TABLE 5

Significant differences (P < 0.05) in mutational direction in synonymous sites

Amino acidCodon change (count in CRS)No. of observed changesa to/fromPP
AlaGCG (8) to GCA (80)9/53 × 10−72 × 10−4
GCU (43) to GCC (123)19/82 × 10−60.002
AsnAAU (32) to AAC (132)13/137 × 10−40.042
AspGAU (15) to GAC (51)12/52 × 10−40.004
GlnCAG (8) to CAA (82)7/90.0010.018
GluGAG (24 )to GAA (64)18/104 × 10−40.046
GlyGGG (34) to GGA (67)44/370.005
GGU (24) to GGC (87)11/120.014
IleAUU (124) to AUC (196)38/260.002
LeuCUG (45) to CUA (276)39/591 × 10−70.006
UUG (19) to CUG (45)4/30.099
UUA (73) to CUA (276)28/184 × 10−82 × 10−4
CUU (65) to CUC (167)25/181 × 10−40.032
UUG (19) to UUA (73)14/115 × 10−40.048
LysAAG (10) to AAA (85)6/100.004
MetAUG (40) to AUA (167)31/295 × 10−60.008
PheUUU (77) to UUC (139)24/170.006
ProCCG (7) to CCA (52)14/101 × 10−53 × 10−4
CCU (41) to CCC (119)22/143 × 10−40.008
SerAGU (14) to AGC (39)7/30.02
UCG (7) to UCA (83)5/100.02
UCU (32) to UCC (99)14/79 × 10−50.008
ThrACU (52) to ACC (155)27/166 × 10−70.002
ACG (10) to ACA (134)24/119 × 10−169 × 10−13
TryUGG (11) to UGA (93)18/365 × 10−40.031
TyrUAU (46) to UAC (89)22/170.01
ValGUU (31) to GUC (48)15/60.008
TotalNNG (223) to NNA (1256)229/2374.6 × 10−525.3E-19
NNU (596) to NNC (1444)249/1622.8 × 10−341.8E-27
ND6NNG (62) to NNA (35)14/190.03 inverse
NNU (72) to NNC (6)10/61.1 × 10−3
  • P is a chi-square probability assuming equal rates of codon exchange and estimates the difference from the expected number of changes, given the codon frequencies in the reference mtDNA sequence (Andrews et al. 1999). P′ is binomial probability taking into account additional transitional biases observed over the whole mitochondrial genome favoring transitions G to A over A to G and T to C over C to T by factors of 2.33 and 1.93, per respective nucleotides.

  • a Number of changes corresponds to mutations (including multiple hits per site) inferred in phylogenetic analysis (Figure 1).