Loss of heterozygosity due to genetic drift:

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Loss of heterozygosity due to genetic drift We
have already seen that genetic drift causes a
gradual loss of heterozygosity in small
populations. As pointed out in the text, in terms
of average heterozygosity, this loss can be
quantified Ht H0(1-1/2Ne)t Where
t the number of generations
H0 starting
heterozygosity
and Ne (effective) population
size Suppose that a population of an endangered
species in nature has an average heterozygosity
(H0) of 20 A zoo wishes to help conserve this
species, but can only afford to keep 3 males
and 3 females in every generation. What is the
average heterozygosity of the zoo population
after 4 generations?
H4 .2(1-1/2(6))4 .2(.71) 0.14
That is, after 4 generations the zoo population
has retained only about 14/20 or 70 of its
original average heterozygosity. In 8
generations it will only retain a half of the
starting value. Obviously, this loss of
heterozygosity can be of serious concern to
conservation biologists
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SOMETHING TO THINK ABOUT If you ran a zoo, what
might you do to (partially) to counteract the
loss of heterozygosity due to drift?
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THE CONCEPT OF EFFECTIVE POPULATION SIZE
1. The population size in the previous
examples is really the effective population
size, Ne. Many populations contain individuals
who do not breed (e.g, post-reproductives,
juveniles or immatures, losers in territorial
bouts, etc.). These are part of the census
size of the population, but they are not
included in its effective size.

• An ideal population" contains an equal number of
  reproductively
• active males and females and contains no
  individuals who do
• not reproduce.

• Ne is the size of an ideal population that loses
  average
• heterozygosity at the same rate as the real
  population. Ne is
• almost always smaller than the census size of a
  population.
• The concept of Ne sometimes seems needlessly
  technical to
• students, but, as we will see, it involves some
  interesting and
• relevant biology.

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When sex ratios are uneven, it can be shown
that Ne 4NmNf / (Nm Nf)
where Nm the number of males Suppose that
there are 50 reproductively active members of a
given population, but there are 45 females and
only 5 males
Ne 4NmNf / (Nm Nf)
4(45)(5)/ 50 18 (!)
Thus, while the census size of this population
might be 50, its effective size is only 18 due
to the imbalance of sex ratios.
In what natural circumstances might this effect
be important? How might this sex ratio effect
influence hunting practices and/or regulations?
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• Fluctuations from generation to generation in
  population size also
• markedly influence Ne
• 1/Ne 1/t ? 1/Nt or 1/tt 1/t1
  1/t2 1/t3.
• where t number of generations and Nt size in
  each generation
• and tt is the total number of generations.
• Suppose a population of mice had the following
  sizes in each generation
• gen size
• 500
• 350
• 400
• 470
• 25
• 400
• .

1/Ne 1/6 1/500 1/350 1/400
1/470 1/25 1/400 .167.002 .0029
.0025 .0021 .04 .0025 .167(.052)
.00868 Ne 115 (!) The arithmetical
average size of this population over the
same generations is 358! It is more than 3X
larger than Ne.
The smallest population has had a
disproportionate influence on Ne. Note the
formula above is for the harmonic mean, which
does have this property.
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NON-RANDOM MATING
INBREEDING Mating between related individuals at
a level higher than that of random encounters.
ASSORTATIVE MATING Mating based on phenotype.
Positive vs
Negative
or
Assortative vs Disassortative
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INBREEDING DOES NOT CHANGE GENE FREQUENCIES BUT
DOES REDUCE HETEROZYGOSITY
We will use the most intense form of
inbreeding, self-fertilization, to show this

• Start with a popln at HW equilibrium
• p2 AA 2pqAa q2 aa

• Let each genotype self fertilize
• p2 AA -gt p2 AA q2 aa -gt q2 aa
• 2pq Aa -gt 2pq(1/4 AA 1/2 Aa 1/4aa) pq/2
  AA pqAa pq/2 aa

• AA p2 pq/2 aa q2 pq/2 Frequency of
  both homozygotes has increased by pq/2.
• Aa pq Frequency of heterozygotes has
  dropped by pq.

4. p1 AA Aa/2 p2 pq/2 pq/2 p2
pq p2 p (1 - p) p
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In general, the decay of heterozygosity with
inbreeding is more rapid than with genetic drift.
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• Lets take a moment to consider to combined
  effects of drift
• and inbreeding on small, endangered
  populations
• Drift results in the gradual loss of
  heterozygosity.
• The level of inbreeding by random contact goes
  up.
• Probability of random contact leading to
  inbreeding is
• roughly 1/2Ne. When Ne is small, this
  probability
• increases.
• As the text indicates, these two effects can
  combine to
• very nearly doom a small population to
  extinction
• Heres an example of such a doom cascade
• I. Inbreeding results in homozygosity of
  deleterious alleles.
• II. Homozygosity for these alleles
  reduces fertility of the endangered population.
• III. Reduced fertility reduces population
  size.
• IV. Reduced population size leads to
  further inbreeding and drift.

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Inbreeding depression is a very common phenomenon
in laboratory lines and domestic animals. It is
especially noticeable when lines have been
derived from outcrossing species with large
population sizes. Why might this be so?
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Inbreeding depression has been measured
historically in our own species by levels
of infant mortality. Here is a notable example.
The probable source of many of the deleterious
recessive mutations which are segregating in
homozygous form is, unfortunately, too obvious to
mention.
Vocabulary consanguinity or consanguinous
same blood blood relationship. For
example, Second cousins are less consanguinous
than are first cousins. Likewise, a
marriage between cousins, uncle and niece,
etc. is a consanguinous marriage.
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Inbreeding depression, regardless of its cause,
generally lowers the fitness of organisms, and
many organisms have developed mechanisms that
prevent or reduce inbreeding (especially
self-fertilization). These range from incest
taboos, a widespread feature of our own species,
to self-incompatibility genes in various plants.
When present, the latter act to prevent/reduce
self-fertilization even in monoecious species.
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Even though inbreeding depression is both real
and frequently encountered, some organisms have
mating or social systems which promote some level
of inbreeding. We will briefly consider three
of these 1. The naked mole rat, Heterocephalus
glaber. 2. The mangrove Rivulus, Rivulus
marmoratus (a fish). 3. The common or
orange-spotted jewelweed, Impatiens capensis
(also called the touch-me-not).
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The naked mole rat, Hetero- cephalus glaber,
lives in colonies and has a social system much
like termites and ants one queen does all the
breeding. As is evident from the DNA
fingerprint data (right), it is highly inbred.
http//www.lincolnzoo.org/vid-molerat.html
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Rivulus marmoratus is the only vertebrate known
to reproduce by self-fertilization. Since
self-fertilization is the ultimate form of
inbreeding, it occurs in nature as arrays of
homozygous clones. Yet it lives in mangrove
forests, very challenging environments.
http//www.bsi.vt.edu/rivmar/
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Impatiens capensis, the spotted jewelweed,
occurs as both outcrossing and
self-fertilizing forms. In some populations, the
extent of self-fertiliza- tion vs outcrossing
seems to be regulated by population density (high
density leads to outcrossing). In other
populations, the breeding system seems to be much
less flexible and does not respond to density.
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• Humans often mate assortatively for many traits.
  
• How many can you think of
• Height (rank order only)
• Weight (rank order only)
• Hair color (some negative here also)
• Skin color (culturally variable)
• Eye color (some negative here also)
• Language/enthnic origin (culturally variable)
• Religion (culturally variable)
• Age (rank order only)
• Similar Infirmity
• IQ (weak and culturally variable)
• Shoe size (rank order only) (?)
• Specific components of body odor or other
  pheromones
• (? MHC phenotype) -- negative only
• 13. Facial symmetry (rank order only)

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An example of positive assortative mating in
humans level of educational
attainment
Note In this table, a score of 0.5 would
indicate no significant assortative mating. A
score of 0.6 or above indicates a significant
level of assortative mating. This is a rank
order correlation and does not imply the same
level of education for both spouses.
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Does assortative mating lead to changes in gene
frequency in natural populations? The answer is
complex To the extent that positive assortative
mating resembles inbreeding, the answer is
generally no. However, there are mating
systems in which one sex seeks mates with a
particular suite of characters (so these systems
can be considered a type of assortative
mating). These cases are generally termed
sexual selection and the frequencies of genes
underlying their traits can sometimes change
very rapidly.