My sailboat, a 23ft trailerable keelboat, is currently stuck fast in 12 inches of ice at Lake Clinto

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• My sailboat, a 23ft trailerable keelboat, is
  currently stuck fast in 12 inches of ice at Lake
  Clinton (you can walk across the lake).

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3
Lecture 13 Genetics Gene pools and populations
Assigned Readings Ch. 23 23.1 - 23.3
Hardy-Weinberg equilibrium random mating
equilibrium conditions Genetic drift chance
allele frequency change Mutations silent,
missense, nonsense, insertions and deletions,
frameshifts, deleterious, neutral, beneficial
Population genetics the mechanics
(engineering) of evolution microevolution
population, agriculture, medical
genetics Examples of genetic variation terms
(gene pool standing variation, mutation)s,
examples, human genetic variation Describing
variation frequencies (percentages), allele,
genotype, and phenotype frequencies, normal curve
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Lakes in Michigan, www.egr.msu.edu
Population genetics population microevolution agri
culture medicine
A population is a group of individuals living in
a particular area. Individuals in a population
usually mate with other individuals from that
population.
Largemouth bass, a lake fish
5
Population genetics population microevolution agri
culture medicine
Fig. 23.3. One species, two popuations. The two
populations can interbreed perfectly, but most
matings are within a herd (population).
6
Figure 23.2 Individuals are selected populations
evolve. Grass genotypes tolerant of heavy-metal
poisoning survive and reproduce.
Population genetics population microevolution agri
culture medicine
7
Population genetics population microevolution agri
culture medicine
Each tomato variety is a distinct population with
a unique genotype, kept distinct by controlled
breeding.
http//www.hort.purdue.edu/fruit/rep_pres/2002prio
r/insidebackcover-tomatoes.jpg
8
Figure 23.13 Mapping malaria and the sickle-cell
allele (ignore malaria for now). Note how the
frequency (percentage of the allele in the
population) changes from place to place.
Population genetics population microevolution agri
culture medicine
9
Fig. 23.1, Fig. 24.3. All life is this variable.
The sum of all the alleles of all the genes in
all the individuals in a population is called the
gene pool. At any given time the gene pool has
many old mutations (standing variation), plus new
mutations are always occurring.
Genetic variation terms examples human genetic
variation
10
Genetic variation terms examples human genetic
variation
Multicolored Asian Ladybird Beetle, Harmonia
axyridia
11
Figure 23.9 Nonheritable variation within a
population
Genetic variation terms examples human genetic
variation
But one must always be aware that nongenetic
variation (that is, environmental variation) is a
possibility. Genetic variation must be shown to
exist by crosses or other tests.
12
Figure 23.11 Does geographic variation in yarrow
plants have a genetic component? Plants develop
different sizes even when grown in a common
garden experiment.
Genetic variation terms examples human genetic
variation
13
Genetic variation terms examples human genetic
variation
The OCA2 gene on chromosome 15 is the major
determinant of eye color. Perhaps as many as 6
other genes affect eye color. Two particular
OCA2 alleles are strongly associated with brown
and with green-hazel eyes.
Eye color portals into pigmentation genes and
ancestry. R. A. Sturm and T. N. Frudakis. 2004.
Trends in Genetics 20 327-332.
14
Describing variation frequencies allele,
genotype, phenotype normal curve
If we have discrete (clear-cut) variation, we can
use frequencies (proportions) to describe it. We
need frequencies for the phenotypes, the
genotypes, and the alleles. Frequencies are
probabilities and obey the multiplicative and
additive rules of probability.
15
Describing variation frequencies allele,
genotype, phenotype normal curve
A population - color is determined by one gene,
with 2 alleles showing partial dominance.
16
Describing variation frequencies allele,
genotype, phenotype normal curve
total
3
10
5
2
Phenotype frequencies (/100)
3/100.3
5/100.5
2/100.2
17
Describing variation frequencies allele,
genotype, phenotype normal curve
Genotype frequencies are the same as phenotype
frequencies in this case.
total
3
10
5
2
3/100.3
5/100.5
2/100.2
But this will not be the case if there is
dominance. If there is dominance, test crosses
may be needed to count genotypes.
18
Describing variation frequencies allele,
genotype, phenotype normal curve
The third kind of number is perhaps the most
important - allele frequencies. We will use p
and q to denote allele frequencies.
total
6 CW
20
5 CW, 5 CR
4 CR
(65)/20 0.55 p
(45)/20 0.45 q
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Polygenic inheritance additive effects
(essentially, incomplete dominance) of multiple
genes on a single trait
Describing variation frequencies allele,
genotype, phenotype normal curve
Although this hypothetical example shows a normal
(or bell) curve resulting from an F2 cross, it is
also representative of typical population data
for polygenic traits (or characteristics), in
which there is often an environmental component
as well as polygenic inheritance.
20
Hardy-Weinberg random mating equilibrium condition
s
Genotype frequencies in many populations conform
to what is called a Hardy-Weinberg Equilibrium
(HWE). This is an extremely important
generalization about variation in nature. It
arises because in many populations, we see
approximately random mating. This does not mean
that all mate choice is random, but that mating
is random for many traits (think of
microsatellite loci as a type of variation not
visible to animals).
21
Hardy-Weinberg random mating equilibrium condition
s
If there is random mating (and this is not always
the case), then the genotype frequencies and
allele frequencies are related as below. Assume
two alleles (A and a, but we are not assuming
complete dominance), with the allele frequency of
A of p, and that of a being q. We will
symbolize the genotype frequencies as AA P, Aa
H, and aa Q.
22
Hardy-Weinberg random mating equilibrium condition
s
Then if some assumptions hold (in a second), we
find that frequency of AA P p2 frequency of
Aa H 2pq frequency of aa Q q2 because if
there is random meeting of gametes, then for
example the probability of an A sperm meeting an
A egg and producing an AA zygote is p x p
(multiplicative rule). The others are similarly
derived (slide from book following). Note that
this is just a binomial expansion, (p q)2 p2
2pq q2
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Figure 23.5 The Hardy-Weinberg theorem
Hardy-Weinberg random mating equilibrium condition
s
24
Figure 23.4 Mendelian inheritance preserves
genetic variation from one generation to the next
Hardy-Weinberg random mating equilibrium condition
s
Please note that HWE can be described for more
than 2 alleles (p q r)2, where p, q and r are
the frequencies of 3 alleles.
A special case to make a point progeny from one
F2 cross. It is more accurate to say that HWE
does not change allele frequencies.
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Hardy-Weinberg random mating equilibrium condition
s
The book emphasizes on p. 458 that prefect HWE is
only possible in perfect populations (no
mutation, infinitely large populations, etc).
But the book misses the point. HWE is quite
robust, and gives a good approximation to
genotype frequencies even if the conditions are
violated. For example, if allele frequencies
(p, q) change but there is random mating, the new
genotype frequencies will be different from
before but still following p2 2pq q2.
26
Genetic drift chance allele frequency change
Allele frequencies do not remain exactly the same
from generation to generation, especially in very
small populations. A process called genetic
drift - random changes in allele frequencies -
occurs in all populations.
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Figure 23.7 Genetic drift
Genetic drift chance allele frequency change
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Genetic drift chance allele frequency change
In any population, but especially small
populations, allele frequencies change over time
by chance.
An allele frequency graph
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Genetic drift chance allele frequency change
1
0.8
If you follow allele frequency change in several
small populations, you get a different result
each time. One possible outcome is allele
fixation - loss of one allele.
0.6
0.4
0.2
0
0
1
2
3
4
5
6
7
8
9
generations
An allele frequency graph
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Genetic drift chance allele frequency change
1
0.9
0.8
N 10 beetles in population
0.7
0.6
0.5
red
freqency b allele
0.4
0.3
b b
0.2
0.1
0
A real experiment with the b locus in flour
beetles.
0
2
4
6
8
10
12
14
16
18
20
generations (time)
1
brown
0.9
b b
0.8
0.7
0.6
0.5
frequency b allele
0.4
N 50 beetles in population
0.3
0.2
black
0.1
0
b b
0
2
4
6
8
10
12
14
16
18
20
generations (time)
Note effect of population size
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Genetic drift can be shown in the lab, using
populations of different sizes and initial 5050
frequencies of two neutral alleles.
1.0
0.5
allele A neither lost nor fixed
0
1
50
5
10
15
20
25
30
35
40
45
Generation (500 flies at the start of each line
or population)
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In small populations one or other of the alleles
is inevitably lost.
1.0
AA in five populations
0.5
allele A lost from four populations
0
1
50
5
10
15
20
25
30
35
40
45
Generation (25 flies at the start of each line or
population)
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Figure 23.8 A special case of genetic drift The
bottleneck effect
Genetic drift chance allele frequency change
34
Cheetahs are another example of a species that
appears to have experienced a severe bottleneck
in the relatively recent past, because their
genetic variability is extremely low. For
example, skin grafts from one cheetah to another
are no rejected.
35
Polydactyly in Pennsylvania Old Order Amish
(founding population approximately 200 people,
almost always marry within the group)
Johns Hopkins University Press
36
Genetic drift chance allele frequency change

• Some facts about genetic drift
• 1. It occurs the same way if there are more than
  2 alleles, it just produces a more
  complicated-looking graph.
• 2. It is most powerful in small populations, but
  is inevitable even in large populations.
• 3. If it goes on long enough, it is possible for
  one allele to become the only allele in the
  population. This allele is now said to be
  fixed.
• The opposite of fixation is allele loss or allele
  extinction. New mutants run a huge risk of going
  extinct, but some do increase, and even become
  fixed, by chance.
• Over truly long periods drift and mutation are
  the primary causes of changes in nucleotides
  sequence in non-coding parts of genomes.

37
Mutations types rates effects
All variation (all alleles) must originate at
some point by mutation. A mutation is
essentially an error in DNA replication. We will
follow the book with a very simple classification
of mutations, specifically in genes. Point
mutation - change in a single base. These can
either have no effect (silent mutation - remember
that the genetic code is redundant), change an
amino acid (missense mutation), or form a new
stop codon leading to truncation of the encoded
protein (nonsense mutation). Insertions and
deletions - if these are a multiple of three they
lead to gain or loss of amino acids. If they are
not a multiple of three they cause frameshifts,
leading to truncated strange proteins.
38
Mutations types rates effects
Mutations are low probability events, one in a
million events, but one must remember how many
DNA replications there are in the development of
an organism, and that population sizes can be in
the billions. Thus, mutations are inescapable.
The probability of a mutation is called its
mutation rate.
39
Mutations types rates effects
The effects of mutations range from one extreme
to the next. Many are deleterious - they have a
negative effect on the organism (often only in
homozygous condition). A great many are what we
will call neutral - they have no effect on the
organism. Microsatellite alleles are an example.
A small number are actually beneficial to the
organism. Mutations for insecticide resistance
are an example.