Hypothesis Testing

Goodness of Fit Chi Square

By Rhondene Wint
CAPE BIOLOGY

Chi-Square Test
A fundamental problem is genetics is determining

whether the experimentally determined data fits

the results expected from theory (i.e. Mendels
laws as expressed in the Punnett square).

Problem
A geneticist is researching if a certain gene in a group

of offspring follows the Mendelian pattern of

inheritance, when two heterozygote parents were
crossed for the presence the dominant phenotype (A)
and the recessive phenotype (a).
Table 4. Results of a monohybrid cross between two heterozygotes for the 'a' gene.

A
a
Totals

A
10
33
43

a
42
15
57

Totals
52
48
100

Hypothesis Testing
Hypothesis testing is a systematic way to test claims

or ideas about a group or population based on a

sample
Null hypothesis HO: A claim that there is no

difference between an observation and an

expected/theoretical claim
Alternative Hypothesis Ha: A claim that the
observation and expected claims are different

How To: Hypothesis Testing

Step 1: State the hypotheses.

Step 2: Set the criteria for a decision.

Step 3: Compute the test statistic.
Step 4: Make a decision

Step 1:
State the Null Hypothesis:
The gene Aa is inherited according to the Mendelian

heterozygote ratio 3 dominant:1 recessive

State the alternative hypothesis:
The gene Aa is not inherited according the

Mendelian heterozygote ratio of 3 dominant:1

recessive

Confidence Limit
To set the criteria for a decision, we state the

level of significance for a test.

The level we set, called the alpha level or p
value.
The p value is the probability of rejecting the null,
when it is actually true

Goodness of Fit Chi Square

How "close" are the observed values to

those which would be expected under

the fitted- ideal model?
This test allows us to compare a
collection of categorical data with some
theoretical expected distribution. This
test is often used in genetics to compare
the results of a cross with the theoretical
distribution based on genetic theory.

Obser Expect (O (O E)2

ved
ed
E)

(O E)2/ E

A- 85
typ
e

75

10

100

1.33

a- 15
typ
e

25

10

100

4.0

Tota 100 100

5.33

Critical Chi-Square
Critical values for chi-square are found on

tables, sorted by degrees of freedom and

probability levels. Be sure to use p = 0.05.
If your calculated chi-square value is greater
than the critical value from the table, you
reject the null hypothesis.
If your chi-square value is less than the critical
value, you fail to reject the null hypothesis
(that is, you accept that your genetic theory
about the expected ratio is correct).

 Teach by organising data into tables

Interpreting Chi square confidence limit degrees

of freedom
D.f (# of row 1) x (# columns-1)
when the computed x2 statistic exceeds the
critical value in the table for a 0.05 probability
level, then we can reject the null hypothesis of
equal distributions
Since our x2 statistic (3.418) did not exceed the
critical value for 0.05 probability level (3.841)

Chi-Square Table

 3.A genetics engineer was attempting

to cross a tiger and a cheetah. She

predicted a phenotypic outcome of the
traits she was observing to be in the
following ratio 4 stripes only: 3 spots
only: 9 both stripes and spots. When
the cross was performed and she
counted the individuals she found 50
with stripes only, 41 with spots only
and 85 with both. According to the
Chi-square test, did she get the
predicted outcome?