Measuring genetic variability

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Measuring genetic variability
Studies have shown that most natural populations
have some amount of genetic diversity at most
loci locus physical site where a gene resides
on a chromosome plural is loci
For instance, you can measure the number of
different alleles of a given protein using gel
electrophoresis

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Protein electrophoresis
-
A gel is a porous slab of jello-like material,
which large molecules like proteins can slowly
move through By running a current across the
gel, one end becomes positively
charged Proteins with a negative charge will
move towards the end of the gel

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Protein electrophoresis
Why might proteins carry a negative charge?
Some amino acids are negatively charged in
solution (glutamate, aspartate) Some
are positively charge (lysine, arginine,
histidine) By adding up the total number of
and charged amino acids, you can figure out
the total (or net) charge of a protein The net
charge of Lys-Asp-Asp-Ser-Thr-Arg-Glu-Glu
- - - -

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Protein electrophoresis
The net charge of Lys-Asp-Asp-Ser-Thr-Arg-Glu-Glu
-2 - -
- - - but different
alleles may change the total charge on a
protein Consider a different allele of this
protein Lys-Asp-Thr-Ser-Thr-Arg-Glu-Glu
- - - This
allele has a net charge of -1 -
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Sampling variation in a population
-
(1) Sample many individuals (2) Grind them up
and load a drop of the mush onto each lane
of a gel (3) Run a current across the gel (4)
Stain the gel by adding a chemical that
will turn dark when a particular enzyme
reacts with it -


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Variation in a population Allozyme
electrophoresis
-
Different protein alleles that show up on such
a gel are termed allozymes
This individual was homozygous for the most
common allele -

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Variation in a population Allozyme
electrophoresis
-
Different protein alleles that show up on such
a gel are termed allozymes
This individual was heterozygous - -


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Variation in a population Allozyme
electrophoresis
-
What is the frequency of a allele in this
population?
A a a

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Variation in a population Allozyme
electrophoresis
-
What is the frequency of a allele in this
population?
total of a alleles 10 total of alleles
12 frequency of a 10/12 83.3
A a a

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Population Genetics
Integrates Darwinian evolution by natural
selection with Mendelian principles of
inheritance Shows how changes in the frequency
of alleles in a population affect the
frequency of the traits they control   Evolution
change in allele frequency over generations How
do alleles behave in a sexually reproducing,
diploid population?
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Population Genetics
In a population where adults mate randomly every
generation, does the frequency of alleles
change over time?   Assume a population where
there are two alleles of a gene, A and a
- frequency of allele A in the gene
pool is 60, or 0.6   - in other words,
60 of sperm and 60 of eggs made by
adults in this population carry the A allele  
- frequency of allele a in the gene pool is
40, or 0.4
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What will be the frequencies of the various
genotypes (AA, Aa, aa) after one round of
random mating?   odds that an A sperm will meet
an A egg   (frequency of X (frequency of
frequency of A sperm)
A egg) AA zygote   0.6 X
0.6 0.36
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Egg Sperm Zygote Probability   A A
AA 0.6 x 0.6 0.36   A a Aa 0.6 x
0.4 0.24   a A aA 0.4 x 0.6 0.24
  a a aa 0.4 x 0.4 0.16
Aa
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0.36 0.48 0.16 1 These probabilities
are the genotype AA Aa aa
frequencies of the next generation So what will
the allele frequencies be after this generation
reproduces? (will the frequencies
change?) Calculate new gamete frequencies, as
before AA is 36 of the population (0.36), so
36 of gametes are A Aa is 48 of the
population, so 24 of gametes are A and
24 are
a aa is 16 of the population, so 16 of
gametes are a New allele frequencies A
0.36 0.24 0.6 a 0.24 0.16 0.4
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Hardy-Weinberg Equilibrium
The allele frequencies for the A and a alleles do
not change from generation to generation -
they are in equilibrium - hence, the population
does not evolve   This illustrates an example
that is true in general allele frequencies do
not change from generation to generation The
general case is stated algebraically as the
Hardy-Weinberg equilibrium principle  
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Hardy-Weinberg Equilibrium
frequencies in the parental gametes
The frequency of A in the population is called
p   The frequency of a in the population is
called q   When there are only 2 alleles, p q
1   What are the odds of each genotype after a
round of mating?   AA Aa aa p x p (p x q)
(q x p) q x q p2 2pq q2
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Hardy-Weinberg Equilibrium
AA Aa aa p x p (p x q) (q x p) q x
q p2 2pq q2   so, weve gone from allele
frequencies in the parental gene pool to
genotype frequencies among the offspring What
happens when these offspring reproduce?
  Calculate new gamete frequencies, as before
  AA has frequency p2, so p2 gametes will carry
the A allele   Aa has frequency 2pq, so ½
(2pq) or pq gametes will carry A
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Hardy-Weinberg Equilibrium
AA has a frequency p2, so p2 gametes will carry
the A allele   Aa has a frequency 2pq, so ½
(2pq) or pq gametes will carry A   New allele
frequency A p2 pq The frequency of A can
be re-stated as   p2 pq p(p q) Since
p q 1 p(1) p 
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Hardy-Weinberg Equilibrium
Thus, we can draw 2 conclusions from the
Hardy-Weinberg equilibrium
principle   1) frequency of an allele stays the
same over generations - it doesnt matter
what the particular allele frequencies are
- it doesnt matter how many alleles there are
for a gene   2) when allele frequencies are
given as p and q, the genotype frequencies will
be p2 2pq q2 The Hardy-Weinberg
principle predicts that evolution will not
happen in a population -- unless one of the
underlying 5 assumptions is violated
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Hardy-Weinberg Assumptions
The 5 assumptions   1) There is no natural
selection - all individuals survive and
reproduce equally - if individuals of some
genotypes survive and reproduce more than
others, then allele frequencies may change
from one generation to the next   2) There is
no mutation - alleles dont change to
other existing alleles or new alleles
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Hardy-Weinberg Assumptions
The 5 assumptions   3) There is no
migration - no individuals moved into or out of
the population - if individuals with certain
genotypes leave the population, then the
allele frequencies may change  
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Hardy-Weinberg Assumptions
The 5 assumptions   4) There were no chance
events that caused some individuals to
pass on more alleles to the next generation -
this is termed genetic drift - commonly happens
in small populations - genetic drift causes
evolution by changing allele frequencies -
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Hardy-Weinberg Assumptions
The 5 assumptions   5) Individuals mate at
random - individuals are not more likely to
mate with others of their own
genotype examples a) big individuals do not
prefer big individuals b) habitat
choice mate where you like to hang When
individuals mate non-randomly, genotype
frequencies change over generations and the
model is violated
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Use of Hardy-Weinberg
How do scientists use Hardy-Weinberg equilibrium
theory? - useful as a null model-- something to
be disproven -   Go out into the field, sample
allele and genotype frequencies - if
allele frequencies change over time, or if
genotype frequencies cannot be predicted from
allele frequencies, then the null
model (H-W equilibrium) is not correct
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Use of Hardy-Weinberg
If null model is wrong, one of the assumptions is
being violated - indicates that selection,
mutation, or other force is acting on a
population - functions as a spotlight,
drawing attention to potential cases
where a population may be evolving   You cant
easily go out into the field and tell if a
population is under natural selection or
experiencing high migration....
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Selection
Happens when individuals with certain phenotypes
survive or reproduce at higher rates than
others - bottom line differential reproductive
success - when phenotype is derived largely
from genotype, evolution can happen
selection on phenotype
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Selection and Allele Frequencies
When selection increases the reproductive success
of certain genotypes, do allele frequencies
change over generations?   Take the earlier
example frequency of allele A was 60, and
the frequency of allele a was 40, in a
population that makes 1,000
zygotes AA Aa aa 360 480 160 (actual of
individuals)  
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Selection and Allele Frequencies
When selection increases the reproductive success
of certain genotypes, do allele frequencies
change over generations?   Take the earlier
example frequency of allele A was 60, and
the frequency of allele a was 40 AA Aa aa 360
480 160   Now assume that genotypes differ in
their rates of survival (due to effects on
phenotype) - all AA survive - only 75 of Aa
survive - 50 of aa survive
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Selection and Allele Frequencies
AA Aa aa 360 480 160 x 100 x 75 x
50 360 360 80 800
survivors When this generation makes gametes,
what will the allele frequencies be? First
calculate genotype frequencies   Total
individuals of each genotype / total of
individuals   AA 360/800 0.45 Aa 360/800
0.45 aa 80/800 0.1
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Selection and Allele Frequencies
Total individuals of each genotype / total of
individuals AA 360/800 0.45 Aa 360/800
0.45 aa 80/800 0.1 Calculate allele
frequencies, when these individuals make
gametes   Frequency of A allele frequency of
AA ½ frequency of Aa (0.45) ½
(0.45) 0.45 0.225 0.675
Frequency of allele A was originally 0.6
- selection changed allele frequencies -
thus, the population evolved in response to
selection
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Artificial selection experiments
 Laboratory experiments using fruit fly
Drosophila melanogaster have shown that
many forms of artificial selection cause
rapid evolution by changing allele frequencies in
experimental populations - scientists
change the conditions of experimental
populations - after many generations, check to
see if allele frequencies have changed,
relative to control populations  
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Artificial selection experiments
 Change conditions of 2 experimental populations
add ethanol After 50 generations, allele
frequencies had changed relative to
control populations  
flies fed ethanol- spiked food
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Selection and Genotype Frequencies
In the previous case, selection changed allele
frequencies Can selection change genotype
frequencies, instead?   Consider this
population   Frequency of A 0.5 after one
round a 0.5 of random
mating   Genotype AA Aa aa frequency
0.25 0.5 0.25 250 500 250 ( out of
1,000 individuals)  
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Selection and Genotype Frequencies
Genotype AA Aa aa frequency
0.25 0.5 0.25 250 500 250 Now introduce
selection only 50 of homozygotes survive
AA Aa aa of adults 125 500 125
(750 survivors) New genotype frequencies (total
of each genotype / total of individuals in
population) AA 125 / 750 0.167 Aa 500 / 750
0.667 aa 125 / 750 0.167
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Selection and Genotype Frequencies
New genotype frequencies (total of each
genotype / total individuals in the
population) AA 125 / 750 0.167 Aa 500 / 750
0.667 aa 125 / 750 0.167 New allele
frequencies, when these individuals produce
gametes   Frequency of A allele frequency of
AA ½ frequency of Aa (0.167) ½
(0.667) 0.167 0.334 0.5
This was the initial frequency of the A allele!
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Selection and Genotype Frequencies
Despite strong selection against homozygotes,
allele frequencies didnt change
population did not evolve Conclusion 1 of
Hardy-Weinberg wasnt violated by
selection .... what about conclusion 2 can
you still predict genotypes from the
new allele frequencies?
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Selection and Genotype Frequencies
Can you still predict genotypes from the new
allele frequencies? New allele frequencies A
0.5 a 0.5 New genotype frequencies AA 125 /
750 0.167 Aa 500 / 750 0.667 aa 125 / 750
0.167 Frequency of the A allele
0.5 Predicted frequency of the AA genotype
(0.5)2 0.25 Actual frequency of the AA
genotype 125/750 0.167
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Selection and Genotype Frequencies
Frequency of the A allele 0.5 Predicted
frequency of the AA genotype (0.5)2
0.25 Actual frequency of the AA genotype
125/750 0.167 Selection took the population
out of Hardy-Weinberg equilibrium Conclusion 2
(genotypes are predicted from allele
frequencies) is violated ?