Out of sync: monitoring the time of sea entry of wild and hatchery salmon Salmo salar smolt using floating passive-integrated transponder antennae.

Floating passive-integrated transponder (PIT) antennae and smolt traps were used to study the time of sea entry and relative recapture of wild and hatchery-reared Atlantic salmon Salmo salar smolt released below and above a lake formed in the Vosso River. In total, 8.4 and 4.1% of the tagged wild and hatchery fish, respectively, were detected leaving the river (i.e. sea entry). Wild smolts released below the lake were detected leaving the river 16 days before smolts released above the lake, which also showed a 52% lower probability of detection during out-migration. Hatchery smolts were out of sync with the wild smolts and were detected approximately 2 months later than the wild smolts from both release locations, with an 84% lower likelihood of detection than wild fish. Size selection was evident for wild fish released above the lake, but not below the lake, with an overall likelihood of detection increasing by 2.6% per cm total length (LT ). Wild fish caught in the tributaries and transported to the main river had a 64% lower likelihood of detection than fish caught and released in the main river. This study demonstrates that floating PIT antennae out-performed the traditional rotary screw trap in the ability to detect tagged smolts and that it is an efficient tool for evaluating the time of sea entry of S. salar smolts in a large river system.

Relating target fish DNA concentration to community composition analysis in freshwater fish via metabarcoding.

Metabarcoding has been widely accepted as a useful tool for biodiversity assessment based on eDNA. The method allows for the detection of entire groups of organisms in a single sample, making it particularly applicable in aquatic habitats. The high sensitivity of the molecular approaches is especially beneficial in detecting elusive and rare fish species, improving biodiversity assessments. Numerous biotic and abiotic factors that affect the persistence and availability of fish DNA in surface waters and therefore affecting species detectability, have been identified. However, little is known about the relationship between the total fish DNA concentration and the detectability of differential abundant species. In this study three controlled mock-community DNA samples (56 individual samples) were analyzed by (i) metabarcoding (MiSeq) of 12S rDNA (175 bp) and by (ii) total freshwater fish DNA quantification (via qPCR of 12S rDNA). We show that the fish DNA quantity affects the relative abundance of species-specific sequences and the detectability of rare species. In particular we found that samples with a concentration between 1000 pg/µL down to 10 pg/µL of total fish DNA revealed a stable relative frequency of DNA sequences obtained for a specific fish species, as well as a low variability between replicates. Additionally, we observed that even in complex mock-community DNA samples, a total fish DNA concentration of 23 pg/µL was sufficient to reliably detect all species in every replicate, including three rare species with proportions of ≤0.5 %. We also found that the DNA barcode similarity between species can affect detectability, if evenness is low. Our data suggest that the total DNA concentration of fish is an important factor to consider when analyzing and interpreting relative sequence abundance data. Therefore, the workflow proposed here will contribute to an ecologically and economically efficient application of metabarcoding in fish biodiversity assessment.