Non-Invasive Underwater DNA Sampling Illuminates Red Sea Echinoderm Diversity

Species-specific non-invasive underwater DNA sampling remains largely understudied for marine invertebrates despite its potential to revolutionise biodiversity assessment of vulnerable species or fragile ecosystems. Comprehensive species-specific DNA barcode databases are essential for accurate species identification and taxonomic assignment, particularly at a time of increasingly employed metabarcoding monitoring of marine biodiversity. We present an in situ swab-based protocol adapted for underwater collection of genetic material, using Red Sea echinoderms as a case study. We sampled 308 individuals from over 50 species across all five echinoderm classes using a newly designed underwater sampling kit applying sterile buccal swabs and an underwater sampling container. The novel sampling protocol was compared to traditional tissue-based DNA extractions and tested for preservation conditions (fixatives, temperatures and durations). DNA yield from swabs was lower than from traditional tissue biopsies, yet sufficient for all downstream applications. Overall PCR amplification success was 88% (240/274 echinoderm swabs), with a 94% sequencing success rate (202/214), and no significant difference in DNA integrity between swab and tissue methods. Phylogenetic analyses of 231 specimens revealed 37 clades, including 20 novel Red Sea lineages and provisional identifications of cryptic and rare species. Our results demonstrate that underwater swabbing is a rapid (< 1 min per sample), cost-effective, and non-destructive, suitable for generating high-quality genetic data under challenging field conditions. We propose this protocol as an alternative to traditional DNA sampling, providing an efficient approach for studying at-risk ecosystems and species while prioritising conservation and sustainability and facilitating large-scale genetic screening of wild populations.