Evaluating manta ray mucus as an alternative DNA source for population genetics study: underwater-sampling, dry-storage and PCR success

Abstract

13Sharks and rays are increasingly being identified as high-risk species for extinction, 14prompting urgent assessments of their local or regional populations. effectively collected underwater using a toothbrush. DNA stored on cards was found to be 24 reliable for PCR-based population genetic studies. We successfully amplified mtDNA ND5, 25 nuclear DNA RAG1, and microsatellite loci for all samples. As the yields of DNA with the 26 tested method were low, further improvements are desirable for assays that may require larger 27 amounts of DNA, such as population genomic studies using emerging next-gen sequencing.

Towards more compassionate wildlife research through the 3Rs principles: moving from invasive to non-invasive methods

“…(Kawai et al 2004), polyplacophoran molluscs (Ischnochiton spp.) (Palmer et al 2008), freshwater pearl mussels Margaritifera margaritifera (Karlsson et al 2013) and fish (Manta birostris, Oreochromis niloticus) (Kashiwagi et al 2015, Taslima et al 2016.…”

Feeding ecology and habitat use of the giant manta ray Manta birostris at a key aggregation site off mainland Ecuador

“…Preliminary findings from this work suggest that mucus could be useful as a material in elasmobranch dietary studies using SIA. Particular benefits of mucus use relate to the minimally-invasive method of collection, its potential in exploring seasonal shifts in diet, and even its use in molecular genetics studies (Kashiwagi et al 2015). The use of mucus may prove particularly valuable for elasmobranch species for which stomach content data are unavailable.…”

Use of mucus as a non‐invasive sampling method for DNA barcoding of stingrays and skates (batoid elasmobranchs)

“…However, the use of this tool is still very dependent on tissue sampling ( e.g ., muscle, scale and blood), usually obtained from dead animals in fish markets and fishing vessels or from live animals, with many challenges involving the angling and handling processes, such as physical injuries and pathology due to hook removal or retention, and post‐release survivorship (Danylchuck et al ., ). On the other hand, less invasive procedures for DNA extraction has been tested in a wide variety of vertebrates (including large species of elasmobranchs) to assess information on genetic population, forensic identification, sex determination and genetic diversity (Alvarado Bremer et al ., ; Hilsdorf et al ., ; Kashiwagi et al ., ; Lieber et al ., ; Presti et al, ). Such outcomes demonstrated the feasibility of non‐destructive approaches to DNA extraction and its use in different analyses, at a low cost and with a high degree of sensitivity and confidence.…”

“…Scraping mucus proved to be effective for DNA barcoding and for a preliminary analyses on the genetic diversity and phylogeny of mobulids, providing a reliable method and quality DNA from the studied species through rapid handling and with no injuries to animals. Although the DNA quantity ranged from different values, it was enough to amplify coI region from mucus, such as already observed for others organism such as bony fishes, and elasmobranchs (Kashiwagi et al ., ; Lieber et al ., ; Mirimin et al ., ). In times where populations of sharks and rays are declining worldwide, the increasing of studies considering the development of non‐lethal methods can improve genetic monitoring and other conservation strategies for elasmobranchs.…”