Download Population Genetics Outline Population Genetics Allele Frequency

4/29/2009
Outline
• Population genetics
– Definition
– Modern evolutionary synthesis
– Allele frequency
– Evolutionary forces
– Application of population genetics
– References
Population Genetics
SCBI 113 Essential Biology
Nuttaphon Onparn, PhD.
April 30, 2009
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Population Genetics
Allele Frequency
• Definition
• Definition
– The study of the allele frequency distribution and
changes.
– The number of copies of a particular allele
divided by the number of copies of all alleles at
the locus in a population.
– Changes due to evolutionary forces
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– Allele
Natural selection
Genetic drift
Mutation
Gene flow
• Alternate version of a gene.
– Classical model: 2 alleles per gene (wild-type, mutant)
– Balance model: more than 2 alleles per gene
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Calculation
• Calculating allele frequency
– There are 90 TT, 60Tt and 50tt (200 indv.)
Using numerical gene counts
AA
AA
n(A) = 8
n(a) = 2
n(A) + n(a) = 10
AA
AA
freq(A) = 8/10 = 0.8
freq(a) = 2/10 = 0.2
freq(A) + freq(a) = 1.0
aa
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Using genotype frequencies
n(T) = 2(90) + 60 = 240
freq(TT) = 90/200 = 0.45
n(t) = 2(50) +60 = 160
freq(Tt) = 60/200 = 0.30
n(T) + n(t) = 240 + 160 = 400
freq(tt) = 50/200 = 0.25
freq(T) = 240/400 = 0.6
freq(TT)+freq(Tt)+freq(tt) = 1
freq(t) = 160/400 = 0.4
freq(T) = 0.45 + ½ (0.30) = 0.6
freq(T) + freq(t) = 0.6+0.4 = 1.0
freq(t) = 0.25 + ½ (0.30) = 0.4
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Probability
Conservation of Allele Frequencies
• Probability of picking up gamete from a gene
pool.
• Hardy-Weinberg theorem (1908)
– Frequencies of alleles and genotypes remain constant
from generation to generation.
– Probability of getting gamete A is p.
– Probability of getting gamete a is q.
– Probability of getting gamete A or a is p+q=1
– Probability of getting AA is pxp = p2.
– Probability of getting Aa is pxq or qxp = 2pq.
– Probability of getting aa is qxq = q2.
– Probability of getting AA or Aa or aa is p2+2pq+q2=1.
• Not evolving gene pool.
• Only Mendelian segregation and recombination occur.
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Modern Evolutionary Synthesis
Godfrey Harold Hardy
Wilhelm Weinberg (1862 — 1937)
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Natural Selection
• Modern synthesis of evolution theory
• Natural selection
– The integration of Darwinism, Mendelian
genetics, and mathematics.
– Differential fitness leads to changes in allele
frequencies.
• Population genetics show that Mendelian genetics
was consistent with natural selection and gradual
evolution.
• If indv. with AA is better, then freq(A) will increase
whereas freq(a) will decrease.
From left to right:
•Sir Ronald Aylmer Fisher
•John Burdon Sanderson Haldane
•Sewall Green Wright
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Genetic Drift
• Genetic drift
– Random changes in allele frequencies with
unpredictable direction or magnitude.
• Sampling errors due to small population
• Bottleneck event
• Founder effect
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Mutation
• Mutation
– Any event that changes genetic structure
• Mutation from A to a will lead freq(A) to decrease,
freq(a) to increase.
– Mutation rate is low in animals and plants (1 mutation in
100,000 genes per generation)
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Gene Flow
• Gene flow
– The transfer of alleles from one population to
another population.
• If indv. with AA migrate into a population, freq(A) will
increase.
Diverse colour pattern of these mustangs are the product of past mutations.
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Combination of Forces
• Mutation-selection balance
– Equilibrium frequency of allele will be obtained
when mutation rate equal selection rate.
• Gene flow and selection balance
– Allele frequencies were change due to both gene
flow and natural election.
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Adaptation
• Adaptation
– The process that make an organism becomes
better suited to its habitats.
• Fitness of the organisms will increase.
• Frequencies of alleles in these organisms will increase.
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Speciation
Extinction
• Spciation
• Extinction
– The process that makes new species arises.
– The death of every member of species or group
of taxa.
• Species are isolated genetically, accumulating
different mutations.
• Prior to extinction, allele frequencies might be at
fixation or allele lost (frequencies of 1.0 or 0.0).
– Allele frequencies of species A should be significantly
different from species B.
– Gene flow reduction between species A and species B
– Low genetic diversity population might not be able to adapt.
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Perfect Organisms
• Why could natural selection not create
“perfect organism”?
– Evolution is limited by historical constraints.
– Adaptations are often compromises.
– Chance and natural selection interact.
– Selection can only edit existing variations
Extinction Vortex
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References
• Textbooks
– Campbell, N. A. (2008). Biology. San Francisco,
Pearson Benjamin Cummings.
– Cummings, K. (1997), Concepts of Genetics (the
5th edition). Prentice Hall. USA.
• Internets
– Population Genetics, http://en.wikipedia.org/wiki/Population_genetics
(retrieved April 29, 2009)
– Modern synthesis of evolution,
http://en.wikipedia.org/wiki/Modern_evolutionary_synthesis (retrieved
April 29, 2009)
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