Knudsen, S. W. | Search bioRxiv

bioRxiv2026

Metabarcoding replicate detection frequency tracks ddPCR copy number for cod and herring eDNA in ancient marine sediments

O_LIDetecting environmental DNA (eDNA) from rare or low-abundance aquatic species remains a major challenge, particularly when it is highly degraded, present at low concentrations, and dominated by DNA from non-target taxa. These challenges are further amplified in sedimentary ancient DNA (sedaDNA) studies, where thousands of years can degrade eDNA further, making the detection and quantitative interpretation of weak biological signals difficult. C_LIO_LIMetabarcoding is commonly used to produce high-throughput community-level data from eDNA but is inherently compositional and influenced by amplification biases. Nonetheless, metabarcoding read abundance or PCR replicate detection frequency are increasingly used as proxies for relative DNA concentration, but their quantitative interpretation has rarely been evaluated against independent measures of absolute DNA abundance. C_LIO_LIWe used droplet digital PCR (ddPCR) to quantify mitochondrial DNA from Atlantic cod (Gadus morhua) and Atlantic herring (Clupea harengus) in 136 ancient eDNA extracts from Icelandic marine sediment cores spanning the last three millennia. We compared ddPCR copy number estimates with metabarcoding (18S) derived relative abundance and detection frequency, and evaluated whether temporal DNA trends corresponded with proxy reconstructed sea surface temperature (SST) variability. C_LIO_LIWe found that ddPCR-measured fish sedaDNA abundance was positively correlated with the proportion of metabarcoding PCR replicates for both Atlantic cod and Atlantic herring. Moreover, temporal trends in Atlantic herring DNA abundance were consistent with proxy reconstructed SST variability, supporting the ecological relevance of the molecular signal. C_LIO_LIOverall, our results show that ddPCR-derived DNA concentrations and metabarcoding PCR replicate detection frequency capture consistent patterns in low-abundance fish sedaDNA from marine sediments. The observed agreement between approaches supports the use of PCR replicate detection frequency as a semi-quantitative proxy for low-abundance sedaDNA. C_LI

genetics↗

bioRxiv2022

Holistic monitoring of freshwater and terrestrial vertebrates by camera trapping and environmental DNA

The anthropogenic impact on the worlds ecosystems is severe and the need for non-invasive, cost-effective tools for monitoring and understanding those impacts are therefore urgent. Here we combine two such methods in a comprehensive multi-year study; camera trapping (CT) and analysis of environmental DNA (eDNA), in river marginal zones of a temperate, wetland Nature Park in Denmark. CT was performed from 2015 to 2019 for a total of 8,778 camera trap days and yielded 24,376 animal observations. The CT observations covered 87 taxa, of which 78 were identified to species level, and 73 were wild native species. For eDNA metabarcoding, a total of 114 freshwater samples were collected from eight sites in all four seasons from 2017 to 2018. The eDNA results yielded a total detection of 80 taxa, of which 74 were identified to species level, and 65 were wild native species. While the number of taxa detected with the two methods were comparable, the species overlap was only 20 %. In combination, CT and eDNA monitoring thus yielded a total of 115 wild species (20 fishes, four amphibians, one snake, 23 mammals and 67 birds), representing half of the species found via conventional surveys over the last ca. 20 years (83% of fishes, 68 % of mammals, 67 % of amphibians, 41 % of birds and 20 % of reptiles). Our study demonstrates that a holistic approach combining two non-invasive methods, CT and eDNA metabarcoding, has great potential as a cost-effective biomonitoring tool for vertebrates.

zoology↗