Sawyer's Runs Tests

This test looks for evidence of recombinational exchanges within a set of aligned sequences by determining if regions of sequence pairs have more consecutive identical polymorphic sites in common than would be expected by chance (Sawyer, 1989; Drouin et al, 1999).  Pair-wise comparisons of derived sequences containing only silent polymorphic sites (condensed sequences) are made.  Each pair of sequences is partitioned into fragments containing runs of identical sites.   The lengths of all the fragments found between every pair-wise comparison are used to obtain two values: the sum of the squares of condensed fragments (SSCF) and the maximum condensed fragment (MCF).   A gene conversion event tends to increase the values of SSCF and MCF as it results in an identical region within two sequences and may produce an unusually long fragment.  Provided the mutation rate is constant across sequences, SSCF and MCF are not significantly influenced by mutational hot and cold spots.

Alternative measures of the sizes of conserved segments are obtained by performing the tests on all nucleotide sites (uncondensed sequences).  For each pair-wise partition, fragment boundaries are defined by the presence of a discordant silent polymorphic site.  The corresponding uncondensed fragment statistics, SSUF and MUF, are more likely to resolve large conversion events but do not control for mutational hot and cold spots.

This analysis requires both allelic profiles and the allele sequences to be loaded.  Again, individual isolates may be selected or deselected from inclusion using the 'Isolate Selection' dialog reachable from the 'Options' menu.  This analysis also requires that the open reading frames are identified for each locus and the program will prompt for this information.  If necessary, it will take you to the 'Reading Frames' dialog where these can be auto-detected.

To run the analysis, click 'Analysis ... Tests for Recombination ... Sawyer's Runs Tests'.  A dialog will then appear prompting you to select which loci to perform the tests on, the number of trials and whether you wish to analyse either condensed or uncondensed fragments, or both.

sawyer's runs test

The program outputs values for SSCF, MCF, SSUF and MUF with their appropriate P values.  It will also display the number and types of degenerate sites and the length and identity of the four largest fragments at each locus.

Program Output:

Locus SSCF SSCF P value MCF MCF P value SSUF SSUF P value MUF MUF P value
abcZ 93335 0.0000 54 1.0000 7270579 0.0000 433 1.0000
adk 6890 0.0342 15 0.8954 7852119 0.0958 444 0.9514
aroE 50901 0.0032 46 1.0000 15933752 0.6362 489 1.0000

Silent polymorphic sites

Locus Silent polymorphic sites Twofold degenerate sites Threefold degenerate sites Fourfold degenerate sites Mixed degenerate sites
abcZ 54 19 4 13 18
adk 16 8 0 5 3
aroE 46 12 3 20 10

abcZ largest condensed fragments

Length Condensed Fragment Sequences
54 1 - 54 abcZ2 / abcZ21
49 1 - 49 abcZ1 / abcZ20
12 43 - 54 abcZ1 / abcZ16
12 43 - 54 abcZ1 / abcZ12

abcZ largest uncondensed fragments

Length Uncondensed Fragment Sequences
433 1 - 433 abcZ2 / abcZ21
416 1 - 416 abcZ1 / abcZ20
98 1 - 98 abcZ1 / abcZ7
66 368 - 433 abcZ1 / abcZ6