5.2.5 Cladistics

• The term clade can be defined as
  • A group of organisms that have all descended from a common ancestor

• Cladistics is the branch of science in which scientists put organisms into clades
  • It involves classification that is based on homologous characteristics rather than analogous characteristics
• Clades are formed on the basis of evolutionary relationships i.e. who is descended from which ancestor
• Note that while taxonomy is about classifying and then naming organisms, cladistics is about identifying evolutionary relationships between organisms
  • A taxon is a group of organisms that have been given a group name by taxonomists on the basis on their shared features
  • A clade is a group of organisms classified together on the basis of their shared descent from a common ancestor

• If taxonomy is carried out correctly then all of the members of a taxon should form a clade, but due to historical errors and the difficulties in distinguishing between true homologous characteristics and those that have come about by convergent evolution, this is not always the case
• Clades can include both living and extinct species
  • Some of the descendants of a common ancestor may have gone extinct
  • The common ancestor species itself may have gone extinct
• Clades can be large or small depending on the common ancestor being studied

• In the past, scientists encountered many difficulties when trying to determine the evolutionary relationships between species
  • Using the physical features of species has limitations and can often lead to organisms being put into groups that are not true clades
  • This would mean that all of the organisms in a group are not descended from a common ancestor
    • Some descendants might be missing
    • Some organisms might have been included that descend from a different ancestor

• Advances in sequencing technology have allowed scientists to further investigate the evolutionary relationships between species
• Sequence data that can be used to investigate evolutionary relationships can come from
  • DNA
  • mRNA
  • Amino acids in polypeptides

• Sequencing technology can determine the order of DNA bases, mRNA bases and amino acids
• For all types of sequence data, it can be said that the more similar the sequences, the more closely related the species are
  • Two groups of organisms with very similar sequences have separated into separate species more recently than two groups with less similarity in their sequences
  • Species that have been separated for longer have had a greater amount of time to accumulate mutations and changes to their DNA, mRNA and amino acid sequences
• Sequence analysis and comparison can be used to create family trees that show the evolutionary relationships between species

• The evolutionary relationships between species can be determined by analysing sequence data from e.g. DNA, mRNA, or amino acids in polypeptides
• The number of differences between sets of sequence data provides information on how closely related two species are
  • The more differences there are between the sequences, the longer ago the species diverged, and vice versa
• The differences between sequence data can also be used to produce a quantitative estimate for how long ago two species diverged from each other
  • Differences in sequence data come about due to mutations in the DNA
  • Evidence suggests that mutations occur at a constant rate
  • This means that the number of mutations that have occurred gives an indication of the amount of time that has passed since two species diverged
    • Scientists refer to the constant rate of mutation as the molecular clock

• Analysing the differences in sequence data allows evolutionary biologists to determine the order in which different species diverged from a common ancestor, and therefore how closely related species are

Differences in DNA sequence data show how much time has passed since species diverged from each other, enabling the relationships between species to be established

• Homologous traits can be defined as
  • Characteristics that may differ in form and function in different species but that have shared evolutionary origins

• Homologous traits, or characteristics, indicate common ancestry, and are useful for classifying organisms into true clades
  • An example of a homologous characteristic is the pentadactyl limb; limbs in different species of animal differ significantly in their shape and role, but similarities in overall structure indicate common ancestry
• The difficulty with using homologous traits in classification is that it is not always obvious whether characteristics are homologous or analogous
• Analogous traits can be defined as
  • Characteristics with the same function but which do not share an evolutionary origin
• Such characteristics have evolved independently of each other from different ancestors, enabling organisms to adapt to similar environments
  • This is known as convergent evolution

• Analogous characteristics look similar, hence the danger of confusing them with homologous characteristics
• Classifying organisms on the basis of analogous characteristics will not produce an accurate clade
  • This has led to errors of classification in the past
  • For this reason, sequencing data is now used for classification instead of observable characteristics

The body shape of sharks/dolphins and the wings of butterflies/bats are both examples of analogous structures

• Evolutionary relationships between species can be represented visually using a diagram called a cladogram
• Cladograms are evolutionary trees that show probable order of divergence from ancestral species and therefore probable relationships between species
  • The point at which two branches separate is known as a node
  • Nodes represent common ancestor species

• The information used to build cladograms most often comes from sequence data due to difficulties in the use of observable characteristics
  • It can be difficult to be sure whether observable traits are homologous or analogous
• Sequence data can provide information about how different species are from each other, as well as how much time has passed since divergence from a common ancestor took place
  • The constant rate at which mutations accumulate can be used as a molecular clock

• Computers use the information from sequence data to build the most likely cladogram
  • This is done using the principle of parsimony, which states that the simplest explanation is preferred
    • The computer builds the shortest possible cladogram with the smallest number of divergence events to fit the available data
  • We say that cladograms show the most probable divergence times and relationships rather than providing definite conclusions

Cladograms that include humans and other primates

• Analysis of sequence data for humans and other primate groups show that humans are most closely related to chimps and bonobos, and that the next closest relative is the gorilla
• Humans are thought to have diverged from chimps and bonobos between 5-7 million years ago

A cladogram showing humans and other primates