers rather than picked one or two at a time.
Because it weighs many characters at once, a natural system usually brings together organisms that are, in fact, related, even though it was not designed around evolution as such.
The standard example is Bentham and Hooker’s system of classification.
Phylogenetic Classification
A phylogenetic system goes one step further and asks the evolutionary question directly: which organisms descended from a common ancestor?
Groups in such a system are meant to reflect branches of the tree of life. Organisms sharing a recent common ancestor are placed close together; those whose ancestries separated long ago are placed far apart.
Engler and Prantl’s classification is the example given for this type. You will meet another one shortly — the three domains of life, which is phylogenetic in exactly this sense.
Taxa and Categories
Two words appear again and again once a classification is in place: “category” and “taxon” (plural, taxa).
Each category is a unit of classification. It represents a rank — a level in the classification scheme — and such a unit is commonly termed a taxon.
You will see in the sections that follow how these ranks stack one above the other, from species at the bottom to kingdom and domain at the top.
For examinations, this section is most often tested through match-the-following items pairing a system with its type — Linnaeus with artificial, Bentham and Hooker with natural, Engler and Prantl with phylogenetic — and through assertion–reason questions asking why an artificial system can group unrelated organisms together.
2.3 Three Domains of Life
From Simple Beginnings to Diverse Life
It is believed that life originated on the earth in a very simple form. The early living beings faced a constant struggle to survive, and out of that struggle arose more and more perfect forms of life.
This struggle and progress is what we call evolution, and it is evolution that led to the appearance of the diverse life forms we see today. Any classification that hopes to be truthful must therefore reflect this branching history.
Woese’s Three Domains
Carl Woese, in 1990, proposed three domains of life to classify all living forms. They are Archaea, Bacteria and Eukarya.
A domain is a unit larger than kingdom in the system of classification. In other words, it sits above kingdom — several kingdoms can fall within a single domain, which makes domain the broadest rank in use today.
The relationship between the three domains is shown in Fig. 2.1. Notice that all three lines are traced back to a single point marked “common ancestor” — the diagram is making a claim about descent, not merely about resemblance.
Diagram
Fig. 2.1 – Phylogenetic descent: three branches labelled Bacteria, Archaea and Eukarya arising from a single line labelled Common ancestor.
Cell Type: The First Great Divide
Bacteria and Archaea both have prokaryotic cells, whereas Eukarya have eukaryotic cells.
A prokaryotic cell has no true nucleus — its genetic material lies free in the cytoplasm, without a nuclear membrane around it — and it lacks membrane-bound organelles. A eukaryotic cell has a proper nucleus enclosed by a nuclear membrane, along with membrane-bound organelles such as mitochondria.
Why rRNA Was the Deciding Evidence
All three domains have very unique ribosomal RNA (rRNA). Ribosomal RNA is the RNA that forms part of the ribosome, the structure on which every cell builds its proteins.
Because protein synthesis is essential to every living thing, rRNA is present in all organisms and changes only very slowly over evolutionary time. That combination makes it an excellent molecular yardstick: small, steady differences in rRNA sequence reveal how long ago two lineages parted company, even when the organisms look identical under a microscope.
Archaea and Bacteria: Alike in Appearance, Not in Ancestry
Archaea are known for their survival in very extreme conditions — high temperature, high salinity, acidic conditions, and the like. Environments that would kill most cells are, for them, ordinary living conditions.
Bacteria, though they are also prokaryotes, differ from Archaea in the structure of the cell wall. This difference in wall chemistry, along with the rRNA evidence, is what justifies keeping them in separate domains.
In examinations, this section commonly appears as a direct question on who proposed the three domains and in which year, and as assertion–reason items testing whether you understand that domain ranks above kingdom, and that Bacteria and Archaea are separated on the basis of rRNA and cell wall structure rather than on appearance.
2.4 Chemotaxonomy
Chemotaxonomy is a method of biological classification based on the similarities and differences in the structure of certain compounds found among the organisms being classified. In short, it is classification based on the chemical constituents of organisms.
The reasoning behind it is simple. The chemicals a cell builds are made by its enzymes, and those enzymes are coded by its genes. So a shared chemical usually means shared genetic instructions, and shared instructions point to shared ancestry.
Cell Wall Chemistry as Evidence
The cell wall gives a clear example. The Archaea have a cell wall without peptidoglycan, while that of Prokarya is with peptidoglycan. Peptidoglycan, as its name suggests, is a mesh built from sugar chains cross-linked by short chains of amino acids.
Among Eukarya the same test separates two kingdoms neatly: fungi have a chitinous cell wall, while plants have a cellulosic cell wall. Cellulose and chitin are both long chains of sugar units, but they are not the same polymer, and no organism builds both as its wall material.
Chemotaxonomy is not restricted to cell walls. In flowering plants, biologists compare pigments, alkaloids and other chemical products, and members of a family very often share a distinctive chemical signature.
In examinations, this section is usually tested through match-the-following items pairing a group with its wall material, and through assertion–reason questions on why Archaea and Bacteria are separated even though both are prokaryotes.
2.5 Numerical Taxonomy
Numerical taxonomy is a system based on the quantification of characters, which then develops an algorithm for classification. Instead of describing an organism in words, the taxonomist converts each of its features into a number.
The scoring itself is straightforward. A large number of characters is listed, and for every organism each character is recorded as present or absent, or given a measured value, so that the whole organism becomes a row of figures.
The basic aim of this taxonomy was to create a classification using numeric algorithms, such as cluster analysis, rather than using a subjective evaluation of the properties of organisms. Cluster analysis is a computational method that measures how similar every pair of organisms is, and then places the most similar ones together in groups.
This system was first proposed by R. Sokal and P. Sneath in 1963. The sequence of steps they set out is summarised in FC 2.2.
Flowchart
FC 2.2 – Steps in numerical taxonomy: select the organisms to be classified → list a large number of characters → score every character for every organism as a numerical value → calculate a similarity value for each pair of organisms → apply cluster analysis → obtain groups in which the most similar organisms fall together
For examinations, remember the names Sokal and Sneath with the year 1963, the term cluster analysis, and the key idea that all characters are given equal weight.
2.6 Cladogram
A cladogram is a typical branching pattern used to show relationships between organisms. The diagram of the three domains of life that you saw earlier, in Fig. 2.1, is itself a cladogram.
Every such diagram has two kinds of features. The ends of the branches carry the organisms or groups being compared, while each point where a line splits stands for a common ancestor from which those branches descended.
A cladogram represents a hypothetical relationship, denoting a comparison of organisms and their common ancestors. The word “hypothetical” is important: no one has ever seen the ancestor sitting at a branch point. Its existence is inferred from the characters shared by the organisms above it.
In examinations, cladograms usually appear as diagram-based questions: you may be shown a branching pattern and asked which two groups are most closely related, or asked to identify what a particular node represents.
2.7 Phylogeny
Phylogeny is the evolutionary relationship of an organism — the history of descent that connects it to every other form of life.
It is an important tool in classification because it takes into account not merely the morphological status of an organism, but also the relationship of one group of organisms with other groups of life. Morphological status means the external form and structure of the organism: its shape, its size, the arrangement of its parts.
Two organisms may be alike in form and yet belong to lineages that parted long ago, so form alone cannot settle the question of relationship. Phylogeny therefore asks a wider question — not “what does this organism look like?” but “where does it sit on the tree of life?”
The phylogenetic approach helps us to understand evolution, and it also focuses on the similarities of metabolic functioning among organisms. Metabolism is the whole set of chemical reactions by which a cell obtains energy and builds its materials.
Such reactions are inherited, step by step, along with the genes that code for the enzymes carrying them out. When two groups run the same biochemical pathway in the same way, that shared machinery is strong evidence of a shared ancestor. The kinds of evidence used, from the most obvious to the most refined, are set out in FC 2.3.
Flowchart
FC 2.3 – Evidence used in building a phylogeny: morphology (external form) → internal anatomy and development → metabolic and biochemical pathways → molecular sequences such as rRNA → phylogenetic relationship of the group
Woese’s three domain concept, which you have already studied, and Whittaker’s five kingdom system, which you will meet later in this chapter, are both very good examples of phylogenetic relationship. Neither was built simply on how organisms look; both attempt to place organisms according to how they are related by descent.
For examinations, be clear that phylogeny means evolutionary relationship, that it goes beyond morphology to include metabolic similarities, and that both the three domain concept and the five kingdom system are cited as examples of phylogenetic classification.
2.8 DNA Barcoding
DNA barcoding is a new method for the identification of any species, based on its DNA sequence obtained from a tiny tissue sample of the organism under study.
A DNA sequence simply means the order in which the four bases — adenine, thymine, guanine and cytosine — are arranged along a stretch of the DNA molecule. That order differs slightly from species to species, and it is this difference that the method reads.
The name is borrowed from the barcode printed on packaged goods in a shop. Just as a scanner reads a pattern of lines and matches it against a list of products, a laboratory reads a short standard stretch of DNA and matches it against a list of species.
Why the Method Is Valuable
DNA barcoding helps in the study of newly identified species. When a specimen does not match anything in the library, that itself is a signal — the organism may belong to a species not yet described.
It also helps in understanding the ecological and evolutionary relationships between living beings, since the degree of difference between two sequences reflects how closely or distantly the two organisms are related.
There is a further practical advantage. Identification no longer depends on having a whole, undamaged, adult specimen. A fragment of tissue, an egg, a larva or a piece of dried plant material carries the same DNA as the complete organism.
How Barcoding Is Done
The process of DNA barcoding includes two basic steps. The first is collecting DNA barcode data of known species, so that a reference library is built up. The second is matching the barcode sequence of the unknown sample against that barcode library for identification. The sequence of operations is set out in FC 2.4.
Flowchart
FC 2.4 – DNA barcoding: collect tissue samples of correctly identified known species → sequence the standard DNA region from each → store the sequences to build a barcode library → take a tiny tissue sample of the unknown organism → sequence the same DNA region → match the sequence against the library → if a match is found, the species is identified; if no match is found, the organism may belong to a species not yet recorded
Applications
DNA barcoding has many applications. A few worth noting are the protection of endangered species, the preservation of natural resources, pest control in agriculture, the identification of disease vectors, the authentication of natural health products, and the identification of medicinal plants.
Each of these rests on the same requirement: a correct name for the organism, arrived at quickly and from very little material.
In examinations, DNA barcoding is commonly tested through short answer questions on its two basic steps, and through application-based items asking which method would be suitable for identifying an organism from a damaged or incomplete sample.
2.9 Taxonomic Categories
Classification is not a single step process. It involves a hierarchy of steps, in which each step represents a rank or category.
Working in steps is what makes the system usable. Rather than deciding in one jump that an organism is a mango tree, the taxonomist narrows the field stage by stage — first the broadest group, then a narrower one within it, and so on until only one kind of organism remains.
Since a category is part of the overall taxonomic arrangement, it is called a taxonomic category. All the categories, taken in their increasing or retrogressive order, together constitute the taxonomic hierarchy.
Increasing order means moving upward, from the smallest category to the largest. Retrogressive order means moving the other way, downward from the largest to the smallest. Either direction describes the same ladder; only the starting point changes.
The Compulsory Categories
Kingdom, division, class, order, family, genus and species are the categories in hierarchical sequence, and they are shown in order in FC 2.5. These are the compulsory categories — every organism that is classified must be placed in each one of them.
Flowchart
FC 2.5 – Sequence of compulsory taxonomic categories, largest to smallest: Kingdom → Division → Class → Order → Family → Genus → Species
The Facultative Categories
Besides the compulsory categories, there are some facultative categories, such as sub-order and sub-family, which are used as per need.
Facultative means optional. When a group contains a very large number of members that clearly fall into smaller clusters, a taxonomist may insert an extra level — a sub-family within a family, for instance — to keep the arrangement precise. When no such need exists, the extra level is simply left out.
In examinations, this section usually appears as sequence-ordering questions asking you to arrange the categories from largest to smallest, or as short questions on the difference between a compulsory and a facultative category.
2.10 Taxonomic Hierarchy
What a Taxon Is
Once the ladder of categories exists, each rung has to be filled with an actual group of organisms. Such a group is called a taxon.
A taxon is a taxonomic group of any rank in the system of classification. This definition was given by H. J. Lam in 1948.
The phrase “of any rank” is the key to the idea. A taxon is not tied to one particular level — a kingdom is a taxon, and so is a family, and so is a single species.
In the plant kingdom, for example, each of the following represents a taxonomic group, that is, a taxon: Angiospermae, Dicotyledonae, Polypetalae and Malvaceae. They sit at four different ranks, yet every one of them is a taxon.
Two Organisms Placed in the Hierarchy
The clearest way to understand the hierarchy is to follow one plant and one animal all the way down it. Table 2.2 does exactly this for the China-rose and the cobra.
Table 2.2 Classification of China-rose and Cobra
| Category | Taxon | Taxon |
|---|---|---|
| Kingdom | Plantae | Animalia |
| Division/Phylum | Angiospermae | Chordata |
| Class | Dicotyledonae | Reptilia |
| Sub-class | Polypetalae | Diapsida |
| Series | Thalamiflorae | – |
| Order | Malvales | Squamata |
| Family | Malvaceae | Elapidae |
| Genus | Hibiscus | Naja |
| Species | rosa-sinensis | naja |
Read the table downwards and you will see the groups getting smaller at every step. Kingdom Plantae holds every plant on earth; by the time you reach the genus Hibiscus, only a small set of closely similar plants remains; and the species rosa-sinensis is the China-rose alone.
Notice also that the first column contains two categories you were told are optional. Sub-class and series are facultative categories, brought in here because the plant kingdom is large enough to need those extra steps. In the animal column the row for series is left blank, since that category is not used for animals.
Putting the last two rows together gives the complete scientific name of each organism: Hibiscus rosa-sinensis for the China-rose and Naja naja for the cobra.
In examinations, this section is most often tested by giving you a partly filled hierarchy and asking you to complete it, or by asking which category a named taxon such as Malvaceae or Elapidae belongs to.
2.11 Units of Classification
You have seen the ladder of categories and you have seen two organisms placed on it. Now each rung deserves a closer look, because every category has its own defining idea. We shall climb from the bottom upwards, from species to kingdom.
Species
Species is the principal lowest natural taxonomic unit, ranking below a genus, and it is denoted by a Latin binomial — a two-word Latin name. It is considered to be the basic unit of classification.
Biologically, a species is a group of organisms that can interbreed under natural conditions to produce fertile offspring. Read that definition carefully, because each part of it is doing work. “Under natural conditions” rules out crosses forced in captivity, and “fertile offspring” means the young must themselves be able to reproduce.
For a long time, a species was thought to be an indivisible, stable and static unit — a fixed kind of organism that neither changed nor could be broken down further.
Modern taxonomy takes a different view. Sub-divisions of species, such as sub-species, varieties and populations, are now recognised and are given more importance, because members of a single species living in different places are often measurably different from one another.
Genus
Genus is a higher taxonomic rank, or category, than species. It is used in the biological classification of both living and fossil organisms.
A genus is a group of species bearing close resemblance to one another in their morphological characters, but which usually do not interbreed. So a genus collects the near relatives of a species — organisms clearly built on the same plan, yet reproductively separate.
The tiger, the leopard and the lion all belong to the same genus, Panthera, yet each is different from the others. Anyone can see that the three are variations on one design, and that is exactly what a genus records.
The genus Solanum gives a plant example. Brinjal and potato both belong to this genus, although one is grown for its fruit and the other for its underground tuber.
Family
Family is one of the major hierarchical taxonomic ranks. A family represents a group of closely related genera.
Among plants, genera such as Hibiscus, Gossypium, Sida and Bombax are included in the same family, Malvaceae. Notice that Hibiscus appeared in Table 2.2 — the China-rose sits inside this very family.
Among animals, the cat belongs to the family of leopards, tigers and lions, the family Felidae. The dog, however, belongs to a different family, Canidae.
Cohort / Order
Order, also called cohort, is a taxonomic rank used in the classification of organisms and recognised by nomenclature codes. An order is a group of closely related families showing definite affinities, and it is thus a step higher than family in the taxonomic hierarchy.
Because an order is a wider group, members belonging to the same order but to different families may show very few dissimilarities. In other words, being in different families does not always mean looking very different.
The families Papavaraceae, Brassicaceae, Capparidaceae and others share parietal placentation — an arrangement in which the ovules are attached to the wall of the ovary — and on this evidence they are grouped in the order Parietales.
The animal example follows the same logic. The families of dogs and cats are different, yet both belong to the same order, Carnivora.
Class
The class is a distinct taxonomic rank of biological classification, having its own distinctive name. It is a group of higher taxonomic rank than order, and it is an assemblage of closely related or allied orders.
The order Carnivora and the order Primates both belong to the class Mammalia. So monkeys, gorillas and gibbons, which are Primates, and dogs, cats and tigers, which are Carnivora, all belong to the same class.
Read the table upwards and you can see exactly where the two animals separate: they share the same class and the same order, and part company only at the level of family.
Division / Phylum
The division is a category composed of closely related classes. For example, the division Angiospermae includes two classes — Dicotyledonae and Monocotyledonae.
In animal classification, division is a sub-unit of the category phylum. This is why the same row of Table 2.2 was headed “Division/Phylum” — plant taxonomists use the term division at that level, while animal taxonomists use phylum.
Sub-kingdom
Different divisions having some similarities form a sub-kingdom.
The divisions Angiospermae and Gymnospermae together form the sub-kingdom Phanerogams, also called Spermatophyta. What they share is the production of seeds, which sets them apart from plants that reproduce by spores.
Kingdom
Kingdom is the highest taxonomic category, composed of different sub-kingdoms.
The sub-kingdoms Phanerogams and Cryptogams together form the plant kingdom, Plantae, which includes all the plants, while all animals are included in the kingdom Animalia.
The whole plant arrangement, from kingdom down to class, is set out in FC 2.6.
Flowchart
FC 2.6 – Plant kingdom worked downwards: Kingdom Plantae → sub-kingdoms Phanerogams (Spermatophyta) and Cryptogams → Phanerogams → divisions Angiospermae and Gymnospermae → Angiospermae → classes Dicotyledonae and Monocotyledonae
Climbing the Ladder: What Changes at Each Step
The taxonomic categories considered so far are broad categories. Scientists have added sub-categories to these in order to place organisms in a more scientific and precise manner.
As you go higher in the taxonomical ladder, the number of common characters shared by the members goes on decreasing. Members of a species share almost everything; members of a family share a good deal; members of a kingdom share only a few very general features.
This has a practical consequence. If we are comparing two organisms that are related to each other only at the division or phylum level, their classification may become difficult, since so few characters are common between them that there is little to work with.
In examinations, this section is a favourite source of match-the-following and odd-one-out questions — pairing a genus with its family, or asking which organism does not belong to a given group — and of assertion–reason items on why the number of common characters falls as one moves from species towards kingdom.
2.12 Nomenclature
Any object that becomes known to human intelligence must possess a name. Describing an object every time we wish to speak about it is neither possible nor convenient, so a name is what allows ideas about it to be communicated.
The art of naming objects is, in fact, a science, and that science is called nomenclature. All living organisms are known by a particular name.
Two kinds of names are in use for organisms, and they serve very different purposes.
Vernacular, Local or Common Names
Widely distributed organisms have a large number of common names. The more useful and the more widespread an organism is, the more names it accumulates.
The pansy (Viola tricolor L.), grown in most European and American gardens, has about fifty common English names — and that is in a single language.
In a multilingual country like India the problem multiplies. Almost all useful plants have local names, which differ from language to language and even from dialect to dialect. In Ayurveda, the mango (Mangifera indica L.) is known by over fifty different names, all of them in Sanskrit alone.
Hence common names obviously have limited usage. For universal application, a unique name for a particular organism is very much essential.
Scientific Names
Scientists have given scientific names to all the known organisms in order to overcome the difficulties raised by common names. These names are systematic, and they therefore provide a means for international communication: a botanist in Jaipur and a botanist in Brazil use exactly the same name for the same plant.
Initially the polynomial system was used, in which an organism was named by a string of Latin words that described it. Such names were accurate but long and awkward, and different authors described the same plant differently, so the names themselves varied.
Carl Linnaeus then used the binomial system of nomenclature, in which the scientific name consists of two epithets, or parts. He introduced this system in his book Species Plantarum, published in 1753.
The International Code of Botanical Nomenclature (ICBN) has been set up to confirm the scientific names.
Reading a Scientific Name
According to this system, the scientific name of the sunflower is Helianthus annuus. Here Helianthus indicates the name of the genus, called the generic epithet, and the second word, annuus, denotes the name of the species, called the species epithet.
The two words together do more than label the plant. They also place it, because the first word tells you the genus, and therefore tells you which other plants are its close relatives. The parts of a complete scientific name are labelled in Fig. 2.15.
Diagram
Fig. 2.15 – The scientific name Mangifera indica L. written out, with arrows labelling the generic epithet (capital first letter), the species epithet (small first letter), the italic type, and the author abbreviation.
Rules of the Binomial Nomenclature System
The binomial nomenclature system follows certain rules.
- The name of an organism is composed of two Latin or Greek words.
- The generic epithet is a simple noun. It should come first and begin with a capital letter.
- The specific epithet is a descriptive adjective. It should come later and begin with a small letter.
- The scientific epithet must be underlined separately if handwritten, and must be in italics when printed.
- The generic and specific epithet should not have less than three letters and more than thirteen letters.
- Usually the name of the author who names a plant or animal is also written in full or in abbreviated form after the scientific name. For example, in Mangifera indica L., the letter L stands for Linnaeus.
In examinations, this section is tested very directly: you may be given a scientific name written in several ways and asked which one is correct, or asked why binomial nomenclature is important, or asked what the abbreviation after a scientific name stands for.
2.13 Salient Features of Five Kingdoms
Why Two Kingdoms Were Not Enough
For a long time, living organisms were sorted into just two kingdoms — plants and animals. The scheme was simple, and for the organisms people saw around them every day it worked well enough.
It broke down the moment biologists looked closely at the microscopic world. Some organisms would not stay in either box, and one organism could show characters of both kingdoms at the same time. A system that cannot place an organism is not doing its job.
The five kingdoms and the main criteria that separate them are set out in FC 2.7.
Flowchart
FC 2.7 – Five Kingdom system: All organisms → if prokaryotic → Kingdom Monera; if eukaryotic → if unicellular → Kingdom Protista; if multicellular → if autotrophic with cellulosic wall → Kingdom Plantae; if heterotrophic with chitinous wall and extracellular digestion → Kingdom Fungi; if heterotrophic without cell wall, holozoic → Kingdom Animalia
Kingdom Monera
These are unicellular organisms with a prokaryotic cellular organization. Monera includes unicellular, prokaryotic organisms only.
They are omnipresent. They are found in all types of environment, including habitats that are not generally inhabited by any other living beings — which is why members of this kingdom turn up in boiling springs, in ice, in deep rock and inside other organisms.
Nutritionally, a few are photoautotrophs or chemoautotrophs, but the majority are heterotrophic in nature. A photoautotroph makes its own food using light energy, a chemoautotroph makes it using energy released from chemical reactions, and a heterotroph must obtain ready-made organic food from outside.
Cell Structure of Monerans
These organisms do not have a well defined nucleus. Their DNA exists as a simple, double stranded, circular, single ring without a nuclear membrane, and this chromosome is called the nucleoid.
Smaller circular molecules of DNA are often present as extra-chromosomal genetic elements, and these are called plasmids. Being separate from the main chromosome, plasmids can be gained or lost without disturbing the essential genes of the cell.
The cell wall is made up of peptidoglycan, also called murein, which is a polymer of sugars and amino acids.
Membrane bound organelles — for example mitochondria, chloroplast and endoplasmic reticulum — are absent. Ribosomes are present, but they are smaller in size, 70S, than those of eukaryotic cells.
The mode of reproduction in Monera is asexual, taking place with the help of binary fission or budding. Very rarely, sexual reproduction occurs by the conjugation method.
Shapes of Bacteria
Morphologically, bacteria are categorised into four groups: the spherical Coccus, the rod-shaped bacillus, the comma or kidney shaped vibrio, and the spring like spiral spirillum. These shapes, along with some related forms, are shown in Fig. 2.3.
Diagram
Fig. 2.3 – Different shapes of bacterial cells: Coccus, Coccobacillus, Vibrio, Bacillus, Spirillum and Spirochete, each drawn and labelled.
Shape is one of the first things recorded when an unknown bacterium is examined, because it can be seen directly under the microscope and needs no special equipment.
On the basis of evolution, bacteria can be classified as Archaebacteria and Eubacteria. This division is shown in FC 2.8.
Flowchart
FC 2.8 – Kingdom Monera on the basis of evolution: Bacteria → Archaebacteria (extremophiles, cell wall without peptidoglycan) and Eubacteria (true bacteria, cell wall of peptidoglycan) → Eubacteria → autotrophs (photosynthetic or chemosynthetic) and heterotrophs
a. Archaebacteria
These are differentiated from other bacteria on the basis of their different cellular features. These bacteria are mostly found in extreme environments, and are hence termed extremophiles.
They are found in a wide variety of places, from volcanic craters to salty lakes and hot springs. Their ability to withstand such hostile environments speaks of their capacity to survive in very severe conditions.
Bacteria that can withstand high salinities are called halophiles, while those that withstand extreme temperature are known as thermophiles.
A very common example is that of the methanogenic bacteria found in the gut of ruminants such as cows and buffaloes. These bacteria help in the production of methane in biogas plants.
Their cell wall is without peptidoglycans, and reproduction takes place by binary fission.
b. Eubacteria
These are commonly referred to as true bacteria. They have a cell wall of peptidoglycan.
They are found as both autotrophs and heterotrophs. The autotrophs can be photosynthetic, like Chlorobium (green sulphur bacteria) and Chromatium, or chemosynthetic, like the sulphur bacteria.
Filamentous Cyanobacteria
Some members are mostly multicellular filamentous forms living in fresh water. The body is covered by a mucilagenous sheath, a slimy layer that holds the filament together and protects it from drying.
The genetic material is typical prokaryotic — a circular DNA ring with no nuclear membrane, exactly as described earlier.
Chlorophyll-a, chlorophyll-b, carotenes and xanthophylls are the photosynthetic pigments present in them. Because they carry a range of pigments, they can absorb light of several different wavelengths.
The filaments show heterocysts, which help in nitrogen fixation. Nitrogen fixation is the conversion of nitrogen gas from the air into a combined form that living cells can use. A typical filamentous form is shown in Fig. 2.4.
Diagram
Fig. 2.4 – Cyanobacterium (Nostoc): a coiled filament of cells, with the heterocyst and the mucilagenous sheath labelled.
Heterotrophic Bacteria
Heterotrophs are the most abundant of all bacteria. Most of them are decomposers, known for breaking down large molecules into simpler molecules or minerals.
This work is what keeps the biosphere running. Without decomposers, the carbon and nitrogen locked in dead bodies and waste would never return to circulation.
They can be anaerobes, that is, organisms that live without oxygen, and they include forms that help in the curdling of milk (Lactobacilli), in the fixation of nitrogen (Azotobacter), in antibiotic production (Streptomyces), and in composting and the degrading of oil.
But the story does not end here. Some of them are pathogens, that is, they cause disease — typhoid, cholera, tuberculosis and tetanus are all caused by bacteria.
Mycoplasma
These are the smallest of the living forms. They do not have a cell wall at all.
Many forms are pathogenic. They are found to be resistant to common antibiotics due to the absence of a cell wall.
Kingdom Protista
This group includes all the unicellular but eukaryotic organisms. That single sentence carries both criteria — one cell, and a true nucleus.
These organisms show a link with all the eukaryotic kingdoms, namely Plantae, Fungi and Animalia. Some of them feed like plants, some like animals, and some like fungi, which is why the kingdom is often described as the meeting point of the eukaryotic world.
The three groups of protists are shown in FC 2.9.
Flowchart
FC 2.9 – Kingdom Protista: Protists → plant-like protists (Chrysophytes — diatoms; dinoflagellates; euglenoids) → animal-like protists (protozoans — amoeboid, flagellated, ciliate, sporozoan) → fungi-like protists (Myxomycetes)
a. Plant-like Protists
They are also termed Chrysophytes, and are commonly called phyto-planktons. They are microscopic and mostly photosynthetic, and they are the major producers in the oceans.
That last point deserves emphasis. Nearly all life in the sea ultimately depends on the food these microscopic drifting cells manufacture.
Most of them are referred to as diatoms, as they have a body wall made up of two soap-box like fitting silica covers. Fig. 2.5 shows the variety of patterns these covers can take.
Diagram
Fig. 2.5 – Diatoms: a field of diatom cells of several shapes, showing the patterned silica walls.
“Diatomaceous earth” is nothing but these shells, left behind over so many years. Diatomaceous earth is granular, and hence finds use in polishing and in filtration.
Dinoflagellates. These are aquatic, mostly marine, and photosynthetic. The cell wall is made up of stiff cellulosic plates, and they possess a pair of flagella.
They have a wide range of photosynthetic pigments, which can be yellow, green, brown, blue and red. Gonyaulax is a dinoflagellate that is responsible for the famous ‘red tide’; it makes even the sea appear red. Its structure is shown in Fig. 2.6.
Diagram
Fig. 2.6 – Gonyaulax: ventral view labelled with apical horn, epitheca, cingulum, hypotheca, sulcus, flagella and flagellar pores, alongside a dorsal view showing the plates and anatomical horns.
Euglenoids. They lack a cell wall but have a tough covering of proteinaceous pellicle, which keeps the shape of the cell while still allowing it to bend.
They possess two flagella, one short and the other long. They behave as heterotrophs in the absence of light, but they also possess pigments similar to those of higher plants, with which they carry out photosynthesis. The structure of Euglena is shown in Fig. 2.7.
Diagram
Fig. 2.7 – Euglena: an elongated cell labelled with flagellum, photoreceptor, contractile vacuole, chloroplasts, mitochondria, nucleus with nucleolus, Golgi apparatus, endoplasmic reticulum and stored carbohydrate.
This double ability is exactly why the two kingdom system failed. In the light, Euglena behaves like a plant; in the dark, it behaves like an animal; and it is the same organism throughout.
b. Animal-like Protists
They are also termed protozoans. They lack a cell wall and they are heterotrophs. They are believed to be primitive animal forms.
Amoeboid protozoans have pseudopodia as locomotory organs. Pseudopodia are temporary extensions of the cell that flow forward, allowing the cell both to move and to engulf food. Amoeba is a free living form, but Entamoeba is an endoparasite and causes amoebic dysentery.
Flagellated protozoans have flagella as their locomotory organ. Trypanosoma is a common flagellated pathogen, which causes sleeping sickness.
Paramoecium is a ciliate protozoan having cilia for locomotion. In Paramoecium, the gullet, which is a cavity, opens on the cell surface. Its structure is shown in Fig. 2.8.
Diagram
Fig. 2.8 – Paramoecium: a slipper-shaped cell labelled with cilia, oral groove, gullet, cytopyge, food vacuoles, contractile vacuole, macronucleus, micronucleus, lysosomes and trichocysts.
Plasmodium is a sporozoan protozoan. It causes malaria, and it forms spores in one of its life stages.
c. Fungi-like Protists
They are commonly from the group Myxomycetes. These are saprophytic organisms found on decaying leaves, meaning that they feed on dead and decaying organic matter.
Their cells aggregate to form a large cell mass called a plasmodium. The spores produced by the plasmodium are very tough and survive even very harsh conditions, which is how the organism outlasts periods when there is nothing to feed on. An example is Stemonitis.
Kingdom Plantae
The kingdom is dominated by autotrophs — organisms that manufacture their own food.
It also includes some semi-autotrophic members, the insectivorous plants such as the Venus fly trap, the pitcher plant and the bladderwort. These plants photosynthesise like any other plant, but they trap and digest insects as well, which supplies the extra nitrogen that their soils lack.
The kingdom further includes heterotrophic parasitic members like Cuscuta, which has lost the ability to feed itself and draws nourishment from the host plant it twines around.
Members of this kingdom are multicellular, having eukaryotic cells containing chlorophyll. Their cells have a cell wall mostly made up of cellulose.
Plants exhibit alternation of generations, that is, the life cycle has two distinct phases. Kingdom Plantae is divided into two major groups, Cryptogamae or Cryptogams and Phanerogamae or Phanerogams.
We will study this kingdom in detail in the next chapter.
Kingdom Fungi
These are eukaryotic heterotrophs showing extracellular digestion. They are found in warm and humid places.
Extracellular digestion means that the organism releases its digestive enzymes onto the food outside its body, and then absorbs the simple molecules that result. The food is digested first and taken in afterwards — the reverse of what happens in animals.
They have a simple body, which may be unicellular or made up of long thread like structures called hyphae. Large fungi such as mushrooms have a compact mass of cells. Unicellular organisms have a protoplast with many nuclei, as in Rhizopus and Saccharomyces, the unicellular yeast fungus.
Structure of the Fungal Body
Filamentous fungi consist of a body called the mycellium, in which hyphae are present.
The hyphae may be with septa or without septa — that is, they may or may not be divided by cross walls — and they may be uni- or multinucleate. The non-septate multinucleate hyphae are called coenocytic hyphae.
The cell wall in fungi is composed of chitin, a polysaccharide, also called fungal cellulose.
The fungi exhibit a heterotrophic mode of nutrition. Mostly they are saprophytic; some are parasitic or predators.
They reproduce sexually as well as asexually. Asexual reproduction takes place by fragmentation, fission and budding.
Some fungi are symbiotic. They either live with algae as lichens, or as mycorrhiza in association with the roots of higher plants.
Useful and Harmful Fungi
Fungi are useful as well as harmful, and the same kingdom supplies both food and disease.
Mushrooms are consumed as food, and yeast is used in bakery and breweries. Penicillium, a fungus, is well known for antibiotic production.
Harmful fungi cause diseases in plants and animals, for example Puccinia.
The fungi are further classified on the basis of their structure, mode of spore formation and fruiting bodies, as shown in FC 2.10.
Flowchart
FC 2.10 – Classification of fungi: Fungi → Phycomycetes (algal fungi, aseptate coenocytic hyphae) → Ascomycetes (sac fungi, branched septate hyphae) → Basidiomycetes (club fungi, branched septate hyphae) → Deuteromycetes (imperfect fungi, only asexual reproduction)
a. Phycomycetes
These are commonly called algal fungi. The mycelium is made up of aseptate coenocytic hyphae.
They commonly grow in moist and damp habitats, on decaying organic matter, as well as in aquatic habitats or as parasites on plants.
Examples are Mucor, Rhizopus (bread mould) and Albugo (a parasitic fungus on mustard). The structure of one of them is shown in Fig. 2.9.
Diagram
Fig. 2.9 – Mucor: a photomicrograph alongside a line drawing labelled with sporangium, sporangiophore and hypha.
b. Ascomycetes
These are called sac-fungi. These fungi are mostly multicellular; rarely, unicellular varieties include yeast. The hyphae are branched and septate.
Sac fungi can be decomposers, parasites, or coprophilous, meaning that they grow on dung.
Morels and truffles are varieties of sac fungi that are consumed as delicacies. Neurospora is useful in genetic and biochemical assays.
Examples are Aspergillus, Penicillium, Claviceps, Neurospora and Saccharomyces. One of them is shown in Fig. 2.10.
Diagram
Fig. 2.10 – Aspergillus: a photomicrograph of the growing fungus beside a line drawing of the conidial head showing the swollen tip bearing chains of spores.
c. Basidiomycetes
These are commonly called club fungi. They have branched, septate hyphae.
Examples include Agaricus (mushrooms), Ganoderma (bracket fungi), Ustilago (smuts) and Puccinia (rusts). A familiar member is shown in Fig. 2.11.
Diagram
Fig. 2.11 – Mushroom: a mushroom growing in grass, one specimen cut lengthwise to show the stalk, cap and gills.
d. Deuteromycetes
These are called imperfect fungi, which are known to reproduce only asexually. They are called “imperfect” because the sexual stage of their life cycle has never been observed.
Examples are Alternaria and Colletotrichum. The effect of one of them on a leaf is shown in Fig. 2.12.
Diagram
Fig. 2.12 – Alternaria: spores of the fungus as seen under the microscope, alongside an infected leaf showing dark spots.
Diagram
Fig. 2.16 – Lichen (Parmelia): a flat, leafy, grey-green lichen spreading over the bark of a tree.
Kingdom Animalia
Members of this kingdom are heterotrophs, adapted to holozoic nutrition. Holozoic nutrition means that food is taken into the body as solid material, digested inside it, and the waste then thrown out.
Most of them have the capacity of locomotion. This follows from the way they feed — an organism that must find and capture its food has to be able to move to it.
They are multicellular eukaryotes, in which the cells lack chlorophyll as well as a cell wall. The absence of a rigid wall is what allows animal cells to change shape, and it is what makes muscle and nerve tissue possible.
Growth is determinate, that is, it follows a definite pattern. An animal grows to a characteristic size and shape and then stops, unlike a plant, which can go on adding new parts throughout its life.
In chapter four, we will study Kingdom Animalia and its further classification.
In examinations, this section supplies a very large share of the questions: match-the-following items pairing an organism with its kingdom or class, odd-one-out questions on heterotrophic bacteria or on fungal classes, diagram-labelling of Euglena, Paramoecium or Mucor, and assertion–reason items on why Euglena could not be placed in the two kingdom system, or why Mycoplasma resists common antibiotics.
2.14 Acellular Organisms
Viruses and viroids are groups of acellular organisms that are not included in Whittaker’s Five Kingdom classification.
The word acellular means “not made of cells”. Since the five kingdom system sorts organisms by the kind of cell they possess, a particle that has no cell at all simply cannot be placed anywhere in it.
a. Viruses
Viruses were named so by Louis Pasteur, considering the meaning of the word — venom, or poison.
These obligate parasites were given the name ‘virus’ by M. J. Beijernck, after his observation that they were able to migrate in an agar gel. Being an infectious soluble agent, he called the filtrate ‘contagium vivum fluidum’, which means a living infectious fluid. An obligate parasite is one that cannot live independently at all, but must depend on a host.
It was the scientist Stanley who demonstrated that viruses are inert when outside the host cell and can be crystallised. They are made up of proteins.
Why a Virus Is Called Acellular
Viruses lack their own cell machinery. They have a protein coat, the capsid, around a nucleic acid strand, and nothing more — no cytoplasm, no ribosomes, no membrane-bound organelles. They are therefore considered to be acellular organisms.
Viruses are inactive outside a host cell. But once they enter their specific host cell, they take charge of the cellular machinery of the host cell and duplicate themselves.
Viruses can thus be called infectious nucleoprotein particles — “nucleoprotein” because they consist of a nucleic acid together with protein, and “infectious” because that simple combination is enough to cause disease.
Flowchart
FC 2.11 – Multiplication of a virus: virus reaches specific host cell → nucleic acid enters the cell → host’s cellular machinery taken over → viral nucleic acid and capsid proteins manufactured → new virus particles assembled → particles released to infect further host cells
Structure of the Virus
The protein coat, called the capsid, is made up of smaller units, the capsomeres. Capsomeres are arranged in polyhedral or helical forms. The capsid protects the genetic material.
The helical arrangement can be seen clearly in the tobacco mosaic virus, shown in Fig. 2.13, where the capsomeres are stacked in a spiral around a hollow core containing the RNA.
Diagram
Fig. 2.13 – Tobacco mosaic virus (TMV): a helical rod of capsomeres around a hollow core, labelled with RNA, capsomeres, hollow core, radius 40 Å and pitch 23 Å, beside a photograph of an infected tobacco leaf showing mosaic patches.
The dimensions marked on the figure are given in ångström units. One ångström equals \(1\ \text{Å} = 10^{-10}\ \text{m}\), so a radius of \(40\ \text{Å}\) is four billionths of a metre — a reminder of just how small these particles are. The pitch of \(23\ \text{Å}\) is the distance along the axis covered by one complete turn of the helix.
Types of Viruses
As per their genetic material, viruses are grouped as DNA viruses or RNA viruses.
The genetic material in viruses is usually either single-stranded RNA — and very rarely double stranded RNA — or double stranded DNA, and rarely single stranded DNA.
Viruses that infect bacterial cells are called bacteriophages, which normally have double-stranded DNA. The structure of a bacteriophage is shown in Fig. 2.14.
Diagram
Fig. 2.14 – Bacteriophage: a virus with a polyhedral head containing the core, and a collar, sheath, basal plate and tail fibers, all labelled, beside an electron micrograph of the same.
Diseases Caused by Viruses
Viruses cause disorders such as leaf curling, yellowing and mosaic formation in plants.
In animals, foot and mouth disease and swine flu are viral diseases. In human beings, the list runs from small pox, mumps and herpes to the common cold, and it includes AIDS as well.
b. Viroids
Potato spindle tuber disease was found to be caused by a single stranded RNA which lacks a protein coat.
T. O. Diener, in 1971, reported that this is a low molecular weight RNA, and smaller in size than viruses. These infectious RNA strands are called viroids.
So a viroid is a virus stripped of everything but its message — a bare strand of RNA that is nevertheless able to enter cells, multiply and cause disease.
In examinations, this section is tested through assertion–reason questions on whether viruses are living or non-living, through diagram-labelling of the bacteriophage and TMV, and through direct questions asking which infectious agent lacks a protein coat — a question whose answer is the viroid.
2.15 Summary
The great diversity of organisms around us led humans to identify and differentiate them, and this effort grew into classification and eventually into systematics.
Systematics is the study of the kinds and diversity of organisms and of their comparative and evolutionary relationships (G. Simpson, 1961).
Taxonomy means classification carried out according to fixed rules or principles. The word comes from the Greek taxis (arrangement) and nomos (law). The term was first introduced by A. P. de Candolle, a Swiss botanist (1778–1841).
Classification is the arrangement of organisms or groups of organisms into distinct categories according to a well-established scheme, on the basis of their similarities and dissimilarities.
Classification systems are of three types. Artificial systems use a few easily observed, non-evolutionary features such as habit and colour, often ignoring affinity (example: the Linnaeus system). Natural systems use objectively significant characters rather than characters chosen for convenience (example: Bentham and Hooker’s system). Phylogenetic systems are based on common evolutionary descent (example: Engler and Prantl’s classification).
A category is a unit of classification representing a rank, and such a unit is commonly termed a taxon.
Carl Woese, in 1990, proposed three domains of life — Archaea, Bacteria and Eukarya. A domain is a unit larger than kingdom.
Bacteria and Archaea have prokaryotic cells, while Eukarya have eukaryotic cells. All three domains have very unique rRNA. Archaea survive in extreme conditions such as high temperature, high salinity and acidic conditions, and Bacteria differ from Archaea in the structure of the cell wall.
Chemotaxonomy classifies organisms on the basis of the chemical compounds present in them — for example, the Archaea cell wall is without peptidoglycan while that of Prokarya has it, and among Eukarya, fungi have chitinous walls while plants have cellulosic walls.
Numerical taxonomy quantifies characters and uses numeric algorithms such as cluster analysis instead of subjective judgement. It was first proposed by R. Sokal and P. Sneath in 1963.
A cladogram is a branching pattern representing the hypothetical relationship between organisms and their common ancestors.
Phylogeny is the evolutionary relationship of an organism. It considers not only morphology but also the relationship of one group with other groups and similarities in metabolic functioning. Woese’s three domain concept and Whittaker’s five kingdom system are good examples of phylogenetic relationship.
DNA barcoding identifies a species from the DNA sequence of a tiny tissue sample. It involves two basic steps: collecting barcode data of known species, and matching an unknown sample against that library. It is used in protecting endangered species, preserving natural resources, pest control, identifying disease vectors, authenticating natural health products and identifying medicinal plants.
Classification is not a single step process; it is a hierarchy of steps, each representing a rank or category. Kingdom, division, class, order, family, genus and species are the compulsory categories, while sub-order, sub-family and similar ranks are facultative categories used as per need.
A taxon is a taxonomic group of any rank in the system of classification (H. J. Lam, 1948).
Species is the lowest natural taxonomic unit, denoted by a Latin binomial, and is a group of organisms that interbreed under natural conditions to produce fertile offspring. Genus is a group of closely resembling species that usually do not interbreed. Family is a group of closely related genera; order is a group of closely related families; class is an assemblage of allied orders; division is composed of closely related classes; sub-kingdom is formed of similar divisions; and kingdom is the highest category, composed of sub-kingdoms.
As one goes higher in the taxonomic ladder, the number of common characters shared by the members goes on decreasing.
Flowchart
FC 2.12 – The taxonomic ladder from the smallest to the largest unit: Species → Genus → Family → Order (Cohort) → Class → Division / Phylum → Sub-kingdom → Kingdom → Domain, with the note that the number of common characters decreases as one moves upward
Nomenclature is the science of naming. Common or vernacular names vary from language to language and dialect to dialect — the pansy (Viola tricolor L.) has about fifty common English names and mango (Mangifera indica L.) has over fifty Sanskrit names — so they are of limited use.
Carl Linnaeus introduced the binomial system of nomenclature in his book Species Plantarum, published in 1753, replacing the earlier polynomial system. A scientific name has two epithets — the generic epithet, a noun beginning with a capital letter, and the specific epithet, an adjective beginning with a small letter, as in Helianthus annuus.
Scientific names must be in italics when printed and underlined separately when handwritten; each epithet has not fewer than three and not more than thirteen letters; and the author’s name may follow, as in Mangifera indica L. Scientific names were confirmed by the ICBN, which after the Shenzhen Congress of 2017 became the ICNAFP, published on 26th June 2018.
The two kingdom classification of Linnaeus could not place organisms such as bacteria, fungi and Euglena, so R. H. Whittaker proposed the Five Kingdom system in 1969 — Monera, Protista, Plantae, Fungi and Animalia.
Kingdom Monera consists of unicellular prokaryotes with a nucleoid, often plasmids, a peptidoglycan (murein) cell wall, no membrane bound organelles and 70S ribosomes; they reproduce by binary fission or budding, and very rarely sexually by conjugation. Bacteria occur as coccus, bacillus, vibrio and spirillum forms, and are grouped as Archaebacteria (extremophiles — halophiles and thermophiles, methanogens, wall without peptidoglycans) and Eubacteria (true bacteria with peptidoglycan walls, autotrophic like Chlorobium and Chromatium or heterotrophic). Filamentous cyanobacteria have a mucilagenous sheath, chlorophyll-a, chlorophyll-b, carotenes and xanthophylls, and heterocysts for nitrogen fixation. Useful heterotrophs include Lactobacilli, Azotobacter and Streptomyces, while pathogenic forms cause typhoid, cholera, tuberculosis and tetanus. Mycoplasma are the smallest living forms, lack a cell wall, and resist common antibiotics.
Kingdom Protista includes all unicellular eukaryotes and links the other eukaryotic kingdoms. Plant-like protists (Chrysophytes) include diatoms with two silica covers, which leave behind diatomaceous earth; dinoflagellates with cellulosic plates and a pair of flagella, including Gonyaulax, which causes red tide; and euglenoids with a proteinaceous pellicle and two flagella of unequal length. Animal-like protists (protozoans) include amoeboid forms (Amoeba, Entamoeba), flagellated forms (Trypanosoma), ciliates (Paramoecium) and sporozoans (Plasmodium). Fungi-like protists are Myxomycetes such as Stemonitis, whose cells aggregate into a plasmodium producing very tough spores.
Kingdom Plantae is dominated by multicellular autotrophs with chlorophyll and cellulosic cell walls, showing alternation of generations. It includes semi-autotrophic insectivorous plants such as the Venus fly trap, pitcher plant and bladderwort, and parasitic members such as Cuscuta. It is divided into Cryptogamae and Phanerogamae.
Kingdom Fungi contains eukaryotic heterotrophs with extracellular digestion, a chitinous wall, and bodies of hyphae forming a mycellium; non-septate multinucleate hyphae are coenocytic. They may be saprophytic, parasitic, predatory or symbiotic, as lichens and mycorrhiza. Fungi are classified as Phycomycetes (Mucor, Rhizopus, Albugo), Ascomycetes (Aspergillus, Penicillium, Claviceps, Neurospora, Saccharomyces), Basidiomycetes (Agaricus, Ganoderma, Ustilago, Puccinia) and Deuteromycetes (Alternaria, Colletotrichum).
Lichens are a symbiosis of an algal phycobiont with a fungal mycobiont; they are pollution indicators and help in soil formation. An example is Parmelia.
Kingdom Animalia contains multicellular heterotrophic eukaryotes with holozoic nutrition, no cell wall and no chlorophyll, mostly capable of locomotion, and with determinate growth.
Viruses and viroids are acellular organisms, and are not included in the Five Kingdom classification. A virus is an obligate parasite made of a nucleic acid strand within a capsid of capsomeres arranged in polyhedral or helical form; it is inert outside the host but takes over host machinery inside it, and is therefore called an infectious nucleoprotein particle.
Viruses carry either DNA or RNA, never both at a time — usually single stranded RNA or double stranded DNA, rarely the other forms — and bacteriophages, which infect bacteria, normally have double stranded DNA. Viruses cause leaf curling, yellowing and mosaic in plants, foot and mouth disease and swine flu in animals, and small pox, mumps, herpes, common cold and AIDS in human beings.
Viroids are infectious, low molecular weight, single stranded RNA strands without a protein coat, smaller than viruses, reported by T. O. Diener in 1971 as the cause of potato spindle tuber disease.
2.16 Points to Ponder
Classification began as a way of telling useful organisms from harmful ones. Does a system built for human convenience ever become a system that describes nature truthfully — and how would you know when it has?
An artificial classification can place a shark, a dolphin and a penguin in one group. If such a system is admitted to be misleading, why has it never been abandoned altogether?
The definition of a species requires interbreeding under natural conditions to produce fertile offspring. How, then, would you decide whether two fossils, or two bacteria that never reproduce sexually at all, belong to the same species?
Modern taxonomy recognises sub-species, varieties and populations within a species. If a species can be divided in this way, in what sense is it still the “basic” unit of classification?
Woese separated Bacteria from Archaea on the evidence of rRNA, not appearance. What does this suggest about which characters a classifier should trust when the evidence of the eye and the evidence of the molecule disagree?
Numerical taxonomy gives every character equal weight in order to remove personal bias. Is treating all characters as equally important itself a kind of assumption?
A cladogram represents a hypothetical relationship, and its branch points stand for ancestors nobody has ever seen. What kind of new evidence would make you willing to redraw a branch?
The number of characters shared by members of a group falls as one moves from species towards kingdom. Does this mean that the higher categories tell us less about an organism, or that they tell us something different?
Common names such as “brahmi” may refer to more than one plant, while a scientific name refers to only one. What is lost when a local name, carrying generations of use and knowledge, is set aside in favour of a Latin binomial?
Euglena photosynthesises in the light and feeds like an animal in the dark. If a single organism can behave in two ways, what does that tell you about the boundaries we draw between kingdoms?
Fungi digest their food outside their bodies and then absorb it, while animals take food in first and digest it inside. Which of these two arrangements places more limits on where an organism can live?
A lichen is so intimate an association that the alga and the fungus cannot easily be told apart as separate beings. Should a lichen be classified as one organism or as two?
A virus can be crystallised like a chemical, yet it carries genetic material and multiplies inside a host. Where would you place it on the line between the living and the non-living, and what would you accept as the deciding property?
A viroid is nothing but a strand of RNA, without even a protein coat, and it is still infectious. What does its existence suggest about the minimum requirement for something to reproduce and cause disease?
2.17 Check Your Concepts
Distinguish between taxonomy and systematics, and state which of the two is the broader term.
A student groups a set of plants only by the colour of their flowers. Name the type of classification the student has used, and explain one serious limitation of that approach.
Why is Bentham and Hooker’s system described as natural while the Linnaeus system is described as artificial?
Arrange the following in the correct sequence, from the largest category to the smallest: Family, Kingdom, Species, Order, Genus, Class, Division.
Distinguish between a taxonomic category and a taxon, giving one example of each.
Why is domain considered a unit larger than kingdom? Name the three domains proposed by Carl Woese.
Bacteria and Archaea are both prokaryotes. On what two grounds are they nevertheless placed in separate domains?
What is chemotaxonomy? Explain how the chemical nature of the cell wall helps to separate fungi from plants.
Why was numerical taxonomy developed, and what is meant by saying that it gives equal weight to every character?
In a cladogram, what does a branch point represent? Why is the relationship shown by a cladogram described as hypothetical?
Explain why similarity in metabolic functioning is considered stronger evidence of relationship than similarity in body shape.
State the two basic steps of DNA barcoding. What happens if the sequence of an unknown sample matches nothing in the barcode library?
What happens to the number of common characters shared by the members of a group as we move from species towards kingdom? Explain the reason behind this trend.
The horse and the ass can be mated, and the offspring is a mule. Why are the horse and the ass still regarded as two different species?
The dog and the cat belong to different families but to the same order. Name the two families and the common order, and state what this tells you about how closely they are related.
Rewrite the following names correctly and state the rule you have applied in each case: mangifera Indica, helianthus annuus, Naja Naja.
What is the full form of ICNAFP, and which earlier code did it replace?
Why did the two kingdom system of classification prove inadequate? Name two organisms it could not place satisfactorily.
What happens to a bacterial cell if its peptidoglycan wall is destroyed while it is in a dilute solution? Use this to explain why Mycoplasma is resistant to antibiotics that act on the cell wall.
Draw a labelled diagram of a filament of Nostoc, and explain how the structure of the heterocyst suits the function it performs.
Kingdom Protista is often described as a link between the other eukaryotic kingdoms. Justify this statement with one example of each kind of protist.
Arrange the following steps in the correct sequence to describe how food is taken in and disposed of by Paramoecium: formation of the food vacuole; removal of undigested matter through the cytopyge; sweeping of food particles by cilia; digestion of food within the vacuole; passage of food along the oral groove into the gullet.
What is diatomaceous earth, how is it formed, and why is it useful in filtration?
Explain why the plasmodium of a slime mould must not be confused with Plasmodium.
Fungi digest their food outside the body and then absorb it. Explain how the thread-like structure of the fungal body suits this mode of nutrition.
Distinguish between septate and coenocytic hyphae, and name one class of fungi in which coenocytic hyphae are found.
Why are Deuteromycetes called imperfect fungi?
Name the two partners of a lichen and state what each contributes to the association. Why are lichens used as pollution indicators?
Give one reason each for the following: animal cells can change shape easily; plants can go on growing throughout life while animals stop at a definite size.
Why are viruses and viroids not included in the Five Kingdom classification?
Arrange the following events in the correct order to describe the multiplication of a virus: assembly of new virus particles; entry of the nucleic acid into the host cell; release of new particles; manufacture of viral nucleic acid and capsid proteins; takeover of the host’s cellular machinery.
Draw a labelled diagram of a bacteriophage and state the type of genetic material it normally contains.
Why is a virus called an infectious nucleoprotein particle? Explain the function of the capsid.
What happens if a viroid, which has no protein coat at all, is compared with a virus? List three differences between the two.
Identify the scientist associated with each of the following, and state the contribution in one line: A. P. de Candolle, G. Simpson, Carl Woese, R. Sokal and P. Sneath, H. J. Lam, Carl Linnaeus, R. H. Whittaker, T. O. Diener.
What are the salient features of Monera?
What will be the shape of a bacillus and of a coccus type of bacteria?
Why is binomial nomenclature important?
Write short notes on the following.
- Useful and harmful bacteria
- Five Kingdom system
- Useful fungi
Complete the tree diagram in detail. (The diagram shows a branching tree in which the branches for Fungi and Protista are labelled, and the remaining branches are left blank.)
Draw neat labelled diagrams.
- Paramoecium
- Euglena
- TMV
Complete the chart and explain in your own words. (The chart begins with “Types of Viruses” and branches into three boxes, of which only “Animals” is filled in.)
Identify the following diagrams, label them, and write detailed information about each in your own words. (Diagrams A to F are provided.)
The scientific name of sunflower is given below in two ways. Identify the correctly written name.
- Helianthus annuus L.
- Helianthus Annuus l.
2.18 Objective Questions
Which of the following shows single stranded RNA and lacks a protein coat?
- Bacteriophage b. Plant virus c. Viroid d. Animal virus
The causative agent of red tide is ____________.
- Dinoflagellate b. Euglenoid c. Chrysophyte d. Lichen
Select the odd one out for heterotrophic bacteria.
- Nitrogen fixing bacteria b. Lactobacilli c. Methanogens d. Cyanobacteria
Paramoecium : Ciliated Protist :: Plasmodium : ____________
- Amoeboid protozoan b. Ciliophora c. Flagellate protozoan d. Sporozoan
Plant-like Protista – ____________
____________ – Entamoeba
Assertion: An artificial system of classification may place a shark and a dolphin in the same group. Reason: Artificial systems use a few easily observable, non-evolutionary features and often ignore the affinity of organisms. Examine whether the assertion and the reason are correct, and whether the reason explains the assertion.
Assertion: rRNA is used for comparing organisms belonging to all three domains. Reason: rRNA is present in every organism and changes only very slowly over evolutionary time. Examine whether the assertion and the reason are correct, and whether the reason explains the assertion.
Assertion: Euglena could not be placed satisfactorily in either Kingdom Plantae or Kingdom Animalia. Reason: Euglena photosynthesises in the presence of light but behaves as a heterotroph in its absence. Examine whether the assertion and the reason are correct, and whether the reason explains the assertion.
Assertion: A virus is described as being at the borderline of the living and the non-living. Reason: A virus can be crystallised and is inert outside a host cell, yet it possesses genetic material and multiplies inside a host cell. Examine whether the assertion and the reason are correct, and whether the reason explains the assertion.
Match the following.
| Kingdom | Example |
|---|---|
| a. Monera | i. Riccia |
| b. Protista | ii. Cyanobacteria |
| c. Plantae | iii. Rhizopus |
| d. Fungi | iv. Diatoms |
- Match the following.
| Class of fungi | Example |
|---|---|
| a. Phycomycetes | i. Alternaria |
| b. Ascomycetes | ii. Agaricus |
| c. Basidiomycetes | iii. Albugo |
| d. Deuteromycetes | iv. Claviceps |