Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms

Table 2 Taxonomic distance-based PERMANOVA results for differences in community composition (genus level) between host species and host environments based on shared abundance (Bray-Curtis) and shared presence (Jaccard), based on whole genome shotgun and different amplicon strategies (P values are adjusted via Hommel’s procedure)

Distance	Factor	Data	Classifier	DF	F	P	P _Hommel	R ²	adj. R²
Bray-Curtis	Organism	Shotgun	MEGAN	10,49	6.3517	0.0001	0.0001	0.5645	0.4756
		Amplicon	V1 V2 one-step	10,43	7.1026	0.0001	0.0001	0.6229	0.5352
			V1 V2 two-step	10,42	4.2297	0.0001	0.0001	0.5018	0.3831
			V3 V4 one-step	10,43	7.8964	0.0001	0.0001	0.6474	0.5654
			V3 V4 two-step	10,41	3.7917	0.0001	0.0001	0.4805	0.3538
	Environment	Shotgun	MEGAN	1,58	5.8958	0.0001	0.0004	0.0923	0.0766
		Amplicon	V1 V2 one-step	1,52	6.1588	0.0001	0.0001	0.1059	0.0887
			V1 V2 two-step	1,51	4.6185	0.0001	0.0001	0.0830	0.0651
			V3 V4 one-step	1,52	5.4975	0.0001	0.0001	0.0956	0.0782
			V3 V4 two-step	1,50	3.3349	0.0001	0.0001	0.0625	0.0438
Jaccard	Organism	Shotgun	MEGAN	10,49	4.7458	0.0001	0.0001	0.4920	0.3883
		Amplicon	V1 V2 one-step	10,43	3.6867	0.0001	0.0001	0.4616	0.3364
			V1 V2 two-step	10,42	2.9760	0.0001	0.0001	0.4147	0.2754
			V3 V4 one-step	10,43	4.0248	0.0001	0.0001	0.4835	0.3633
			V3 V4 two-step	10,41	2.9343	0.0001	0.0001	0.4171	0.2750
	Environment	Shotgun	MEGAN	1,58	4.3872	0.0001	0.0004	0.0703	0.0543
		Amplicon	V1 V2 one-step	1,52	3.8714	0.0001	0.0001	0.0693	0.0514
			V1 V2 two-step	1,51	3.6541	0.0001	0.0001	0.0669	0.0486
			V3 V4 one-step	1,52	4.3213	0.0001	0.0001	0.0767	0.0590
			V3 V4 two-step	1,50	3.6646	0.0001	0.0001	0.0683	0.0497

ISSN: 2049-2618