Water, water everywhere: environmental DNA can unlock population structure in elusive marine species

Abstract

Determining management units for natural populations is critical for effective conservation and management. However, collecting the requisite tissue samples for population genetic analyses remains the primary limiting factor for a number of marine species. The harbour porpoise (Phocoena phocoena), one of the smallest cetaceans in the Northern Hemisphere, is a primary example. These elusive, highly mobile small animals confound traditional approaches of collecting tissue samples for genetic analyses, yet their nearshore habitat makes them highly vulnerable to fisheries by-catch and the effects of habitat degradation. By exploiting the naturally shed cellular material in seawater and the power of next-generation sequencing, we develop a novel approach for generating population-specific mitochondrial sequence data from environmental DNA (eDNA) using surface seawater samples. Indications of significant genetic differentiation within a currently recognized management stock highlights the need for dedicated eDNA sampling throughout the population's range in southeast Alaska. This indirect sampling tactic for characterizing stock structure of small and endangered marine mammals has the potential to revolutionize population assessment for otherwise inaccessible marine taxa.

Invasion genetics from eDNA and thousands of larvae: A targeted metabarcoding assay that distinguishes species and population variation of zebra and quagga mussels

“…Our study results here discerned haplotypic diversity of zebra and quagga mussels that was undetected by conventional sequencing of adults (Marescaux et al, 2016;Stepien et al, 2013). Similar intraspecific approaches using the mtDNA control region have been developed for the whale shark Rhincodon typus (Sigsgaard et al, 2016) and harbor porpoise Phocoena phocoena (Parsons et al, 2018), and with the cytochrome b region for the invasive silver carp Hypophthalmichthys molitrix .…”

“…Our study results here discerned haplotypic diversity of zebra and quagga mussels that was undetected by conventional sequencing of adults (Marescaux et al, ; Stepien et al, ). Similar intraspecific approaches using the mtDNA control region have been developed for the whale shark Rhincodon typus (Sigsgaard et al, ) and harbor porpoise Phocoena phocoena (Parsons et al, ), and with the cytochrome b region for the invasive silver carp Hypophthalmichthys molitrix (Stepien et al, ). Our assay is designed to accurately estimate haplotypic frequencies, as well as relative species proportions, which will be useful for elucidating invasion pathways, along with documenting population relationships across temporal and spatial scales.…”

“…Although those studies detected dreissenids (De Ventura et al, 2017;Egan et al, 2015;Gingera et al, 2017;Ram et al, 2011), their methodology was unable to differentiate between zebra and quagga mussel species using a single assay and could not address population-level variation (e.g., haplotypes). Targeted metabarcoding assays with high-throughput sequencing (HTS) and bioinformatic processing can be designed to simultaneously resolve entire communities to species level, as well as distinguish population genetic variation (Elbrecht, Vamos, Steinke, & Leese, 2018;Parsons, Everett, Dahlheim, & Park, 2018;Sigsgaard et al, 2016;Stepien, Snyder, & Elz, 2019).…”

False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)

“…In this study, the first of its kind, similar mitochondrial haplotype frequencies were recovered from seawater eDNA compared to tissue samples, expanding the applications of eDNA to encompass population genetics of aquatic organisms . A similar study by Parsons et al (2018) on harbor porpoises (Phocoena phocoena) in the inland waters of southeast Alaska revealed indications of significant genetic differentiation within a currently recognized single stock of harbor porpoises and identified two previously undocumented mitochondrial haplotypes from seawater samples. Another, recently published, marine mammal eDNA study confirmed killer whale (Orcinus orca) presence in Puget Sound, North America, and correctly identified the killer whale ecotype present at the time of seawater sampling (Baker et al, 2018).…”

“…Initial aquatic eDNA research was limited to determining the presence or absence of a species in freshwater ecosystems (Dejean et al, 2012;Ficetola et al, 2008;Jerde et al, 2011). Subsequently, many applications have started to emerge, including the use of eDNA to determine species abundance (Pilliod et al, 2013;Thomsen et al, 2016), biomass (Jane et al, 2015;Nevers et al, 2018;Takahara, Minamoto, Yamanaka, Doi, & Kawabata, 2012), and population structure Parsons, Everett, Dahlheim, & Park, 2018). Additionally, eDNA research has developed into sampling in the more challenging marine environment (Baker et al, 2018;Bakker et al, 2017;Foote et al, 2012;Minamoto et al, 2017;Parsons et al, 2018;Sigsgaard et al, 2016;Thomsen, Kielgast, Iversen, Møller et al, 2012;Thomsen et al, 2016;Thomsen & Willerslev, 2015).…”