Table 2

Divergence and polymorphism in reference genes assessed by McDonald-Kreitman test, stratified by level of cross-genus conservation

Conservation level

dN/dS

Adjusted dN/dS

Synonymous

Non-synonymous

Chi-squared

Neutrality Index


Identical

0.030

0.034

D

839

101

8.3 × 10-15

5.6

P

52

35

Semi-conserved

0.21

0.24

D

186

174

0.22

1.6

P

12

18

Non-conserved

0.35

0.39

D

90

118

0.38

1.5

P

7

14

Non-aligned

0.55

0.64

D

155

402

0.74

1.1

P

12

35

Total

0.15

0.17

D

1270

795

9.5 × 10-6

2.0

P

83

102


dN/dS ratios refer to P. falciparum /P. reichenowi divergence. Conservation levels were based on BLOSUM62 score in P. falciparum - P. chabaudi alignments; identical (+4 and above), semi-conserved (0 to +3), non-conserved (-4 to -1) and non-aligned. Adjusted dN/dS ratios were derived based on the transition: transversion ratio measured at 4-fold degenerate sites (see Table 4). D = divergent mutations, P = polymorphisms. Chi-squared and Neutrality Index are the outputs of the McDonald-Kreitman test; neutrality index indicates the extent to which the levels of variation depart from the expected in the neutral model with values greater than 1 indicating an excess of polymorphism and hence negative selection.

Gardner et al. BMC Evolutionary Biology 2011 11:257   doi:10.1186/1471-2148-11-257

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