Prac 6 Genetic Diversity Answers

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).


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


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 total

Slow 12

Fast 18


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


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 total

Slow 14

Fast 16


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 total

Slow 8

Fast 22


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


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


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.


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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Prac 6 Genetic Diversity Answers