. 2024 May 16;17:225. doi: 10.1186/s13071-024-06306-5

Table 4.

Molecular diversity indices based on multiple tests of molecular diversity on the combined β-tubulin genotype dataset

(a) Molecular diversity indices
	Molecular diversity indices			Hardy-Weinberg equilibrium				Population-specific F_IS indices (1023 permutations)
Group	Sample size	No. of haplotypes	Average gene diversity over loci	Locus	Obs. Het	Exp. Het	p-value	F_IS	p-value
Human	286	26	0.591	A	0.224	0.468	< 0.001^a	0.523	< 0.001^a
Human	286	26	0.591	B	0.615	0.714	0.009^a	0.523	< 0.001^a
Pig	474	50	0.681	A	0.325	0.517	< 0.001^a	0.372	< 0.001^a
Pig	474	50	0.681	B	0.544	0.845	< 0.001^a	0.372	< 0.001^a

(b) Analysis of MOlecular VAriance (AMOVA)
Source of variation	d.f	Sum of squares	Variance components	Percentage of variation	Fixation indices		p-value
Among groups	1	1.587	− 0.0128	− 5.07	F_CT	− 0.051	0.853
Among populations within groups	17	29.553	0.047	18.84	F_SC	0.179	< 0.001^a
Among individuals within populations	361	104.882	0.074	29.23	F_IS	0.339	< 0.001^a
Within individuals	380	54.5	0.143	57	F_IT	0.43	< 0.001^a

^aIndicates a p-value < 0.05. Abbreviations: Obs.Het. = observed heterozygosity, Exp.Het. = expected heterozygosity. (a) Hardy-Weinberg equilibrium was calculated for each isotype over 1,000,000 Markov chain steps and the p-value is based on the deviation between the observed and expected values. Population-specific inbreeding coefficient (F_IS) calculated over 1023 permutations is shown for each population with p-values of divergence between random F_IS vs observed F_IS. (b) Analysis of MOlecular VAriance tests to identify sources of variation and calculate fixation indices. Samples (individuals) were grouped by host species and then populations were separated by country, for the UK pig farm data each farm was designated as a separate population. Samples from humans in the UK were grouped with the pigs as they have been previously shown to be of porcine origin. Results show the degrees of freedom (d.f.) sum of squares and variance components which are used to calculate the percentage of variation contained within the sample divisions. Fixation indices are shown for F_CT, F_SC, F_IS and F_IT along with p-values from 1023 permutations. Most variation occurs between individuals within the entire population. Fixation indices show that there is little differentiation between groups but significant differentiation between individuals and populations