Implications for sponge phylogeography and population genetic studies
The RADseq strategy was effective in detecting two major genetic lineages (Lineage A and B) (Becking et al. , 2013). When combining both lineages significantly less markers were recovered than when analyzing lineages separately. Based on our filters requiring a read depth of at least 3X and loci having to be present in at least 70% of the individuals, we retained 541 SNPs when including both lineages, compared to 4,826 SNPs when analyzing only Lineage B. This is more than a 90% loss of common markers and indicates the resolution of RADseq generated markers can be less effective when one (unknowingly) includes multiple lineages. Given that there is a prevalence in morphologically cryptic species in sponges (e.g. Becking, 2013; Swierts et al. , 2013; Morrow and Cárdenas, 2015), it may be advised to first verify broad genetic lineages using common single markers before starting an extensive sponge population genetic study implementing high resolution markers. Perhaps the low number of SNPs recovered in the previous two studies on sponges (Brown, Davis and Leys, 2017; Leiva et al. , 2019) was caused by including different lineages. Further, our adjustments to the existing low-cost protocol of Peterson et al.(2012) with a step-by-step protocol presented in Maas et al.(2018) can help to retrieve extensive data for non-model marine organisms in general and tropical sponges in particular, thus benefitting future studies. Our strategy for bioinformatically filtering out possible microbial contamination proved effective since we did not detect congruence between host population structure and microbial community structure. We further showed that reduced representation genome sequencing can work for DNA that was extracted for other purposes and stored for long times in a -20°C freezer before sequencing, or suboptimal removal of contamination before sequencing. Recent developments with capture based methods such as hyRAD (Suchan et al. , 2016) can further exploit the potential of older DNA extractions. This gives hope to the wealth of knowledge to be gained from extractions from past sponge studies across the world.
Assessing genetic connectivity between populations is crucial to determine the scale of marine reserves (Richards et al. , 2016). Moving on from studying few genetic markers to (reduced representation) genome sequencing provides the potential to look for genetic basis of adaptation (Catchen et al. , 2017), a major goal in molecular ecology. As the oceans are changing, it is imperative how sponge host and its associated microbe community will respond (Pita et al. , 2018). Understanding within- and between population diversity, demography and connectivity serves to facilitate conservation management decisions. It is important to ensure connectivity between marine populations where necessary, while also allowing crucial local adaptation, in view of projected climate change and habitat fragmentation (IPCC, 2019).