iDNA at Sea: Recovery of Whale Shark (Rhincodon typus) Mitochondrial DNA Sequences from the Whale Shark Copepod (Pandarus rhincodonicus) Confirms Global Population Structure

Abstract

The whale shark (Rhincodon typus) is an iconic and endangered species with a broad distribution spanning warm-temperate and tropical oceans. Effective conservation management of the species requires an understanding of the degree of genetic connectivity among populations, which is hampered by the need for sampling that involves invasive techniques. Here, the feasibility of minimally-invasive sampling was explored by isolating and sequencing whale shark DNA from a commensal or possibly parasitic copepod, Pandarus rhincodonicus that occurs on the skin of the host. We successfully recovered mitochondrial control region DNA sequences (∼1,000 bp) of the host via DNA extraction and polymerase chain reaction from whole copepod specimens. DNA sequences obtained from multiple copepods collected from the same shark exhibited 100% sequence similarity, suggesting a persistent association of copepods with individual hosts. Newly-generated mitochondrial haplotypes of whale shark hosts derived from the copepods were included in an analysis of the genetic structure of the global population of whale sharks (644 sequences; 136 haplotypes). Our results supported those of previous studies and suggested limited genetic structuring across most of the species range, but the presence of a genetically unique and potentially isolated population in the Atlantic Ocean. Furthermore, we recovered the mitogenome and nuclear ribosomal genes of a whale shark using a shotgun sequencing approach on copepod tissue. The recovered mitogenome is the third mitogenome reported for Meekan et al. Whale Shark DNA from Copepod the species and the first from the Mozambique population. Our invertebrate DNA (iDNA) approach could be used to better understand the population structure of whale sharks, particularly in the Atlantic Ocean, and also for genetic analyses of other elasmobranchs parasitized by pandarid copepods.

Vertebrate diversity revealed by metabarcoding of bulk arthropod samples from tropical forests

“…Since the field of iDNA originated, targeted collection followed by iDNA analyses of gut contents has been carried out on different invertebrate taxa such as leeches (Drinkwater et al, 2019;Pérez-Flores, Rueda-Calderon, Kvist, Siddall, & Oceguera-Figueroa, 2016;Schnell et al, 2018;Weiskopf et al, 2018), sand flies (Kocher, De Thoisy, et al, 2017), blow and flesh flies Hoffmann et al, 2018;Lee, Gan, Clements, & Wilson, 2016;Lee, Sing, & Wilson, 2015;Rodgers et al, 2017;Schubert et al, 2015), mosquitoes (Kocher, De Thoisy, et al, 2017), ticks (Gariepy et al, 2012), marine copepods (Meekan et al, 2017), and shrimps (Siegenthaler et al, 2019). This has offered a new and promising tool to complement traditional vertebrate monitoring methods, something of great value in the ongoing biodiversity monitoring efforts (Bohmann et al, 2013).…”

Beyond Biodiversity: Can Environmental DNA (eDNA) Cut it as a Population Genetics Tool?

“…Previous non-invasive genetic techniques for terrestrial organisms have been able to assume different individuals from separate scats [34,45] or feeding sites [39,40,84]. Additionally, DNA extracted from invertebrate stomachs (iDNA) has also been used to obtain host DNA [28,[85][86][87]. [18].…”

“…[18]. Indeed, whale shark population structure was confirmed using iDNA from a whale shark copepod (Pandarus rhincodonicus) parasite [28]. However, capture of whole, discrete fecal matter beyond initial deposition, feeding traces, or parasites may be challenging in environmental sampling scenarios.…”

“…More recently, non-invasive sampling techniques have been developed to reduce harm and expense [23]. In marine environments, for example, fecal plumes, respiratory blow, parasites, and shed skin have proven to be useful DNA sources [24][25][26][27][28]. Such indirect samples have been used to amplify mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) markers, allowing measurement of allelic diversity, kinship, sex ratios, abundance and effective population size, density, evolutionary significant units, mating systems, and patterns of dispersal in species that might otherwise be difficult to sample [26,27,[29][30][31][32][33][34][35][36].…”

Advancing Research for the Management of Long-Lived Species: A Case Study on the Greenland Shark

“…Genomic and genetic resources, such as numerous single nucleotide polymorphism (SNP) loci and highly polymorphic nuclear microsatellites, may provide the tools for determining the number of extant populations and the extent of connectivity among them (Milano et al, 2014). Novel sampling methodologies, such as the collection of external parasites to obtain host mitochondrial DNA sequences (Meekan et al, 2017), have proven effective for obtaining genetic samples for such analyses. These invertebrate DNA (iDNA) sequences have helped resolve the genetic structure and connectivity of global whale shark populations (Rhincodon typus; Meekan et al, 2017) and could be similarly applied using copepods sampled from parasitized Greenland sharks.…”