The mate recognition protein gene mediates reproductive isolation and speciation in the Brachionus plicatiliscryptic species complex

Table 4 Branch-Site models and tests of selection

Branch	model	Parameter estimates					lnL	p
Branch	model	Site class	0	1	2a	2b	lnL	p
Harvey	M2 H₀	p_n	0.712	0.044	0.230	0.014	−1939.35	0.65
		back ω	0.046	1.000	0.046	1.000
		fore ω	0.046	1.000	1.000	1.000
	M2 H₁	p_n	0.744	0.046	0.197	0.012	−1939.25
		back ω	0.047	1.000	0.047	1.000
		fore ω	0.047	1.000	1.440	1.440
Ibericus	M2 H₀	p_n	0.866	0.040	0.090	0.004	−1945.76	0.29
		back ω	0.055	1.000	0.055	1.000
		fore ω	0.055	1.000	1.000	1.000
	M2 H₁	p_n	0.897	0.042	0.058	0.003	−1945.51
		back ω	0.055	1.000	0.055	1.000
		fore ω	0.055	1.000	2.437	2.437
Harvey	M3 H₁	p_n	0.587	0.249	0.115	0.049	−1916.07	0.0005
		back ω	0.003	0.221	0.004	0.221
		fore ω	0.003	0.221	1.497	1.497
Ibericus	M3 H₁	p_n	0.622	0.357	0.013	0.008	−1925.01	0.017
		back ω	0.004	0.198	0.004	0.198
		fore ω	0.004	0.198	2.549	2.549
Clade B	M3 H₁	p_n	0.605	0.356	0.025	0.015	−1921.68	0.33
Clade B	M3 H₁	back ω	0.002	0.169	0.002	0.169	−1921.68	0.33
		fore ω	0.002	0.169	0.694	0.694

Branch refers to the branch allowed to have a dN/dS distribution independent of the rest of the tree; Model refers to the Nsites value in codeml; M2 is the branch-site test of positive selection; M3 is the test of divergent selection pressure. For M2:H₀ the foreground ω (branch tested) is fixed at 1; (omega = 1; fix_omega = 1); for M2:H₁ ω is estimated from the data (omega = 0); for M3:H₀ all branches have the same distribution of ω (see Table 4, “M3” for values); for M3:H₁ the branch values are estimated independently from the data. Other parameter values were codon frequency =3, and for M3, ncat = 3. dN/dS and p_n is the proportion of codons with ratio ω_n; κ is the transition:transversion ratio; LnL is the log likelihood, p is the result of χ² test; bold indicates test that were statistically significant.

ISSN: 2730-7182