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Chapter 3 -- Genetics Diversity
Importance of Genetic Diversity -- Maintenance
of genetic diversity is a major focus of
conservation biology.
Environmental change is a continuous process &
genetic diversity is required for populations to
evolve to adapt to such change.
Loss of genetic diversity is often associated
with inbreeding and reduction in reproductive
fitness.
IUCN recognizes the need to conserve genetic
diversity as one of three global conservation
priorities.
Genes are sequences of nucleotides in a particular
segment (locus) of a DNA molecule.
Genetic diversity represents slightly different
sequences.
DNA sequence variants may result in amino acid
variation that may result in functional biochemical
or morphological dissimilarities that cause
differences in reproductive rate, survival, or
behavior of individuals.
Normal hemoglobin
NH2-Val-His-Leu-Thr-Pro-Glu-Glu-COOH
Sickle-Cell hemoglobin
NH2-Val-His-Leu-Thr-Pro-Val-Glu-COOH
Measuring Genetic Diversity
Quantitative Characters: the most important
form of genetic variation is that for reproductive
fitness as this determines the ability to evolve.
These traits and other measurable characters,
such as height, weight, etc. are referred to as
“Quantitative Characters”.
Variation for quantitative characters is due to
both genetic and environmental factors.
Therefore, methods are required to determine
how much of this variation is due to heritable
genetic differences among individuals and how
much is due to the environment.
While genetic variation for quantitative characters
is the genetic diversity of most importance in
conservation biology, it is the most difficult and
time-consuming to measure.
Proteins: The first measures of genetic diversity
using molecular methods were provided in 1966
using protein electrophoresis.
This technique separates proteins according to
their net charge and molecular weight.
Disadvantages of Protein Electrophoresis:
Only about 30% of DNA substitutions result in
charge changes so electrophoresis appreciably
underestimates the full extent of genetic
variation.
Usually uses blood, liver, heart, or kidney in
animals or leaves and root tips in plants therefore
animals must be captured and many times killed.
DNA: There now exists several methods for
directly or indirectly measuring DNA sequence
variation.
Advantages:
Sampling can often be done non-invasively
Polymerase Chain Reaction (PCR) amplification
allows the use of small quantities
of sample.
Restriction Fragment Length Polymorphism
(RFLP)
DNA Fingerprinting
Polymerase Chain Reaction (PCR): Requires only
extremely small quantities of sample to amplify
a target sequence millions fold.
Allows use of remote sampling (hair, skin biopsy,
feathers, sperm, etc) and the use of degraded
samples.
Randomly Amplified Polymorphic DNA (RAPD)
Microsatellite Repeats:
Tandem repeats of short DNA fragments
Typically 1 - 5 bp is length -gtagacGTGTGTGTGTGTGTGTccatag
catcagCACACACACACACACAggtatc
Number of repeats is highly variable due
to “slippage” during DNA replication.
Genotyping with microsatellites
Locus G10C
BIBE1
BIBE15
BIBE16
DNA Sequencing
Terms:
Genome: The complete genetic material of a
species or individual. All the DNA, all the
loci, or all the chromosomes.
Locus (loci): A segment of DNA (e.g., microsatellite)
or an individual gene.
Alleles: Different forms of the same locus that
differ in DNA base sequence: A1, A2, A3, etc.
Genotype: The combination of alleles present at a
locus in an individual.
Homozygote: An individual with two copies of the
same allele at a locus -- A1A1
Heterozygote: An individual with two different
alleles at a locus -- A1A2
Allele Frequency: Frequency of an allele in a
population (often referred to a gene frequency).
Example: If a population has 8 A1A1 individuals
and 2 A1A2 individuals, then there are 18 copies
of the A1 allele and 2 copies of the A2 allele.
Thus, the A1 allele has a frequency of 18/20 = 0.9
and the A2 allele has a frequency of 2/20 = 0.1
Polymorphic: Having genetic diversity. A locus in
a population is polymorphic if it has more than
one allele.
Polymorphic loci are usually defined as having
the most frequent allele at a frequency of
less than 0.99 or less then 0.95.
Monomorphic: Lacking genetic diversity. A locus
in a population is monomorphic if it has only
one allele present in a population or if the
frequency of the most common allele is
greater than 0.99 or 0.95.
Prorportion of loci polymorphic (P): Number of
polymorphic loci divided by the total number
of loci sampled.
Example: If you survey genetic variation at 10
loci and only 3 loci are polymorphic then,
P = 3/10 = 0.3
Average Heterozygosity (H): Sum of the
proportion of heterozygotes at all loci
divided by the total number of loci sampled.
Example: If the proportions of individuals
heterozygous at five loci in a population are:
0, 0.1, 0.2, 0.05, and 0, then
H = (0 + 0.1 + 0.2 + 0.05 + 0)/5 = 0.07
Allelic Diversity (A): Average number of alleles
per locus.
Example: if the number of alleles at 6 loci are 1,
2, 3, 2, 1, 1
Then A = (1 + 2 + 3 + 2 + 1 + 1) = 1.67
Haplotype: Allelic composition for several loci
on a chromosome, e.g., A1B3C2
This term is also used to refer to unique mtDNA
sequences for a particular locus.
Polymorphic sites within mtDNA haplotypes
of 144 southwestern black bears
Variable nucleotide positions
Haplotype
A
B
C
D
E
36
T
.
.
C
C
93
T
.
.
C
C
351
T
.
–
.
–
352 462 466
T A
G
–
.
.
–
.
.
–
G A
–
G A
BIBE
N = 31
MM
N = 29
B
E
A
D
BGWMA
N=9
SDB
N = 60
B
SDC
N=5
B
A
B
SMM
N=4
B
Haplotype Diversity (h): this is also known as
Gene Diversity and is equivalent to expected
heterozygosity for diploid data.
It is defined as the probability that two
randomly chosen haplotypes are different
in the sample.
k
h = (n/n-1)(1-pi2)
i=1
Where n is the number of gene copies in the sample,
k is the number of haplotypes, and pi is frequency
of the ith haplotype
Example: population size = 50, 5 haplotypes.
A
B
C
D
E
n
46
1
1
1
1
pi
0.92
0.02
0.02
0.02
0.02
pi2
0.8464
0.0004
0.0004
0.0004
0.0004
0.848
h = 50/49(0.848) = 0.1551
n
10
10
10
10
10
pi
0.2
0.2
0.2
0.2
0.2
pi2
0.04
0.04
0.04
0.04
0.04
0.2
50/49(0.8) = 0.8163
Nucleotide diversity (): also known as average
gene diversity over L loci and is the
probability that two randomly chosen
homologous nucleotides are different.
This is equivalent to gene diversity at the nucleotide
level.
k
= (n/n-1)(
pipjdij)
i=1 j<i
Where pi is the frequency of haplotype i and pj is
the frequency of haplotype j, and dij is an
estimate of the number of mutations having
occurred since the divergence of haplotypes i and
j, k is the number of haplotypes.
Example: 2 populations of size 30, each having
3 haplotypes.
Population A
A
10
B
10
C
10
Population B
F
10
G
10
H
10
Haplotype diversity in each population = 0.6897
What is nucleotide diversity in each population?
Sequenced 478 bp and obtained the following:
Population 1
Haplotype A
10
A
Haplotype B
10
B
Haplotype C
10
C
Nucleotide Diversity = 0.0019
Population 2
Haplotype D
10
D
Haplotype E
10
E
Haplotype F
10
F
Nucleotide Diversity = 0.0115
A
-1
1
B
C
-2
1
D
-8
11
E
F
-5
--
SEQUENCED 478 BP
A
B
C
A
--0.0021
0.0021
B
1
--0.0042
C
1
2
---
D
E
F
D
--0.0167
0.0230
E
8
--0.0105
F
11
5
---
Population 1
pi
A vs. A
0.333
A vs. B
0.333
A vs. C
0.333
B vs. B
0.333
B vs. C
0.333
B vs. A
0.333
C vs. C
0.333
C vs. A
0.333
C vs. B
0.333
pj
0.333
0.333
0.333
0.333
0.333
0.333
0.333
0.333
0.333
dij
0
0.0021
0.0021
0
0.0042
0.0021
0
0.0021
0.0042
ij
0
0.00023
0.00023
0
0.00047
0.00023
0
0.00023
0.00047
0.00186
 = (30/29) X 0.00186 = 0.00192
YOU SHOULD DO THE
CALCULATIONS FOR
POPULATION #2
Probability of Identity (PI): Probability of
randomly pulling two individuals from a population
and them having the exact same genotype at all
loci examined.
Probability of Identity (PI): Probability of
randomly pulling two individuals from a population
and them having the exact same genotype at all
loci examined.
The unbiased estimate of PI over multiple loci is:
PI = 
n3(2a22 - a4) - 2n2(a3 + 2a2) + n(9a2 + 2) - 6
(n - 1)(n - 2)(n - 3)
n = sample size, ai = pji where
pj = frequency of jth allele.