RAPDs and AFLPs

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RAPDs and AFLPs

• Good for distinguishing between populations
• Often used for trait mapping studies because they
  are variable between the populations that are
  crossed

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VNTR variable number tandem repeats

• Non-coding regions
• Several to many copies of the same sequence
• Large amount of variation among individuals in
  the number of copies

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Microsatellites

• Not a tiny orbiting space craft
• Most useful VNTRs
• 2, 3, or 4 base-pair repeats
• A few to 100 tandem copies
• Highly variable
• Many different microsatellite loci (1000s) in any
  species

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Microsatellites

• Design primers to flanking regions

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Microsatellite Gels
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Microsatellites

• Advantages highly variable, fast evolving,
  co-domininant
• Relatively expensive and time consuming to develop

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Microsatellites

• Used for within-population studies not as much
  for between-population studies b/c they evolve
  too fast
• Paternity analysis and other studies of kinship

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Microsatellites

• Questions
• Is the locus represented by the bands at the
  arrow polymorphic?
• If it is polymorphic, how many individuals are
  heterozygous?
• How many individuals are homozygous for the
  short allele?

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Sequencing
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Sequencing

• Often used for phylogenetics (especially
  sequences of mitochondrial genes).
• Also used for studies of molecular evolution
  (e.g., compare rates of synonymous vs.
  non-synonymous substitution)

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Quantifying variation (single locus)

• Allele frequency (gene frequency)
• Genotype frequency

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Example using allozyme (protein) data
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Protein (allozyme) data

• PGM locus, Daphnia obtusa,
• Ojibway Pond (Spitze 1993)
• Genotypes Number
• MM 57
• MS 53
• SS 18
• Q Calculate genotype and allele frequencies

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Genotype Number MM 57
MS 53 SS 18 128

• Genotype freqs
• MM
• MS
• SS
• Allele freqs
• Freq of M
• Freq of S

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Allele frequency

• If there are two alleles at a specific locus, we
  usually designate the frequency of one allele p
  and the frequency of the other as q.
• When there are only two alleles q1-p.
• If there is a third allele, its frequency is
  usually designated as r.

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Microsatellite Data Ridleys sea turtle

• How many alleles?
• Which individuals are homozygous for a short
  allele which for a long allele?
• Genotype and allele frequencies?

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Where does genetic variation come from?

• And why does it persist?

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What is the ultimate source of all genetic
variation?
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Given that that variation arises, what happens to
it over time?
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• A population of light brown deer mice is
  monomorphic for genotype bb at a locus
  controlling coat color. A mutation occurs and a
  single deer mouse is born with dominant melanic
  mutation genotype Bb. Lets start a new
  population with the black female mouse and a
  single light brown male. What will happen to the
  new B allele in this population if mice of all
  colors have equal fitness (e.g., there is no
  selection on color)? Assume no genetic drift.
• What is the initial allele frequency of the B
  allele in the new population (one Bb mouse
  and one bb mouse)?
• What are the genotype frequencies?
• What will be the genotype frequencies in the F1
  offspring of these parents?
• What will be the allele frequencies in the F1
  offspring of these parents?

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Allele frequency in F2?

• Random mating in a population in which
• p freq of b allele 0.75 and
• q freq of B allele 0.25
• Expected freq of bb homozygotes?
• Expected freq of BB homozygotes?
• Expected freq of Bb heterozygotes?

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p2 bb 2pq Bb q2 BB
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Will the allele frequencies change after another
generation of random mating?Will the genotype
frequencies change?
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Hardy-Weinberg Principle

• Allele frequencies remain constant from
  generation to generation unless some outside
  force is acting to change them
• After the first generation of random mating,
  genotype frequencies also remain constant

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Assumptions of H-W

• Mating (union of gametes) is random across the
  entire populationno segregation distortion and
  no subpopulations that differ in allele
  frequencies
• All genotypes have equal viability and fertility
  (no selection)
• Migration into the population can be ignored
• Mutation does not occur, or is so rare it can be
  ignored
• Population is large enough that the allele
  frequencies do not change from generation to
  generation due to chance (random genetic drift).
• Allele frequencies are the same in females and
  males.

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Usefulness of H-W

• If you know the allele frequencies, you can
  predict the genotype frequencies

One implication homozygotes for a rare allele
will be ____________.
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Usefulness of H-W

• If you know the frequency of one of the
  homozygous genotypes, you can estimate allele
  frequencies, and predict the frequencies of the
  other genotypes

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Northern Leopard Frog
Rana pipiens-normal phase burnsi
phase (wild type) Burnsi allele dominant to
normal. In a sample of 2000 frogs 200 were
burnsi, and 1800 were normal. What are the
allele frequencies and expected genotype
frequencies?
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R. pipiens Data
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Why do we care?

• What if you can actually genotype the individuals
  at a locus that controls the color pattern?

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R. pipiens Data, p0.95, q0.05
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Why do we care?

• If we can conclude that the observed genotype
  frequencies are really different from expected,
  what can we infer?

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Review use of HW w/ sex linked genes
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Multiple Alleles ABO blood types

• p freq of A allele
• q freq of B allele
• r freq of O allele
• Expansion of p q r2
• p2 q2 r2 2pq 2pr 2qr

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Calculate allele frequencies and expected
genotype frequencies from the following observed
genotype frequencies

• AA Aa Aa aa aa aa
• 8 38 121 27 252 401

Is the population in H-W equilibrium? Do this
before next class period.
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Summary measures of variation

• Single loci
• Heterozygosity Obs Het/Tot Ind
• Expected Heterozygosity 1-?pi2
• Multiple loci
• Polymorphism proportion loci that are
  polymorphic in a sample

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Grad students

• Read section of lecture notes on
• Measures of variation for DNA sequence data