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. 2009 Jan 6;26(4):843–857. doi: 10.1093/molbev/msp001

Table 3.

HKA and MK Tests Comparing the MEA Promoter to Silent Sites within the MEA Gene and the 5′ Flanking Gene

Nsequencesb
 Test # Polymorphic/#Differencesc
 MEA promoter versusd
Taxona 5′Gene + Promoter MEA Gene 5’ Gene syn MEA prom. MEA syn. Introns 1–2 Introns 3–16 5’ Gene syn MEA synonymous MEA introns 1–2 MEA introns 3–16
Arabidopsis lyrata 23 28 MK 9/6 67/57 18/39 48/31 57/116 P = 0.786 P =0.006 P = 0.385 P = 0.0003
HKA 9/9.2 67/74 18/38 48/44 57/128 χ2 = 0.02, ns χ2 = 1.36, ns χ2 = 0.05, ns χ2 = 2.00, ns
Arabidopsis lyrata lyrata 10 13 MK 4/8 40/63 6/40 33/42 30/123 P = 0.766 P = 0.002 P = 0.538 P = 0.0009
HKA 4/9.3 40/76 6/38 33/57 30/131 χ2 = 0.06, ns χ2 = 2.83, P = 0.09 χ2 = 0, ns χ2 = 2.46, ns
Arabidopsis lyrata petraea 13 15 MK 5/7 49/57 13/39 46/33 40/122 P = 1.000 P = 0.014 P = 0.137 P = 0.0003
HKA 5/9.0 49/75 13/39 46/46 40/134 χ2 = 0.05, ns χ2 = 1.14, ns χ2 = 0.31, ns χ2 = 2.16, ns
Arabidopsis thaliana 18 13 MK 2/9 15/71 5/43 7/70 24/122 P = 1.000 P = 0.322 P = 0.167 P = 0.857
HKA 2/9.3 15/75 5/41 7/72 24/131 χ2 = 0.01, ns χ2 = 0.22, ns χ2 = 0.97, ns χ2 = 0, ns
a

 One A. thaliana sequence was used as the outgroup for A. lyrata diversity tests, and one A. l. petraea sequence was used as the outgroup for A. thaliana.

b

 Number of sites used in the analysis are 80–87 (5′ gene), 747–756 (MEA promoter), 429–436 (MEA synonymous), 480–721 (MEA introns 1–2), and 1208–1269 (MEA introns 3–16).

c

 The two tests use different methods to calculate the number of polymorphic sites and differences; MK test uses fixed differences, whereas HKA test uses average pairwise differences.

d

 Fisher's exact test was used to calculate significance for the MK test. Chi-square tests based on coalescent simulations implemented in the HKA software were used for HKA tests.