Habitat selection and migration of the common shrimp, Palaemon paucidens in Lake Biwa, Japan—An eDNA‐based study

Abstract

Palaemon paucidens has a large population and is an important food source for fish in Lake Biwa, Japan. They are abundant in shallow waters from spring to summer, after which most individuals migrate to offshore deep areas where they remain during autumn and winter. However, some individuals are nonmigratory, remaining in shallow waters over winter. It has been reported that P. paucidens individuals have declined in recent years; a better understanding of its seasonal distribution is needed to manage this species, and basic information on its seasonal distribution is indispensable. We tracked the environmental DNA (eDNA) distribution of P. paucidens in Lake Biwa over a year using a quantitative real-time polymerase chain reaction method.We collected water samples from offshore (both from the surface and from the benthic) and from shallow shore sites adjacent to the shorelines of the main lake and connecting freshwater lagoons. Offshore sampling took place in summer and winter, and shallow shore and lagoon sampling in all four seasons. During summer, eDNA concentrations were significantly higher in shallow and lagoon areas than offshore bottom sites. Conversely, during winter, eDNA concentrations were higher in offshore bottom sites, and relatively high and low eDNA concentrations in lagoons and shallow shore, respectively. These results most likely reflect the spatial and temporal distribution of this species in Lake Biwa. The eDNA concentrations peaked in early August at shallow shore sites in the main lake, with a significant decline in mid-October, while low eDNA concentrations were recorded at offshore bottom sites in late August. These results suggest that P. paucidens migrates from shallow waters to offshore bottom sites between early August and mid-October. These results provide important information for the management of this species. K E Y W O R D Senvironmental DNA (eDNA), Lake Biwa, migration, Palaemon paucidens, quantitative real-time PCR, spatial and temporal distribution | 55 WU et al.

Development and evaluation of fish eDNA metabarcoding assays facilitate the detection of cryptic seahorse taxa (family: Syngnathidae)

“…Therefore, there may be a greater probability of detection using shorter amplicon assays relative to longer ones. While there is an increase in detection rates, previous studies have shown that assays targeting longer DNA fragments will selectively detect newly released eDNA (Jo et al., 2017; Wu et al., 2019), providing a more contemporary insight to fish community assemblage.…”

Particle size influences decay rates of environmental DNA in aquatic systems

“…For example, target eDNA copy number is often found to correlate with species abundance in ponds and mesocosms (e.g., Lacoursière‐Roussel et al, 2016; Takahara et al, 2012), a correlation strengthened when allometric scaling is considered (Yates et al, 2021). Other recent studies have noted that the eDNA signal can vary spatially, revealing patterns of habitat use by target species (e.g., Oka et al, 2021; Wu et al, 2019). However, separating the signal of abundance from longitudinal information (i.e., where and when an organism was present) within these observations requires a deeper understanding of “eDNA ecology” (Barnes & Turner, 2016; Hansen et al, 2018), a term that encompasses rates of shedding, transport, and decay in the environment, and how these rates are influenced by various biotic and abiotic factors.…”

Estimating the spawning activity of fish species using nuclear and mitochondrial environmental DNA concentrations and their ratios

“…Because this method relies simply on collecting DNA fragments that exist in the water for analysis, it can be used to investigate biological population structures in a body of water without damaging the organisms and with a greatly decreased expenditure of time and labour. This technique has been widely used to investigate fish (Takahara et al, 2012; Thomsen et al, 2012), amphibians (Goldberg et al, 2011; Pilliod et al, 2013), reptiles (Davy et al, 2015; Hunter et al, 2015), crustaceans (Tréguier et al, 2014; Wu et al, 2019) and other organisms. Previous studies have shown that eDNA concentrations increase sharply during fish spawning periods (Buxton et al, 2017; Spear et al, 2015; Tsuji & Shibata, 2021).…”