Elucidating the evolutionary history and expression patterns of nucleoside phosphorylase paralogs (vegetative storage proteins) in Populusand the plant kingdom

Table 3 Results of the tests for episodic diversifying selection among the 13 NP-like genes assayed within Populus trichocarpa

Branch		ω^-	Pr[ω = ω^-]	ω^N	Pr[ω = ω^N]	ω⁺	Pr[ω = ω⁺]	LRT	p-value	Corrected p-value
VSP425	0.911	1.0	0.888	1.0	0.009	10000.0	0.102	120.182	0.0	0.0
VSP840	1.078	0.607	0.968	1.0	0.004	72.780	0.028	12.596	0.0	0.004
VSP87A	10.0	0.0	0.748	0.0	0.071	10000.0	0.180	8.721	0.002	0.033
Node3	1.855	0.0	0.653	0.0	0.052	21.384	0.296	8.193	0.002	0.042
BSPA	0.394	0.279	0.996	0.281	0.0	10000.0	0.004	8.079	0.002	0.043
BSPC	0.899	0.0	0.673	0.0	0.236	12.791	0.091	8.013	0.002	0.042
Node2	0.324	0.202	0.934	1.0	0.002	24.413	0.064	5.244	0.011	0.187
BSPB	0.595	0.059	0.959	0.197	0.001	21.161	0.040	3.666	0.028	0.444
NP880	0.155	0.094	0.959	0.841	0.0	593.764	0.041	2.912	0.044	0.660
NP157	0.545	0.0	0.499	0.857	0.0	2.940	0.501	0.754	0.193	1.0
NP860	0.174	0.108	0.855	0.730	0.120	684.793	0.026	0.587	0.222	1.0
Node12	0.446	0.302	0.881	0.650	0.0	3.380	0.119	0.277	0.299	1.0
Node9	10.0	0.0	0.240	0.0	0.111	10000.0	0.649	0.245	0.310	1.0
Node14	0.375	0.150	0.832	0.993	0.0	2.068	0.168	0.186	0.333	1.0
Node5	0.163	0.0	0.404	0.321	0.554	3333.11z	0.042	0.172	0.339	1.0
PNI288	0.540	0.0	0.428	0.999	0.0	1.192	0.572	0.108	0.371	1.0
VSPXIII	0.973	0.986	0.0	0.984	0.0	1.040	1.0	0.001	0.486	1.0
NP870	0.301	0.165	0.867	1.0	0.060	3.224	0.073	-0.380	0.500	1.0
Node7	0.0	0.0	0.885	0.996	0.0	2.106	0.115	-0.001	0.500	1.0
Node1	10.0	0.093	0.971	0.894	0.028	8.630	0.001	-0.001	0.500	1.0
Node21	10.0	0.095	0.009	0.897	0.010	8.819	0.980	-0.001	0.500	1.0
Node17	10.0	0.054	0.370	0.492	0.232	0.293	0.398	0.0	1.0	1.0
WIN4	0.545	0.714	0.0	0.722	1.0	1.578	0.0	0.0	1.0	1.0

Branch = The name of the branch (see tree plot on the main analysis page for the location of automatically named internal branches). $\bar{ω}$ = The ω ratio inferred under the MG94xREV model that permits lineage-to-lineage but no site- to-site ω variation.
ω^- = The maximum likelihood estimate (MLE) of the first rate class with ω ≤ 1.
Pr[ω = ω^-] = The MLE of the proportion of sites evolving at ω-.
ω^N = The MLE of the second rate class with ω ≤ 1.
Pr[ω = ω^N] = The MLE of the proportion of sites evolving at ωN.
ω⁺ = The MLE of the rate class with unconstrained ω.
Pr[ω = ω+] = The MLE of the proportion of sites evolving at ω + .
LRT = Likelihood ratio test statistic for ω + = 1 (null) versus ω + unrestricted (alternative).
p-value = The uncorrected p-value for the LRT test.
Corrected p-value = The p-value corrected for multiple testing using the Holm-Bonferroni method.

ISSN: 1471-2229