Differential strengths of selection on S-RNases from Physalis and Solanum(Solanaceae)

Table 3 Sites predicted to be under differential positive selection using the Bayesian ratio of omegas (ω₁/ω₂) 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 ω_p/ω_s 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 ω₁/ω₂ 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.

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