1. What are the Patterns Of Nucleotide Substitution Within Coding and
Non-coding Gene Regions?
Mouse vs Human
T = 80,000 my
rate = substitutions / site / 109 years

2. (1) Rates of substitution are extremely variable,
more so for nonsynonymous substitutions.
NSyn Rate
Syn Rate
# Codons

3. (2) In the majority of genes, the synonymous substitution
rate greatly exceeds the nonsynonymous rate.
NSyn Rate
Syn Rate
# Codons

4. (3) Overall rate of substitution is lowest for non-
degenerate sites, highest for 4-fold degenerate sites.
(4) Rate of transversional substitution is lower at
2-fold vs 4-fold degenerate sites.

5. (5) Rate of transitional substitution is higher than
transversional substitution at 4-fold sites.
(6) At nondegenerate sites, rate of transitional and
transversional substitution are similar.

6. Schematic of Eukaryotic Protein-Coding Locus
5’ UTR
3’ UTR
Intron 1
Intron 2 5’ 3’
Exon 1
Exon 2
Ex 3
GT AG
GT AG
Signal
Sequences
Initiation
codon
Stop
codon

8. Percent divergence between cow and
goat b- and g-globin genes and between cow and
goat b-globin pseudogenes.
Region K
5’ flanking
5’ untranslated
4-fold degenerate
Introns
3’ flanking region
3’ untranslated
Pseudogenes

10. Causes of Variation in Substitution Rates
Rate of Substitution is determined by:
(1) Mutation rate
Among genes
Among gene regions
(2) Probability of fixation
Neutral, advantageous, deleterious

12. Functional constraint: Range of alternative nucleotides
that is acceptable at a site without negatively affecting
the function or structure of a protein.
Total Mutation
Rate per Unit Time
Fraction of
Selectively Neutral
Mutations
Rate of Neutral
Mutation
V0 = vT fo
Neutral Theory Predicts k = V0 :
Rate of Substitution
So,
k = vT fo

13. k = vT fo i.e. Highest Rate of Substitution is Expected in
So, rate of substitution will be greatest when fo is 1.0
i.e.
Highest Rate of Substitution is Expected in
Sequence That Does Not Have A Function
Pseudogenes!

15. Expect an inverse relationship between the intensity of the
functional constraint and the rate of neutral evolution

16. Also, expect higher rates of substitution for
Given this relationship:
Also, expect higher rates of substitution for
synonymous vs nonsynonymous sites.
Logic:
(1) Mutations that result in amino acid replacements have
a higher probability of causing a deleterious effect on the
structure/function of the protein.
(2) Accordingly, the majority of nonsynonomous mutations
will be eliminated from the population by purifying selection.
(3) As a result, there will be a reduction in the rate of
nonsynonymous substitution vs synonymous substitution.

17. Causes of Variation in Substitution Rates
Rate of Substitution is determined by:
(1) Mutation rate
Among genes
Among gene regions
(2) Probability of fixation
Neutral, advantageous, deleterious

19. Functional constraint: Range of alternative nucleotides
that is acceptable at a site without negatively affecting
the function or structure of a protein.
Total Mutation
Rate per Unit Time
Fraction of
Selectively Neutral
Mutations
Rate of Neutral
Mutation
V0 = vT fo
Neutral Theory Predicts k = V0 :
Rate of Substitution
So,
k = vT fo

20. k = vT fo i.e. Highest Rate of Substitution is Expected in
So, rate of substitution will be greatest when fo is 1.0
i.e.
Highest Rate of Substitution is Expected in
Sequence That Does Not Have A Function
Pseudogenes!

22. Expect an inverse relationship between the intensity of the
functional constraint and the rate of neutral evolution

23. Also, expect higher rates of substitution for
Given this relationship:
Also, expect higher rates of substitution for
synonymous vs nonsynonymous sites.
Logic:
(1) Mutations that result in amino acid replacements have
a higher probability of causing a deleterious effect on the
structure/function of the protein.
(2) Accordingly, the majority of nonsynonomous mutations
will be eliminated from the population by purifying selection.
(3) As a result, there will be a reduction in the rate of
nonsynonymous substitution vs synonymous substitution.

24. Why is the rate of substitution at 4-fold sites lower
than the rate within pseudogenes?
Synonymous substitutions are not selectively neutral!
Codon Usage is non-random: species-specific, and
patterns may vary among genes within a genome.