Identifying spawning sites and other critical habitat in lotic systems using eDNA “snapshots”: A case study using the sea lamprey Petromyzon marinus L.

Abstract

Many aquatic species of conservation concern exist at low densities and are inherently difficult to detect or monitor using conventional methods. However, the introduction of environmental (e)DNA has recently transformed our ability to detect these species and enables effective deployment of limited conservation resources. Identifying areas for breeding, as well as the ecological distribution of species, is vital to the survival or recovery of a conservation species (i.e., areas of critical habitat). In many species, spawning events are associated with a higher relative abundance of DNA released within an aquatic system (i.e., gametes, skin cells etc.), making this the ideal time to monitor these species using eDNA techniques. This study aims to examine whether a “snapshot” eDNA sampling approach (i.e., samples taken at fixed points in chronological time) could reveal areas of critical habitat including spawning sites for our target species Petromyzon marinus. We utilized a species‐specific qPCR assay to monitor spatial and temporal patterns in eDNA concentration within two river catchments in Ireland over three consecutive years. We found that eDNA concentration increased at the onset of observed spawning activity and patterns of concentration increased from downstream to upstream over time, suggesting dispersal into the higher reaches as the spawning season progressed. We found P. marinus to be present upstream of several potential barriers to migration, sometimes in significant numbers. Our results also show that the addition of a lamprey‐specific fish pass at an “impassable” weir, although assisting in ascent, did not have any significant impact on eDNA concentration upstream after the pass had been installed. eDNA concentration was also found to be significantly correlated with both the number of fish and the number of nests encountered. The application of snapshot sampling techniques for species monitoring therefore has substantial potential for the management of low‐density species in fast‐moving aquatic systems.

Evaluation of environmental DNA surveys for identifying occupancy and spatial distribution of Pacific Lamprey (Entosphenus tridentatus) and Lampetra spp. in a Washington coast watershed

“…River kilometer has been found to be a strong predictor of relative abundance for larval E. tridentatus (Torgersen & Close, ). While a link between eDNA concentration and density requires enumerating individuals, which was beyond the scope of our study, several studies covering diverse aquatic species have observed positive relationships between eDNA concentration and biomass/density (Bracken et al, ; Doi et al, ; Lacoursiere‐Roussel et al, ; Pilliod et al, ; Takahara et al, ; Thomsen et al, ; Wilcox et al, ), supporting our conclusion that E. tridentatus eDNA concentrations within each river reflected a density gradient.…”

“…Entosphenus tridentatus adults migrate into freshwater in summer and fall (Beamish, 1980;Keefer, Moser, Boggs, Daigle, & Peery, 2009) and hold in overwintering habitats until they begin their spawning migration in spring. Positive relationships between eDNA concentration and adult density have been observed in Sea Lamprey (Petromyzon marinus Linnaeus, 1758) (Bracken et al, 2019;Schloesser et al, 2018), and, therefore, would likely be observed in adult E. tridentatus also. We observed no adult E. tridentatus at the time of electrofishing and it is unknown if adults were present at the time when eDNA samples were collected.…”

“…Studies on organisms residing in streams indicate that eDNA may be detected over hundreds of meters to several kilometers downstream from the source (Deiner & Altermatt, 2014;Tillotson et al, 2018;Wilcox et al, 2016). Therefore, eDNA can provide information on spatial distributions of aquatic species, and with consistent monitoring over time, can provide information on temporal changes in distributions (Bracken, Rooney, Kelly-Quinn, King, & Carlsson, 2019).…”

A non-invasive eDNA tool for detecting sea lamprey larvae in river sediments: analytical validation and field testing in a low abundance ecosystem

“…Recently, an eDNA assay using water samples was developed to identify key spawning areas for sea lamprey, including an investigation of the impact of physical barriers that prevent the species fully utilizing its potential spawning habitat (Bracken et al, 2019). Whilst useful for mapping the spatial distribution of spawning areas, the utility of the tool is limited by the short temporal window during which spawning occurs.…”

“…Correspondingly, the application of eDNA detection to monitoring biodiversity is now well established, with a broad range of applications, including species detection in either an ancient or contemporary context, from the reconstruction of past faunal or floral assemblages to the identification of range expansions / biological invasions (Bohmann et al, 2014). In the freshwater environment, it has been used to document habitat utilisation, detect the presence of rare and invasive species, and quantify spawning activity in pre-defined areas (Bracken, Rooney, Kelly□Quinn, King, & Carlsson, 2019; Stoeckle, Soboleva, & Charlop-Powers, 2017; Thomsen & Willerslev, 2015b), including the extent of upstream spawning migrations in anadromous fish species (Antognazza et al, 2019).…”