Table 3

Sites predicted to be under differential positive selection using the Bayesian ratio of omegas (ω12) test, the fixed effects likelihood comparison of selective pressures (FEL-CSP), and FEL-Clade tests

S-RNase Region (codon positions)


Test

HVa (1-38)

HVb (44-62)

C3 (63-68)

V1 (69-84)

C4 (85-93)

V2 (94-131)


ωp/ωsα

Physalis codons

7,8, 10,

11, 13,14,

15, 26, 33

44, 46, 49

52, 53,

56 (0.97), 59

62

-

-

-

-

69, 71, 84

87 (0.98)

9, 101, 104, 110, 111,

112, 119 (0.96), 120 (0.96),

123, 124 (0.97), 125

127 (0.95), 129, 131


FEL CSPb

Physalis codons

8, 9,13, 24,

26 (0.08), 31

46, 53

-

84

87

96, 99, 116, 125

127, 129, 131


FEL Clade A

Physalis codons

3, 6, 9,

10, 13

46, 56

-

87, 89, 90

96, 99, 110, 121


FEL Clade C

Physalis codons

9, 14, 24

44, 57

-

92

97, 127, 129


FEL Clade Sc

Solanum codons

21, 22, 23, 29

30, 32, 34, 35, 38

60

Clade A as forground

-

77

103, 106, 109


FEL Clade Sc

Solanum codons

23, 31

47, 48, 50

Clade C as forground

-

80

124


Bold indicates sites predicted to be under stronger selection in Physalis than in Solanum by both ωps and FEL CSP tests. FEL-Clade tests comparing clades A and C show mostly different sites under selection as well as several different sites selected in Solanum depending on the foreground Physalis clade present.

a) For the ω12 test codons had a posterior probability score ≥ 0.99 unless otherwise indicated in parentheses.

b) For the FEL test all sites listed had a p-value ≤ 0.05 except site 26.

c) The FEL Clade Tests had either Clade A or Clade C as the foreground with all other Physalis alleles removed from the alignment and phylogeny.

Paape and Kohn BMC Evolutionary Biology 2011 11:243   doi:10.1186/1471-2148-11-243

Open Data