Download Lecture 11 Molecular evolution

Lecture 11
Molecular evolution
Jim Watson, Francis Crick, and DNA
Molecular Evolution
3 characteristics
1.  c-value paradox
2.  Molecular evolution is sometimes decoupled
from morphological evolution
3. Molecular clock
Molecular Evolution
paradox
1.  c-value
Navicola (diatom) Drosophila (fruitfly)
Gallus (chicken)
Cyprinus (carp)
Boa (snake)
Rattus (rat)
Homo (human)
Schistocerca (locust)
Allium (onion)
Lilium (lily)
Ophioglossum (fern)
Amoeba (amoeba)
Kb
35,000
180,000
1,200,000
1,700,000
2,100,000
2,900,000
3,400,000
9,300,000
18,000,000
36,000,000
160,000,000
290,000,000
Isochores
Cold-blooded vertebrates
L
(low GC)
Warm-blooded vertebrates
L
(low GC)
H1
L
H2
L
H3
(high GC)
Isochores
- 
- 
- 
- 
- 
Chromatin structure
Time of replication
Gene types
Gene concentration
Retroviruses
Warm-blooded vertebrates
L
(low GC)
H1
L
H2
L
H3
(high GC)
Human Genome Map
Molecular Evolution
2. Molecular evolution is sometimes decoupled
from morphological evolution
Morphological
Similarity
Genetic
Similarity
1. low
2.  high
low
high
3. high
4. low
low
high
Molecular Evolution
Morphological
Similarity
3.
high
Genetic
Similarity
low
Living fossils
Latimeria, Coelacanth
Limulus, Horseshoe crab
Molecular Evolution
Morphological
Similarity
4. 
low
Genetic
Similarity
high
- distance between humans and
chimpanzees is less than
between sibling species of
Drosophila.
- for example, from a sample of
11 proteins representing 1271
amino acids, only 5 differ
between humans and chimps.
- the other six proteins are
identical in primary structure.
- most proteins that have been
sequenced exhibit no amino
acid differences - e.g.,
alphaglobin
Pan, Chimp
Homo, Human
Molecular clock
- when the rates of silent substitution at a gene are compared to its rate of
replacement substitution, the former typically exceeds the latter by a factor
of 5-10.
Conclusion: the majority of evolution involves the substitution of silent
mutations – likely by random drift.
- these observations led to the proposal of the neutral theory of molecular
evolution in 1968 by Motoo Kimura.
“the survival of the luckiest”
Motoo Kimura
1924-1994
The neutral theory of molecular evolution
1.  most mutations are harmful and thus removed by “negative”
(or “purifying”) natural selection.
2. some mutations are neutral and thus accumulate in natural
populations by random genetic drift.
3. very rarely, beneficial mutations occur and are fixed by “positive”
Natural selection.
4. The rate of evolution of a molecule is determined by its degree of
“functional constraint”.
Genetic Code
The neutral theory of molecular evolution
1.  most mutations are harmful and thus removed by “negative”
(or “purifying”) natural selection.
2. some mutations are neutral and thus accumulate in natural
populations by random genetic drift.
3. very rarely, beneficial mutations occur and are fixed by “positive”
Natural selection.
4. The rate of evolution of a molecule is determined by its degree of
“functional constraint”.
The neutral theory of molecular evolution
5. neutral mutations and random genetic drift are responsible for
virtually all molecular evolution.
- this theory gave rise to a bitter dispute known as the neutralistselectionist controversy.
- the controversy raged throughout the 1970’s and 1980’s and has not
been satisfactorily resolved.
- the essence of this controversy is not whether natural selection or
random genetic drift operate at the molecular level, but rather what is
the relative importance of each.
- Testing the validity of the neutral theory has been very difficult.
“Classical” versus “balanced” views of
genome structure
• controversy began in the 1920’s with the establishment
of two schools of genetics.
• the “Naturalists” studied natural populations (e.g.
Dobzhansky, Mayr).
• the “Mendelians” studied genetics exclusively in the
laboratory (e.g., Morgan, Sturtevant, Muller).
Classical
Balanced
+
+
-
+
+
+
A1 B2 C1 D4 E3 F6
+
+
+ +
+
+
A3 B2 C4 D5 E5 -
Most loci homozygous
for “wild type” alleles
Most loci heterozygous
Polymorphism rare
Polymorphism common
+ = “wild type” allele
- = deleterious recessive allele
Why is this distinction important?
Classical
Balanced
Difficult
Easy
(mutationlimited)
(opportunitylimited)
Selection
Purifying
Balancing
Population
variation
Inter > Intra
Intra > Inter
Polymorphism
transient
balanced
(short-lived)
(long-lived)
Speciation
Allozyme electrophoresis setup
Starch gel stained for
Phosphoglucomutase (Pgm)
Extensive allozyme variation exists in nature
Vertebrates
(648 species)
Extensive allozyme variation exists in nature…
…so this confirms the balanced view?
Vertebrates
(648 species)
NO! MOST
POLYMORPHISMS
MAY BE NEUTRAL!
The neutral theory of molecular
evolution
• first proposed by Motoo Kimura in 1968.
The neutral theory of molecular
evolution
• first proposed by Motoo Kimura in 1968.
• two observations led Kimura to develop neutral
theory:
1. “Excessive” amounts of protein (allozyme)
polymorphism
• this would impart a severe "segregational load" if
adaptive.
Example: sickle cell anemia
Genotype
Fitness
HbAHbA
HbAHbS
HbSHbS
1-s
1
1-t
s=0.12
t=0.86
Segregational load = st/(s + t)
= 0.11
• this means that 11% of the population dies every
generation because of this polymorphism!
2. The molecular clock
• first reported by Zuckerkandl and Pauling in 1962.
2. The molecular clock
• first reported by Zuckerkandl and Pauling in 1962.
Method:
1.  Obtain homologous amino acid sequences from a
group of taxa.
2. Estimate divergence times (from the fossil record)
3.  Assess relationship between protein divergence and
evolutionary time.
The molecular clock
α-globin gene in
vertebrates
No. of amino
acid substitutions
100 
200
300
400
Time (millions of years)
500
The molecular clock ticks at different rates for
synonymous and nonsynonymous mutations
Kimura argued that the molecular clock
reflects the action of random drift, not
selection!
α-globin gene in
vertebrates
No. of amino
acid substitutions
100 
200
300
400
Time (millions of years)
500
Main features of the neutral theory
1. The rate of protein evolution is roughly
constant per site per year.
- this is the "molecular clock" hypothesis.
- why per site PER YEAR, not per site PER GENERATION?
2. Rate of substitution of neutral alleles equals
the mutation rate to neutral alleles.
• let µ = neutral mutation rate at a locus.
• the rate of appearance of a neutral allele = 2Nµ.
• the frequency of the new neutral allele = 1/2N.
• this frequency represents the allele’s probability of
fixation.
2. Rate of substitution of neutral alleles equals
the mutation rate to neutral alleles.
Rate of evolution = rate of appearance x
probability of fixation
= 2Nµ x 1/2N
= µ
• this rate is unaffected by population size!
3. Heterozygosity (H) levels are determined by
the “neutral parameter”, 4Neµ.
H = 4Neµ/(4Neµ + 1)
4. Rates of protein evolution vary with degree
of selective constraint.
• “selective constraint” represents the ability of a protein to
“tolerate” random mutations.
• for highly constrained molecules, most mutations are
deleterious and few are neutral.
• for weakly constrained molecules, more mutations are
neutral and few are deleterious.
Degree of constraint dictates rate of evolution
α-globin
No. of amino
acid substitions
histone H4
100 
200
300
400
Time (millions of years)
500
high constraint → low µ → low H, slow rate of
evolution
low constraint → high µ → high H, fast rate of
evolution
Testing the neutral theory by studying DNA
sequences
1. Comparisons of polymorphism and divergence
• studying DNA sequences enables the comparison of
replacement and silent mutations!
D. melanogaster
D. simulans
N
AAT
--C
---------
A
GCG
------C
-----
E
GAA
-----T-T-T-
R
CGG
-----------
T
ACT
--T--------
R
CGT
------C
--C
--C
D. melanogaster
D. simulans
N
AAT
--C
---------
A
GCG
------C
-----
E
GAA
-----T-T-T-
R
CGG
-----------
Mutations are either:
1. fixed between species
2. polymorphic within species
Mutations are also either:
1. silent
2. replacement
T
ACT
--T--------
R
CGT
------C
--C
--C
Replacement
Silent
Polymorphic
a
b
Fixed
c
d
• the degree of selective constraint determines the ratio of
a:b and c:d.
• however, because polymorphism is a transient phase of
molecular evolution, the neutral theory predicts that
ratio a:b = ratio c:d
↑
↑
short term evolution = long term evolution
This is the McDonald-Kreitman test
Two examples:
1. The alcohol dehydrogenase (Adh) locus in Drosophila
melanogaster, D. yakuba and D. simulans
polymorphic
replacement
silent
2
42
fixed
7
17
G = 7.43, P < 0.001
Conclusion: too many fixed replacements!
Two examples:
2. The glucose-6-phosphate dehydrogenase (G6pdh)
locus in D. melanogaster and D. simulans.
polymorphic
replacement
silent
2
36
fixed
21
26
G = 19.0, P < 0.0001
Conclusion: too many fixed replacements!
2. Tests for positive selection
• positive selection occurs when the rate of replacement
substitution exceeds the rate of silent substitution.
• although rare, is widely documented at two broad classes
of genes:
1. Genes involved in host-pathogen interactions
• notably the major histocompatibility complex (MHC) and
pathogen surface coat proteins.
2. Genes functioning in reproduction
• notably seminal fluid proteins and surface proteins on
sperm and egg.
Conclusion: Natural selection may be more
important in directing molecular evolution
than previously believed!