Maximum Chi-squared Test

The maximum chi-squared test is used to identify potential recombination events between two sequences or between two sequences and a putative derived sequence.  The test compares the distribution of polymorphic sites along such sequences with those expected to occur by chance (Maynard-Smith, 1992).

The test looks at every position along aligned sequences and creates a 2x2 matrix, containing the number of differences to the left and to the right of the current position.   When comparing just two sequences, one row of the matrix consists of the proportion of differences and the other contains the proportion of identities.   When comparing two parental sequences and a derived sequence, the matrix rows contain the proportion of differences between each parental sequence and the derived sequence.  The value of chi-squared is determined for this matrix.  The position at which the maximum value of chi-squared is obtained is identified as a putative recombination point.

To test whether this putative recombination point is significant, trials are run where random sequence pairs of the same length and the same number of polymorphic sites are created.  The significance level is determined as the proportion of trial pairs with greater max chi squared values than the observed data.

This analysis only uses sequence data and so only requires the allele sequences to be loaded.  To run the analysis, click 'Analysis ... Tests for Recombination ... Maximum Chi-Squared'.

max chi squared test

When the test is selected, a dialog box is displayed with which you select whether the test is for two sequences or two sequences and a derived sequence, the number of trials to perform to test the significance level and the sequences to be used.  You may also select a nucleotide range.

Program Output

Locus fumC, nucleotide range 1 - 465
Alleles fumC39 and fumC40
Possible recombination site after nucleotide 9
Max Chi Squared: 0.1176
Significance value, P = 0.013