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Table 2 Rubisco L-subunit sites candidate to positive selection

From: Exploring molecular evolution of Rubisco in C3 and CAM Orchidaceae and Bromeliaceae

Dataset

Na

Site models

M2a vs. M1a test

Site model

M8 vs. M8a test

M0

M2a

M8

ωb

p2c

ω2d

Selected sitese

p-valuef

p1

ω

Selected sites

p-value

Orchids

78

0.12

0.89

0.02

89***, 251***, 449**, 461*, 478*, 479**, 481**

1

0.001

999.0

89***, 142*, 225**, 251***, 265*, 449***, 461**, 468**, 470*, 477*, 478*, 479**, 481**

1

Bromeliads

130

0.17

0.91

0.01

28***, 91***, 142***, 225**, 251*, 449**, 468***, 478***

1

0.001

999.0

28***, 91***, 142***, 225***, 251**, 255*, 270*, 449***, 468***, 478***

1

  1. aNumber of species
  2. bdN/dS ratio averaged across all branches and codons
  3. cProportion of codons in a class under positive selection
  4. ddN/dS ratio in a class under positive selection
  5. eSites marked with *, ** and *** are under positive selection with posterior probability higher than 0.90, 0.95 and 0.99, respectively
  6. fp-value refers to likelihood ratio tests (LRTs) calculated between nested models of codon evolution M1a-M2a and M8-M8a