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Biodiversity & Ecosystems Measuring Genetic Diversity 1
Practical 6 Measuring Genetic Diversity
Step 1 To measure how genetic variation is spread within and between populations
you first need to determine allele frequencies in each population. The particular
allozyme locus examined has two alternate forms. The identity of the two alleles in
each individual is reflected directly by the banding patterns within each lane on the gel.
For example, the first individual in the first lane of the first gel is heterozygous, that is,
the two alleles it has are different and are indicated (+) by both a Fast and a Slow
moving band on the gel. In contrast, the individual in the second lane is homozygous, as
indicated by having a single band representing two Slow alleles.
Determine the allele frequencies in each population for the Fast-moving allele
(p) and the Slow-moving allele (q) by counting the number of alleles for
individuals in each population (remember that a homozygote has two alleles the
same so you have to count the + twice, and the total number of alleles for the 15
individuals is 2 x 15 = 30). The, divide that by the total number of alleles
present in the population (always equal to two times the number of individuals).
Biodiversity & Ecosystems Measuring Genetic Diversity 2
Pterostylis isozymus, Population 1 (individual 1 to 15 from left to right)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 total
Slow 23
Fast 7
Pterostylis isozymus, Population 2 (individual 1 to 15 from left to right)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 total
Slow 12
Fast 18
Pterostylis isozymus, Population 3 (individual 1 to 15 from left to right)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 total
Slow 4
Fast 26
Pterostylis polyzymus, Population 1 (individual 1 to 15 from left to right)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 total
Slow 12
Fast 18
Pterostylis polyzymus, Population 2 (individual 1 to 15 from left to right)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 total
Slow 14
Fast 16
Pterostylis polyzymus, Population 3 (individual 1 to 15 from left to right)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 total
Slow 8
Fast 22
Biodiversity & Ecosystems Measuring Genetic Diversity 3
Step 2. Next, you need a measure of genetic difference between populations. A commonly
used measure is Wright’s fixation index, or Fst, which ranges from 0, indicationg no
difference between populations, upwards, indicating increasing difference. To determine Fst,
you need to calculate the expected heterozygosity for each species (Hs). Do
this by multiplying 2pq for each population and then averaging these values over all three
populations within each species.
Allele frequencies for Pterostylis isozymus
Fast allele p Slow allele q = 2 x p x q
population 1 7/30 = 0.23 23/30 = 0.77 2 x 0.23 x 0.77 =
0.35
population 2 18/30 0.60 12/30 0.40 0.48
population 3 26/30 0.87 4/30 0.13 0.23
average = 1.06/3
(Hs) = = 1.06/3 = 0.35
Allele frequencies for Pterostylis polyzymus
Fast allele p Slow allele q = 2 x p x q
population 1 18/30 0.60 12/30 0.40 0.48
population 2 16/30 0.53 14/30 0.47 0.50
population 3 22/30 0.73 8/30 0.27 0.39
average = 1.37/3
(Hs) = 1.37/3=0.46
Hs is heterozygosity if populations were isolated ie. not interbreeding
Biodiversity & Ecosystems Measuring Genetic Diversity 4
Step 3. Now, calculate the expected heterozygosity if all three populations were
part of the same, extended breeding population (Ht). Do this by averaging p and q
over all three populations within each species, and then multiplying 2 x the average p x
the average q This would be the expected frequency of heterozygotes in the population if
it acted as one large breeding pool with no genetic differences at the local population level.
Expected heterozygosity (Ht) for Pterostylis isozymus
Fast allele p Slow allele q
population 1 7/30 = 0.23 23/30 = 0.77
population 2 18/30 0.60 12/30 0.40
population 3 26/30 0.87 4/30 0.13
average allele
frequency
1.70/3
=0.57
1.30/3
=0.43
(Ht).= 2 x the average p x the average q = 2 x 0.57 x 0.43 =0.49
Expected heterozygosity (Ht) for Pterostylis polyzymus
Fast allele p Slow allele q
population 1 18/30 0.60 12/30 0.40
population 2 16/30 0.53 14/30 0.47
population 3 22/30 0.73 8/30 0.27
average allele
frequency
1.86/3
=0.62
1.14/3
=0.38
(Ht).= 2 x the average p x the average q = 2 x 0.62 x 0.38 = 0.46
Biodiversity & Ecosystems Measuring Genetic Diversity 5
Step 4. OK, now you need to calculate the amount of local, within-population variation!
Deviations of the frequency of heterozygotes in separate
populations (Hs) from what you would expect to find if they were
all part of the same larger population (Ht) provide an index of the amount of
genetic variation that is found only in local populations. Thus, Fst = (Ht - Hs) / Ht, where
values of Fst < 0.01 indicate little divergence between populations, and values Fst > 0.1
indicate great divergence between populations (that is, the populations are genetically
different from each other). Values in-between indicate some genetic divergence
Follow the examples provided, calculate the fixation index for each species, and then
compare the indices between the two species.
Pterostylis isozymus
Fst = (Ht - Hs) / Ht = 0.49 – 0.35 / 0.49 = 0.29
Fst > 0.1 and indicates great divergence between populations of P. isozymus
almost none
Pterostylis polyzymus
Fst = (Ht - Hs) / Ht = 0.02
Fst <0.1 and indicates no/some/great divergence between populations of P.polyzymous
Populations of Pterostylis isozymousare more divergent than populations of Pterostylis
polyzymous. That is, the populations of Pterostylsi polyzymous, are genetically most
similar to each other.
Biodiversity & Ecosystems Measuring Genetic Diversity 6
Your Report
In your report you should outline the original problem, and discuss the following questions in an
“essay style” report (about 600 words). Use your calculations to support your discussion. Make sure
you correctly reference your discussion
Are the populations of each species different from each other ? Does one species have
more “between population” diversity than the other? Which one ?
How will you allocate your scarce funds for wetland acquisition ? Justify your decision in
terms of preserving the maximum amount of genetic diversity that characterizes these two
species.
What considerations other than genetic ones might influence your choice ?
Recall that our goal in this exercise is to capture as much of the genetic diversity that
characterizes these species as is possible, given a limited budget. Note that both alleles at
the locus surveyed are already found in each population of both species. Why does it
matter that more than a single population of each species be protected ?
In the reading by Eldridge(1998) “Trouble in Paradise”, how did the scientists maximize
the genetic diversity in the re-introduced population? Why didn’t they just choose to use
animals from just one of the islands ?
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