Welcome back to IB 150'''

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Welcome back to IB 150...
Channel 12, 8 PM Sept. 26 27 he not busy being
born is busy dying
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Lecture 13 Microevolution
Assigned Readings Ch. 23 (rest of chapter)
Putting genetic drift and mutation together
allele gain and loss infinite alleles model
neutral evolution Predicting genotype
frequencies from allele frequencies - the
Hardy-Weingberg equilibium random mating Forensic
genetics
microsatellites
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IB 150 EXAM ONE INFORMATION-Fall 2005 WHEN
THURSDAY, September 29th , 7-9 PM  LOCATIONS-You
must go to your assigned room.   1 IF YOUR TA
IS ROSE or DEVI GO TO 314 ALTGELD HALL 2 IF
YOUR TA IS BEN or ADAM GO TO 112 GREGORY HALL
3 IF YOUR TA IS DOMINIC or LIZ GO TO 228
NATURAL HISTORY 4 IF YOUR TA IS MONI, MAHESHI,
or BETH GO TO 213 GREGORY HALL BRING TO
EXAM 1 Sharpened PENCILS 2 NON-PROGARAMMABLE
CALCULATOR IT IS PAST THE DEADLINE TO SIGN UP
FOR THE CONFLICT
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A Hardy-Weinberg Equilibrium is just like a
Punnett square except for a population rather
than a single pair cross. Gamete frequencies are
the same as the allele frequencies.
Sperm with allele A p
Sperm with allele a q
pq Aa
p2 AA
Ova with allele A p
pq Aa
q2 aa
Ova with allele a q
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Fig. 23.5 Note exam questions only on general
issues, calculations on next exam
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If the genotype frequencies predicted from the
allele frequencies turn out to be close to those
observed in the population, the population is
said to be in a Hardy-Weinberg Equilibrium. A
perfect Hardy-Weinberg equilibrium is seen only
if there is no genetic drift, no mutation, no
subdivision of populations, no natural selection,
etc., but it is in fact rather robust to
violations of these conditions.
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Using H-W to determine frequencies of carriers in
a population (must assume at least approximately
random mating)
Phenylketonuria recessive Mendelian
trait 1/10,000 children born in the US have the
disease What proportion of the population are
carriers?
q2 0.0001
q 0.01 p 0.99
2 of the population are carriers
2pq 0.0198
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The Hardy-Weinberg Equilibrium is important
because 1. It helps us understand human genetic
diseases - (e.g., why are carriers so much more
common than affected people?) 2. It is robust to
many assumptions. 3. It is basic to a lot of
more complex population genetics. 4. It is used
in forensic genetics
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Forensic genetics uses variation such as
microsatellite variation - differing numbers of
short DNA repeats such as AC or AG or ATG. The
replication enzymes tend to make frequent
mistakes once a few repeats are in place, adding
more repeats. Deletions also occur from time to
time, so microsat loci do not grow infinitely
long.
One strand of a DNA molecule shown
repeats length ...AATGCGTTAGCACACACGCTAGTACCG
CATAG... 3 32 ...AATGCGTTAGCACACACACGCTA
GTACCGCATAG... 4 34 ...AATGCGTTAGCACACACACACG
CTAGTACCGCATAG... 5 36
These are 3 alleles of a microsatellite locus.
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Vocero-Akbani et al. 1996. Mapping human
telomere regions with YAC and P1 clones
Chromosome specific markers for 27 telomeres
including 149 STSs and 24 polymorphisms for 14
proterminal regions. Genomics 36492-506 .
Microsatellite variation - differing numbers of
short DNA repeats - an actual example with a
pedigree. The DNA is run in an electrophoresis
gel (bottom towards top), and the bands represent
DNA fragments of a given size like 150 base
pairs, etc.)
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Examples of calculations of genotype frequencies
using microsatellite variation - the more
alleles, the more genotypes, and the lower the
frequency will be for each. Note allele
frequencies are all the same in each case just to
simplify calculations! Try the Punnett square
yourself! Forensics uses Hardy-Weinberg
Equilibrium (HWE)!
(Alleles) All. p HWE genotype frequencies
11 12 22 2 0.5 0.25 0.50 0.25
11 12 13 22 23 33 3
0.33 0.11 0.22 0.22 0.11 0.22 0.11
11 12 13 14 22 23 24 33
44 4 0.25 0.06 0.13 0.13 0.13 0.06 0.13
0.13 0.13 0.06
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Frequencies become even lower when multiple loci
(genes) are considered. If the genes are
unlinked, you can determine the genotype
frequencies for the two-locus genotypes by just
multiplying the single locus HWE genotypes. Here
the allele frequencies for the A gene are freq.
A1 p 0.5, A2 q 0.5, and for the B gene
are B1 r 0.4, B2 s 0.6.
Thus, with enough alleles and enough loci, the
frequency (probability) of any genotype is very
small - so we are all unique!
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Lecture 13 Microevolution
Assigned Readings Ch. 23 (rest of chapter)
Putting genetic drift and mutation together
allele gain and loss infinite alleles model
neutral evolution Predicting genotype
frequencies from allele frequencies - the
Hardy-Weingberg equilibium random mating Forensic
genetics
microsatellites
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Lecture 13 Natural selection
Assigned Readings Ch. 23
Natural selection
fitness, discrete traits, continuous
traits Patterns of natural selection
directional, balancing, stabilizing,
disruptive, diversifying Sexual selection
secondary sexual
characteristics, intersexual, intrasexual
selection Guppies
natural versus cultivated strains, field
observations of effects of predators on male
color, experiments on balance of natural and
sexual selection, field experiments
Natural selection and the influenza virus
influenza surface
proteins immune response 1918 flue epidemic
antigenic drift antigenic shifts
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Natural selection - examples and details
Anytime there is unequal survival and/or unequal
reproduction of genotypes, there is selection.
It results in changes in the frequencies of
alleles. Fitness a quantitative measure of an
individual organisms ability to survive and
reproduce.
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There are 3 basic patterns of natural selection
(same 3 occur with artificial selection
also) They are basically the same whether one
is studying selection on discrete characters -
e.g., white flowers vs purple flowers or
quantitative characters - (polygenic or
multifactorial characters) - e.g., height,
weight, etc.
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A useful term - polymorphism - A population is
said to be polymorphic for a character if two or
more distinct morphs are each represented in high
enough frequency to be readily noticeable. (p
453)
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Selection on discrete traits
fitness
AA
Aa
aa
AA
Aa
aa
AA
Aa
aa
Balancing or stabilizing selection Aa has higher
fitness than AA and aa Outcome alleles A and B
can be maintained (not fixed by drift)
Directional selection
Diversifying or disruptive selection Aa has a
lower fitness than AA and aa Outcome alleles A
and B can be maintained (not fixed by drift).
Special conditions.
AA has higher fitness than Aa and aa Outcome
allele A replaces a
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Assuming independent assortment there are 23 8
gamete type (ABC, Abc, AbC, Abc, aBC, aBc, abC,
abc) which can be combined in 64 ways, to produce
27 genotypes, and in this example, 7 phenotypes.
Selection on continuous traits - look back at
normal curve. Fig. 14.12
Aabbcc - 2 ways aaBbcc - 2 ways aabbCc - 2 ways
aabbcc
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Fig. 23.11 - a common garden experiment tells
us if the continuous variation we see has a
genetic basis.
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Fig. 23.12 - patterns of selection on a
continuous trait.
Dark individuals have high fitness
Dark and light individuals have high fitness
Intermediate individuals have high fitness
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Figure 23.16x1 Sexual selection and the
evolution of male appearance
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Figure 23.16x2 Male peacock
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Another type of selection is called sexual
selection. This often involves secondary sexual
characteristicts. In one common type of sexual
selection (intersexual selection), females choose
males that have the most conspicuous ornaments.
In another (intrasexual selection), males fight
for access to females.
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In intersexual selection, natural selection is
still really occurring - males that can survive
when burdened with lots of ornaments must have
good genes for running ability, flight ability,
etc.
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Examples of natural and sexual selection Guppies
(Poecillia reticulata) are small tropical
American fish that have become good examples of
microevoluton because 1. Spectacular success in
artificial selection. 2. Observations on the
interaction of natural and artificial selection
in the field (nature). 3. Experimental
replication of natural and artificial selection
in the lab. 4. Experimental studies on the
interaction of natural and artificial selection
in the field (nature).
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From Dr. K. Hughes web site at UIUC. The three
guppies in the middle are females, which show no
pronounced color variation. The males on either
side are representative of the enormous variation
in this species - effectively all male have a
different appearance.
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Domesticated guppies
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Above falls, predators only of baby guppies
(killifish).
Below falls, predators of adult guppies (pike
cichlid).
Field observation male size and coloration
differs even in the same stream, and seems to be
related to the presence or absence of predators
of adult guppies. Can this observation be acted
upon with experiments?
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Yes. Lab experiments (in above ground swimming
pools in a greenhouse at Princeton) showed that
the amount of color on male guppies increases due
to sexual selection - females prefer to mate with
brightly colored males. Adding killifish (prey
only on baby guppies) does not affect the
increase in male brightness. But adding a pike
cichlid to a pool results in the fish evolving
back to the appearance of below-falls fish -
dul colored males. Can this experiment be done
in the field?
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Yes, in one direction (brighter males). Small
streams can be found (in Trinidad) which do not
have guppies or pike cichlids (although even the
smallest streams have killifish) Moving guppies
from a below-falls population (dull males) to
an empty stream results in males evolving to be
brighter. So both lab and field experiments have
corroborated the field observations about the
balance of sexual and natural selection in
guppies.
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Fig. 22.12 Other features of guppies have also
been found to be subject to experiments on
natural selection.
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Natural selection and medicine

• An example using the influenza virus.

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The influenza virus

• Causes the flu symptoms we all know, but is not
  the only virus to cause runny noses, fevers, and
  all the rest of the symptoms.
• Is an RNA virus that replicates itself in animal
  cells. Like all viruses, it is a complete
  parasite, and cannot replicate unaided.

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The influenza virus in the electron microscope.
Note the projections on the outside, and in the
photo on the left, indications of structures
inside the capsule.
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The projections are two types of proteins,
haemaglutinin and neuramindase, which are
antigens - molecular sites to which the human
body can make antibodies.
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The other player in this story is the human
immune system. It is capable of making
antibodies to various chemicals that are
introduced into the body. Such chemicals are
called antigens. Viral coat proteins are
important antigens. A key fact is that it takes
about 2 weeks for humans to make a new antibody.
Once a human has made an antibody, it can be made
more rapidly the second time (antibody memory).
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Influenza coat protein evolution The human
immune system usually (given 2 weeks) destroys a
virus infection (but often not before it is
transmitted to another person). Eventually,
almost all of the people who get the virus become
immune and second infections fail. But the
influenza virus is constantly giving rise to new
mutations, with different amino acid sequences in
coat proteins. Such a new sequence (surviving in
a few people) can re-infect many people the next
flu season because antibodies cannot be made
rapidly against it. Thus there is continual
evolution of new viral sequences. This process
is called, confusingly, antigen drift. But
this process is not caused primarily by genetic
drift, but by selection.
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A really remarkable tree Haemaglutinin gene
evolution in influenza type A strains from 1985 -
1996. This represents 1348 base
substitutions! Where are the side
branches? Evidence for strong selection.
From Bush et al. 1999. Positive Selection on the
H3 Hemagglutinin Gene of Human Influenza Virus A.
Mol. Biol. Evol. 1614571465. 1999
In medical terminology this is called antigen
drift, but it is primarily selection, not
genetic drift.
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But there is also a process of antigen shift,
which comes about from reshuffling of the
genome of the influenza virus. Such a shift
seems to have been responsible for the 1918 flu
epidemic that killed some 20 million people.
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Influenza A has a large number of subtypes that
infect birds and pigs as well as humans.
Some of these types can infect humans (avian
flues and swine flues). If a person is
infected with human type, and a pig or bird type,
some cells can be infected with both types at the
same time, so that a new type with alleles from
both types can be created. Such a flu can be a
surprise to the human immune system.
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Influenza A subtypes (not all shown in this tree
of haemaglutinin sequences) which infect birds
and pigs as well as humans. Note the arrow
showing the position of the 1918 sequences.
However, the 1918 sequences have avian features
as well.
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Every year, researchers at the Centers for
Disease Control and elsewhere try to guess what
next years flu strain will be, so that vaccines
can be made. Most of the searching is done in
China, where there is a very high human
population density, and many people still live in
close proximity to pigs as well as ducks and
other birds. Three Chinese strains are chosen
and used to make the next years vaccines. This
process involves growing the flu strains in
millions of eggs!
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(No Transcript)
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Why is there such rapid virus evolution? Viruses,
especially RNA viruses (which use RNA instead of
DNA for genes) have 1) an extraordinarily high
rate of mutation (as large as a 10-4 probability
of a base not being replicated correctly per
generation) and 2) extremely short generation
times (for example, 1.2 days for HIV
virus). Plus, there is a lot of drift and
selection...
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Lecture 13 Natural selection
Assigned Readings Ch. 23
Natural selection
fitness, discrete traits, continuous
traits Patterns of natural selection
directional, balancing, stabilizing,
disruptive, diversifying Sexual selection
secondary sexual
characteristics, intersexual, intrasexual
selection Guppies
natural versus cultivated strains, field
observations of effects of predators on male
color, experiments on balance of natural and
sexual selection, field experiments
Natural selection and the influenza virus
influenza surface
proteins immune response 1918 flue epidemic
antigenic drift antigenic shifts