## Table 5 |
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Probabilities, on null hypothesis, of frequency similarities at PEPCK polymorphic
codons in two Colias species |
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Amino acid polymorph |
Probability calculations |
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counts |
(t/2N_{e} = 1.8) |
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θ_{ss}from 5 genes |
θ_{ss}from PEPCK |
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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 |

x^{2} = − 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.

Watt * et al.*

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