Brandao-Dias, P. F. | Search bioRxiv

bioRxiv2025

Estimating Organism Abundance Using Within-Sample Haplotype Frequencies of eDNA Metabarcoding Data

Environmental DNA (eDNA) metabarcoding provides powerful insights into species presence and community composition, but remains limited in its ability to quantify species abundance or structure. Here, we show that deviation between observed haplotype frequencies within a given sample and the population haplotype frequencies can be used to infer the number of individual contributors to an eDNA sample. We also lay out the theory for how population haplotype frequencies can be approximated from eDNA data alone, enabling broad applicability even in the absence of tissue-based references. We then present an estimator to derive the number of individual contributors to a given eDNA sample and validate its performance using simulations with variable allele frequencies and noise. Our framework demonstrates that differences between expected and observed frequencies carry meaningful biological information in eDNA data. Our results show that the number of contributors can be recovered under a range of conditions, particularly with hypervariable markers and sufficient sampling. This approach complements existing molecular methods and opens a new avenue for inferring abundance from eDNA metabarcoding datasets.

molecular biology↗

bioRxiv2025

Differential Decay of Multiple eNA Components from a Cetacean

Environmental nucleic acids (eNA), such as DNA and RNA, are powerful tools for monitoring biodiversity. Yet, interpreting eNA detections requires understanding of their environmental persistence. We conducted a decay experiment using seawater from an open enclosure to track degradation of six eNA components derived from Tursiops truncatus: mitochondrial eDNA of varying lengths, ribosomal eRNA, and messenger eRNA. Targets were quantified over seven days via digital droplet PCR (ddPCR). Decay followed a biphasic exponential model with rapid initial loss ([~]24 hours at 15 {degrees}C), followed by slower degradation. Cytb messenger eRNA was least stable, disappearing within four hours. Ribosomal eRNA persisted longer but degraded slightly faster than its eDNA counterpart ({lambda} = 0.236 vs. 0.165 hr-{superscript 1}). Longest eDNA fragments decayed more rapidly ({lambda} = 0.190 hr-1) than shorter ones ({lambda} = 0.114 hr-1). These findings support the use of eDNA fragment length as a proxy for degradation state and reinforce that combining multiple eNA components with distinct stabilities can potentially provide a molecular clock for inferring eNA age. This approach improves the spatiotemporal resolution of eNA-based monitoring, particularly for rare marine-mammal that act as point sources. We also emphasize the importance of explicitly distinguishing between RNA types (ribosomal vs. messenger) in environmental studies, given their divergent stability and interpretability.

molecular biology↗