Chapter 2 Genetic diversity
Molecular markers > asses genetic diversity: Know how to calculate allelic diversity,
He,observed / He,expected;
Genetic diversity is required for populations to adapt to environmental change. Large
populations of naturally outbreeding species usually have extensive genetic diversity, but it
is typically reduced in endangered species.
Importance of genetic diversity
● Environmental change is a continuous process and genetic diversity is required
for populations to evolve to adapt to such change
● Loss of genetic diversity is usually associated with inbreeding and overall
reduction in reproduction and survival (fitness)
What is genetic diveristy
Is the variety of alleles and genotypes present in the group under study (population,
species or group species)
Genes are sequences of nucleotides in a particular region (locus) of a DNA molecule.
Genetic diversity represent slightly different sequences. And DNA sequence variation may
expresses in amino acid sequence difference > different functional biochemical, morphology
or behavior)
The genetic composition of a population is usually described in terms of allele frequencies,
number alleles and heterozygosity. (TABLE 2.1 PAG. 14)
Measuring genetic diversity
Molecular techniques such as allozyme electrophoresis measure genetic diversity at
individual loci.
Genotype frequencies > the proportion of the total sample of that type genotype frequency
Allele frequencies > p and q letters (relative frequencies for the two alleles at the locus)
p= (2*FF) +FS / 2 * total and p+q = 1.0
Observed heterozygosite (H0) is simply the proportion of the samples individuals that are
heterozygotes. When we are comparing the extent of genetic diversity among populations
or species use average heterozygote (H).
Allelic diversity (A)
Is the average number of alleles per locus it is used to characterize genetic diversity
Hardy weinberg equilibrium
In large, random mating populations, allele and genotype frequencies at an autosomal locus
attain equilibrium after one generation when there are no perturbing forces (no mutation,
migration or selection)
A1 A1 = p * p = P2
A2 A2 = q * q = q2
,A1 A2 = 2 * p * q (A2 A1)
P2 + 2pq + q2 = (p+q)2 = 1.0
Hardy Weinberg equilibrium is expected for all loci, expect for those located on sex
chromosomes.
GRAPG 2.1 PAG. 17
Heterozygote cannot be greater than 0.5
Assumption:
- A large population size
- A closed population (no migration)
- No mutation
- Normal mendeliam segregation of alleles
- Equal fertility of parent genotypes
- Random union gametes
- Equal fertilizing capacity of gametes
- Equal survival of all genotpyes
Example calculation:
- First calculate allel frequencies with used of observerd numbers (O)
- Than the HW equilibrium
- Expected numbers (E)= expected frequencies * total)
Deviations from hardy weinberg equilibrium
Provides null hypothesis that allows us to detect of the population has non random
mating, migration or selection
Expected heterozygosity
He= 2pq (gene diversity).
When there a more than two allels it is simpler to calcuate expected hterozygosity as
one minus the sum of the squared allele frequencies
He= 1- SOM pi2
Estimating the frequency of recessive allele
> aa= q2= wortel van q2 = a
Extent of genetic diversity
Large populations of naturally outbreeding species usually have extensive genetic diversity
Example dog breeds > variation due to non genetic variation due to environment and
genetic variation due to alleles and heterozygosity at many loci.
Genetic diversity can be measured at a number of difference levels > measurable
characters > quatitative variation
Quantitative variation
The characters of most importance in conservation are those that determine the health and
reproductive fitness. All qualitative characters in outbreeding species exhibit genetic
diversity (reproductive, growth rate, chemical composition behaviour)
Wil be determined by many loci (quantitative trait loci > QTL)
, Deleterious alleles
All outbred populations contain a load of rare deleterious alleles that can be exposed by
inbreeding. These alleles reduce viability and reproduction fitness when they become
homozygous through inbreeding. D. Alleles are constantly generated by mutation and
removed by selection.
Proteins
electrophoresis is been used to obtain information on genetic diversity, which separates
molecules according to their net change and molecular mass in an electrical potential
gradient. (underestimated > 30 percent of changes in DNA leads to charge change.)
Average heterozygosity within species (H) is lower in vertebrate than invertebrate or plants
possible due to lower population sizes in vertebrate.
DNA
Dna will be collected to measure genetic diversity
PCR > polymerase chain reaction > specific DNA sequence
A major advantage of measuring DNA variation, as opposed to protein variation is that
sampling can often be taken non invasively and genotypes identified following DNA
amplification (veel makkelijker dan via de protein dinges )
To amplify a DNA segment of interest specific invariant sequences on either side of the
segment of interest must be identified to design primers for the pcr reaction. The segment
to be amplified is defined by and lies between the primers. Copies of these sequences are
synthensized (oligonucleotides) and used in pcr reaction. Primer sequences can often be
deduced from publishes sequence information for mitochondrial DNA (mtDNA)
Microsatellite (variable number short tandem repeats) have become the marker of choice
for population studies. Advantage: are highly variable, individual genotypes can be directly
inferred and individuals can be typed following non invasive sampling. Disadvantage: the
primers must be developed anew for eacht species, although primers from closely related
species will other work in both species.
mtDNA
Contain small circular DNA molecules that are maternally inherited in most species.
Sequencing of mtDNA has advantage over other techniques that it can be done following
non invasive sampling, that mtDNA has high mutation rate and is highly variable and that it
can be used to specifically trace female lines of decent or migration patterns. Disadvantage:
it traces only a single maternally inherited unit.
Levels of genetic diversity in DNA
The highest levels of genetic diversity in DNA are typically found in sequences with little
functional significance. These variations either do not code for functional products, or
substitutions do not change the function of the molecule. There fore selection does not act
against such changes.
The lowest genetic diversity is found in de functionally regio of molecules. Much DNA in an
organism does not code for a function
Molecular markers > asses genetic diversity: Know how to calculate allelic diversity,
He,observed / He,expected;
Genetic diversity is required for populations to adapt to environmental change. Large
populations of naturally outbreeding species usually have extensive genetic diversity, but it
is typically reduced in endangered species.
Importance of genetic diversity
● Environmental change is a continuous process and genetic diversity is required
for populations to evolve to adapt to such change
● Loss of genetic diversity is usually associated with inbreeding and overall
reduction in reproduction and survival (fitness)
What is genetic diveristy
Is the variety of alleles and genotypes present in the group under study (population,
species or group species)
Genes are sequences of nucleotides in a particular region (locus) of a DNA molecule.
Genetic diversity represent slightly different sequences. And DNA sequence variation may
expresses in amino acid sequence difference > different functional biochemical, morphology
or behavior)
The genetic composition of a population is usually described in terms of allele frequencies,
number alleles and heterozygosity. (TABLE 2.1 PAG. 14)
Measuring genetic diversity
Molecular techniques such as allozyme electrophoresis measure genetic diversity at
individual loci.
Genotype frequencies > the proportion of the total sample of that type genotype frequency
Allele frequencies > p and q letters (relative frequencies for the two alleles at the locus)
p= (2*FF) +FS / 2 * total and p+q = 1.0
Observed heterozygosite (H0) is simply the proportion of the samples individuals that are
heterozygotes. When we are comparing the extent of genetic diversity among populations
or species use average heterozygote (H).
Allelic diversity (A)
Is the average number of alleles per locus it is used to characterize genetic diversity
Hardy weinberg equilibrium
In large, random mating populations, allele and genotype frequencies at an autosomal locus
attain equilibrium after one generation when there are no perturbing forces (no mutation,
migration or selection)
A1 A1 = p * p = P2
A2 A2 = q * q = q2
,A1 A2 = 2 * p * q (A2 A1)
P2 + 2pq + q2 = (p+q)2 = 1.0
Hardy Weinberg equilibrium is expected for all loci, expect for those located on sex
chromosomes.
GRAPG 2.1 PAG. 17
Heterozygote cannot be greater than 0.5
Assumption:
- A large population size
- A closed population (no migration)
- No mutation
- Normal mendeliam segregation of alleles
- Equal fertility of parent genotypes
- Random union gametes
- Equal fertilizing capacity of gametes
- Equal survival of all genotpyes
Example calculation:
- First calculate allel frequencies with used of observerd numbers (O)
- Than the HW equilibrium
- Expected numbers (E)= expected frequencies * total)
Deviations from hardy weinberg equilibrium
Provides null hypothesis that allows us to detect of the population has non random
mating, migration or selection
Expected heterozygosity
He= 2pq (gene diversity).
When there a more than two allels it is simpler to calcuate expected hterozygosity as
one minus the sum of the squared allele frequencies
He= 1- SOM pi2
Estimating the frequency of recessive allele
> aa= q2= wortel van q2 = a
Extent of genetic diversity
Large populations of naturally outbreeding species usually have extensive genetic diversity
Example dog breeds > variation due to non genetic variation due to environment and
genetic variation due to alleles and heterozygosity at many loci.
Genetic diversity can be measured at a number of difference levels > measurable
characters > quatitative variation
Quantitative variation
The characters of most importance in conservation are those that determine the health and
reproductive fitness. All qualitative characters in outbreeding species exhibit genetic
diversity (reproductive, growth rate, chemical composition behaviour)
Wil be determined by many loci (quantitative trait loci > QTL)
, Deleterious alleles
All outbred populations contain a load of rare deleterious alleles that can be exposed by
inbreeding. These alleles reduce viability and reproduction fitness when they become
homozygous through inbreeding. D. Alleles are constantly generated by mutation and
removed by selection.
Proteins
electrophoresis is been used to obtain information on genetic diversity, which separates
molecules according to their net change and molecular mass in an electrical potential
gradient. (underestimated > 30 percent of changes in DNA leads to charge change.)
Average heterozygosity within species (H) is lower in vertebrate than invertebrate or plants
possible due to lower population sizes in vertebrate.
DNA
Dna will be collected to measure genetic diversity
PCR > polymerase chain reaction > specific DNA sequence
A major advantage of measuring DNA variation, as opposed to protein variation is that
sampling can often be taken non invasively and genotypes identified following DNA
amplification (veel makkelijker dan via de protein dinges )
To amplify a DNA segment of interest specific invariant sequences on either side of the
segment of interest must be identified to design primers for the pcr reaction. The segment
to be amplified is defined by and lies between the primers. Copies of these sequences are
synthensized (oligonucleotides) and used in pcr reaction. Primer sequences can often be
deduced from publishes sequence information for mitochondrial DNA (mtDNA)
Microsatellite (variable number short tandem repeats) have become the marker of choice
for population studies. Advantage: are highly variable, individual genotypes can be directly
inferred and individuals can be typed following non invasive sampling. Disadvantage: the
primers must be developed anew for eacht species, although primers from closely related
species will other work in both species.
mtDNA
Contain small circular DNA molecules that are maternally inherited in most species.
Sequencing of mtDNA has advantage over other techniques that it can be done following
non invasive sampling, that mtDNA has high mutation rate and is highly variable and that it
can be used to specifically trace female lines of decent or migration patterns. Disadvantage:
it traces only a single maternally inherited unit.
Levels of genetic diversity in DNA
The highest levels of genetic diversity in DNA are typically found in sequences with little
functional significance. These variations either do not code for functional products, or
substitutions do not change the function of the molecule. There fore selection does not act
against such changes.
The lowest genetic diversity is found in de functionally regio of molecules. Much DNA in an
organism does not code for a function
