For endangered species, quantitative variation for

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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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
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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.
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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.
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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.
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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.
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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
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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.
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Therefore, VP VG VE 2CovGE More
specifically, VP VA VD VI VE 2CovGE
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Evolutionary Potential and Heritability Conservat
ion 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.
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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.
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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.
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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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