Five and three domain classification of living organisms

By | August 24, 2021
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Our Earth exhibits a large variety of living organisms, be it different kinds of plants, insects, sea creatures or other animals. In addition to these living forms, there are many organisms which we cannot see with our naked eye but are present around us. There are an estimated 1.5 – 1.7 million named species on earth (E. O. Wilson, 2001). Of these, invertebrates account for >99%. This refers to biodiversity on earth or simply number of types of organisms present on earth.

Since it is nearly impossible to study all the extant species on earth, there should be a way to make it possible. In order to study all the living forms, it is vital to separate them into domains or group based on the some common criteria ( such as plants or animals, sea and land creatures etc.) This is termed as classification. It is similar to arranging our cupboard with clothes. if we put all our clothes in one compartment , we will need more time to find the things which we require. However, if we arrange our trousers, shirts and jackets in different compartments, then it will be easy to find them.

Advantages of Classification :

Classification or sorting of organisms into groups serves many purposes

  • It allows us to understand biodiversity better.
  • It makes study of different organisms easier.
  • To give specific names to the organisms and identify various species.
  • For finding the evolutionary relationships between the organisms.
  • It allows us to study how complex organisms evolve from simpler organisms.

Biological classification of living forms is continuously evolving with emerging techniques. Classification has come a long way from the days of two kingdom type of classification ( division in to plants and animals) of Carolus Linnaeus in mid 1700’s. This kind of classification fail to distinguish between eukaryotic or prokaryotes, single celled or multi cellular organisms, photosynthetic or non-photosynthetic organisms. Another reason for failure of two kingdom system is that it couldn’t accommodate many organisms which don’t fall in plants or animals category.

Five kingdom classification of R.H.Whittaker:

In a bid to overcome the shortcomings of earlier attempts of classification of life forms, Whittaker in 1969 had proposed a Five kingdom classification. The five kingdoms of his classification were : Monera, Protista, Fungi, Plants and animals. The important features considered as basis for classification are cell structure, body organization, mode of nutrition, reproduction and phylogenetic relationships.

Cell TypeProkaryoticeukaryotic eukaryotic eukaryotic eukaryotic
Cell wallNon cellulosicPresent in someChitin cell wallCellulose cell wallAbsent
Body organizationCellularCellularMulticellularTissue or organsTissue/organ/organ system
Mode of nutritionAutotrophic and Heterotrophic Autotrophic and Heterotrophic HeterotrophicAutotrophicHeterotrophic
ExamplesBacteria, ArchaebacteriaEuglina, slime moulds, Protozoans etc.Penicillium, aspergillus etc.All plantsAll animals

Three domain system / Carl Woese  and George Fox’s  classification:

As mentioned above that the two kingdoms classification was prevalent before 1969. After that, the five domain system of Whittaker was followed two decades. One of the main drawbacks of five domain system was that it fails to explain how organisms within Kingdoms or between kingdoms are related each other or in other words does not throw any light on the evolutionary relationships among the organisms from different domains or kingdoms.

The pioneering work of Carl Woese and George Fox,(published in PNAS in 1977) laid the foundation of the widely accepted three domain system in the year 1990. The main difference between the Woese’s system and earlier classifications was in using the molecular or genetic details of the organism instead of morphological/ phenotypic characters for comparison.

Carl Woese , who was working at the University of Illinois, proposed a new  classification system by comparing  nucleotide sequence of 16S rRNA molecules from prokaryotic and eukaryotic species. Since smaller sub unit of ribosome is common to both prokaryotes and eukaryotes and hence serves as molecular marker to compare between all the life forms. This results in a “tree” of related organisms (as proposed by Charles Darwin in his landmark book origin of species) which are connected by common ancestry at the base.

Why rRNA sequence is best for creating phylogenetic trees or for comparisons to find evolutionary relatedness between organisms – Read here

This classification system divides the life forms into three domains:  archaea, bacteria and eukaryotes. The main difference when compared to five kingdom system of whittaker is that the prokaryotes are divided in bacteria and archaea. Another aspect is the four kingdoms (protista, fungi, animals and plants) are grouped into single domain of eukaryotes. Hence woese’s classification is also called as three domain and six kingdom classification.

Phylogenetic trees:

The word phylogeny can be described as the evolutionary history of an organism / group of organisms. It describes the organism’s relationships, such as from which organisms it may have evolved, or to which species it is most closely related. A phylogenetic tree is a diagram reflecting the evolutionary relationships among different groups of organisms. This tree of life generated by comparing rRNA nucleotide sequences from different life forms, yields the following

Phylogenetic trees show the relationship of the three domains of life—Bacteria, Archaea, and Eukarya

In a rooted tree :

  • The branching indicates evolutionary relationships.
  • The point where a split occurs is called branch point.
  • Two lineages separating from the same branch point are termed as sister taxa.
  • The species of interest are found at the tips of tree’s branches.

In a simple phylogenic tree, the current day or extant species are present at the tips of branches or lines. In the example below


A simple phylogenetic tree

The five species A, B, C, D and E are present at tip of branches. Their most recent common ancestors are represented by red arrows. The pattern in which the branches are present is based on how the species in the tree evolved from a series of common ancestors. Each branch point represents a splitting event of a single group into two descendant groups.

These trees also allows us to find the species which are more related to each other. In trees, two species are considered more closer or related to each other, if they have a more recent common ancestor and distant related if they have a less recent common ancestor. For the above diagram, we can say that species A and B are more related than A and C or D because A and B share most recent ancestor. In the samilar manner species C and D are closely related than C and E.

To generate these kinds of phylogeny trees, scientists use many characteristics such as morphological characters, biochemical pathways, DNA and protein sequences, and sometimes characteristics of fossils.

The phylogeny trees or diagrams allows us to trace the evolutionary history of an organism or group of organisms. If we want to trace the history of a species, we need to just track back towards the “trunk” of the tree. While doing so we we can figure out its ancestors and also the entire relationship with the other organisms (liked by other branches of the tree of life). The greater the similarities in these compared sequences, the more closely related organisms are thought to be present on the nearby branches of the phylogeny tree.

The pioneering work from Woese and many other scientists, by comparing DNA sequences from a variety of prokaryotic organisms has led to two main domains among the prokaryotes . They are termed as “true” bacteria, or eubacteria, and archaea (also called archaebacteria or Archaean’s).

According to the above tree, the archaea and the eukaryotes diverged from the true bacteria before they diverged from each other. This means, in spite of being prokaryotes , Achaea is evolutionarily much closer to eukaryotes than bacteria. Archaea and all eukaryotes share a common ancestor ( Purple box in figure), which went on to form a separate lineage after getting branched out or separated from common ancestor of all life forms (represented by red box in figure). This works on the hypothesis that organisms with more similar genes evolved from a common ancestor more recently than those with more dissimilar genes.

All cells are thought to have evolved from a common progenitor because the structures and molecules in all cells have many similarities. As predicted by Charles Darwin in his famous “Origin of species” book – The entire Tree of Life is a nested hierarchy and we’re all related.

Page from Darwin’s notebooks around July 1837, showing his first sketch of an evolutionary tree, with the words “I think” at the top

References :

Woese CR, Fox GE (November 1977). “Phylogenetic structure of the prokaryotic domain: the primary kingdoms”. Proceedings of the National Academy of Sciences of the United States of America. 74 (11): 5088–90.

doi:10.1073/pnas.74.11.5088. PMC 432104. PMID 270744.

Woese CR, Kandler O, Wheelis ML (June 1990). “Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya”. Proceedings of the National Academy of Sciences of the United States of America. 87 (12): 4576–9.. doi:10.1073/pnas.87.12.4576. PMC 54159. PMID 211274

Gregory, T.R. Understanding Evolutionary Trees. Evo Edu Outreach 1, 121–137 (2008).

Image credit :

Modified from Openstax biology

Charles Darwin – Tree of life – Wikipedia Public domain image

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