Cladistics (HL) (HL IB Biology)

• Historically organisms would have been classified on the basis of morphology, which often led to organisms being classified into groups that were not all close relatives
• The development of DNA sequencing technology means that classification can now be carried out on the basis of evolutionary relationship
  • Organisms grouped together using this method of classification form groups known as clades; every member of a clade shares a recent common ancestor
    • A common ancestor is a shared ancestor, e.g.
      • The most recent common ancestor of siblings is their parents
      • The most recent common ancestor of cousins is their grandparents
  • Clades are monophyletic groups, meaning that they contain all of the descendants of a common ancestor

Advantages of classification by evolutionary relationship

• Classifying organisms correctly according to their clade ensures that groups of organisms are close evolutionary relatives rather than arbitrary groups that happen to look similar
  • The characteristics within a clade are often inherited from a common ancestor, so are likely to be shared
    • This means that scientists need to be careful not to accidentally place organisms together on the basis of analogous characteristics; not all species with shared characteristics are closely related
• The use of DNA sequencing has allowed some organisms to be reclassified into more accurate groups
  • Some species have been reclassified into different groups of organisms
  • Some groups of organisms have been split 
  • Some groups have been merged

Cladistics

• Cladistics is the branch of science in which scientists put organisms into clades
• The term clade can be defined as

A group of organisms that have all descended from a common ancestor

• • 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
• 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 this is not always the case

Identifying members of a clade

• In cladistics, it is important that species are placed into true clades; this avoids mistakes such as:
  • Some descendants of a common ancestor being placed in a different clade to each other
  • Some organisms that descend from a different ancestor being included in the same clade

Sequence data

• The most objective method for grouping species into clades is the use of sequence data from:
  • DNA bases
  • mRNA bases
  • Amino acids in polypeptides
• For all types of sequence data, it can be said that the more similar the sequences, the more closely related the species
  • 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

Morphology

• Species that share a recent common ancestor are more likely to share similar morphologies than species that diverged a long time ago, so identifying members of a clade can sometimes be done on the basis of morphology
• This method is considered to be more subjective, and has led to classification errors in the past
  • Similar morphology can be a sign that convergent evolution has occurred rather than a sign of recent common ancestry
• When classifying organisms in this way it can be difficult to decide on which characteristics classification should be based
  • E.g. should we classify bats along with birds on the basis of their wings, or with mammals on the basis of their fur?
• In order to choose the most important characteristic, scientists need to decide which characteristics are primitive, and which are derived
  • Primitive traits evolve early in the lineage of a clade and are found in all clade members, e.g.
    • All vertebrates have spinal cords
    • All insects have six legs
  • Derived traits evolve later and can differ between clade members
    • E.g. within the vertebrate clade, birds have feathers while mammals have fur
  • Note that a derived trait in one clade could be an ancestral trait in another
    • E.g. fur is a primitive trait within the mammal clade, but a derived trait within the vertebrate clade
• More closely related species will share a larger number of derived traits

• The evolutionary relationships between species can be determined by analysing sequence data from, e.g. DNA bases, mRNA bases, 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 number of differences between sequences can be determined using a method known as DNA hybridisation
    • Sections of single-stranded DNA from corresponding parts of the genome are taken from two species
    • The two complementary strands are allowed to bind to each other, or hybridise
    • The points on the DNA strand that do not bind show where bases are different to each other
    • The number of differences are recorded
• 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 fairly 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
      • It is worth noting that the assumed rate of mutations does not always match with the actual rate at which mutations occur, so the molecular clock provides estimates rather than exact time periods
      • The rate at which mutations accumulate can ne affected by, e.g.
        • Generation time
        • Population size
        • Selection pressures
• 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

Evolutionary tree diagram

The relatively consistent rate at which mutations occur in DNA provides scientists with a molecular clock. Differences in DNA sequence can therefore show how much time has passed since species diverged from each other.

• 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 base or amino acid sequence data due to difficulties in the use of observable characteristics
  • Observable characteristics can be misleading as they are not always the result of shared ancestry
• 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
• The reliability of a cladogram may vary depending on the amount of sequence data used to construct it
  • A cladogram based on the sequencing of one gene will be less reliable than a cladogram based on the sequencing of several genes
• 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 may change in the future if new evidence comes to light

Primate cladogram diagram

A cladogram for primates shows that humans are most closely related to chimps and bonobos, and that the next closest relatives are gorillas. Humans are thought to have diverged from chimps and bonobos between 5-7 million years ago.

NOS: Different criteria for judgement can lead to different hypotheses

• Cladograms are constructed using available evidence and on the basis of the principle of parsimony
  • Cladograms show the probable relationships between species, so they form a hypothesis
• The principle of parsimony states that the simplest explanation is the most likely
  • E.g. it is more likely that the characteristic of fur evolved once than twice, so cladograms place mammals as the descendants of one common ancestor, rather than appearing in several places in the cladogram
• The principle of parsimony provides the criteria for the construction of cladograms
  • Without this criteria, cladograms might look different

• Analysis of a cladogram can provide several pieces of information
  • The point at which two branches separate is known as a node, and represents common ancestor species
    • A node immediately adjacent to a pair of clades indicates that these two clades share a recent common ancestor
      • This shows that the two clades are more closely related to each other than they are to any other clade in the cladogram
    • If several nodes need to be traced back before two clades can be joined, this indicates a more distant relationship between two clades
  • The root of a cladogram is found at its base, and represents the common ancestor of all of the organisms within the cladogram
    • The root of a cladogram will represent organisms that were present a long way back in evolutionary history
  • The terminal branch represents the most recent species in an evolutionary lineage
  • Cladograms sometimes show numbers along the branches; these indicate the number of base or amino acid changes that have occurred between one node and the next or between a node and an emerging clade or species
    • The constant rate at which mutations accumulate means that these numbers can be used as a molecular clock to calculate how much time has passed
  • Some cladograms have a time scale to show how many millions have years have passed

Cladogram analysis diagram

Multiple conclusions can be drawn from a large cladogram such as this vertebrate cladogram. 

Note that this cladogram contains no numbers or time scale, so it does not show the number of base or amino acid changes that have occurred between one node and the next, or how much time has passed between nodes.