IUCN recognizes the need to conserve genetic

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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.
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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.
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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.
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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.
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Disadvantages of Protein Electrophoresis Only
about 30 of DNA substitutions result in charge
changes so electrophoresis appreciably underestima
tes 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.
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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.
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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.
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Microsatellite Repeats Tandem repeats of short
DNA fragments Typically 1 - 5 bp is length --
gtagacGTGTGTGTGTGTGTGTccatag catcagCACACACACAC
ACACAggtatc Number of repeats is highly
variable due to slippage during DNA
replication.
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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.
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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
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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
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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.
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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
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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
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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
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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.
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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)
i1 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
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Example population size 50, 5
haplotypes. n pi pi2 n pi pi2 A 46 0.92 0.846
4 10 0.2 0.04 B 1 0.02 0.0004 10 0.2 0.04 C 1 0.0
2 0.0004 10 0.2 0.04 D 1 0.02 0.0004 10 0.2 0.04
E 1 0.02 0.0004 10 0.2 0.04 0.848 0.2 h
50/49(0.848) 0.1551 50/49(0.8) 0.8163
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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.
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• k
• (n/n-1)(? ?pipjdij)
• i1 jlti
• 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.

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Example 2 populations of size 30, each having 3
haplotypes. Population A Population
B A 10 F 10 B 10 G 10 C 10 H 10 Haplotyp
e diversity in each population 0.6897 What is
nucleotide diversity in each population?
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Sequenced 478 bp and obtained the
following Population 1 A B C Haplotype
A 10 A -- Haplotype B 10 B 1 -- Haplotype
C 10 C 1 2 1 Nucleotide Diversity
0.0019 Population 2 D E F Haplotype
D 10 D -- Haplotype E 10 E 8 -- Haplotype
F 10 F 11 5 -- Nucleotide Diversity 0.0115
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Population 1 pi pj dij ?ij A vs.
A 0.333 0.333 0 0 A vs. B 0.333 0.333 0.0021 0.00
023 A vs. C 0.333 0.333 0.0021 0.00023 B vs.
B 0.333 0.333 0 0 B vs. C 0.333 0.333 0.0042 0.00
047 B vs. A 0.333 0.333 0.0021 0.00023 C vs.
C 0.333 0.333 0 0 C vs. A 0.333 0.333 0.0021 0.00
023 C vs. B 0.333 0.333 0.0042 0.00047 0.0
0186 ? (30/29) X 0.00186 0.00192
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YOU SHOULD DO THE CALCULATIONS FOR POPULATION 2
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Probability of Identity (PI) Probability of
randomly pulling two individuals from a
population and them having the exact same
genotype at all loci examined.
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