Molecular Evolution Lecture Notes: Anders Gorm Pedersen
Molecular Evolution Lecture Notes: Anders Gorm Pedersen
Lecture Notes
Anders Gorm Pedersen
[email protected]
February 4, 2005
Contents
1 Brief Introduction to Evolutionary Theory
1.1 Classification . . . . . . . . . . . . . . . . .
1.2 Darwin and the Theory of Evolution . . . .
1.3 Natural Selection . . . . . . . . . . . . . . .
1.4 The Modern Synthesis . . . . . . . . . . . .
1.5 Mendelian Genetics . . . . . . . . . . . . . .
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9
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10
13
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15
21
23
24
25
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28
29
ii
Chapter 1
Brief Introduction to
Evolutionary Theory
1.1
Carl Linnaeus
(17071778)
Classification
One of the main goals of early biological research was classification, i.e., the
systematic arrangement of living organisms into categories reflecting their
natural relationships. The most successful system was invented by the swede
Carl Linnaeus, and presented in his book Systema Naturae first published
in 1735. The system we use today is essentially the one devised by Linnaeus.
It is a hierarchical system with seven major ranks: kingdom, phylum, class,
order, family, genus, and species.
Specifically, groups of similar species are placed together in a genus,
groups of related genera are placed together in a family, families are grouped
into orders, orders into classes, classes into phyla, and phyla into kingdoms.
When depicted graphically, the Linnean system can be shown in the form
of a tree with individual species at the tips, and with internal nodes in
the tree representing higher-level categories (Fig. 1.1). Along with this
classification system, Linnaeus also developed the so-called binomial system
in which all organisms are identified by a two-part Latinized name. The
first name is capitalized and identifies the genus, while the second identifies
the species within that genus. For example the genus Canis includes Canis
lupus, the wolf, Canis latrans, the coyote, and Canis familiaris, the domestic
dog. Similarly, the genus Vulpes contains Vulpes vulpes, the red fox, Vulpes
chama the Cape fox, and others. Both genera (Canis and Vulpes) belong
to the family Canidae, which in its turn is part of the order Carnivora, the
carnivores.
Note that it is non-trivial to come up with a generally applicable definition of what exactly a species is. According to the so-called biological
species concept, a species is a group of actually or potentially interbreeding natural populations which are reproductively isolated from other such
groups. This definition is due to the evolutionary biologist Ernst Mayr
(1904) and is perhaps what most people intuitively understand by the word
species. However, the biological species concept does not address the issue
of how to define species within groups of organisms that do not reproduce
sexually (e.g., bacteria), or when organisms are known only from fossils.
An alternative definition is the morphological species concept which states
that species are groups of organisms that share certain morphological or
biochemical traits. This definition is more broadly applicable, but is also
far more subjective than Mayrs.
1.2
species of animals. Linnaeus believed that God was the ordering principle
behind this classification system, and that its structure somehow reflected
the divine master plan.
It was not until after the 1859 publication of Charles Darwins On the
Origin of Species that an alternative explanation was widely accepted. According to Darwin (and others), the ordering principle behind the Linnean
system was instead a history of common descent with modification: all life
was believed to have evolved from oneor a fewcommon ancestors, and
taxonomic groupings were simply manifestations of the tree-shaped evolutionary history connecting all present-day species (Fig. 1.2).
The theory of common descent did not in itself address the issue of how
evolutionary change takes place, but it was able to explain a great deal
of puzzling observations. For instance, similar species are often found in
adjacent or overlapping geographical regions, and fossils often resemble (but
are different from) present-day species living in the same location. These
phenomena are easily explained as the result of divergence from a common
ancestor, but have no clear cause if one assumes that each species has been
created individually.
1.3
Natural Selection
The mechanism that Darwin proposed for evolutionary change is called natural selection. This is related to artificial selectionthe process of intenc Anders Gorm Pedersen, 2005
1.4
Charles Darwin
(1809-1882)
1.5
Mendelian Genetics
Figure 1.3: Mendelian genetics. Each diploid parent contains two alleles. The s
allele is recessive and results in wrinkled peas when present in two copies.
be homozygous for that allele (it is a homozygote). If it has two different alleles present at a locus, then it is said to be heterozygous for that
allele (and is then referred to as a heterozygote). The total complement of
alleles present in an organism is its genotype. If we are interested in one
particular locus where the alleles A and a occur, then a diploid organism
might for instance have the genotype AA or Aa. A haploid organism
might have the genotype a at such a locus. Depending on the molecular nature of the different alleles present at a locus in a diploid organism,
one allele may not make an impact on the organisms appearance (its phenotype). It is then said to be a recessive allele. An allele that is fully
expressed in the organisms phenotype is called dominant. For instance,
Fig. 1.3 shows two different allelesthe dominant S allele and the recessive
s alleleof a gene controlling wrinkledness in peas. Occasionally the alleles
will be co-dominant, and this will result in an apparent blending of parental
characteristics. In diploid organisms, one allele comes from the mother, one
from the father. When diploid organisms reproduce sexually, it occurs via
an intermediate, haploid sex cell called a gamete (the gamete is an egg
cell if it is produced by a female, and a sperm cell if it is produced by a
male). During gamete formation, genetic material from the two parents is
mixed by the process of recombination. Recombination is one stage of
the special type of cell division termed meiosis which ultimately results in
formation of the haploid gamete. At any one locus, there will (by necessity)
be only one allele present in the gamete. The diploid cell formed by fusion
of two gametes is called a zygote. Sexually reproducing organisms have life
cycles that alter between a haploid stage and a diploid stage. In some organisms most of the life cycle is diploid (e.g., humans, where only the sex cells
are haploid), while the situation is reversed for other organisms (including
some algae where the diploid zygote quickly undergoes meiosis to form new
c Anders Gorm Pedersen, 2005
Chapter 2
Brief Introduction to
Population Genetics
10
2.1
Introduction
The science of population genetics deals with genetic variation within populations, and with the forces that change this variation. I will now give you
a very brief introduction to a few important results in the field.
My goal with this section is mostly to make you aware of some of the
ways in which evolutionary theory can be approached in a stringent, quantitative manner. Specifically, we will discuss the effects that growth, selection,
mutation, and genetic drift have on the genetic composition of a population.
Most of the concepts will be introduced in the context of haploid, asexually
reproducing organisms since that makes the analysis easier.
The material covered here does not directly relate to reconstruction of
phylogenetic trees. However, any evolutionary history is necessarily the
result of processes that resemble the ones described in this section, and it
is therefore relevant to have at least passing knowledge of the underlying
theory.
2.2
2.2.1
Population Growth
Exponential Growth
We will start by analyzing the characteristics of a growing population. Imagine that we are examining a population of asexually reproducing organisms
where each individual produces 200 offspring per generation and then dies.
The number 200 is called the fecundity of the organism and is usually denoted m. For various reasons only 2% of the offspring survive sufficiently
long to produce offspring of their own. This is the survival rate and is usually denoted L. We can easily see that each individual organism will have
a net life-time production of m L = 200 2% = 4 descendants. This
number is the so-called per capita reproductive rate (R) of the population.
It is also clear that since each individual leaves more than one descendant,
then the population will grow. But how exactly will that growth proceed?
Let us first assume that the numbers L and m remain constant in subsequent generations, and that generations are discrete and non-overlapping.
This means that for every organism that was present at some point in time,
there will be R individuals present after one generation (4 in the example
above). Thus, the population size after one generation (N1 ) can be computed from the initial population size (N0 ) as follows:
N1 = N0 R
The population size after two generations can be found by multiplying this
c Anders Gorm Pedersen, 2005
11
900000
800000
Population size, N
700000
600000
500000
400000
300000
200000
100000
0
0
Generation no., t
(2.1)
12
900000
800000
Population size, N
700000
600000
500000
400000
300000
200000
100000
0
0
Generation no., t
13
2.2.2
Nt
log N
0
log R
Logistic Growth
Nt =
1+
K
N0
1 ert
(2.3)
2.3
14
10000
Population size, N
8000
6000
4000
2000
0
0
10
12
Generation no., t
Figure 2.3: Logistic growth. The plot shows the growth of a population with
initial size N0 = 100, rate of increase r = 1.1, and carrying capacity K = 10, 000.
NA,1
pN0 R
=
=p
N1
N0 R
2.4
Selection
Let us now consider the more interesting case where two haploid genotypes
do not have the same absolute fitness. We will again investigate an example
where the alleles A and a are present at a locus in a haploid organism that
reproduces as described above. Let us imagine that the absolute fitness of
genotype A is RA = 4, while that of genotype a is Ra = 2. Recall that
for organisms such as the one we are examining here, R is the product of
fecundity and survival rate. It is therefore possible that the difference in
fitness between the two genotypes is caused by differential fecundity, differential survival rate, or both. Let us say, for instance, that genotype A
c Anders Gorm Pedersen, 2005
15
16
20000
Genotype A
Genotype a
Population size, N
15000
10000
5000
0
0
Generation no., t
has a fecundity of 200 offspring per generation, and a survival rate of 2%,
giving RA = 200 2% = 4. We may further imagine that genotype a has
a higher fecundity (400 offspring per generation) but a much lower survival
rate (0.5%) resulting in an overall fitness that is half that of genotype A
(Ra = 400 0.5% = 2).
The number of individuals with genotype A therefore grows faster than
the number of individuals with genotype a. An example of this is shown
in Figure 2.4. Table 2.1 gives the corresponding genotype numbers and
frequencies, and includes a few extra generations compared to the figure.
In this example, the initial population consists of one single individual with
genotype A (perhaps a newly created mutation), and 99 individuals with
genotype a. It can be seen how the proportion of individuals with genotype
A rapidly increases from the initial 1%, and after 7 generations A is the
predominant genotype. After only 10 generations genotype A makes up more
than 90% of the population, and intuitively it seems to be approaching 100%
asymptotically (Table 2.1). But instead of guessing, we should of course
develop a mathematical model that we can use to predict the genotype
frequencies at any time t.
c Anders Gorm Pedersen, 2005
17
NA
1
4
16
64
256
1024
4096
16384
65536
262144
1048576
Na
99
198
396
792
1584
3168
6336
12672
25344
50688
101376
Ntot
100
202
412
856
1841
4192
10432
29056
90880
312832
1149952
p
0.01
0.02
0.04
0.07
0.14
0.24
0.39
0.56
0.72
0.84
0.91
q
0.99
0.98
0.96
0.93
0.86
0.76
0.61
0.44
0.28
0.16
0.09
NA,t
p(RA )t
pN0 (RA )t
=
=
Ntot,t
pN0 (RA )t + qN0 (Ra )t
p(RA )t + q(Ra )t
Where the last simplification was obtained by eliminating N0 . The expression can be further simplified by dividing both the numerator and the
denominator with (RA )t :
pt =
p(RA )t
)t
(p(RA + q(Ra
1
(RA )t
)t )
1
(RA )t
=
p+
(Ra )t
q (R
t
A)
p
Ra t
p + q( R
)
A
(2.4)
Ra
The term R
is the so-called relative fitness of allele a. The relative fitness
A
of a genotype (usually denoted W ) is the fitness of that genotype relative
18
Genotype A
Genotype a
Genotype frequency
0.8
0.6
0.4
0.2
0
0
10
12
14
16
18
Generation no., t
Figure 2.5: Change in genotype frequencies as a result of natural selection. Genotype A (initial number NA,0 = 1) has the fitness RA = 4, while genotype a
(Na,0 = 99) has a lower fitness (Ra = 2).
p
p + qWat
(2.5)
And here, finally, is our result: equation 2.5 enables us to compute how
natural selection changes the frequencies of genotypes A and a over time
(The frequency of genotype a can, for instance, be found by qt = 1 pt .) An
important conclusion from equation 2.5 is that the effect of natural selection
only depends on the relative fitness. This means that we would get the same
change in frequency regardless of whether the absolute fitnesses of A and a
were, for instance, 10 and 5, or 6 and 3, or even 0.8 and 0.4 respectively.
The so-called selection coefficient (s) is often used instead of the relative
fitness W . The selection coefficient against the least fit allele is defined as
s = 1 W where W is the relative fitness of the least fit allele. This means
that W = 1 s and equation 2.5 can of course be rewritten by substituting
(1 s) for Wa , if one is interested in expressing the frequencies in terms of
selection coefficients instead of relative fitness.
c Anders Gorm Pedersen, 2005
19
Figure 2.5 shows how the genotype frequencies change over time in our
example (i.e., when Wa = 0.5). A relative fitness of 0.5 corresponds to a
selection coefficient of s = 1 0.5 = 0.5. It can be seen that even though
genotype A has an initial frequency of only 1%, it has essentially reached
fixation after just 16 generations. It should be noted that a selection coefficient of 0.5 is quite high, but it is not unrealistic. For instance it has been
estimated that natural selection acting on the so-called melanic peppered
moths, that spread in industrial Britain during the 1800s, involved a selection coefficient of approximately 0.3. It is believed that this selection was
driven by the dark, melanic forms being harder to detect on soot-covered
tree bark compared to the lighter, more easily spotted form of the moth.
Selection for drug resistance in HIV and pesticide resistance in mosquitoes
has also been reported to be of this magnitude.
Figure 2.6 shows another example where the a allele has a relative fitness
of 0.99 (corresponding to a selection coefficient s = 0.01). In this example
genotype A has essentially reached fixation after 1000 generations. It is
important to note that there are situations where natural selection will not
lead to fixation of one allele, but will instead act to maintain a certain level
of diversity at a locus. One example of this is when a diploid organism
that is heterozygous at some locus has higher fitness then either of the two
homozygotes.
There is one final issue we can investigate using this simple model of
selection. You may have noted from figures 2.5 and 2.6 that the frequency of
A appears to change rapidly when both genotypes are fairly common, while
it changes more slowly when one genotype predominates. Let us derive an
expression that sheds light on this problem. The frequency of genotype A
is initially p. Using equation 2.5, we can see that after one generation, the
frequency of A will be:
p
p1 =
p + qWa
We can rewrite this expression using that p = 1 q and that Wa = (1 s):
p1 =
p
p
p
=
=
(1 q) + q(1 s)
1 q + q sq
1 sq
(2.6)
This expression tells us the frequency after one generation has passed. The
amount of change during one generation can now be seen to be:
p = p1 p0 =
p
p
1 sq
Multiplying p by 1sq
1sq (i.e., multiplying by 1) allows us to collect all the
terms in one single fraction:
p =
p
p(1 sq)
p p(1 sq)
p p + spq
=
=
1 sq
1 sq
1 sq
1 sq
20
Genotype A
Genotype a
Genotype frequency
0.8
0.6
0.4
0.2
0
0
200
400
600
800
1000
1200
Generation no., t
Figure 2.6: Change in genotype frequencies as a result of natural selection. Relative fitness of genotype a is 0.99 corresponding to a selection coefficient of s = 0.01
spq
1 sq
(2.7)
Since 1 > s > 0 (genotype a has a lower fitness than genotype A), it can be
seen from equation 2.7 that p must be positive. This is consistent with the
fact that genotype A is more fit than genotype a and that selection should
therefore act to increase its frequency. The change in frequency of the less
fit genotype is simply:
q = p =
spq
1 sq
(2.8)
Plotting p as a function of p for a given value of s, results in a singlehumped curve with a maximum in the middle (for an example see Fig. 2.7).
The exact location of the maximum depends on the value of s, but for
small s, p is essentially driven by the numerator of this equation and will
be highest when p q. We will use equation 2.7 below when considering
the interplay of mutation and selection.
c Anders Gorm Pedersen, 2005
21
0.40
0.35
0.30
0.25
0.20
0.15
0.10
0.05
0.00
0
0.2
0.4
0.6
0.8
Figure 2.7: Change in p (i.e., the frequency of genotype A) during one generation,
as a function of the current value of p. In this example the selection coefficient
against allele a is s = 0.8
2.5
Mutation-Selection Balance
22
(p)
selection
G2
(p )
mutation
G2
(p1 )
...
Here, p is the frequency of A in generation 1 organisms just prior to reproduction; p is the increased frequency of A in generation 2 after selection
has acted (via fecundity and survival rate); p1 is the final frequency of A
in adult generation 2 organisms after one full life-cycle has elapsed, and
mutation has decreased the frequency of A (thereby producing more a).
To find the equilibrium value, you should first recall that equation 2.6
(page 19) tells us that the natural selection step will change the frequency
of genotype A as follows:
p
p =
(2.9)
1 sq
We now need to figure out how the mutation step will change this frequency.
Note that the mutation rate m gives the fraction of A alleles that will change
into a in the course of one generation. The fraction of A individuals that
remain A must therefore be 1 m and we consequently have that:
p1 = p (1 m)
Substituting the expression in equation 2.9 for p gives us:
p1 =
p(1 m)
1 sq
(2.10)
This expression tells us how the forces of selection and mutation combine
to change the frequency of A (from p to p1 ) in one generation. We can now
find the equilibrium frequency by using the following insight: at equilibrium
the frequency of A is constant. From this it follows that the frequency of
A after one generation (p1 ) must equal the frequency of A in the previous
life-cycle (p). Substituting p for p1 in equation 2.10 gives us:
p=
p(1 m)
1 sq
23
m
s
(2.11)
Equation 2.11 shows us that the equilibrium frequency of the disadvantageous allele depends on only the mutation rate and the selection coefficient
in a very simple way. In our example we find that the equilibrium frequency
of a is:
107
m
=
= 2 106
q=
s
0.05
The conclusion from the analysis presented here, is that when both selection and mutation are acting at the same time, then a constant and
predictable level of genetic diversity will be maintained in the population.
2.6
24
2.7
Genetic Drift
In the discussion presented above we have been using models that are deterministic. Deterministic models are characterized by always giving a specific
result when starting from a specific set of conditions. For instance, when we
investigated exponential growth above, it was assumed that if a population
has growth rate R = 4 and initially consists of N0 individuals, then there
will be exactly 4 N0 individuals in the next generation. Based on this assumption we showed that the proportions of different genotypes will remain
constant provided that the genotypes have the same fitness (section 2.3).
This is, however, a simplification. Different individuals will not leave
exactly the same number of offspring, and death will also not remove exactly
the same fraction of different broods. This means that for every generation
there is some chance that the frequency of a genotype will change, even
though it has the same fitness as all other alleles at the locus (alleles with
the same fitness are said to be neutral).
The frequency of an allele has an equal chance of changing to a higher
or a lower value. This is true for every consecutive generation, regardless
of what the frequency has been at any previous time. Imagine for instance
that an allele has changed from its initial value of p = 0.3 to p = 0.26. In
the next generation the chance of ending with a frequency that is higher
than 0.26 will be the same as the chance of ending with a frequency that
is lower than 0.26. If, after 100 generations, the frequency has changed to
c Anders Gorm Pedersen, 2005
2.8
2.9
Genetic drift ultimately results in the loss of genetic diversity, but since this
loss is the result of random fluctuations, drift is not a particularly strong
or fast-acting evolutionary force. It can be shown that, on average, it takes
2N generations for a new mutation to reach fixation in a haploid, asexually
reproducing population of N individuals. The process takes 4N generations
for diploid, sexually reproducing organisms. We will not prove this but
c Anders Gorm Pedersen, 2005
25
26
Genotype
frequency
A2
A4
A3
A1
t1
t2
t3
t4
Time
only note that, for some organisms, 2N (or 4N ) generations is a very long
time indeed. (This obviously depends on both the population size and the
generation time). You should compare these time spans to the speed with
which natural selection leads to fixation of an advantageous allele (section
2.4).
The loss of genetic diversity caused by genetic drift is, however, counterbalanced by the constant production of new mutations. The net result is
a dynamic equilibrium where the population maintains a certain amount of
variation, but the specific alleles making up this variation are changing over
time. This process is illustrated in figure 2.8 where we follow the frequencies
of alleles at a specific locus. Initially, alleles A1 and A2 are present. At time
t1 , allele A3 is produced by mutation. Allele A1 is lost by drift at time t2 ,
and a new allele (A4 ) subsequently arises by mutation at time t3 . Later,
allele A3 is again lost by drift. Note that the average level of variability
at the locus remains roughly constant over time, but that the actual alleles
(and their frequencies) accounting for this variability changes over time.
We will now consider some aspects of how genetic drift interacts with
selectively neutral mutations that are generated at a constant rate. Let us
again assume that we are examining a haploid, asexual population with a
constant size of N individuals. Mutations are constantly being produced at
a rate . This rate is fairly constant and is perhaps mostly controlled by the
c Anders Gorm Pedersen, 2005
27
Genotype
frequency
2N
1/u
Time
Figure 2.9: The average time it takes for a neutral mutation to reach fixation
(in a population of haploid organisms) is 2N . The average time between the
fixation of different alleles at a locus is 1/u.
interplay between the error rate of the DNA polymerase during replication
and the activity of DNA repair systems. A certain fraction f0 of mutations
are neutral. These are produced at the rate u = f0 . Note that u only refers
to the neutral mutation rate and that this is lower than the total mutation
rate. Most newly arisen neutral mutations are immediately lost due to
genetic drift, but some eventually become fixed. We are now interested in
determining the over-all rate at which neutral mutations become fixed in the
population. This rate of fixation tells us how quickly the DNA sequences
of two isolated populations drift apart.
The number of mutations produced per generation (at the locus we are
examining) is N u. For instance, if u = 2 107 mutations per generation
for this locus, and if N = 106 then an average of 2 107 106 = 0.2
new mutations will be produced at this locus per generation in the entire
population (corresponding to one new mutation every five generations). In
the previous section we found that a single gene in a population of N haploid
individuals has the probability N1 of being fixed by genetic drift. This must
therefore also be the probability a newly arisen neutral mutation has of
becoming fixed, since the mutant allele will initially be present as a single
copy among a total of N genes.
Recall that the rate of fixation is the number of new mutations that
become fixed in a given population per generation (or any other unit of
time). We can now determine this rate simply by multiplying the number of
mutations produced per generation (N u) by the probability that a mutation
eventually becomes fixed ( N1 ). Denoting the rate of fixation by k we therefore
c Anders Gorm Pedersen, 2005
28
1
uN = u
N
(2.12)
This simple but slightly surprising result shows that the rate, at which neutral mutations become fixed, is independent of the population size. Moreover, the rate of fixation is simply equal to u - the neutral mutation rate.
Note that the average time between fixation of different alleles at a locus
is t = k1 = u1 . In our example from before, we have that k = u = 2 107
fixed mutations per generation. The average time between fixations is there1
fore t = k1 = 210
7 = 5, 000, 000 generations per fixed mutation (at this
locus). You should distinguish between the average time it takes for a mutation to reach fixation (2N generations in a haploid) and the average time
between fixation of different mutants ( k1 ; figure 2.9).
2.10
2.11
In addition to the issue of the surprisingly high level of polymorphism, another observation was also taken as evidence for the neutral theorythe
constancy of the rate of molecular evolution.
If a particular protein is examined in a number of species, then it isfor
each pair of speciespossible to determine (1) the approximate time since
the species diverged, and (2) the number of differences between the protein
sequences. Strikingly it was observed that if divergence time was plotted
against genetic distance for many pairs of species, then the points would fall
on a straight line. Figure 2.10 shows an example where the number of differences have been computed from a collection of 4 different proteins (-globin,
globin, cytochrome c, and fibrinopeptide A) from various mammalian
groups. (Note that here the difference between sequences is expressed as
replacements per site. This simply means that the number of differences
have been divided by the total length of the protein).
Since genetic distance is approximately proportional to divergence time,
it appears that molecular evolution must be proceeding at a roughly constant
rate. In figure 2.10 the distance between pairs of sequences is increasing at
a rate of approximately 0.006 amino acid replacements per site per million
years (i.e., for every 1000 amino acids in the protein, 6 differences accumulate every 1 million years). If this is true of most molecular evolution, then
sequences may be used to estimate approximate divergence times for species
that lack an informative fossil record.
c Anders Gorm Pedersen, 2005
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Figure 2.10: The molecular clock. Genetic distance (number of amino acid
replacements per site) plotted against a geological estimate of divergence
times for various pairs of mammalian groups. Combined sequence data
from -globin, globin, cytochrome c, and fibrinopeptide A. (From Graur
and Li, 2000, Molecular Evolution, 2nd edition, Sinauer Associates Inc.)
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