Evidence of functional divergence in MSP7 paralogous proteins: a molecular-evolutionary and phylogenetic analysis

Garzón-Ospina, Diego; Forero-Rodríguez, Johanna; Patarroyo, Manuel A.

doi:10.1186/s12862-016-0830-x

BMC Ecology and Evolution

Table 2 In silico assessment of functional divergence between paralogous and orthologous MSP7 proteins

From: Evidence of functional divergence in MSP7 paralogous proteins: a molecular-evolutionary and phylogenetic analysis

#	Cluster A	Cluster B	θ_D	LRT_θD	RELAX (p-value)
1	Clade 1 Primate-parasites	Clade 1 Rodent-parasites	0.54	4.74^a	NP
2	Clade 1 Primate-parasites	Clade 3d Primate-parasites (B/E)	−0.21	0.00	Intensification (0.0038)
3	Clade 1 Rodent-parasites	Clade 3d Primate-parasites (B/E)	0.78	15.19^a	NP
4	Clade 1 Primate-parasites	Clade 3d Primate-parasites (C/H/E/D/I)	0.34	4.25^a	Intensification (0.00006)
5	Clade 1 Primate-parasites	Clade 3c Primate-parasites (G/C/D)	0.90	14.46^a	Relaxation (1)
6	Clade 1 Rodent-parasites	Clade 3c Primate-parasites (G/C/D)	0.54	8.89^a	NP
7	Clade 1 Rodent-parasites	Clade 3d Primate-parasites (C/H/E/D/I)	0.37	13.01^a	NP
8	Clade 1 Primate-parasites	Clade 2 Primate-parasites	0.45	3.79	Relaxation (0,2)
9	Clade 1 Primate-parasites	Clade 2 Rodent-parasites	0.20	0.76	NP
10	Clade 1 Rodent-parasites	Clade 2 Primate-parasites	0.74	13.21^a	NP
11	Clade 1 Rodent-parasites	Clade 2 Rodent-parasites	0.93	24.39^a	Intensification (9.1e-7)
12	Clade 2 Primate-parasites	Clade 2 Rodent-parasites	0.87	12.60^a	NP
13	Clade 1 Primate-parasites	Clade 4 Rodent-parasites	0.15	0.14	NP
14	Clade 1 Rodent-parasites	Clade 4 Rodent-parasites	0.69	22.20^a	Relaxation (0.4)
15	Clade 3d Primate-parasites (B/E)	Clade 3d Primate-parasites (C/H/E/D/I)	0.03	0.14	Intensification (0.04)
16	Clade 3d Primate-parasites (B/E)	Clade 2 Primate-parasites	0.72	18.91^a	Intensification
17	Clade 3d Primate-parasites (B/E)	Clade 2 Rodent-parasites	0.31	4.99^a	NP
18	Clade 3d Primate-parasites (B/E)	Clade 4 Rodent-parasites	0.35	7.76^a	NP
19	Clade 3d Primate-parasites (B/E)	Clade 3c Primate-parasites (G/C/D)	0.37	3.91^a	Intensification (2.8e-7)
20	Clade 2 Primate-parasites	Clade 3d Primate-parasites (C/H/E/D/I)	0.93	37.86^a	Intensification (0.0002)
21	Clade 3d Primate-parasites (C/H/E/D/I)	Clade 2 Rodent-parasites	0.81	20.90^a	NP
22	Clade 3d Primate-parasites (C/H/E/D/I)	Clade 4 Rodent-parasites	0.72	15.04^a	NP
23	Clade 2 Primate-parasites	Clade 4 Rodent-parasites	1.0	27.64^a	NP
24	Clade 3c Primate-parasites (G/C/D)	Clade 3d Primate-parasites (C/H/E/D/I)	0.45	9.55^a	Relaxation (0.000008)
25	Clade 2 Primate-parasites	Clade 3c Primate-parasites (G/C/D)	1.0	23.68^a	Relaxation (0.5)
26	Clade 3c Primate-parasites (G/C/D)	Clade 2 Rodent-parasites	0.46	3.04	NP
27	Clade 3c Primate-parasites (G/C/D)	Clade 4 Rodent-parasites	0.44	3.94^a	NP
28	Clade 4 Rodent-parasites	Clade 2 Rodent-parasites	0.57	8.56^a	Intensification (0.03)

The coefficients of divergence (θ_D) and their LRT values from pairwise cluster comparisons in the msp7 multigene family. LRT_θD is the (log) score for the likelihood ratio test against the null hypothesis (θ_D = 0) [5]. It is the output of DIVERGE and it follows a chi-square distribution with one degree of freedom; thus, values greater than or equal to 3.84 (^a) indicate functional divergence between pairwise clusters. Selection intensity (relaxation or intensification) found by the RELAX method is shown for paralogous pairwise comparisons (see Additional file 8). Comparisons 2, 4 and 15 revealed fewer positive selected sites on test branches than on reference branches as well as an intensification of negative selected sites and non-significant θ_D. Comparisons 11, 19, 20 and 28 revealed an increased proportion of positive selected sites on the test branches, having an intensification of this kind of selection, while the proportion of negative selected sites stayed the same or decreased. The θ_D values were statistically significant. Comparisons 5 and 24 gave a statistically significant θ_D and relaxed selection (on test branches). NP: analysis was not performed because proteins came from different species

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