Table 2.

Statistical analysis of alpha diversity measures for comparing different breeds or line. p-values were adjusted for false discovery rate (FDR).

Metrics	Mean ± SD Values #				Kruskal–Wallis Test (p-Values)	Dunn Post-Hoc Test—FDR Adjusted p-Values
	B	A	G	N		B vs. A	B vs. G	B vs. N	A vs. G	A vs. N	G vs. N
Richness
Observed richness	513.9 ± 147	902 ± 99	984 ± 243	857 ± 131	0.001	<0.001	<0.001	0.002	0.663	0.688	0.645
Chao1	717 ± 119	1653 ± 223	1601 ± 371	1450 ± 246	<0.001	<0.001	<0.001	<0.001	0.195	0.606	0.721
ACE	755 ± 103	1691 ± 255	1704 ± 392	1557 ± 274	<0.001	<0.001	<0.001	<0.001	0.492	0.530	0.959
Diversity
Simpson	0.938 ± 0.027	0.974 ± 0.015	0.973 ± 0.019	0.976 ± 0.010	0.011	0.018	0.020	0.014	1	1	1
Shannon	4.01 ± 0.54	4.91 ± 0.32	4.95 ± 0.41	4.83 ± 0.34	0.007	0.018	0.015	0.010	0.967	0.865	0.959
Fisher	116 ± 43	240 ± 35	274 ± 99	225 ± 46	0.001	<0.001	<0.001	0.002	0.492	0.530	0.645

^# Sequences were rarefied to the minimum library size (at 12,151 sequences per sample); A, Aseel, B, Broiler, G, Ghagus, N, Nicobari.