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Genetic variation

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Evolucion GuevaraFiore

on 13 October 2015

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Transcript of Genetic variation

Variation
Genetic
There cannot be a response to natural selection, and there cannot be any history recorded by drift, unless there's genetic variation in the population.
evolution is based on genetic change
50's
there wasn't very much genetic variation out there
65's
There is a tremendous amount of genetic variation in Nature.
75-80
Studies
(on the Galapagos finches, on the guppies in Trinidad, on mosquitofish in Hawaii, on the world's fish populations responding to being fished, etc) we know that
evolution
can be very
fast
when there's
strong selection
acting on
large populations
that have lots of
genetic variation.
2013
The rate of
evolution
- the issue of
climate change and global warming:
will all the species on earth be able to
adapt

fast enough
to persist in the face of
anthropogenic change
on the planet?
If there isn't enough
genetic change to adapt,
to the kinds of climatic
changes
that they are going to be encountering, and currently are encountering, they'll go extinct. They have to either
move
to a place which is like the one they're in, or they have to
adapt
to the changed conditions that they're encountering.
MUTATIONS
Mutations
are where genetic differences come from, and they can be
changes

in the
DNA sequence
or
changes
in the
chromosomes.
In the chromosomes they can be changes in
how many chromosomes
there are or in aspects of
chromosome structure
(e.g. there can be gene duplications).
Most of the mutations that occur naturally are mutations that are occurring during DNA replication.
The probability that a
cancer
will emerge in a tissue is directly proportional to the number of
times cells divide in that tissue;
which is why cancers of
epithelial cells
are much more common than cancers of
cells that do not divide.

An intermediate mutation rate is optimal:
If the mutation rate is
too low,
then the descendants of that gene cannot
adapt to changed conditions.
If it's
too high,
then all the accumulation of information on what has worked in the past will be
destroyed by mutation;
which is what happens to pseudogenes that are not expressed. So some intermediate rate is probably optimal.
Now a
gene
that controls the
mutation rate
will evolve much more easily in an
asexual organism
than in a
sexual species
because sexual recombination uncouples the gene for the benefits of the process.
In a
sexual organism
the gene that's controlling the
mutation rate
becomes
disassociated
from the genes whose mutations it might try to control.
It is much more plausible that we will see
genes
that are
controlling mutation rates
evolving in organisms like
bacteria and viruses
than genes that control mutation rates evolving in us.
In bacteria you can do
experimental evolution
and show that the
mutation rate will evolve
up
or
down,
depending on the
circumstances
that you put the bacteria under.
How frequent is a mutation?

The per nucleotide mutation rate in
RNA
is about 10^-5; in
DNA
it's 10^-9.
DNA is a remarkably
stable molecule.
The
per
gene
rate of mutation
in DNA is about one in a million; so this is like per meiosis.
The
per
trait
mutation rate
is about
10^-3 to 10^-5.

The
rate per
prokaryotic
genome
is about
10^-3,
and
per
eukaryotic
genome
it's between
.1 and 10.
10-3
Viruses and bacteria appear to have
converged
on roughly this
per generation mutation rate,
per genome, which is pretty strong evidence that it's an
optimal rate;
thousands of species have converged on this rate.
40 * 1.6 = 64
What is your mutation rate?
Each of you has about
four new mutations
in you that your parents didn't have, and about
1.6 of those are deleterious.
How many deleterious mutations, unique in this generation, are sitting here in the classroom?
Where did they happen?

50 times more in males
than in females.
There are many
more cell divisions
between the formation of a zygote and the production of a
sperm
than there are between the formation of a zygote and the production of an
egg.

In human development, and in mammal development, egg production pretty much stops in the
third month of embryonic development,
at which point all the women in this room had about seven million eggs in their ovaries.
Since then
oocytic atresia
has reduced the number of eggs in your ovaries. When you were born you had gone from
seven million down to one million
.

When you began menstruating you had about
1500 eggs
in your ovaries. It appears to be a
quality control mechanisms,
ensuring that the oocytes that survive are genetically in really good shape.
There are very, very
different
kinds of biology affecting the production of
eggs and sperm
; females have a
mutation screen
that males do not.
RECOMBINATION
What does recombination do to this mutational variation that builds up in populations?
10 genes, each with 2 alleles, each on a different chromosome, can produce
3^10 different zygotes
~59000 different zygotes in a diploid sexual.
Why?
In a
real eukaryotic genome
that had
free recombination
and
unlimited crossing over
the number of possible zygotes
(3^15,000
-
3^50,000)
is unthinkably larger than the number of fundamental particles in the universe
(10^131).
There is a huge portion of
genetic space
that remains
unexplored,
simply because there hasn't been enough time on the planet for that many organisms to have lived.
There has been an evolution of the chromosome number of a lot of species
Ascaris
Sugar cane
There are some populations within a single species that have a
different chromosome number
than other populations within that species
RECOMBINATION II
CROSSING OVER
The amount of crossing over can be adjusted by structural mutations on chromosomes. Inversions block crossing over.
What would happen in a sexual population if we just
shut off mutation?
How long would it take before we would even notice that evolution had been shut off, if we were just observing the
rate at which that population was evolving?

The impact of recombination on the standing genetic diversity in that population would create so
many new diverse combinations of genes
that it would take about
1000 generations
before we would even notice that mutation has been shut off.
What maintains
genetic variation?
What explains the maintenance of so much genetic variation?
Selection and drift

can
both
explain it.
Difficult to
prove
that it is either one or the other.
Both of them are capable of generating quite a few patterns, and those patterns
overlap.
This may
no
longer be a
productive
question, because it is so hard to answer conclusively.
In specific cases we can usually give the leading role either to selection or to drift, but a general answer continues to elude us, probably because
there is none.
1. A balance between
mutation
and
drift.
2. A balance between
mutation
and
selection.
3.
Heterosis
or
over-dominance
-the heterozygote has an advantage.
4.
Negative frequency dependent selection,
the rare type has an advantage.
Forces that can in principle maintain genetic variation
A balance between mutation and drift
FIXATION PROBABILITY:
The probability that it will spread and be fixed in the population. That's equal to its frequency, at any point in time.

FIXATION TIME
is how long it takes to become fixed in generations, if the mutation gets fixed.
For
neutral alleles,
the fixation rate = the mutation rate. This doesn't depend on population size (in contrast with mutations that are subject to selection).
The probability of fixation = the current fq
For a new mutation, this is1/2N to be fixed, & 1-1/2N to be lost.
That means that most of them are lost.
Fq
Generations
1.0
TIME
The discovery of
large amounts of genetic variation
in nearly all populations led to the formulation of a different question:
How is genetic variation maintained?
Natural selection
removes

genetic variation
by eliminating genotypes that are less fit?
Under frequency-dependent selection, the
fitness
of a genotype
depends on its relative frequency
within the population, with
less-common genotypes being more fit
than genotypes that occur at high frequency.
Changing patterns of selection
over time or space can help to maintain genetic variation in a population.
FIXATION

is the change in a gene pool
from a situation where there exists at least two variants of a particular gene
(allele)
to a situation where only
one of the alleles remains.
The term can refer to a gene in general or particular nucleotide position in the DNA chain (locus).

In the process of
substitution,
a previously non-existent allele arises by
mutation
and undergoes fixation by
spreading through the population
by random genetic drift and/or positive selection. Once the frequency of the allele is at
100%
, i.e. being the only gene variant present in any member, it is said to be
"fixed"
in the population.
1
2
3
4
A balance between mutation and selection
Heterosis or over-dominance
Negative frequency dependent selection
Because there are
2N
copies of the gene in the population, and if
u
is mutation rate, then there are
2Nu
new mutations of that gene per generation.
For each of them the probability of fixation is
1/2N.
So the rate of fixation of new mutations is
2Nu x 1/2N = u
(mutation rate).
That's about 10^-5 to 10^-6 per gene,

Thus the molecular clock is ticking once every
100,000 to once every 1,000,000 generations per neutral gene.
The
fixation rate
doesn't depend on N.
The
probability that a mutation will occur
in a population depends upon
how many organisms
are there.
The
bigger
the population, the
longer
this process takes. But the bigger the population, the
more
of these are actually moving through to fixation.
Those two things exactly compensate.
In a
small population
most of them are
lost.
The few that do reach fixation, reach it
rapidly,
and in
large populations
more new mutations are fixed, but each one does it more
slowly.
The fixation rate doesn't depend on population size, if you're looking at the whole genome.
Unlike the fixation rate, which does not depend on population size, if we concentrate just on those
mutants that do become fixed,
their expected time to fixation is
4Ne generations,
where Ne =
EFFECTIVE POPULATION SIZE.

Ne=
the size of a
random mating
population,
unchanging in time
, whose
genetic dynamics
would match those of the real population under consideration.
Factors causing the
effective genetic size
of a population to differ from its actual size:
Variation in family size
Inbreeding
Variation in population size
Variation in the number of each sex breeding.
Cattle in North America.
100,000,000 female cattle that are fertilized by 4 males. Genetically speaking, how big is the population?
1/Ne=1/4Nm+1/4Nf or Ne=4NmNf/(Nm+Nf)
It's just about 16.
Fq
Generations
1.0
The amount of genetic variation in a population, in a mutation-drift balance is a snapshot of the neutral genes that are continually drifting through it.
Mutation brings things into the population. Selection takes them out.
The key idea:
At mutation-selection balance, the
same number
must be removed each generation (the number going in equals the number going out).
That's what would keep this mechanism
balancing the amount of genetic variation
in the population.
i.e. some rare human genetic diseases
Phenylketonuria (PKU) -inability to metabolise phenylalanine, 1 in 20,000 in Caucasians & Chinese.
Low fq, but present in the pop. Disadvantage. It keeps mutating and coming back in, and it keeps getting selected out.
The result is balance.
If selection patterns fluctuate over time, different alleles or genotypes may enjoy
greater fitness at different times.
The overall effect may be that both alleles persist in a population.
If selection patterns
vary
from one place to another as a result of differences in habitat and environment. The prevalence of different genotypes in different habitats, combined with
gene flow
between habitats, can result in the maintenance of multiple alleles in a population.
Grasshopper
characterized by two color morphs, a brown morph and a green morph.
Earlier in the year, habitat is more brown.
Later in the season, the environment is greener.
Copper toxicity in species of grass.

Copper-tolerant alleles are common in areas adjacent to copper mines.
They are not expected in un-contaminated areas, (they are
less fit
than normal alleles).
Grass species are wind pollinated, gametes can travel considerable distances, and copper-tolerant alleles are often found in areas where they are at a
selective disadvantage.
Balancing selection occurs when there is
heterozygote advantage
at a locus, a situation in which the heterozygous genotype (one including two different alleles) has
greater fitness
than either of the two homozygous geno-types (one including two of the same allele).
A classic example of
heterozygote advantage
concerns the allele for sickle-cell anemia. Individuals who are
homozygous

for the sickle-cell allele
have sickle-cell anemia, which causes the red blood cells to become sickle-shaped when they release oxygen.
Heterozygotes,
however, have
normal, donut-shaped blood cells
and do not suffer from sickle-cell anemia. In addition, they enjoy a benefit of the sickle-cell allele, which offers
protection from malaria.
Consequently, heterozygous individuals have
greater fitness
than individuals who have two copies of the normal allele.
These sickle-shaped cells become caught in narrow blood vessels,
blocking blood flow.
Prior to the development of modern treatments, the disease was associated with very low fitness, since
individuals usually died before reproductive age.
Under heterozygote advantage, both alleles involved will be maintained in a population.
Heterozygote advantage
in this system is believed to have played a critical role in allowing a disease as harmful as sickle-cell anemia to
persist in human populations.
Evidence for this comes from an examination of the
distribution of the sickle-cell allele,
which is only found in places where
malaria
is a danger.
Frequency-dependent selection is believed to be fairly
common in natural populations.
For example, in situations where there is
competition for resources,
individuals with rare preferences may enjoy greater fitness than those who have more common preferences.
Frequency-dependent selection may also play a role in
predation:
if predators form a search image for more common prey types, focusing on capturing those,
less common phenotypes
may enjoy better survival.
TODAY´S LECTURE:
Genetic variation
What maintains genetic variation?
Genetic variability in a population is important for biodiversity, because without variability, it becomes difficult for a population to adapt to environmental changes and therefore makes it more prone to extinction.
Genetic transmission
is the mechanism that drives evolution.
DNA
encodes all the information necessary to make an organism. Every organism's DNA is made of the same basic parts, arranged in different orders.
DNA is divided into
chromosomes
, or groups of genes, which code for proteins.
Asexually reproducing organisms
reproduce using
mitosis
, while
sexually reproducing organisms
reproduce using
meiosis
.
Both these mechanisms involve
duplication of DNA,
which then gets passed to offspring.

RNA
is a key component in the duplication of DNA.
It is distinguished from
genetic variability,
which describes the tendency of genetic characteristics to vary.
Genetic variation (diversity/variance),
the level of biodiversity, refers to the total number of genetic characteristics in the genetic makeup of a species.
The phenotypic and genotypic differences among individuals in a population.
Genetic variation refers to diversity in gene frequencies.
Genetic variation can refer to differences between individuals or between populations.
VARIATION
Mutation is the ultimate source of genetic variation, but mechanisms such as sexual reproduction and genetic drift contribute to it as well.
Genetic variability is a measure of the tendency of individual genotypes in a population to vary from one another.
If a population lacks sufficient genetic variability, it also lacks the potential to evolve and adapt.
VARIABILITY
You never get a
cancer
in your heart muscle, and you frequently get cancers on your skin, and in your lungs, and in the lining of your gut, and that's because
every mitotic event
is a potential mutation event.
In positive (or diversifying)
frequency-dependent selection, the fitness of a phenotype increases as it becomes more common.
In negative (or purifying)
frequency-dependent selection, the fitness of a phenotype increases as it becomes rarer. This is an example of balancing selection.
The frequency of the
scale-eating cichlid,
Perissodus microlepis, oscillates around 50%. Each year, the prey species
learn to look
over a particular "shoulder" to guard against predation by the scale-eaters.
The rarer morph
(e.g., Left-jawed in 1984) has an
advantage
and increases in frequency. The following season the other morph becomes rare (e.g., right-jawed in 85) in the following season (Hori 1993)
DNA recombination
involves the exchange of genetic material either between multiple
chromosomes
or between
different regions
of the same chromosome.
EFFECTIVE POPULATION SIZE
The origin and maintenance of
genetic variation
are key issues; mutations are the origin.
Recombination
has huge impact.
There's a tremendous amount of genetic variation in natural populations.
We can explain the maintenance of this variation by various kinds of mechanisms, principally for
balance between mutation and drift, between mutation and selection, and by some kind of balancing selection,
either heterosis or frequency dependent selection.
CONCLUSION
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