Lineage divergence
The phylogenetic tree based on pairwise genetic distances showed two divergent lineages (Fig. 2, Supplemental Table 3). These lineages are concordant with Lineage A and B as defined in Becking et al. (2013). Lineage A was only represented by individuals of B.3. The remaining populations fell under Lineage B. For this lineage, two sub-clades could be identified: B-I representing regions in Australia and Berau, and B-II representing the region Raja Ampat. For the Australia/Berau clade, lagoon populations Bay and DAR appeared to be ancestral to the lake populations. Within Raja Ampat, lake P.4 was most distant from the other lakes.
The number of genetic markers retained strongly differed depending on the inclusion/exclusion of Lineages. When including both lineages, 541 SNPs were retained. When only including Lineage B, the number of SNPs increased almost 9-fold to 4,826. All subsequent analyses were run for Lineage B for 105 individual sponges.