A genetic polymorphism evolving in parallel in two cell compartments and in two clades

Table 5 Probabilities, on null hypothesis, of frequency similarities at PEPCK polymorphic codons in two Colias species

	Amino acid polymorph		Probability calculations
	counts		(t/2N_e = 1.8)
			θ_ss from 5 genes		θ_ss from PEPCK
Codon	C. eurytheme	C. meadii	P	ln P	P	ln P
11	16 K, 20 R	36 K, 0 R	1.0	0.0	1.0	0.0
335	20 G, 16 S	15 G, 21 S	0.018	−4.02	0.019	−3.96
503	7 D, 29 E	4 D, 32 E	0.011	−4.51	0.014	−4.29
629	18 I, 18 V	6 I, 30 V	0.067	−2.70	0.086	−2.45
	x² = − 2Σ ln P:		22.46		21.40
	Probabilities of joint neutrality
	including codon 11, df = 8		P = 0.004		P = 0.006
	omitting codon 11, df = 6		P = 0.001		P = 0.002

Site-specific probabilities estimated by simulation as described in the text and given in Table 4. t/2N_e estimate (actually 1.828) calculated as described in the text. Fisher’s method [27] is used to assemble joint probabilities of neutrality. Analysis using θ_ss from 5 genes tests basic neutral hypothesis vs. selective alternative; analysis using θ_ss from PEPCK tests whether an elevated mutation rate component of θ_ss could allow the null hypothesis to be sustained. See the text for details.

ISSN: 2730-7182