Fish eDNA Abundance from Aquaria Experiment Using Quantitative Sequencing

Tatsuhiko Hoshino from the Japan Agency for Marine-Earth Science and Technology applied quantitative sequencing (qSeq) to environmental DNA (eDNA) analysis. The dataset likely contains quantitative eDNA measurements for five fish species (Hemigrammocypris neglectus, Candidia temminckii, Oryzias latipes, Rhinogobius flumineus, and Misgurnus anguillicaudatus) sampled from aquaria across four days. The study validated qSeq results against digital PCR measurements, finding correlation coefficients of 1.052, 1.074, and 1.114 for three of the species.

Use Cases

• Validate quantitative sequencing (qSeq) methods for eDNA based on the described experimental comparison with digital PCR.
• Model species abundance from eDNA concentration based on the quantitative data generated for five fish species.
• Investigate PCR amplification bias in biodiversity surveys based on the described discrepancy between high-throughput sequencing reads and quantitative analyses.
• Benchmark bioinformatics pipelines for eDNA quantification based on the provided correlation metrics between qSeq and dPCR.

Strengths

• Includes validation data with correlation coefficients (e.g., 1.114 for M. anguillicaudatus) comparing qSeq to digital PCR.
• Data covers five distinct fish species and sampling across a four-day time series.
• Methodology is described in detail, involving a controlled aquaria environment.

Limitations

• Row count and dataset scale are unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• Last update date is unknown; freshness unverified.

Provenance

Source

Tatsuhiko Hoshino, Japan Agency for Marine-Earth Science and Technology

Collection Method

Environmental DNA extracted from aquaria, quantified via microfluidic digital PCR and quantitative sequencing (qSeq).

Time Range

Sampling occurred across four days; specific dates unknown.

Geography

Data originated from a controlled laboratory (aquaria) environment; specific location not stated.