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Table 5 Comparison of positive selection in rbcL of different lineages detected by PAML (M8 model) and by SLR (probability ≥0.95)

From: Exceptionally high rates of positive selection on the rbcL gene in the genus Ilex (Aquifoliaceae)

Lineages N. seqa dN/dSb %pc PALMd SLRd
Ilex, the 20-species alignment 20 20.5 8.2 26 7
eurosids I-26 (Fagaceae)e 21 62.0 (61.0) 0.4 (0.4) 2 (2) 1
euasterids I-9 (Lamiaceae)e 19 27.9 (26.7) 6.3 (6.0) 3 (2) 0
Coniferales 6 (Pinus)e 35 13.1 (24.8) 1.6 (1.1) 6 (6) 2
commelinids-7 (Cyperaceae)e 27 1.1 (1.2) 12.7 (12.9) 0 (0) 0
Commelinids-15 (Poaceae)e 28 2.4 (2.4) 10.0 (9.9) 15 (15) 0
eurosids I-24 (Fagales)e 20 1.7 (1.6) 7.4 (8.5) 0 (0) 0
euasterids I-8 (Lamiaceae)e 20 2.7 (2.8) 10.7 (10.3) 2 (2) 0
Gnetales-1 (Gnetum)e 23 3.7 (3.5) 8.5 (8.6) 3 (3) 0
Flaveria 16 19.2 1.8 5 1
Nothofagus 24 6.2 5.4 7 1
Populus 14 5.1 3.9 6 0
Potamogeton 18 11.6 1.2 1 1
Quercus 30 18.4 0.6 2 1
Salix 28 2.5 9.7 1 0
Schiedea 27 26.1 0.6 0 0
  1. anumber of sequences
  2. bmean dN/dS, “eleventh class” of the M8 model (PAML)
  3. cproportion of positively selected residues, “eleventh class” of the M8 model (PAML)
  4. dnumber of positively selected sites
  5. ePAML re-calculations from data of Kapralov and Filatov [29], with their published results between brackets