Lab 11 :Test of Neutrality and Evidence for Selection

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Lab 11 Test of Neutrality and Evidence for
Selection
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• Goals
• Calculate the expected number of different
  alleles for a given locus in a population.
• Detect departure from neutrality using
• Ewens- Watterson test.
• Tajimas D test.
• HKA test and
• Synonymous and Nonsynonymous nucleotide
  substitution test

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Infinite Alleles Model (IAM)

• Each mutation produces a new allele
• At equilibrium
• number of alleles constant
• shape of allele frequency distribution constant
• frequency of any given allele not constant
• lost alleles replaced by new mutations

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Ewens -Watterson test
Expected homozygosity under mutation-drift
equilibrium and assuming IAM
P-value lt 0.025 Too even -gt Balancing selection
or recent bottleneck P-value gt 0.975 Too uneven
-gt Directional selection or population growth
Expected homozygosity under HWE
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• Problem 1. Estimates of the long-term effective
  population size of human populations vary widely,
  ranging from as low as 3,000 to as high as
  100,000. To estimate allele frequencies for a
  forensic identification study, you are genotyping
  individuals selected at random from a population
  with an estimated Ne 7,500. You are using one
  allozyme and one microsatellite marker, with
  estimated mutation rates ? 0.7?10-6 and ?
  9.6?10-3, respectively.
• How many different alleles do you expect to find
  for each marker in a sample of
• 5 people?
• 20 people?
• List assumptions that need to be made for these
  calculations to be valid. Discuss which of these
  assumptions (if any) seem reasonable.

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Tajimas D

• Under neutrality, we expect the following
• Two different ways of estimating the same
  parameter
• Deviation of these two indicates deviation from
  neutral expectations
• Assumes neutral alleles and constant population
  size

(Based on number of polymorphic sites)
(Based on nucleotide diversity)
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Tajimas D test
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Under neutrality
d ?? - ?S 0
D
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plantsciences.ucdavis.edu
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• Problem 2. File aspen_phy.arp (which is already
  in Arlequin format) contains sequence data from
  exon 1 of the phytochrome B2 (phyB2) gene of 24
  aspen (Populus tremula) trees sampled along a
  wide latitudinal gradient in Europe. Use Arlequin
  to
• Determine the number of polymorphic sites (S) and
  calculate the nucleotide diversity (?) based on
  these sequences.
• Perform the tests of neutrality developed by
  Ewens-Watterson and Tajima and interpret the
  results.
• Provide a statistical and a biological
  interpretation of the results from the two
  neutrality tests. Is selection the only possible
  reason for significant discrepancies between ??
  and ?S?
• Describe at least one other scenario in which a
  force other than selection would make D
  significantly different from 0.
• Include only a summary of the Arlequin output in
  your report (i.e., values of S and ?, as well as
  test statistics and p-values for the two
  neutrality tests). Do not include the entire
  output.