Assembled loci and SNPs summary
The number of raw reads generated as well as the number of assembled loci and SNPs for each specimen are summarized in Table S2. An average of 918813 (35940 – 3186367) reads per individual were obtained for both species and on average 639727 (24930 – 2393023) reads were retained after demultiplexing. A total of 1218974 loci were genotyped forRadula flaccida (ranging by sample between 3706 – 79145),and mean sample coverage was 5.4x (3.9x, to 11.6x, stdev=1.2x).Cololejeunea surinamensis showed a similar range number of genotyped loci 1306155 (ranging by sample between 3706 – 79145) and with mean sample coverage 4.9x (3.6x to 9.04x, stdev=0.9x). After excluding samples with a high percentage of missing data (>90–98%), the clustering of allele diverging by a maximum of 15% or 20% among individuals resulted in 9562 or 8575 filtered loci for R. flaccida , and 4428 or 3258 loci for C. surinamensis, for the two respective datasets. These matrices present a relatively similar number of SNPs as follows (Table S2): R. flaccida (427 SNPs in n = 105, and 316 SNPs in n = 80); and C. surinamensis (415 SNPs in n = 108, and 456 SNPs inn = 71). The number of genotyped individuals did not bias allelic richness estimates when comparing the two datasets (Figure S3). The number of loci assembled (>400) in the two datasets for both species was enough to discriminate individuals within and between populations with further analyses (Figures S4 & S5).