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Chapter 3
Substitution Patterns
Presented by:
Adrian Padilla
Patterns of Substitutions within
• Mutation rates
• Functional constraint
• Synonymous vs. Nonsynonymous
• Indels and pseudogenes
• Substitutions vs. mutations
• Fixation
Estimating Substitution Numbers
• Jukes-Cantor Model
Variations in Evolutionary Rates
between Genes
Evolution in Organelles
Mutation- Change in a nucleotide
sequence that occurs due to
mistakes in DNA replication or repair
• Deleterious (disadvantageous)
• Advantageous
• neutral
Mutation Rates
Rate of substitution (r)
• r = K/(2T)
K is expressed in terms of the number of
substitutions per site
T is Time
Substitution rates can give insight into the
dates of evolutionary events for which no
other physical evidence is available.
Functional Constraint
Natural selection – Differential success
between individuals in passing on genes to
subsequent generations due to differences
in fitness
• Advantageous, disadvantageous, neutral
Functional constraint – The tendency in
particularly important genes to
accumulate changes very slowly over the
course of evolution
Synonymous vs. Nonsynonymous
Synonymous Substitution - Change
at the nucleotide level of coding
sequences that does not change the
amino acid sequence of the protein.
Nonsynonymous Substitution – Any
nucleotide substitution that alters a
codon to one for a different amino
Synonymous vs. Nonsynonymous
Nondegenerate sites – Codon positions where
mutations always result in amino acid
Twofold degenerate sites – Codon postitions
where two different nucleotides result in the
translation of the same amino acid, but the two
other nucleotides code for a different amino acid.
Fourfold degenerate sites – Codon position where
changing a nucleotide to any of the three
alternatives has no effect on the amino acid that
ribosomes insert into proteins
Indels and Pseudogenes
Indels – Insertion and deletion
mutations for DNA replication.
• Mutations change the gene to give it a
new function that effects the fitness of
the organism.
Pseudogene - Acquires mutations
that make it nonfunctional and
transcriptionally inactive.
Mutations vs. Substitutions
Mutations – any change in nucleotide
sequence that occur due to mistakes
in DNA replication or repair.
Substitution – changes that evolution
has tolerated.
Alleles – Different versions of any
given gene within a species of
Fixation – A condition in which an
allele’s frequency within a population
reaches 100%.
New alleles arise from mutations
occurring to an existing allele within a
single member of a population.
As a result new versions of genes typically
begin at very low frequencies (q).
• q = 1/2N
• N is the number of reproductively active
diploid organisms within the population.
Mutations that make organisms less likely
to survive and reproduce tend to be
removed from the gene pool through the
process of natural selection and their
frequencies eventually return to 0.
When advantageous alleles do arise, their
frequencies should move progressively
toward 1.
Selectively neutral – or neutral mutation
that has no effect on the fitness of an
The probability (P) that the neutral variant
of a gene will eventually be lost from the
population is:
• P = 1 – q (frequency)
The probability that the neutral allele will
be fixed is equal to q.
Saturation mutagenesis – when
molecular biologists make all
possible changes to the nucleotide
sequence of a gene to determine
which alter its function.
Jukes-Cantor Model
Assumes that each
nucleotide is just as
likely to change into
any other nucleotide
at rate a.
PC(t)= 1/4 + (3/4)e-4at
• Probability you end up at
C when starting at C for a
period of time (t).
More substitutions than
observed substitutions.
Transitions and Transversions
Purine – nitrogenous bases that have a two-ring
structure. (Guanine and Adenine)
Pyrimidine – nitrogenous bases with only a onering structure. (Cytocine and Thymine)
Transitions – The exchange of one purine for
another or exchangeing one pyrimidine for
Transversions – The exchange of a purine for a
pyrimidine or vice versa.
Evolutionary Rate
Evolutionary rate – is the rate at
which something has changed.
• Two factors
Differences in mutation frequency.
The extent to which natural selection
affects the organism.
Evolutionary pressure – Pressure
natural selection puts on the gene
to survive.
Evolution in Organelles
Mitochondrial DNA (mtDNA) has a 10-fold
higher rate of mutations than that found
in nuclear DNA.
Higher rate of both synonymous and
nonsynonymous substitutions in mtDNA.
Comparisons of mtDNA are often used to
study relationships between closely
related polpulations of organisms.
Mutation is when there is a change in information
content of a DNA molecule due to replication
error or damage.
Mutations do not affect the fitness of an organism
to the same degree.
Natural selection causes many to be lost from the
gene pool and the changes that remain are
referred to as substitutions.
Substitution rates can be used to measure the
functional importance of a gene.
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