1. Phylogenics & Molecular Clocks
DNA and the Genome
Key Area 8b
Phylogenics & Molecular Clocks

2. (b) Evidence of evolution
Learning Intentions
By the end of this topic you should be able to:
(b) Evidence of evolution
Explain what ‘phylogenetics’ is and how it can be used as evidence for evolution
Explain what ‘molecular clocks’ are and how they can be used as evidence for evolution
Explain the term ‘last universal ancestor’
Explain how the evolution of prokaryotes and eukaryotes provides evidence for the sequence of events in evolution
Describe 2 sources of evidence that can be used to support the sequencing of events in evolution
Name the 3 domains of cellular life
Describe the evidence for the existence of the 3 domains of cellular life

3. Phylogenetics

4. Phlogenetics
Phylogenetics is the study of evolutionary history and relationships It uses comparative genomic data to deduce phlogenies – sequences of events involved in a group’s evolution It then constructs phylogenetic trees – diagrams that show evolutionary relationships Closely related species have genomes that are very similar in the sequence of their nucleotide bases

5. Molecular Phylogenetics
The use of structural features alone is not always enough to determine evolutionary relationships. Instead, molecular phylogentics is used - the use of sequence data to study evolutionary relatedness among groups of organisms. This allows us to:
distinguishes between two groups who may not look structurally alike but are related genetically
distinguishes between two groups that are physically indistinguishable (eg many species of bacteria)

6. Bacteria
Archaea
Eukaryote
Universal Ancestor

7. Sequence Divergence
When 2 closely related groups acquire their own set of mutations, their genomes slowly become more and more altered from each other. When it gets to the stage the changes occurring in one groups genome are distinct to those in the other groups, they are said to have diverged Sequence divergence is used to estimate time since lineages diverged. The greater the difference between two groups nucleotide base sequence the more distantly related the two groups are (and vice versa)

8. Evolutionary Distances
The number of differences per unit length of DNA sequence (quantity of genetic change) between two genomes is a measure of evolutionary distance between the two groups
This is measured by comparing the number of differences in base sequence between the two groups
A few changes means they share a more common ancestor and have diverged recently
The greater the number of changes, the longer since divergence
This information is then used to create a phylogenetic tree

9. One unit of genetic change
Key:
One unit of genetic change
Common Ancestor
Species A
Species B
Species C
Species D
The further apart two species are, the more distantly related to each other they are (A and D).
The closer they are, the more closely related they are (B and C).

10. Fossil Evidence for Evolution
The conversion of hard parts of the body (bone, teeth, shells) into rock is known as fossilisation The age of a fossil can be determined by estimating the age of the rock of which it is composed The older the rock, the less radioactivity it emits This can then be used, along with looking at differences in nucleotide sequences, to build molecular clocks

11. Molecular Clocks
The nucleotide base pair sequence of organisms gradually changes over time due to mutations such as nucleotide substitutions When the equivalent genetic sequence of related groups are examined, the number of changes between their sequences can be counted Molecular clocks are used to show when species diverged during evolution. They assume a constant mutation rate and show differences in DNA sequences or amino acid sequences. Therefore, differences in sequence data between species indicates the time of divergence from a common ancestor.

12. Molecular Clocks
If this is compared to evidence from fossils that provide an geological time from divergence, the number of nucleotide substitutions by which the groups differ is proportional to the length of elapsed time since the groups diverged. A molecule of nucleic acid can therefore be regarded as a molecular clock

13. (Millions of years)
If we graph the number of molecular differences against a time scale (from fossil records) we can date the origins of groups of living things and determine the sequence in which they evolved

14. This molecular clock shows comparisons of the human a- globin gene within a number of different species.
Cows can be seen to have shared a common ancestor with humans around 100 million years ago and have approx. 20 different substitutions in this gene
Shark a-globin has around 4 times more nucleotide substitutions than cow when compared with human a- globin (approx. 80) and last shared a common ancestor with humans 450 million years ago.

15. Which part of the genome to use?
Two regions of DNA which are routinely used in this sort of phylogenetic analysis can be found on:
the male Y chromosome
mitochondrial DNA
When a sperm fertilises an egg, only the egg’s mitochondria are present in the zygote, so the mitochondria are derived from the mother
This allows the molecular clock to be traced through the male or female ancestral lines

16. One advantage of using mitochondrial DNA is the simplicity of a single small chromosome, a haploid genome, which does not have a matching homologous partner with different alleles or crossing over events to complicate the sequence
Mitochondrial chromosomes also have very little non-coding DNA, with genes tightly packed together and with few introns
This is in contrast to normal eukaryote genes, which are usually widely dispersed on a linear chromosome and have numerous introns.

17. Advantages & Disadvantages of Molecular Clocks
As mentioned earlier, molecular clocks (phylogenetics) give a better indication of evolutionary relationships than structural changes between groups of related organisms For instance, molecular clocks show dolphins are evolutionary more closely related to bats than they are to sharks and tuna fish Fossil evidence agrees with this although structurally this would not seem to be the case

18. There is one major flaw with using molecular clocks to plot evolutionary relationships They assume that the mutation rate affecting one type of molecule has been relatively constant over time This is more likely to be true for closely related species but not so for groups that diverge early on in the evolution of life on Earth Molecular clocks become less accurate and reliable when looking at distantly related groups

19. The following animation explains the process of evolution using molecular clocks – go to address and click review the animation at the top
Molecular Clocks

20. Three Domains of Living Things
Based on molecular evidence looking at nucleotide sequences of rRNA from many different organisms, a phylogenetic tree has been constructed for all living things
rRNA was used as the genes that code for it:
are ancient
are present in all living things
have suffered little or no horizontal gene transfer
The evidence supports the idea that living things are made up of three different domains

21. The 3 domains are: Bacteria Traditionally prokaryotes Archaea Mostly prokaryotes that inhabit extreme environments such as hot springs and salt lakes Eukaryotes Fungi, plants and animals

23. Combing the Evidence
Using changes in genome sequences and fossil evidence, the sequence of key events in evolution has been worked out The combined data suggests living things have undergone a series of modifications from the first emergence of life on earth to the present day These modifications have become more complex leading to the variety of species now present

24. Millions of years ago
3500
2700
1850
1200
485
435
Evolution of cells
Evolution of last universal ancestor
Evolution of prokaryotes
Evolution of photosynthetic organisms
Evolution of eukaryotes
Evolution of multicellular organisms
Evolution of animals
Evolution of vertebrates
Evolution of land plants