Download Population Genetics

Population Genetics
The “Modern Synthesis” of evolution is Darwinism
enlightened by the understanding of molecular
genetics which has been gained since Darwin.
The key to understanding how evolution occurs is
a move from viewing genetics in terms of individuals
and their alleles to -the frequencies of those alleles among the genes of
all individuals comprising a population.
We know about genes and particulate inheritance.
Darwin did not. He was neither the first not the
last to accept blended inheritance. He wrote
before Mendel had described recessive traits. To
explain evolution, he fell back into a second error:
the inheritance of acquired traits.
Most phenotypes, resulting from the influence of
many genes, do seem to be inherited as if blended.
Without a mechanism for particulate inheritance,
it was hard to establish the concept.
Mendel’s genetics disappeared into the literature
until the beginning of the 20th century.
The rediscovery of Mendelian genetics led to a
number of leading biologists claiming that evolution
resulted from inheritance of mutations. Evolution, in
this view, moved rapidly and by jumps, rather than
gradually, as Darwin had believed.
Failures to accept “the modern synthesis” of
Mendelian genetics and Darwinian evolution
persisted into and after WWII - e.g. Lysenko.
To understand the modern synthesis, we need to
consider the genetics of populations, rather than
individuals.
Consider a Punnett square for a single trait cross:
 (male)
½A
½a
½A AA
Aa
 (female)
½a
Aa
aa
in describing this cross, we have shown the effects
of meiosis: 1/2 the sperm carry A, 1/2 a, and
similarly for the eggs.
Now recognize that the fractions of these two alleles
in the population may not be equal, and there may be
more than two alleles. The sum of all alleles for a
trait in the population is the gene pool for that trait.
We measure fraction p of the genes in this gene
pool are of type A, and fraction q are type a (assuming
males and females are genetically similar). Now the
Punnett square looks like this:
male
pA
qa
pA p2AA
pqAa
female
qa pqAa
q2aa
A mating like this does not change gene frequencies.
Evolution is a change in the composition of the gene
pool. Gradual change is called microevolution.
In a population that had those allele frequencies,
they would remain unchanged indefinitely if the
conditions for Hardy-Weinberg equilibrium held.
What are the conditions?
1. Large population size
2. No migration (gene flow occurring through
immigration or emigration)
3. No mutation
4. Random mating (no assortative mating)
5. No natural selection
Do the conditions often apply (or apply for long)?
The Hardy-Weinberg Law is a null hypothesis.
It holds (as what is called the Hardy-Weinberg
equilibrium) when things don’t change, i.e.
1. In large populations there is no genetic drift. In
small populations random events (mortality of a
single individual) may materially affect gene
frequency. This happens in small island populations or populations of endo (internal) parasites.
2. There is no movement between populations, that
would be gene flow. The genes moved would
change the frequencies in both source and
recipient populations.
3. There is no mutation. If one A mutated to a per
100 alleles, then what was 50% A in the starting
population would become 49%A after mutation.
Actual mutation rates are about 1/106 per gene,
but that translates to about 1 mutation per
gamete for us. We are, thus, each unique.
4. Mating (fertilization) occurs randomly. If blondes
would only marry blondes (real ones) (blond hair
being recessive), there would be a much higher
frequency of the blond phenotype. Let’s look at an
example of this:
We can figure out gene frequencies in a population
if we know the frequency of the recessive
phenotype. For these individuals, knowing the
phenotype frequency we also know the genotype
and gene frequencies. The frequency of the
recessive phenotype is q2. That is also the frequency
of the homozygous recessive genotype. Then the
frequency of the recessive gene is the square root of
q2 → q.
Now for the example:
We start with 100 people (50% male). 1 out of 10
is a natural blond. That means q2 = .1, and q=.316.
p = 1 – q = .684.
Those would be the values indefinitely if mating were
random, but…
If blondes only mate with blondes, then the 5 blond
males mate with the 5 blond females, and produce
10 blond children in the next generation. As to the
other 90 (or 180 genes):
p2 = (.684)2 (·100) → 46 are homozygous for dark hair
(or 92 dark-haired genes), and
2pq = 2(.684)(.316) (⋅100) → 44 are heterozygous
(another 44 genes for dark hair)
The overall frequency for the dark hair gene among
the mating population of dark-haired individuals is:
136/180 = .755…
Assuming that the dark haired individuals mate
randomly:
male gametes
.75B
.25b
.75B .5625 BB .1875 Bb
female gametes
.25b .1875 Bb .0625 bb
BB and Bb have the dark hair phenotype. Take these
fractions and use them to correct to total 90
individuals to keep the population constant in size →
51BB + 34Bb are dark haired, 5bb are blonds
Add these to the 10 blonds from assortative mating,
and now there are 15 blonds instead of 10 out of 100,
and 85 instead of 90 with dark hair.
The phenotypic and genotypic frequencies have
changed; microevolution has occurred. But, how
often does assortative mating of the sort presented in
this example occur in nature?
5. No natural selection occurs. When natural
selection occurs the survival and reproduction of
different phenotypes differs. Some have higher
survival and/or reproduction; they leave behind a
larger fraction of the offspring that form the next
generation (differential reproductive success).
Their genes represent a greater fraction of the
gene pool in the next generation.
A numerical example: selection against the sickle
cell gene. We will conveniently forget the
advantageous effects of being heterozygous.
An example of selection: Sickle cell anemia
Begin with 50% of the genes S and 50% s.
The initial, randomly mated cross is:
.5S
.5s
.5S .25 SS
.25 Ss
.5s
.25 ss
.25 Ss
We will assume the .25ss die without reproducing.
Now calculate new gene frequencies. The 75% of
the population of offspring surviving to reproduce
are the ‘whole’ population. Now 66% of the genes
are S and .33 are s
The cross in the 2nd generation is:
.66S
.33s
.66S .44SS
.22Ss
.33s .22Ss
.11ss
Natural selection against the homozygous recessives
has reduced the fraction from 25% to 11% in one
generation. It would further reduce the fraction each
generation, but since there are fewer of them, fewer
would be selected against, as well.
N.B. natural selection
- acts on phenotypes
- selects only among variants present
Natural selection acts on phenotypic variation.
Where does the variation come from?
Ultimately, all genetic variation in living organisms
originates as mutations.
The variation we observe in a population is also
determined by:
1) recombination (sexual reproduction)
2) the spread of variants in a population due to drift,
and
3) the effects of environmental variation on the
relative success of different phenotypes.
One view of the amount of genetic variation in a
species is the fraction of its genes that are heterozygous. That fraction in part indicates the amount
of outcrossing (breeding with unrelated members of
the species) and in part reflects the history of the
species.
Cheetahs went through a severe bottleneck
within the last 10,000 years; only 0.07% of their
genes are heterozygous.
Humans have not gone through a bottleneck like that;
7% of our genes are heterozygous.
Why are so many genes not heterozygous?
- because altered alleles are not as ‘good’ as
the ones that persist. Others have been
removed by selection.
While examples indicate how gene frequencies can
change, the most common cause of genetic change
(microevolution) in natural populations is natural
selection…
Natural selection can occur in different ways. We
categorize the basic types of natural selection into
three forms: stabilizing selection, directional
selection, and diversifying (or disruptive) selection.
Modes of Natural Selection
1) Stabilizing selection - acts against extreme forms, favors intermediates
- one example: human birth weights
2) diversifying (or disruptive) selection
- acts against intermediates, favors extremes
- example - selection of different coloration
patterns in Papilio to resemble noxious
but unrelated butterflies
3) directional selection
- favors one extreme, selects against the opposite
extreme
- shifts the phenotype distribution curve in one
direction. Numerous examples:
industrial melanism
pesticide or drug resistance
There is another form of selection:
4) sexual selection
- leads to evolution of secondary sexual characters
- results in sexual dimorphism
- usually males evolve showy characters, e.g.:
a) tails of peacocks; peahens are drably colored
b) antlers of deer or caribou - females lack
antlers
c) colors of male mallards at breeding time,...
- Why?
usually females choose mates, showiest or most
dominant male gets a large harem, others
remain generally unmated
So, to take a human view, imagine John Travolta in
Saturday Night Fever, or...
(Sorry, I couldn’t find a good copy of the classic
pose in a white polyester suit, strutting his stuff)
These are Wodaabe
men from Niger in a
pose off, where the
women select the most
beautiful men. They are
wearing lipstick and
other makeup, where the
males of many animal
species are naturally
decorated (e.g. cardinals,
peacocks, birds of
paradise).
Questions about selection:
1) Are most genes subject to the intense natural
of (most) of these examples?
No! These extreme examples make evolution
more apparent, and occurring more rapidly.
2) Are some genes strongly conserved through the
varieties of living things?
Yes! For example, there have been only a handful
of changes in the base sequence of cytochrome C
from bacteria to man.
3) Is all genetic variation adaptive?
No! Much of the variation is neutral. None of the
variants confers a selective advantage.
Does natural selection “perfect” organisms?
No! Why?
1. Organisms are locked into historical constraints.
2. Adaptations are compromises.
3. Not all evolution is adaptive. Chance frequently
plays a large role.
4. Selection can only act on (and edit) variations
(phenotypes) that exist.