Individual haplotyping of whale sharks from seawater environmental DNA

Water samples were collected over two weeks directly behind individual whale sharks at Ningaloo Reef, Australia in May, 2019. A total of 56 seawater samples were collected, filtered immediately through sterile 0.22 μm filters, and stored at -80°C. Tissue biopsy samples were then taken from the same animal using a hand spear with a dart head, totalling 77 individual samples.Individual whale sharks were identified by their unique spot and stipe patters through photographs analysed by I³S Classic Software. Re-sightings of the same individual were removed from the dataset. Following photo-identification, a total of 48 unique individuals were confirmed, of which 42 consisted of both tissue and seawater samples. Additional samples were later discarded from the study, resulting in libraries for 28 seawater samples, and whale shark d-loop haplotypes.DNA extractions of the tissue samples were carried out and PCR amplification of the mitochondrial control region and reaction protocol verified. Seawater samples were processed and environmental DNA was extracted. Statistical analysis was performed with R Studio.