Genetic Diversity

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Genetic Diversity

• Eric Anderson
• Wildlife 458/658 Presentation

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Genetic Diversity

• I. Overview
• II. Genetics primer
• III. Measuring genetic diversity
• IV. Values of heterozygosity
• V. Processes that erode genetic diversity
• VI. Applications

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Genetic Diversity - an example
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Genetic Diversity

• All are the same speciesBrassica oleracea !
• GENETIC DIVERSITY IS THE FOUNDATION OF
  BIODIVERSITY
• Without genetic diversity and variation -
  adaptation and evolution cannot occur.

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Genetic Primer

• CHROMOSOMES - consist of long, coiled strands of
  DNA (double helix, coiled ladder)
• GENES - informational units of DNA molecule/
  coded for a specific protein to produce one of
  many attributes of a species

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Genetic Primer

• GENES
• composed of several hundred nucleotides
• position of gene on chromosome is known as locus
  (chromosomes of bacteria contain 1,000 loci,
  fungi about 10,000, mammals about 100,000 and
  700,000 for many flowering plants)
• genes occupying the same locus on a pair of
  chromosomes are called alleles (one allele on
  each chromosome)

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Genetic Primer

• RECOMBINATION - major source of variation
• 1N - haploid - gametes
• 2N - diploid - joined gamete cells - zygote (does
  not result in change in genetic information, but
  provides for different combinations)
• Largest source of variation

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Genetic Primer

• Three possible combination of alleles
• AA Aa aa
• When alleles are the same, called homozygous
• When alleles are different, called heterozygous

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Genetic Diversity - measures

• Hardy-Weinberg equilibrium
• p2 2pq q 2 1
• the equation tells you the approximate
  propor-tions of the population that are
  homozygous AA (p2), homozygous aa (q2), and
  heterozygous Aa (2pq). If the gene frequencies
  deviate signifi-cantly from Hardy Weinberg
  equilibrium, then evolution (natural selection)
  is occurring

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Genetic Diversity - measures

• 5 basic methods to determine which alleles are
  present at a given locus. All techniques use
  electrophoresis
• Protein electrophoresis indirect, but commonly
  done
• Restriction Fragment Length Polymorphism (RFLP)
• Random Amplification of Polymorphic DNA (RAPDs)
• Simple Sequence Repeat (SSR) polymorphisms
• DNA sequencing (fingerprinting)

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Genetic Diversity - Indices to genetic diversity

• Distribution of 2 alleles, MDH-1X and MDH-1Y,
  among 5 bison

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Genetic Diversity - Indices to genetic diversity

• There are 2 basic indices to genetic diversity
• POLYMORPHISM proportion or percentage of genes
  that are polymorphic
• - if freq. of most common allele is less than 95
• - if 23 out of 24 genes sampled had an allelic
  frequency of lt 95 for a single allele, P1/24
  4.2

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Genetic Diversity - Indices to genetic diversity

• HETEROZYGOSITY percentage of genes at which the
  average individual is heterozygous
• if 2 out of 5 bison were heterozygous at the
  MDH-1 locus (but not polymorphic at the other 23
  loci), so heterozygosity is 40 for this gene.
  Heterozygosity is 0.4/24 across all 24 genes
  1.7

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Genetic Diversity - practicing measures
1. What are the frequencies of alleles for each
locus? 2. What are the frequencies for
genotypes for each locus? 3. What is the level
of poly-morphism for this population? 4. What
is the average level of heterozygosity for this
pop.? 5. If this pop. is in Hardy-Wein-berg
equilibrium (locus 1) what are the gene
frequencies?

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Genetic Diversity - practicing measures

• 1. A0.5 a0.5
• B0.9 b0.1
• C1.0 c0.0
• 2. AA0.2 aa0.2 Aa0.6
• BB0.8 bb0.0 Bb0.2
• CC1.0
• 3. 2/3 67 polymorphism
• 4. (0.60.2)/3 27average
  heterozygosity
• 5. AA0.25 aa0.25 Aa0.5

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Genetic Diversity - measures

• What are normal levels of heterozygosity?
• Plants - 7
• Vertebrates - 5
• Invertebrates - 11

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Genetic Diversity The value of heterozygosity

• LOSS of EVOLUTIONARY POTENTIAL - Fundamental
  Theorem of Natural Selection - rate of
  evolutionary change in a population is
  proportional to the amount of genetic diversity
  available
• LOSS OF FITNESS - heterosis - hybrid vigor -
  fitness is enhanced by heterozygosity and
  diminished by homozygosity
• - heterozygous animals tend to be more
  resistant to disease, grow faster, survive longer
  than homozygous individuals

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Genetic Diversity Heterosis
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Genetic Diversity Heterosis
Theoretically
Remember fitness is a measure of lifetime
reproductive success
Fitness
Heterozygosity
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Genetic Diversity The value of heterozygosity

• LOSS of EVOLUTIONARY POTENTIAL - Fundamental
  Theorem of Natural Selection - rate of
  evolutionary change in a population is
  proportional to the amount of genetic diversity
  available
• LOSS OF FITNESS - heterosis - hybrid vigor -
  fitness is enhanced by heterozygosity and
  diminished by homozygosity
• - heterozygous animals tend to be more
  resistant to disease, grow faster, survive longer
  than homozygous individuals
• EXPRESSION OF DELETERIOUS RECESSIVE GENES -

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Genetic Diversity Heterozygositys bottom
line

• SURVIVAL IS POSSIBLE WITHOUT HETEROZYGOSITY,
• BUT THE EXTINCTION PROBABILITY IS HIGH !

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Genetic Diversity
CONCEPT OF NET EFFECTIVE POPULATION

• NET EFFECTIVE POPULATION - not censused N, but
• those genetically unique individuals contributing
  
• offspring to future generations.
• - only net effective population is important in
  loss/retention of heterozygosity

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Genetic Diversity
CONCEPT OF NET EFFECTIVE POPULATION

• Ne N if all individuals in population have
  equal probability of being parents of any
  individual of the next generation (requires
  panmixia, no overlapping generations, closed pop,
  etc.), but usually
• Ne usually lt Nbreeding
• because skewed sex ratios, some non-breeders,
  some degree of inbreeding, variation in progeny
  survival

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Genetic Diversity

• EXAMPLE N100, 90m, 10f,
• polygynous -
• Ne 49010/9010 36
• monogomous
• Ne 41010/1010 20
• Ne roughly 25 of N (for mammals)
• EXAMPLE
• Ne 436 -2/42 142/6 23.6

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Genetic Diversity Processes that erode
heterozygosity

• Founder effect - propagules starting a new
  population contain fewer genes that the mother
  population, hence limited genetic diversity
• Genetic drift - random changes in gene frequency
  that can lead to loss of genetic variation
• the amount of heterozygosity lost depends on pop.
  size
• a few generations of genetic drift at low
  populations is very erosive of genetic variation

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Genetic Diversity Genetic drift
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Genetic Diversity Genetic drift
Genetic drift
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Genetic Diversity Genetic drift
Coin toss example
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Genetic Diversity Processes that erode
heterozygosity

• Founder effect - propagules starting a new
  population contain fewer genes that the mother
  population, hence limited genetic diversity
• Genetic drift - random changes in gene frequency
  that can lead to loss of genetic variation
• Bottlenecks - dramatic reduction in population
  size during a short period of time (single
  generation event)

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Genetic Diversity Bottlenecks

• IMPACTS -
• a. loss of heterozygosity is not severe
• b. loss of alleles at low freq. is serious
• c. genetic variation lost depends on how fast
  population grows and size of bottleneck
  population (if prolonged, genetic drift occurs) -

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Genetic Diversity Bottlenecks

• Affected by pop. size and by length of time
  population is small

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Genetic Diversity Bottlenecks

• Classic study by Wildt
• 55 were homozygous at 17 loci, due to
  bottleneck in past (10,000 YBP)
• low libido
• abnormal sperm (only have 10 of sperm count of
  other felids 70 of sperm are abnormal)
• skin grafts (14 of 14 accepted)

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Genetic Diversity Bottlenecks

• PROBLEMSsusceptible to epizootics
• captive pop. in Oregon saw outbreak of usually
  non-fatal FIP (feline infectious peritonitis)
• killed 29 of 42 cheetahs.
• Pattern repeated for other species

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Genetic Diversity Bottlenecks
EXCEPTIONS Northern elephant seals
No genetic variation at 24 loci, but doing fine
(caused by over-exploitation in late 1800's -
down to 20 individuals by 1890 -now gt100,000)
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Genetic Diversity Processes that erode
heterozygosity

• Founder effect - propagules starting a new
  population contain fewer genes that the mother
  population, hence limited genetic diversity
• Genetic drift - random changes in gene frequency
  that can lead to loss of genetic variation
• Bottlenecks - dramatic reduction in population
  size during a short period of time (single
  generation event)
• Inbreeding/Outbreeding depression - always
  reduces fitness in animals, generally effects
  reproductive rates

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Genetic Diversity Inbreeding/Outbreeding

• Inbreeding mating of individuals related by
  common ancestry
• Inbreeding depression reduction in fecundity,
  offspring size, growth, survivorship, physical
  deformities due to
• Dominance hypothesis - expression of more
  deleterious recessive alleles
• Overdominance hypothesis - loss of heterozygosity
  and fitness advantages

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Genetic Diversity Processes that erode
heterozygosity
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Genetic Diversity Measuring inbreeding
depression

• ? F 1/2Ne rate of loss of heterozygosity per
  generation
• ? F 1-(1-(1/2Ne))t rate of loss of
  heterozygosity over time
• where t of generations involved

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Genetic Diversity Outbreeding depression

• When genetic hybrids have reduced survival
  and/or reproductive rates
• coadaptation
• local adaptation

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General Rules of Conservation Genetics

• Max. tolerable rate of inbreeding is 1,
  therefore
• Ne for short term viability is 50
• Ne for long term viability is 500
• General rule of thumb captive pops. should
  retain 90 of original genetic variation over 200
  years

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The BIG Picture

• Genetic deterioration may be only 1 of many
  perils of a small population and in most cases is
  inconsequential relative to the other factors
  that threaten small populations

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Genetic Diversity - DNA sequencing
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Genetic Diversity - measures