Table 2

Analysis of sequences from various species with the Homoplasy Test and by compatibility matrices

Species, geneNo. of sequencesSites Homoplasy Test Similarity
syn.var.inf.SeobshH
H. pylori
flaA
 Canada3314459401051240.80.44
 S. Africa221564934114550.550.52
flaB
 Germany5411061471102610.830.35
 S. Africa221125038112660.410.38
vacA
 Canada33111412992830.930.42
 S. Africa221244431103360.460.68
D. melanogaster
Adh15253161221040.160.81
Amy10487262340490.270.72
 EST6135282814438100.50.5
white15597272524000610.620.53
geom. mean: 0.340.63
E. coli
putP1248210064400500.390.72
icd173856545320450.410.63
mdh202793325232110.240.86
trpC274196345348230.120.75
geom. mean: 0.260.74
N. meningitidis
abcZ151345737134290.240.78
pdhC241466156146730.340.63
pilA361434942119700.350.51
serC291354326112470.560.43
geom. mean (11 genes): 0.34 0.57
  • syn., all polymorphic first and third codon position sites plus all uniform third codon position sites; var., variable sites; and inf., informative sites. Se, effective site number; obsh, the observed number of homoplasies; and H, homoplasy ratio. Similarity, mean neighborhood similarity for all pairs of informative sites; geom. mean, geometric mean. The number of sites for the white locus consisted of all sites sequenced since most of the locus consists of untranslated introns. The four genes shown for N. meningitidis are those with the lowest and highest H values plus two genes with intermediate values. Data for the other seven genes is available on request from the authors.