Table 2.

α- and β-diversity analysis results by coral species

Species	Rarefaction	α-Diversity			β-diversity
		Observed ASVs (mean ± SE)	Inverse Simpson	Shannon	PERMANOVA (weighted UniFrac matrix)
A. loripes	737 (removed 106 ASVs)	NA 24 ± 2 (n = 46)	PMA (F(1,35) = 12.52, p = 0.0012)	PMA (F(1,35) = 15.75, p = 0.0003)	PMA (F(1,45) = 24.15, p = 0.0001)
		Figure 1A	Figure 1B	Figure 1C	Figure 2A, B
A. millepora	2184 (removed 6 samples and 309 ASVs)	NA 50 ± 10 (n = 43)	NA	Genotype (F(3,34) = 6.44, p = 0.0014)	NA Additional file 2: Fig. S4A
A. kenti	9895 (Removed 3 samples and 151 ASVs)	Genotype (F(3,29) = 8.24, p = 0.0004) A-568 ± 113 (n = 9) B-213 ± 39 (n = 10) C-211 ± 55 (n = 8) D-135 ± 23 (n = 10)	Genotype (F(3,29) = 15.43, p < 0.0001)	Genotype (F(3,29) = 14.27, p < 0.0001)	Genotype (F(3,39) = 11.52, p = 0.001)
		Additional file 2: Fig. S3A	Additional file 2: Fig. S3B	Additional file 2: Fig. S3C	Additional file 2: Fig. S4B
P. acuta	883 (removed 2 samples and 66 ASVs)	NA 20 ± 2 (n = 48)	NA	NA	PMA (F(1,49) = 1.88, p = 0.0106) Figure 2C-D
P. daedalea	10,489 (removed 5 samples and 243 ASVs)	Genotype (F(4,31) = 3.17, p = 0.0271) A-293 ± 17 (n = 10) B-234 ± 50 (n = 10) C-76 ± 18 (n = 8) D-178 ± 76 (n = 9) E-75 ± 46 (n = 4)	Genotype (F(4,31) = 8.46, p = 0.0001)	Genotype (F(4,31) = 3.40, p = 0.0203)	Genotype (F(4,45) = 52.88, p = 0.001)
		Additional file 2: Fig. S3D	Additional file 2: Fig. S3E	Additional file 2: Fig. S3F	Additional file 2: Fig. S4C
P. lutea	4390 (removed 9 samples and 302 ASVs)	NA 180 ± 22 (n = 41)	NA	NA	Genotype (F(4,49) = 3.30, p = 0.001) Additional file 2: Fig. S4D

Rarefaction levels were chosen based on rarefaction curves for Observed ASVs (Additional file 2: Fig. S2)

A significant main factor effect is denoted by “PMA” or “Genotype;” there were no interactions between main effects. Where there were significant differences, statistics are provided as well as the figure where a given data type is visualized