Table 1.
Analysis of polymorphism and selection in Pf38 sequences (85-892 bp) in different P. falciparum populations
| Codon based Z tests (p-value) | McDonald-Kreitman | Allele frequency based tests | |||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| n | Sa | dN | dS | h | Hd | Π (×103) | K (×103) | HKAr | dN = dS | dN > dS | dN < dS | SYN | NONSYN | Tajima's D | Fu & Li F | ||||
| Fixed | Poly | Fixed | Poly | p-value | |||||||||||||||
| Full (85-892bp) | |||||||||||||||||||
| Mugil | 36 | 10 | 9 | 0 | 11 | 0.88 | 3.24 | 18.97 | 0.17 | 0.014* | 0.007* | 1 | 4 | 0 | 9 | 9 | 0.115 | 0.331 | 0.303 |
| Wosera | 23 | 8 | 7 | 0 | 9 | 0.86 | 2.81 | 18.24 | 0.15 | 0.067 | 0.035* | 1 | 4 | 0 | 9 | 7 | 0.248 | 0.151 | -0.397 |
| Gambia | 88 | 13 | 11 | 1 | 36 | 0.95 | 4.04 | 19.09 | 0.21 | 0.015* | 0.007* | 1 | 4 | 1 | 9 | 11 | 0.321 | 0.432 | 1.057 |
| Domain I (85-466bp) | |||||||||||||||||||
| Mugil | 36 | 6 | 6 | 0 | 6 | 0.82 | 5.74 | 18.33 | 0.31 | 0.023* | 0.012* | 1 | 4 | 0 | 1 | 6 | 0.015* | 1.407 | 1.475# |
| Wosera | 23 | 7 | 7 | 0 | 8 | 0.85 | 5.71 | 17.53 | 0.33 | 0.026* | 0.012* | 1 | 4 | 0 | 1 | 7 | 0.010* | 0.475 | 0.108 |
| Gambia | 88 | 9 | 8 | 1 | 23 | 0.90 | 6.69 | 17.85 | 0.37 | 0.021* | 0.009* | 1 | 4 | 1 | 1 | 8 | 0.0229* | 1.106 | 0.908 |
| Domain II (467-892bp) | |||||||||||||||||||
| Mugil | 36 | 4 | 3 | 0 | 5 | 0.35 | 0.99 | 19.55 | 0.05 | 0.101 | 0.052 | 1 | 0 | 0 | 8 | 3 | n/a | -1.3773 | -1.336 |
| Wosera | 23 | 1 | n/a | n/a | 2 | 0.09 | 0.20 | 18.88 | 0.01 | 0.295 | 1 | 0.151 | 0 | 0 | 8 | 0 | n/a | -1.161 | -1.640 |
| Gambia | 88 | 4 | 3 | 0 | 4 | 0.60 | 1.63 | 20.20 | 0.08 | 0.32 | 0.154 | 1 | 0 | 0 | 8 | 3 | n/a | -0.247 | 0.668 |
*significant (p < 0.05) #aproaching significance (p < 0.10) n/a = not applicable
n = number of sequences, S = number of polymorphic sites, dN = nonsynonymous polymorphisms, dS = synonymous polymorphisms, h = haplotypes, Hd = Haplotype diversity, Π = nucleotide diversity, K = interspecific divergence, HKAr = HK, A ratio (Π/K)
aThere is a polymorphism within an incomplete codon at the 3' end of the sequence, preventing determination of NS or Syn, which explains the lower number of dN+dS than S