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Table 2 Lineage-specific substitutions at synonymous (S) and non-synonymous (NS) sites, preferred and unpreferred codons (UP and PU) and A/T and mutations (WS and SW).

From: Molecular evolution of synonymous codon usage in Populus

Species S NS PU UP G a d UP-PU SW WS G b d WS-SW
Pd 292 203 72 102 5.17* 0.172 89 75 1.20 0.085
Pe 561 392 201 181 1.05 -0.052 162 152 0.32 0.032
Pn 282 212 87 84 0.05 -0.018 87 87 0.0 0.000
Pta 548 386 123 227 30.9*** 0.297 120 137 1.12 0.066
Ptr 202 120 73 64 0.59 -0.066 36 53 3.24 -0.191
Pd/Ptr 17 49 4 7 0.82 0.273 18 20 0.11 -0.053
Pe/Pta 81 78 33 21 2.67 -0.222 4 12 4.0* -0.050
Pe/Pta/Pn 54 21 11 6.23* 1.26 0.333 26 31 0.44 -0.087
Total 2037 1461 604 708 8.24** 0.079 559 550 0.07 -0.081
  1. aHeterogeneity of PU and UP mutations in each lineage
  2. bHeterogeneity of SW and WS mutations in each lineage