Table 5

Probabilities, on null hypothesis, of frequency similarities at PEPCK polymorphic codons in two Colias species
Amino acid polymorph Probability calculations
counts (t/2Ne= 1.8)
θssfrom 5 genes θssfrom 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/2Ne estimate (actually 1.828) calculated as described in the text. Fisher’s method [27] is used to assemble joint probabilities of neutrality. Analysis using θss from 5 genes tests basic neutral hypothesis vs. selective alternative; analysis using θss from PEPCK tests whether an elevated mutation rate component of θss could allow the null hypothesis to be sustained. See the text for details.

Watt et al.

Watt et al. BMC Evolutionary Biology 2013 13:9   doi:10.1186/1471-2148-13-9

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