Transcript Lab9 :Test of Neutrality and Evidence for Selection

Lab 11 :Test of
Neutrality and Evidence
for Selection
Goals:
1. Calculate the expected number of different
alleles for a given locus in a population.
2. Detect departure from neutrality using:
1. Ewens- Watterson test.
2. Tajima’s D test.
3. HKA test and
4. Synonymous and Nonsynonymous
nucleotide substitution test
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
Ewens -Watterson test
E (k ) 
2 N 1




   i  1    1    2  ...    2 N  1
i 0
Where,  4 Neu
Expected homozygosity under mutation-drift equilibrium and assuming IAM:
fe 
1
4N e   1
Expected homozygosity under HWE:
f HW   p
2
i
P-value < 0.025: Too even -> Balancing
selection or recent bottleneck
P-value > 0.975: Too uneven -> Directional
selection or population growth
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:
a)5 people?
b)20 people?
c)List assumptions that need to be made for these calculations to be
valid. Discuss which of these assumptions (if any) seem reasonable.
Tajima’s D
• Under neutrality, we expect the following:
(Based on
nucleotide
diversity)
  m
S 
S
n 1
1
i i
(Based on
number of
polymorphic
sites)
– Two different ways of estimating the same parameter
– Deviation of these two indicates deviation from neutral
expectations
– Assumes neutral alleles and constant population size
Tajima’s D test
.
Under neutrality:
d =  − S = 0
D=
d
SE(d )
D  0  Purifying/positiveselectionor populationgrowth
D  0  Balancingselectionor recentbottleneck
plantsciences.ucdavis.edu
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:
a) Determine the number of polymorphic sites (S) and calculate the nucleotide diversity ()
based on these sequences.
b) Perform the tests of neutrality developed by Ewens-Watterson and Tajima and interpret the
results.
c) 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?
d) 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.