Discussion
A major objective of marine molecular ecology is to obtain accurate estimates of subtle genetic structure, as it can inform efforts to identify units of management and design effective marine protected areas (Kelley et al. , 2016; Selkoe et al. , 2016). By comparing sponge populations in Indo-Pacific marine lakes and lagoons at different spatial scales, varying in degree of connection to the sea and differing in local environmental conditions, we were able to study fine-scaled genetic structure and the drivers of genetic diversity and differentiation of marine populations. Using a reduced representation genomic approach, we confirmed broad-scale patterns of structure identified in a prior single-marker study and provided new evidence of small-scaled structure for sessile species with a short dispersive larval stage. Furthermore, we found no associations between sponge host population patterns and previously studied microbial community patterns, suggesting that sponge host and associated microbes may be on different eco-evolutionary tracts. Below, we discuss our findings on population structure for marine lake sponges, the possible drivers of diversity, microbe versus host patterns and finally the implications for future phylogeographic and population genetic studies on sponges.