2. 5.4 Cladistics
Essential idea: The ancestry of groups of species can be deduced by comparing their base or amino acid sequences.
The images above are both cladograms. They show the statistical similarities between species based on their DNA/RNA. The cladogram on the left show bacteria classified using the 16 S ribosomal RNA gene. The cladogram on the right uses retroviral sequences which have been incoporated into ape DNA and then inherited to build a picture of the relationships between apes. It’s an Interesting fact that humans have around 100,000 endogenous retroviruses incorporated into their DNA.
By Chris Paine

3. Understandings, Applications and Skills
Statement
Guidance
5.4.U1
A clade is a group of organisms that have evolved from a common ancestor.
5.4.U2
Evidence for which species are part of a clade can be obtained from the base sequences of a gene or the corresponding amino acid sequence of a protein.
5.4.U3
Sequence differences accumulate gradually so there is a positive correlation between the number of differences between two species and the time since they diverged from a common ancestor.
5.4.U4
Traits can be analogous or homologous.
5.4.U5
Cladograms are tree diagrams that show the most probable sequence of divergence in clades.
5.4.U6
Evidence from cladistics has shown that classifications of some groups based on structure did not correspond with the evolutionary origins of a group or species.
5.4.A1
Cladograms including humans and other primates.
5.4.A2
Reclassification of the figwort family using evidence from cladistics.
5.4.S1
Analysis of cladograms to deduce evolutionary relationships.

4. 5.4.U5 Cladograms are tree diagrams that show the most probable sequence of divergence in clades.
A cladogram is a tree diagram showing the similarities and differences between different species
The branching points on cladograms are called nodes.
Nodes denote a speciation event when a common ancestor splits into two, or more, species.
Cladograms are mostly based on DNA base sequences or the amino acid sequences in a protein.
Software applications combine multiple sequences* to find the most probable pattern of divergence.
*Cladograms can show different relationships between species depending on the DNA/amino acid sequences used in the analysis. It is important therefore to use multiple sequences when trying to identify the true evolutionary relationships between species.

5. 5.4.U1 A clade is a group of organisms that have evolved from a common ancestor.
Species may evolve over time to form a new species. Consequently there are groups of species derived from a common ancestor. Such groups are called Clades.
Clades can be small
Clades can be large (large clades can contain smaller clades)
Not all members of a clade may exist today, e.g. dinosaurs
Common ancestors often do not exist, as they have evolved into modern species or have become extinct.

6. 5.4.A1 Cladograms including humans and other primates.
The DNA evidence used to build this cladogram of primates, including humans. can also be used to estimate when species diverged and hence when the common ancestor existed.

7. 5.4.U2 Evidence for which species are part of a clade can be obtained from the base sequences of a gene or the corresponding amino acid sequence of a protein. 5.4.U3 Sequence differences accumulate gradually so there is a positive correlation between the number of differences between two species and the time since they diverged from a common ancestor.
Mutations in DNA that persist and are inherited* occur at a predictable rate#.
For example mitochondrial DNA from humans and primates has been completely sequenced and used to construct cladogram between them.
The rate at which mutations occur at can be used as a molecular clock to calculate how long ago species diverged.
If the DNA base sequences or two species are similar …
… then few mutations have occurred …
… therefore the species only diverged relatively recently
The length of the lines separating species on cladograms is often used to represent the estimated time since they diverged.
* In species that reproduce sexually for mutations to be inherited they must occur duration the creation of sex cells.
#When considering multiple changes in the base sequence of DNA. The sample size is large enough to estimate a mean rate of mutation.

8. 5.4.S1 Analysis of cladograms to deduce evolutionary relationships.
What animal is most closely related to a squirrel?
What animals are more closely related to humans that old world monkeys?
Tarsiers share a common ancestor with which animals?
Elephant shrews, Elephants, Manatee and dugong all share a common ancestor. Which animal diverged from the ancestor first?

9. 5.4.S1 Analysis of cladograms to deduce evolutionary relationships.
What animal is most closely related to a squirrel?
What animals are more closely related to humans that old world monkeys?
Guinea pig
Tarsiers share a common ancestor with which animals?
Elephant shrews, Elephants, Manatee and dugong all share a common ancestor. Which animal diverged from the ancestor first?

10. 5.4.S1 Analysis of cladograms to deduce evolutionary relationships.
What animal is most closely related to a squirrel?
What animals are more closely related to humans that old world monkeys?
Guinea pig
Gibbons, Orangutans, Gorillas,
Bonobos, and Common Chimpanzees
Tarsiers share a common ancestor with which animals?
Elephant shrews, Elephants, Manatee and dugong all share a common ancestor. Which animal diverged from the ancestor first?

11. 5.4.S1 Analysis of cladograms to deduce evolutionary relationships.
What animal is most closely related to a squirrel?
What animals are more closely related to humans that old world monkeys?
Guinea pig
Gibbons, Orangutans, Gorillas,
Bonobos, and Common Chimpanzees
Tarsiers share a common ancestor with which animals?
Elephant shrews, Elephants, Manatee and dugong all share a common ancestor. Which animal diverged from the ancestor first?
New world monkeys, Old world monkeys,
Gibbons, Orangutans, Gorilla, Humans,
bonobos, common chimpanzees

12. 5.4.S1 Analysis of cladograms to deduce evolutionary relationships.
What animal is most closely related to a squirrel?
What animals are more closely related to humans that old world monkeys?
Guinea pig
Gibbons, Orangutans, Gorillas,
Bonobos, and Common Chimpanzees
Tarsiers share a common ancestor with which animals?
Elephant shrews, Elephants, Manatee and dugong all share a common ancestor. Which animal diverged from the ancestor first?
New world monkeys, Old world monkeys,
Gibbons, Orangutans, Gorilla, Humans,
bonobos, common chimpanzees
Elephant shrew

13. 5.4.U4 Traits can be analogous or homologous.
Homologous structures are similar because of common ancestry
Analogous structures are similar because of convergent evolution
e.g. pentadactyl limbs
e.g. the human eye and the octopus eye
Both have similar structures to provide similar function, but have evolved independently.
In the past relying on homologous structures to classification has led to mistakes in classification. Distinguishing between homologous and analogous structures is not straightforward

14. DNA evidence identified the different common ancestors
5.4.A2 Reclassification of the figwort family using evidence from cladistics.
5.4.U6 Evidence from cladistics has shown that classifications of some groups based on structure did not correspond with the evolutionary origins of a group or species.
DNA evidence identified the different common ancestors
The similarities among the members of the old Scrophulariaceae family were superficial.
The general flower shape and form of the seed capsule evolved many times from different ancestors (convergent evolution). Different plant species adapted to similar pollinators and adopted similar seed dispersal strategies.
DNA evidence has cast doubt on some traditionally classified groups, but equally it has given support to others.
Though DNA evidence is very important, it must be remembered that is not the only evidence used to decide evolutionary relationships.

15. Bibliography / Acknowledgments
Jason de Nys