1. Section 2 -- Genetics Diversity
Importance of Genetic Diversity -- Maintenance
of genetic diversity is a major focus of
conservation biology and 1 of 3 global conservation
issues of IUCN
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.

2. Characterizing Genetic Diversity: Quantitative Variation
Quantitative (metric or polygenic) characters of
Most concern to conservation biology are those
Related to reproductive fitness such as:
Number of fertile offspring contributed by an
Individual that survive to reproductive age.

3. For endangered species, quantitative variation for
reproductive fitness is involved in the major
genetic concerns in conservation biology, namely:
Reduction in reproductive fitness due to inbreeding
(inbreeding depression)
Loss of evolutionary potential due to small
population sizes.

4. Impact of crossing between different populations
on fitness, whether beneficial (heterosis) or
deleterious (outbreeding depression).
Effects of translocating individuals from one
environment to another.
Correlations between molecular and quantitative
measures of genetic diversity are low. Therefore,
molecular measures of genetic variation provide,
at best, only a very imprecise indication of
evolutionary potential.

5. Quantitative characters typically have continuous,
approximately normal distributions and include
characters such as reproductive fitness, longevity,
height, weight, disease resistance, etc.
It is not possible to directly infer genotype from
observed phenotype for quantitative characters.
Individuals with the same genotype may have
different phenotypic values and individuals with
the same phenotypic values may have different
genotypes.

6. Underlying genetic basis to quantitative characters
is that they are affected by a number of loci,
each possessing alleles that add to or detract from
the magnitude of the character.
Loci affecting quantitative characters, individually,
show usual Mendelian properties of segregation
and linkage.

7. A major challenge in the study of quantitative
genetics is to determine how much of the observed
variation is due to genetics and how much is due
to environment.
One of the central concepts of quantitative genetics
is heritability.
Heritability is the proportion of the total
phenotypic variance in a population due to genetic
differences among individuals.

8. Algebraically, we can define the phenotypic value
Of an individual as the consequence of the alleles
It inherits together with environmental influences
As:
P = G + E
Where P = phenotype, G = Genotype, and
E = Environment.

9. The genetic component can be partitioned from
the environmental component as:
VP = VG + VE + 2CovGE
Where, CovGE is the covariance between genetic
and environmental effects.
The covariance for this component is expected
to be 0 if conditions for different genotypes
are equalized by randomly allocating individuals
across the range of environment, which is
difficult to achieve in wild populations.

10. For example, in territorial species of birds and
mammals, the genetically fittest parents may
obtain the best territories.
Offspring inheriting the best fitness genotypes
also inherit the best environments.
This results in a genotype X environment
correlation that increases phenotypic resemblance
among relatives.

11. Differences in performance of genotypes in
different environments is referred to as
Genotype X Environment Interactions.
These develop when populations adapt to particular
environmental conditions, and survive and
reproduce better in their native conditions than
in other environments.
Genotype X Environment Interactions are of major
significance to the genetic management of
endangered species as follows:

12. Reproductive fitness of translocated individuals
cannot be predicted if there are significant
Genotype X environment interactions.
Success of reintroduced populations may be
compromised by genetic adaptation to captivity.
For example, superior genotypess under captive
conditions may perform relatively poorly when
released to the wild.

13. Mixing of genetic material from fragment
populations may generate genotypes that do not
perform well under some, or all, conditions.
Knowledge of genotype X environment interactions
can strongly influence the choice of populations
for return to the wild.
Genotype X Environment interactions must be
distinguished from the genotype X environment
covariances and correlations.

14. Genotype X environment correlations occur when
genotypes are non-randomly distributed over
environments.
By contrast, genotype X environment interactions
are detected by comparing all genotypes in
several common garden environments; if their
relative performances differ in the different
environments there is a genotype X environment
interaction.

15. Likelihood of genotype X environment interaction
increases with the magnitude of both genetic
and environmental differences.
Thus, it is more likely to be detected in species
with wide geographic, ecological, or altitudinal
ranges.
Further, quantitative traits closely associated with
reproductive fitness appear to be more prone to
genotype X environment interactions than
characters more peripheral to fitness.

16. Quantitative genetic variation has contributions
from the average effects of loci VA, from their
dominance deviations VD, and from interactions
(epistatic) deviations among gene loci VI as:
VG = VA + VD + VI
These are referred to as additive genetic
variance (VA), dominance variance (VD), and
interaction variance (VI).
Each of these has major conservation implications
as follows:

17. VA and especially the ratio VA/VP (heritability)
reflect the adaptive evolutionary potential of the
population for the character under study.
VD reflects susceptibility to inbreeding depression.
VI influences the effects of outbreeding, whether
beneficial or deleterious.

18. VP = VA + VD + VI + VE + 2CovGE
Therefore, VP = VG + VE = 2CovGE
More specifically,
VP = VA + VD + VI + VE + 2CovGE

19. Evolutionary Potential and Heritability
Conservation genetics is concerned with the
evolution of quantitative traits and how their ability
to adapt is affected by reduced population size,
fragmentation, and changes in the environment.
Immediate evolutionary potential of a population is
determined by the heritability which is defined
as the proportion of total phenotypic variation
due to additive genetic variation or h2 = VA/VP.

20. Heritabilities range from 0 to 1.
Heritabilities of 0 are found in highly inbred
populations with no genetic variation.
Heritabilities of 1 are expected for characters with
no environmental variance in an outbred population
if all genetic variance is additive.
Heritabilities are specific to particular populations
living under specific environmental conditions.

21. Heritability and VA are fundamentally measures of
how well quantitative traits are transmitted from
one generation to the next.
Unfortunately, very few heritability estimates
exist for endangered species and there clearly is
need for many more estimates of heritability in
threatened and endangered species.

22. 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.

23. 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.

24. 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.

25. 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

26. 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.

27. 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.

28. Restriction Fragment Length Polymorphism
(RFLP)

29. DNA Fingerprinting

30. 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.

34. Randomly Amplified Polymorphic DNA (RAPD)

35. Microsatellite Repeats:
Tandem repeats of short DNA fragments
Typically bp is length --
gtagacGTGTGTGTGTGTGTGTccatag
catcagCACACACACACACACAggtatc
Number of repeats is highly variable due
to “slippage” during DNA replication.

37. Genotyping with microsatellites
BIBE1
BIBE15
BIBE16
Locus G10C

39. DNA Sequencing

40. 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.

41. 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

42. 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

43. 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.

44. 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

45. 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 = ( )/5 = 0.07

46. 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 = ( ) = 1.67

47. 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.

48. Variable nucleotide positions
Polymorphic sites within mtDNA haplotypes of 144 southwestern black bears
Haplotype
A T T T T A G
B –
C – –
D C C . – G A
E C C – – G A

49. SDC
N = 5 MM
N = 29
BIBE
N = 31
BGWMA
N = 9
SDB
N = 60
SMM
N = 4

50. 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

51. Example: population size = 50, 5 haplotypes.
n pi pi2 n pi pi2 A B C D E
h = 50/49(0.848) = /49(0.8) =

52. 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.

53. 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.

54. Example: 2 populations of size 30, each having
3 haplotypes.
Population A Population B
A F 10
B G 10
C H 10
Haplotype diversity in each population =
What is nucleotide diversity in each population?

55. 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 =
Population 2 D E F
Haplotype D 10 D --
Haplotype E 10 E 8 --
Haplotype F 10 F
Nucleotide Diversity =

56. A B C A B C
D E F D E F
SEQUENCED 478 BP

57. Population 1
pi pj dij ij
A vs. A
A vs. B
A vs. C
B vs. B
B vs. C
B vs. A
C vs. C
C vs. A
C vs. B
 = (30/29) X =

58. YOU SHOULD DO THE
CALCULATIONS FOR
POPULATION #2

59. 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:
n3(2a22 - a4) - 2n2(a3 + 2a2) + n(9a2 + 2) - 6
(n - 1)(n - 2)(n - 3)
PI = 
n = sample size, ai = pji where
pj = frequency of jth allele.