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POPULATION GENETICS BIO 208
revised 2009
I. ANALYSIS OF PV92 GENOTYPIC AND ALLELIC FREQUENCIES
Go to http://www.dnalc.org
Scroll to the right and click on BIOSERVERS. Then enter.
Select Allele Server
Now, add your data to the BIO20809 database.
 Select Add Data
 CHOOSE BIO20809 from the pull down menu
 Your password is BIO208
 Obtain your number from the instructor
 Fill in your gender and genotype (leave the mother and father descent blank), click OK
Before proceeding, you must wait for the entire class to upload the genotype data.
Go to
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MANAGE GROUPS
Select group type: Classes
Select the correct time period
Select the box to the left to choose BIO20809
View the data by clicking the box and VIEW.
1. Determine the genotype distribution for the class by counting the number of students of each
genotype (++, +-, --). For example, 2 +/+ genotypes in a class of 10 individuals is a
genotypic frequency of 0.2. Fill in below with the frequency of each genotype.
genotype
Number of individuals Genotypic frequency
in class
+/+ individuals
+/- individuals
-/- individuals
2. An allele frequency is a ratio comparing the number of copies of a particular allele in a
population to the total number of alleles for that gene present in that population. Remember,
humans are diploid and have 2 alleles at the PV92 locus.
How many total PV92 alleles are present in the data group (all individuals)? _____________
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3. Use the formula below to calculate the frequency (f) of each allele.
Formula:
f (+ allele) = p =
Total number of + alleles in the class
Total # PV92 alleles in class
= ___________________
Don't forget to add all + alleles from the +/+ homozygotes AND + alleles from heterozygotes.
f (- allele) = p =
Total number of - alleles in the class
Total # PV92 alleles in class
= ___________________
4. The Allele Server will perform a Chi Square analysis on your observed data and the genotype
frequencies predicted from a population in Hardy-Weinberg equilibrium. Remember, the Chi
Square provides a statistical measure of the difference between the two sets (observed and
expected) of data. In general, the higher the Chi Square value, the greater the difference between
observed and expected data sets. The Chi Square will determine if the population in the BIO208
class is in genetic equilibrium.
Select the circle to the right of the BIO 208 sequence. Select ANALYZE to perform the Chi
Square. Read the explanation of the results.
Convert frequencies to numbers of individuals.
a. How many individuals are expected to exhibit the ++ genotype? _____observed? _____
b. How many individuals are expected to exhibit the +- genotype? _____observed? _____
c. How many individuals are expected to exhibit the -- genotype? _____ observed? _____
d. What is the p (probability) value?
_____________
5. A p value <0.05 indicates that the observed frequencies do not approximate those expected IF
the population is in Hardy Weinberg equilibrium. A p value <0.05 indicates that there is
SIGNIFICANT difference between observed and expected data.
If the p value is > 0.05, the null hypothesis is accepted and we conclude that the observed data is
not significantly different from the expected data (i.e. the population is in genetic equilibrium).
Is the BIO 208 class in Hardy-Weinberg equilibrium? Explain. (Reading the explanation on the
screen will assist you).
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II. POPULATION SIMILARITIES AND DIFFERENCES
Go to MANAGE GROUPS. Choose REFERENCE on the pull down menu for group type.
Select 3 groups to examine (check box to the left of the group). The groups you select may be
from the same continent or from different world regions.
1. Record the groups picked in the correct geographical location on the map below.
2. Perform a comparative Chi Square analysis. The Chi Square will analyze how closely related
two groups are – if allele frequency differences between 2 groups are statistically different. Click
the box to the left of 2 of the groups. Make sure the boxes next to the other groups in your
collection are not clicked.
3. Analyze two groups at a time and all combinations. Select the desired groups and click on
COMPARE. For each comparison, look at the pie charts. How do the populations seem to
compare? Record the p-value for each comparison in the grid below. Identify the populations on
the lines provided.
Table of p-values
Names of populations
p-value
population 1: population 2
population 1: population 3
population 2: population 3
4. To interpret the results, you need to understand what the test is looking at. The “null
hypothesis” states that the two groups have the same genotypic frequencies. If the p-value is
<0.05, than the null hypothesis is rejected and we conclude that the two groups are significantly
different. If the p-value is >0.05, we conclude that there is no significant difference between the
two populations examined (or that the test was inconclusive and more data is needed).
Remember, you are formulating hypotheses based on a single genetic location, PV92.
a. Which groups are most similar with respect to the PV92 Alu element genotypic frequencies?
b. Which groups are most dissimilar?
c. Were any of the results surprising or not what you expected? Explain.
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III. Molecular Evolution:
MITOCHONDRIAL DNA TO STUDY RELATEDNESS BETWEEN
POPULATIONS
Modern Human
Neandertal
Homo erectus
chimpanzee
male gorilla
Objectives
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To study the history of Neandertal man (handout)
To utilize the Cold Spring Harbor Sequence Server and Clustal Alignment program
To compare human, Neandertal, and primate mitochondrial DNA sequences
To identify transitions and transversion differences between mtDNA sequences
To formulate ideas and synthesize conclusions on the evolutionary relationships between
primates based on analysis of mt DNA sequence
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DOLAN DNA LEARNING CENTER/COLD SPRING HARBOR http://www.dnalc.org
Scroll to the right and click on BIOSERVERS
1. Select SEQUENCE SERVER. Click on ENTER. Click on MANAGE GROUPS and bring
down the prehistoric DNA sequences under Sequence Sources. These are mitochondrial
DNA sequences obtain via the PCR.
 Select a Neanderthal sequence (ancient human from about 30,000 years ago).
 Go back to sequence sources and click the box to select non-human DNA and find and
select the chimpanzee sequences.
 Now you will select two modern human sequences (do not choose European, the
sequence is too short). There are many others to choose from. Click on VIEW to the right
of the sequence name to select a specific population of humans.
 CLICK OK to move all four sequences into your workbook You now have four
sequences in your workbook:
Neanderthal man (record the name of the specific sequence)
Non-human primate (chimp)
Modern Human 1 (record the specific population you choose)
Modern Human 2 (record the specific population you choose)
 Make sure only two modern human sequences are checked and RUN the CLUSTAL
PROGRAM (click COMPARE).
 Examine the aligned nucleotide sequences for ONLY 200 bases! Pick a group of bases
internal to the ends of the aligned sequences.
a. How many total DNA differences are there between the two groups? (Do not count gaps,
only base changes).
b. Record the specific base changes observed (transition or transversion) in the data table
below.
Example if there is a G to C change. Fill in G->C, TV
Transition = purine for purine or pyrimidine for pyrimidine change.
G<-> A
C<-> T
Transversion =purine for pyrimidine change or visa versa.
G<->C
A<->T,
G<->T
C<-> A
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Base Change/ TS or TV
Base change/ TS or TV
Base change /TS or TV
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c. What percent of the changes are transitions?
_______
transversions?
_______
2. RUN the CLUSTAL alignment program on one modern human and the Neanderthal sequence.
a. How many total DNA differences are there between the two groups? _________
b. Of these, what percent are transitions?_____________ transversions?_____________
c. Do you observe any difference in the ratio of transitions to transversions when comparing 2
modern humans versus comparing a modern human to a Neanderthal?
3. RUN the CLUSTAL alignment program on the same modern human and the chimp sequence.
a. How many total DNA differences are there between the two groups? _________
b. Of these, what percent are transitions?_____________ transversions?_____________
c. Comment on the ratio of transitions to transversions (is the ratio larger or smaller than when
two modern humans or modern human and Neandertal sequences are compared?)
4. Transitions usually predominate between two closely related groups. The substitution of a
purine for purine or pyrimidine for pyrimidine occurs more frequently than transversions.
Groups that are less closely related also exhibit transitions, but have also accumulated
transversions. Do your data support this? Discuss the results of the comparisons. Include:
Human/Human:
Human/Neanderthal:
Human/Chimp:
Conclusion: