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School Biology Notes: How we classify living organisms

CLASSIFICATION of living organisms

e.g. domain, kingdom, phylum, class, order, family, genus, species - some modern developments - Carl Woese, classification diagrams - the earlier work of Carl Linnaeus and evolutionary tree of life diagrams and know how organisms are named

See also Cell Structure - eukaryotes and prokaryotes

 Doc Brown's school biology revision notes: GCSE biology, IGCSE  biology, O level biology,  ~US grades 8, 9 and 10 school science courses or equivalent for ~14-16 year old students of biology

Sub-index for this page

(a) The traditional method of classifying living organisms - Linnaean system of five kingdoms

(b) Modern developments in the classification of living things - three domain system

(c) Evolutionary Trees - An evolutionary tree of life

(d) The naming of organisms - Linnaeus Latin names of the binomial system



(a) The traditional method of classifying living organisms

In biology, a classification system is a way of organising living organisms into groups.

Early classification systems used observable features to place organisms in groups - sometimes referred to as an artificial classification system - although now regarded as outdated and not suitable in the light of more advanced knowledge, such systems have their use in e.g. identifying animals using a key system.

As we understanding of evolutionary relationships developed there was a need for a more advanced classification system, sometimes referred to as natural classification system.

Natural classification systems look at an organism's common ancestors and common structural features to help out organisms into suitable groupings.

e.g. bats and humans have many different features, the pentadactyl hands of them means they are both grouped together.

The traditional 'natural' system, still in wide use today, is based on the classification work of Carl Linnaeus working in the 18th century.

His system grouped living things according to their particular observable physical characteristics and structural features seen with an optical microscope.

This gives rise to the 'Linnaean system' in which living organisms are first divided up into five kingdoms.

You are basically looking at similarities and differences between species and the data is expressed in the idea of a five kingdom system.

Up to the 1970s scientists considered the five kingdoms of life were sub-divided as follows:

The Five Kingdoms of life and their characteristics CAN be defined as ...

animalia - all animals – animals are multicellular (eukaryotic lacking cell wall material, but have a chromosome containing nucleus), do not have cell walls, do not have chlorophyll, feed heterotrophically (heterotrophs can't make their own food) e.g. fish, insects, mammals, reptiles etc.

plantae - all plants - are multicellular (eukaryotic), have cell walls (and a chromosome containing nucleus), have chlorophyll, feed autotroprically (autotrophs can make their own food from photosynthesis) e.g. grasses, flowers, trees etc.

fungi - usually multicellular (eukaryotic), have cell walls, do not have chlorophyll  e.g. mushrooms, toadstools, yeasts. Fungi can (i) feed saprophytically - saprophytes/saprotrophs feed off dead organisms and decaying material, (ii) be parasite symbiont - feeding off another living organism (at its host's expense!) or (iii) symbiosis, where both the fungus and host benefit each other.

protoctista (protists) - usually unicellular (single celled eukaryotes), have a nucleus, protists include algae (can photosynthesise) and protozoa.

prokaryotes - unicellular (single celled prokaryotic organisms), have no nucleus e.g. bacteria, cyanobacteria and archaea.

This 'five kingdom' system is still in use, BUT it is getting out of date.

So that's where I've come from!

With reference to the above diagram of the Linnaean classification system,

the five kingdoms of all organisms of life are sub-divided into:

Phylum – comprising of several classes (us - chordata - vertebrates)

Class – comprising of several orders (us - mammalian)

Order – comprising of several families (us - primate)

Family – comprising of several genera (us - hominidae)

Genus – contains several species with similar characteristics (us - Homo)

Species – groups of organisms that have many features in common (Homo sapien - you and me!)

Reminder: A species is defined as a group of similar organisms that can reproduce to give fertile offspring e.g. cats, humans.

Even for the blue line-text pathway of 'Dr Phil Brown', the diagram ignores many subspecies e.g. vertebrates are part of the phylum Chordata and the vertebrates themselves are sub-divided into five subphyla: Vertebrata - fish, amphibians, reptiles, birds, and mammals.

Examples of ancestry:

Humans and apes share the same ancestry down to the same family (hominidae), but humans and cats only share ancestry down to class (mammals).

Extra note on 'traditional' classification (which you may not need for your GCSE biology exam)

  • Scientists do not classify viruses in any of the five kingdoms and regard them as non-living.
    • Viruses, which are smaller than bacteria, cannot reproduce themselves, have protein coat containing a few genes, they invade cells and make them reproduce the invading virus.
  • The main characteristics of the phylum Chordata as animals with a supporting rod running the length of the body, an example of this being the backbone in vertebrates.
    • Vertebrates are divided into five classes, groups of amphibians, birds, fish, mammals and reptiles
  • Scientists place vertebrates into the five groups based on:
    • a) Oxygen absorption methods – lungs, gills and skin
    • b) Reproduction – internal or external fertilisation, oviparous (lay eggs) or viviparous (give birth to live young)
    • c) Thermoregulation – homeotherms ('warm blooded' - kept at a constant temperature) and poikilotherms ('cold blooded' - body temperature varies with external temperature).
  • There can be problems associated with assigning vertebrates to a specific group based on their anatomy and reproduction methods - why many vertebrates are difficult to classify.
    • e.g. the duck-billed platypus has a bill like a duck, tail like a beaver, its homeothermic, lays eggs but suckles its young. Not an easy one to classify! but its closer to a mammal than any of the other four vertebrate groups!
  • Accurate classification may also be complicated by:
    • a) variation within a species
    • b) hybridisation in ducks produces viable new species
    • c) ring species - a group of related populations that live near each other, neighbouring populations may interbreed but those well separated geographically may not. Sorting out which are genuinely different species is not easy.
  • The definition of a species as organisms that produce fertile offspring may have limitations:
    • Some organisms do not always reproduce sexually and some hybrids are fertile.
    • Some organisms can reproduce asexually but are still classed as the same species.
    • Many closely related species can interbreed producing viable offspring and technically classed as a different species.

 


(b) Some modern developments in the classification system of living things

Since the days of the 18th century Carl `Linnaeus, there have been two very significant developments in the science of living organisms.

(i) Now that we know the structure of DNA and RNA we have a much greater knowledge of the biochemistry of life - new discoveries are being made all the time.

You can now compare DNA sequences for particular genes or the whole genome for different organisms - and all you need is a small sample of cells or a piece of tissue.

You look for DNA similarities or differences between organisms e.g. do they have the same number of genes, do they have a similar number of variants for a gene.

The more similar the DNA sequences of two or more species, the more closely they are genetically related and therefore be more likely to be more correctly classified in the same group.

If two or more organisms share the same number of genes and genetic variants, so they have a similar, but not identical genomes, its likely these organisms have a common ancestor.

(Quote: "94% of the DNA base sequences is the same for chimpanzees and humans". You can therefore deduce we have a common ancestor, and not that long ago in terms of the millions of years of 'geological time'.)

The study of the history of evolutionary relationships at the molecular level is called molecular phylogenetics - looking at DNA sequences of the genome.

In biology, phylogenetics is defined as the study of the evolutionary history and relationships among individuals or groups of organisms to determine the course of evolution.

(ii) Developments in microscopy, using more advanced techniques, enable us to see and understand the most fundamental structures of cells of living organisms e.g. cells, sub-cellular structures e.g. organelles like ribosomes and mitochondria.

This is allowing biological scientists to propose new models of classification - which in time will change too!

The new discoveries are helping to clarify the relationships between organisms.

In the later 1970s onwards scientists like Carl Woese proposed a three domain system.

This was proposed from the evidence of e.g. RNA sequence analysis which showed that some species thought to be closely related, where in fact, quite distinct from each other, and not as closely related as was thought.

The three domain system is based on the following divisions of life forms ..

(1) Eukarya (eukaryota, types of eukaryotes): This our most familiar domain which includes all the life you see around you! e.g. animals, fungi, plants and protists (but you can't see the latter without a microscope!). They are usually multi-cellular organisms.

(2) Bacteria ('true bacteria', types of prokaryotes): These are bacteria, some of whose names we are quite familiar with as examples of infections! e.g. E. coli, Cholera, Chlamydia, Helicobacter, Listeria, Staphylococcus etc.

Although they often look similar to Archaea, there are significant biochemical differences between these domains i.e. there are significant differences in the DNA and RNA sequences of archaea and 'true bacteria'.

(3) Archaea (types of prokaryotes): Archaea may be described as primitive bacteria and often found living in extreme environmental conditions e.g.

around very hot volcanic hydrothermal vents on the seabed - often associated with areas of tectonic activity in the earth's crust,

hot volcanic springs on the surface,

salt lakes - such a high concentration of dissolved salts that few organisms can survive in,

and in very acidic soils or anaerobic environments like marshes and animal guts.

These are environments where few other life forms can survive.

Therefore, many archaea are examples of extremophiles.

Again, although archaea often look similar to 'true' bacteria, there are significant biochemical differences between these to justify the split into two domains.

The ribosomes of archaeans is similar in size and structure to archaeans, yet the DNA/RNA is closer in structure to eukaryotic cells.

Further justification for treating archaea as a separate domain comes from the fact that 2/3rds of the genes in them did not match genes in other organisms.

In a sense archaea were 'discovered' because of their genetic uniqueness, and would have remained a mystery without the advent of modern techniques of genetic analysis - genome sequencing!

As you can see from the diagram, the three domain system is added to the top of the traditional Linnaean classification system, and each domain is the subdivided into kingdoms, phylum, class, order, family, genus and species categories, in a similar way to the traditional classification system.

Strictly speaking, under this system, organisms are classified into three domains and six kingdoms.

As already described, the domains are Archaea, Bacteria, and Eukarya.

However, the six kingdoms can be considered as:

Archaebacteria (ancient bacteria), Eubacteria (true bacteria), Protista, Fungi, Plantae, and Animalia.

 


(c) Evolutionary Trees - An evolutionary tree of life

Evolutionary trees are a way of representing the relationship between species and the pathway they may have evolved.

Evolution and DNA and the evolutionary tree

Scientists can use DNA sequences to estimate how long ago different species separated from each other.

This is worked out from how frequently mutations have occurred giving rise to variants.

By knowing the number of different genetic variants between two species, you can work out how long ago that particular speciation occurred i.e. how long ago did the new species appear in the timeline of evolution.

 

By combining traditional classification data and the new evidence from DNA sequencing, you can join species together to form an evolutionary tree - see examples below.

In an evolutionary tree you connect the species together by lines that come from their most recent ancestor indicating their evolutionary relationship.

The more closely two species are related, the smaller the number of steps between them on the evolutionary tree.

The diagram above illustrates the idea of distant and recent common ancestors (a to o represent species).

e.g. the evolutionary path for species h is a ==> b ==> d  => h

species d would be a recent ancestor, species a would be a more distant ancestor.

Such a diagram shows how closely, or otherwise, how species might be related.

e.g. the characteristics of species h and i would be closely related to each other, and those of j and k would be similar too.

BUT, there would be a greater difference between the species pairs h/i and j/k because they have different previous ancestors of d and e respectively, despite the earlier common ancestor b.

 

Scientists are using all sorts of data these days to try and 'formulate' the evolutionary tree of ALL life.

The diagram above is principally based on (i) structural details and (ii) DNA and RNA sequence analysis of currently existing organisms.

For extinct species, scientists have to rely on fossil evidence, but with modern instrumental techniques, amazing details can be obtained on the structure of long extinct organisms - even those of a 'soft flesh' bodied nature.


(d) The naming of organisms - Linnaeus Latin names of the binomial system

The adoption by biologists of a system of strictly binomial nomenclature is due to Swedish botanist and physician Carl von Linnι, more commonly known by his Latinized name Carl Linnaeus (1707–1778).

In this context, the word binomial means consisting of 'two parts' - usually two Latin words, the first has a capital letter (upper case), the second word has a small letter (lower case).

The name of the organism is written in italics (I may have forgotten this sometimes!)

By using Latin, every name can be unambiguously recognised around the world, no matter what the native language of any scientist.

The use of a universal name avoids confusion in scientific communication.

(I'm afraid its not quite the same in chemistry!)

With millions of species to name, the world of science needs a VERY systematic way of naming life forms.

Although the classification system of Carl Linnaeus is being 'updated' on the basis of modern biological research, his proposed system of naming living organisms is still the basis of today's names.

The name is based on the two 'lowest' sections of the classification systems described above:

The first part gives you the genus of the species.

This gives you information on the organism's ancestry.

In the case of 'us', our genus is Homo.

The second part tells you the specific species.

In the case of 'us', our species is sapiens.

Therefore, as an organism, OUR two-part name is Homo sapiens.

  • So, be able to explain why binomial classification is needed to identify, study and conserve species, and can be used to target conservation efforts.
    • The binomial name of species consists of a two part Latin name (handy for use any country with its own language!).
      • The Latin name cannot be confused linguistically with 'local' or country names.
      • Study and identification produces a common data base of information on species-organisms with a universal name.
      • From the database, species at threat can be identified and preservation strategies put in place.

algae - protists


See also:

Evolution - theories and evidence, variation, speciation - new/old species & extinctions, selective breeding

Adaptations, lots of examples explained including extremophiles  gcse biology revision notes


Doc Brown's School Biology Revision Notes

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