TABLE 2 .
AT-to-GC and GC-to-AT nucleotide substitutions in 29 Salmonella genomes, compared to the predicted state of the common ancestora
| Rate of change to: |
% equilibrium GC | % observed GC | ||
|---|---|---|---|---|
| AT | GC | |||
| Core | ||||
| AT | 46.64 | 54.36 | 54.52 | |
| GC | 39.16 | |||
| SPI-1 | ||||
| AT | 37.77 | 44.47 | 44.65 | |
| GC | 47.17 | |||
| SPI-4 | ||||
| AT | 33.33 | 40.4 | 40.57 | |
| GC | 49.16 | |||
a
Three sets are shown: (i) the concatenated core codon alignments, (ii) the AT-rich SPI-1, and (iii) the AT-rich SPI-4. Maximum composite likelihood estimates were compared for 2,025 single-copy genes, the AT-rich SPI-1 (3009898 to 3046643 in LT2), and SPI-4 (4477857 to 4501818 in LT2). The observed GC is the average GC content of all sequences compared. % equilibrium GC equals the rate of AT-to-GC substitutions divided by the sum of the rate of AT-to-GC substitutions and the rate of GC-to-AT substitutions. Gaps and missing data were excluded from the analysis.