A novel target-enriched multilocus assay for haplosclerid sponges

With declining biodiversity worldwide, a better understanding of species diversity and their relationships is imperative for conservation and management efforts. Marine sponges are species-rich ecological key-players on coral reefs, but their species diversity is still poorly understood. This is particularly true for the demosponge order Haplosclerida, for which the systematic relationships are contentious due to the incongruencies between morphological and DNA sequence-derived phylogenetic hypotheses. The single gene markers applied in previous studies did not resolve these discrepancies, hence, there is a high need for a genome-wide approach to derive a phylogenetically robust classification and to understand the evolutionary relationships within this group. To this end, we developed a target enrichment-based multilocus probe assay for Haplosclerida. This bait set, consisting of 20,000 enrichment probes targeting genome-wide loci, was tested on twenty-six specimens collected from the Red Sea. Our target-enrichment approach correctly placed our samples in agreement with previous haplosclerid phylogenies and resulted in a well-supported phylogeny. Our results demonstrate the applicability of high-resolution genomic methods in a systematically difficult invertebrate group and provide a promising approach for robust phylogenies of Haplosclerida. Subsequently, this will lead to biologically unambiguous taxonomic revisions, better interpretations of biological and ecological observations, open new avenues for applied research, conservation, and management of declining marine diversity.