. 2011 Sep;1(1):46–62. doi: 10.1002/ece3.6

Table 5.

Analysis of molecular variance (AMOVA) based on (A) pairwise differences and frequencies of haplotypes, and (B) only haplotype frequencies; levels of significance from 20,022 random permutations

(A)	Pairwise differences and frequencies of haplotypes

Grouping	Source of variation	df	Fixation index	Percentage of total variation	P-value
Queen morph	Between queen morphs	1	Φ_CT = –0.00727	–0.73	0.52897
	Among populations within queen morphs	46	Φ_SC = 0.41241	41.54	0.00000
	Within queen morphs within populations	82	Φ_ST = 0.40814	59.19	0.00000
	Total	129
Population	Among populations	23	Φ_CT = 0.37574	37.57	0.00000
	Between queen morphs within populations	24	Φ_SC = 0.06494	4.05	0.11093
	Within queen morphs within populations	82	Φ_ST = 0.41628	58.37	0.00000
	Total	129

(B)	Haplotype frequencies only

Grouping	Source of variation	df	Fixation index	Percentage of total variation	P-value
Queen morph	Between queen morphs	1	Φ_CT = –0.00246	–0.25	0.44082
	Among populations within queen morphs	46	Φ_SC = 0.31901	31.98	0.00000
	Within queen morphs within populations	82	Φ_ST = 0.31733	68.27	0.00000
	Total	129
Population	Among populations	23	Φ_CT = 0.10450	10.45	0.00025
	Between queen morphs within populations	24	Φ_SC = 0.24077	21.56	0.00000
	Within queen morphs within populations	82	Φ_ST = 0.32010	67.99	0.00000
	Total	129