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Biology · Natural Selection and Evolution

Classification and Molecular Phylogenetics

There are millions of species on Earth, and biologists need a way to sort them and to name them. This lesson is for both Combined Science and separate Biology. It covers natural and artificial classification, the system started by Linnaeus, binomial names, the three domains, and how DNA sequencing is now used to build evolutionary trees.

  • 10 key terms
  • All boards

Learning Objectives

  1. 1Describe the difference between natural and artificial classification, and explain why natural classification is preferred.
  2. 2Describe the Linnaean classification system, and use the binomial naming of species.
  3. 3Describe how developments in biology, including DNA sequencing, have changed classification, including the three-domain system.
  4. 4Explain how DNA sequences are used to produce evolutionary trees (molecular phylogenetics).

Retrieval practice

  1. 1

    What is a species?

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    A group of organisms that can interbreed to produce fertile offspring.

  2. 2

    What is a mutation?

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    A random change in the base sequence of DNA.

  3. 3

    Why are all living things related?

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    They share common ancestors, because of evolution.

  4. 4

    What do we call the order of the bases along a DNA strand?

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    The base sequence.

Sorting out living things

Biologists have named about two million species and there are many millions more. To study them, they need to sort them into groups and to give each one a name that every scientist can use. How the groups are chosen has changed. At first they were based on what organisms looked like. Now the best groupings are the ones that show how organisms are related, and DNA sequencing allows us to check that.

Artificial and natural classification

There are two ways to build a classification system, and they work in very different ways.

  • Artificial classification

    This groups organisms by a few features that are easy to see and useful to us, such as whether they fly, live in water or are edible. It is quick, but it can put unrelated organisms together, for example bats, birds and butterflies in a group of flying animals.

  • Natural classification

    This groups organisms by many shared features, which they have inherited from a common ancestor. The groups therefore show how closely organisms are related by evolution.

  • Why natural is preferred

    A natural system shows evolutionary relationships and allows predictions. If a newly discovered organism is placed in a group, we can predict many of its features from the others in the group.

  • Example

    A whale and a fish are both streamlined swimmers in water, but a whale has hair, mammary glands and lungs, so it is grouped with mammals, not fish.

Artificial and natural systems

Artificial classification

  • Uses one or a few easily seen features
  • Groups can include unrelated organisms
  • Does not show evolutionary relationships
  • Example: flying animals, or trees and herbs

Natural classification

  • Uses many features, now including DNA
  • Groups contain organisms with a common ancestor
  • Shows evolutionary relationships
  • Example: the Linnaean system, now using DNA

Linnaeus and the hierarchy of ranks

Carl Linnaeus, a Swedish botanist, published a system in the 1700s which is the basis of the modern one.

  • A hierarchy

    Each group sits inside a larger group, like boxes inside boxes. The groups are called ranks. From the largest to the smallest they are kingdom, phylum, class, order, family, genus and species. A phrase such as King Philip Came Over For Good Soup helps to remember them.

  • Going down the ranks

    The groups get smaller. The organisms in a group have more in common with each other, and there are fewer of them.

  • Species at the bottom

    A species is the smallest group, and contains organisms that can interbreed to produce fertile offspring.

  • Linnaeus

    He used five ranks, kingdom, class, order, genus and species. Phylum and family were added later, as more was learned about living things.

Binomial names

Linnaeus also gave every species a two-part Latin name, which is called a binomial.

  • Two parts

    The first part is the genus and the second is the species. The genus has a capital letter and the species has a small letter, and the name is written in italics or underlined: Homo sapiens.

  • One name worldwide

    Common names change from place to place, and one name may be used for different organisms. A binomial is the same in every language, so scientists in every country know which species is meant.

  • Shows relationships

    Species in the same genus are close relatives. The lion, Panthera leo, and the tiger, Panthera tigris, are in the same genus.

  • Examples

    Humans are Homo sapiens, the oak is Quercus robur and the house mouse is Mus musculus.

How developments in biology changed classification

As new techniques were developed, scientists found that some groups did not reflect the relationships between organisms, and they changed them.

  • Microscopes

    Better microscopes showed the structure of cells and the existence of single-celled organisms, so that scientists could group organisms by their cell structure, such as whether there is a nucleus.

  • Biochemistry

    Comparing the proteins of different species showed which are closely related, even if they look different.

  • DNA sequencing

    Since the 1970s scientists have been able to read the base sequence of DNA, and compare it between species. Closely related species have more similar DNA, so this gives a more reliable measure of relationship than appearance.

  • Three domains

    In 1977 Carl Woese compared ribosomal RNA genes and found that the prokaryotes include two very different groups. In 1990 he proposed three domains above the kingdoms: Bacteria, Archaea and Eukaryota.

How DNA is used to build an evolutionary tree

Molecular phylogenetics uses differences in DNA to work out how species are related.

  1. 1 Choose a gene

    Select a gene that all of the species have, so that its sequence can be compared.
  2. 2 Sequence it

    Use DNA sequencing to read the order of the bases in this gene for every species.
  3. 3 Compare

    Line up the sequences and count the bases that are different. Changes build up over time as mutations happen.
  4. 4 Link difference to time

    The more differences there are, the longer ago the two species split from their common ancestor, so they are more distantly related.
  5. 5 Draw the tree

    Species with the fewest differences are placed side by side, joined at a branching point, which is their most recent common ancestor.

Comparing the DNA of apes

A section of a gene has 500 bases. The human sequence differs from the chimpanzee in 6 bases, from the gorilla in 8 bases and from the orangutan in 15 bases. Calculate the percentage difference between the human and each species, and say which species is the closest relative of the human.

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  1. 1 Chimpanzee \(\frac{6}{500} \times 100 = 1.2\) per cent
  2. 2 Gorilla \(\frac{8}{500} \times 100 = 1.6\) per cent
  3. 3 Orangutan \(\frac{15}{500} \times 100 = 3.0\) per cent
  4. 4 Conclude The smallest difference is with the chimpanzee, so it is the closest relative, and the orangutan is the most distant

AnswerThe differences are 1.2 per cent for the chimpanzee, 1.6 per cent for the gorilla and 3.0 per cent for the orangutan. The chimpanzee is the closest relative, because it has the fewest differences.

What DNA has changed

DNA sequences have confirmed some groupings and corrected others.

  • Animals that look alike

    Features can look alike because of the same way of life rather than ancestry. DNA shows that the marsupial mole and the golden mole, which look alike, are not close relatives.

  • Surprising relatives

    The giant panda is classed with the bears, and whales are closest to the hippopotamus among living animals.

  • Fungi

    Fungi are closer to animals than to plants, although they look like plants.

  • Microorganisms

    Without DNA there is not much to compare in microorganisms, and most prokaryotes could not be classified until their DNA could be sequenced.

Case study

Carl Woese and the Archaea

Until the 1970s all prokaryotes, the cells with no nucleus, were put in one group, the bacteria. Carl Woese compared the sequence of a gene for ribosomal RNA, which every living thing has, in many organisms. He found that some of the prokaryotes, which lived in places such as hot springs, were as different from the other bacteria as they were from animals and plants. In 1990 he proposed that there are three domains: Bacteria, Archaea and Eukaryota. The idea has been accepted, because it was supported by evidence from DNA.

1977 Woese publishes the evidence from ribosomal RNA
3 domains Bacteria, Archaea and Eukaryota

The big idea

The best classification shows how organisms are related, and DNA sequencing gives the most reliable evidence of that.

Classification

Classification

  • Artificial

    • few visible features
    • unrelated organisms grouped
    • does not show ancestry

  • Natural

    • many shared features
    • common ancestors
    • shows relationships

  • Linnaeus

    • kingdom, phylum, class, order, family, genus, species
    • binomial names

  • Three domains

    • Bacteria
    • Archaea
    • Eukaryota
    • Woese and ribosomal RNA

  • Molecular phylogenetics

    • DNA sequencing
    • count differences
    • build evolutionary tree

Summary and exam focus

  • Artificial classification uses a few visible features, and natural classification uses many features and shows evolutionary relationships.
  • The Linnaean system has seven ranks, from kingdom to species, and each species has a binomial name of genus and species.
  • Microscopes, biochemistry and DNA sequencing have all changed classification, and Woese's work led to the three domains of Bacteria, Archaea and Eukaryota.
  • In molecular phylogenetics, DNA sequences are compared, and species with fewer differences are more closely related.
  • The results are shown in an evolutionary tree, with branches where species split from a common ancestor.

Exam focus

Describe how scientists use DNA sequencing to find out how closely related different species are, and explain how this has changed classification. (6 marks) (6 marks)

Describe the method in steps: sequencing the same gene in each species, comparing the base sequences and counting the differences. Explain that fewer differences mean a more recent common ancestor. Then give a change, such as the three domains, or the correction of groups that were based on appearance.

Key terms

The words this lesson expects you to use. Each one is linked from the first place it appears above.

Classification
The sorting of living things into groups.
Artificial classification
Grouping organisms by a few easily seen features, which may not show how they are related.
Natural classification
Grouping organisms by many shared features, so that the groups show evolutionary relationships.
Binomial name
A two-part Latin name for a species, made of its genus and species, such as Homo sapiens.
Genus
A group of closely related species.
Domain
The highest rank of classification: Bacteria, Archaea or Eukaryota.
DNA sequencing
Finding the order of the bases along a piece of DNA.
Molecular phylogenetics
Using differences in DNA or protein sequences to work out evolutionary relationships.
Evolutionary tree
A branching diagram that shows how species are related and when they split from common ancestors.
Common ancestor
The species from which two or more other species have evolved.

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