CLASSIFICATION of living organisms

domain, kingdom, phylum, class, order, family, genus, species

modern developments - Carl Woese, classification diagrams

the work of Carl Linnaeus, evolutionary tree of life diagrams

how organisms are named

Doc Brown's Biology Revision Notes

Suitable for GCSE/IGCSE/O level Biology/Science courses or equivalent

See also Cell Structure - eukaryotes and prokaryotes

 



 

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to place organisms in groups - sometimes referred to as an artificial classification system - although now regarded as outdated and not suitable in the light of more advanced knowledge, such systems have their use in e.g. identifying animals using a key system.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

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

animalia - all animals – animals are multicellular, 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, have cell walls, have chlorophyll, feed autotroprically (autotrophs can make their own food from photosynthesis) e.g. grasses, flowers, trees etc.

fungi - multicellular, have cell walls, do not have chlorophyll, feed saprophytically (saprophytes feed off dead organisms and decaying material) e.g. mushrooms, toadstools, yeasts.

protoctista (protists) - unicellular (single celled eukaryotes), have a nucleus, protoctista include algae.

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

This 'five kingdom' system is still in use, BUT it is getting out of date.

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

the five kingdoms of life are sub-divided into

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.

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

Family – comprising of several genera (us - hominidae)

Order – comprising of several families (us - primate)

Class – comprising of several orders (us - mammalian)

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

(Kingdom - animal)

Even for the blue 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.

 

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.

 


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 similarities 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 1990s the scientist 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 see the latter without a microscope).

(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, Helicobacter, Listeria, Staphylococcus etc.

Although they often look similar to Archaea, there are significant biochemical differences between these domains - 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. hot volcanic springs or salt lakes (high concentration of dissolved salts) 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 two domains.

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.

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.

 


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.


APPENDIX - The naming of organisms

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.

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