Download Population Genetics and Evolution

Population Genetics and Evolution
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What happens to genes and alleles of genes in populations?
If a new allele appears because of a mutation, does it…
…immediately disappear?
…become a permanent part of the population?
Does it matter if the allele is beneficial or detrimental?
Does it matter if the population is large or small?
Does it matter if there are lots of alleles or only a few?
Does it matter if the genome is large or small?
Two mathematicians helped resolve these questions in the early
1900s
• Godfrey Hardy and Wilhelm Weinberg
• Developed a concept known now as Hardy-Weinberg Equilibrium
Population Genetics and Evolution
• Terminology
• Population – a group of
interbreeding individuals
• Gene pool – the collection
of genes and alleles in a
population
• Each member of the
population carries a portion
of the gene pool
• H-W equilibrium models
allele frequencies in a
population under certain
theoretical conditions
• Obviously, no real
populations follow these
assumptions
Population Genetics and Evolution
• Assume two alleles of a given gene, A1 and A2
• There are three possible genotypes
• A1A1, A2A2, A1A2
• The frequencies of those alleles are
• f(A1) = p, f(A2) = q, with equal frequencies in males and females
• Assuming only the two alleles, p + q = 1
• q=1-p
• Genotype frequencies can be computed as (p + q)2
• f(A1A1) = p2
• f(A1A2) = 2pq
• f(A2A2) = q2
– With p2 + 2pq + q2 = 1
Population Genetics and Evolution
• Assume f(A1) = p = 0.6 and f(A2) = q = 0.4
• The frequency of A1 in male gametes is 0.6
• Same for female gametes
• The frequency of A2 in gametes is 0.4
– p2 + 2pq + q2 = 1
– 0.62 + 2x0.6x0.4 + 0.42 = 1
– 0.36 + 0.48 + 0.16 = 1
• Random mating produces genotype frequencies that are
predictions of allele/genotype frequencies in the population
• Under H-W assumptions, the frequencies will remain constant
over generations
Population Genetics and Evolution
Population Genetics and Evolution
• An example from this class
• http://myweb.ttu.edu/daray/Genetics/humant
raits_BIOL3416_F15_112315.xlsx
• Tongue rolling is a biallelic dominant trait
• RR, Rr = tongue roller
• rr = non-tongue roller
• 237 people surveyed
• 200 people in the survey can roll their tongue
• Calculate the number of homozygotes from each
category and the number of heterozygotes
• Calculate p and q
Population Genetics and Evolution
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An example from this class
Tongue rolling is a biallelic dominant trait
237 people surveyed
200 people in the survey can roll their tongue
Calculate the number of homozygotes from each category and the
number of heterozygotes
• Calculate the p and q
• Easiest way to start  how many are homozygous recessive?
• 37 = # people with genotype rr
• f(rr) = q2 = 37/237 = 0.156
• q therefore = 0.395
• p therefore = 1 – q = 0.605
• p2 = f(RR) = 0.366
• 2pq = f(Rr) = 0.478
• Check your work
• p2 + 2pq + q2 = 0.366 + 0.478 + 0.156 = 1
Population Genetics and Evolution
• If two populations with unique allele frequencies are merged, a new
equilibrium set of frequencies will result
Population Genetics and Evolution
• Note that each of the original populations
has a distinct set of allele frequencies
• Taking a sample of the population and
determining those frequencies in the
sample can be used to identify the
populations
• Ray et al. 2005 – Forensic Science
International
Population Genetics and Evolution
• H-W equilibrium values can be
determined for cases with more than two
alleles
• Just add a factor
• p+q+r=1
• p2 + 2pq + q2 + 2pr + r2 +2qr = 1
• ABO blood type is the classic example
Population Genetics and Evolution
• H-W equilibrium is unattainable in natural
populations
• Natural selection, non-random
mating, migration, non-infinite
population size, mutation, etc.
• We therefore expect H-W values to be at
least slightly different from expected
values
• Statistical tests such as the Χ2 test can be
used to determine if observed frequencies
are significantly different from what is
predicted
• If so, the reason can be investigated
• How do we measure selection?
Population Genetics and Evolution
• How do we measure selection?
• Fitness = the ability of an organism to
survive and reproduce in an environment
• Relative fitness (w) is determined when
we compare the fitness of some
genotypes relative to others
• Selection coefficient (s) = relative
fitness value for a given genotype
• Genotypes with the highest
reproductive success  w = 1
• Genotypes with other fitness values
=1-s
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Directional selection
Population Genetics and Evolution
• Directional selection
• The phenotype associated with the
homozygous genotype has a higher relative
fitness than others
• Acts to increase the frequency of the ‘better’
alleles
• Example – two codominant alleles of gene B
• w(B1B1) = 1
• w(B2B2) = 0.4 s = 0.6
• w(B1B2) = 0.8 s = 0.2
• The relative success at reproduction are
given by w in each case
• Imagine a population where B1 (p = 0.6) and
B2 (q = 0.4)
Population Genetics and Evolution
• Directional selection
• Example – two codominant alleles of gene B
• w(B1B1) = 1; w(B2B2) = 0.4; w(B1B2) = 0.8
• Imagine a population where B1 (p = 0.6) and B2 (q = 0.4)
• What happens after one generation of breeding?
• Note the change in freqencies
Population Genetics and Evolution
• Directional selection
• If selection is strong enough and/or goes on for enough generations, the
favored allele will eventually become fixed in the population and the
unfavored allele will go extinct
Population Genetics and Evolution
• Directional selection
• Detrimental recessive alleles, even lethal ones can remain in populations
for long periods of time, hidden by the dominant alleles
• Cystic fibrosis
• PKU
• Beta-thalassemia
• Tay-Sachs disease
• Blue diaper syndrome?
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https://en.wikipedia.org/wiki/Category:Autosomal_recessive_disorders
Population Genetics and Evolution
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Directional selection
Classic experiment by Cavener and Clegg
Four subpopulations derived from a single Drosophila population
Measured the frequency of two alleles over 50 generations
• Adh – detoxifies alcohol
• AdhF – better at detoxifying alcohol
• Two subpopulations placed in alcohol-rich environment
• Original frequency of AdhF = 0.38
Population Genetics and Evolution
• Balancing selection
• The heterozygous genotype/phenotype has a
higher relative fitness than others
• Results in a balanced polymorphism –
alternate allele frequencies are maintained
• Classic example – sickle-cell trait
• In regions where malaria is prevalant, having
one recessive sickle-cell allele confers an
advantage
Population Genetics and Evolution
• Genetic drift
• Chance fluctuations in allele frequencies that result from random
breeding/inheritance
• Especially influential in small populations
• Original p=0.72, q = 0.28
p=0.77, q=0.23
Population Genetics and Evolution
• Genetic drift
• Chance fluctuations in allele frequencies that result from random
breeding/inheritance
• Especially influential in small populations
• Original p=0.72, q = 0.28
• Post-apocalypse p=0.74, q=0.26
p=0.77, q=0.23
p=0.86, q=0.14
Final Exam
• December 8; 4:30 – 7:30; LH100 (here)
• Rules:
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Bring ID
All mobile devices must be out of site during the exam
• Exam is cumulative
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20 questions each from Drs. Zhang and Rock
40 questions from Dr. Ray
• Dr. Ray’s portion will cover
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Slides associated with chapters 12, 13, 14, 15 and 22
• No review session this time. Sorry