Comparison of results for the following data after adding an additional filter (Filter2b) for removing outlier samples identified by DAPC and rerunning the full epiRAD pipeline.

Number of individuals left after this additional filter is 33.

1. Filter4: Data obtained post BLAST filter, low read filter and low coverage filter
2. Filter 5a: Data obtained post filter4 AND removing problematic loci identified by rad_haplotyper
3. Filter 5b: Data obtained post filter4 AND keeping only those loci that remain after full SNP filtering pipeline

Filter#	Number of loci	Methylation cutoff
4	7795	-2.848
5a	6809	-2.883959
5b	5912	-2.830382

Result1: MDS without dapc outliers

Filter4	Filter5a	Filter5b

Result2: Methylation heatmap clustered by rows and columns without dapc outliers

Filter4	Filter5a	Filter5b

Result3: %Methylation without dapc outliers

ANOVA for % methylation per site is not significant.

Filter4	Filter5a	Filter5b

Result5a: Pst

	Filter4	Filter5a	Filter5b
Mean Pst	0.127	0.132	0.132

Filter4	Filter5a	Filter5b

Result5b: Pairwise Pst

Table 1 Filter4	Table 2 Filter5a	Table3 Filter5b
| | EOB | PBF | WOB | WOF | |-----|-----|-------|-------|-------| | EOB | x | 0.217 | 0.053 | 0.02 | | PBF | | x | 0.2 | 0.218 | | WOB | | | x | 0.072 | | WOF | | | | x |	| | EOB | PBF | WOB | WOF | |-----|-----|-------|-------|-------| | EOB | x | 0.22 | 0.055 | 0.018 | | PBF | | x | 0.199 | 0.219 | | WOB | | | x | 0.075 | | WOF | | | | x |	| | EOB | PBF | WOB | WOF | |-----|-----|-------|-------|-------| | EOB | x | 0.22 | 0.055 | 0.018 | | PBF | | x | 0.199 | 0.219 | | WOB | | | x | 0.075 | | WOF | | | | x |

Result5c: Pooled Back Reef vs Pooled Fringe Reef Pst

	Filter4	Filter5a	Filter5b
Mean Pst	0.053	0.053	0.053

find.clusters

find.clusters identifies one cluster for data post Filter4,5a,5b.

PERMANOVA

by site

	Filter4	Filter5a	Filter5b
R2	0.12809	0.12993	0.12993
Pvalue	0.011	0.011	0.007

by loc

	Filter4	Filter5a	Filter5b
R2	0.06397	0.06215	0.6215
Pvalue	0.001	0.002	0.003