Biology subjects

Guri, G.

Publications and source records attributed to Guri, G..

5 recordsLinked to original sources

bioRxiv2025

Quantitative, Multispecies Monitoring at a Continental Scale

Molecular data from environmental samples can reflect the abundance of species DNA, an index immediately relevant to natural-resources management at a broad geographic scale. These data commonly derive from assays designed and targeted for individual species (e.g., using qPCR or ddPCR), or from metabarcoding that use more general PCR primers to amplify many species simultaneously. Multispecies analyses make efficient use of field samples and laboratory time, and speak to inherently multispecies questions of management and ecological interest. However, unlike single-species techniques, metabarcoding alone generally reflects only the environmental DNA (eDNA) proportions of target-species DNA present, not their absolute quantities. Here, we combine qPCR and metabarcoding data derived from the same samples to estimate quantities of eDNA from many fish species along the US West Coast in three dimensions, demonstrating a technique of practical relevance for both management and ecology. We derive spatially explicit maps of eDNA abundances for 12 common species of ecological and management importance and point the way to quantitative surveys of wild species using molecules alone. We find that species distribution maps derived from eDNA largely mirror known species niches and known spatial distributions. Notably, our analyses indentify biodiversity hotspots that align with previously documented regions of ecological significance, such as the Columbia River plume and the Heceta Bank.

ecology↗

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

Vertebrate Biodiversity via eDNA at the air-water interface

Although aquatic, aerial, and terrestrial habitats are often treated as separate ecological systems, these environments exist along a continuum of connectivity: flows of biomass and energy routinely create linkages across water and air, blurring traditional boundaries. Here, we use eDNA sequencing to illustrate and quantify the movement of trace genetic information between water and air. We collected 27 paired air-and-water samples from two urban-wildland interface sites using passive air sampling and active water filtering. Metabarcoding with the MiFish-U 12S marker recovered 35 vertebrate taxa, 40% of which were detected in both water and air, ranging from the strictly aquatic salmon to wholly terrestrial cottontail rabbit. This reciprocal relationship suggests that eDNA pools form within each partition (water or air), with the probability of transfer governed by DNA concentration. In this view, detecting aquatic eDNA in the air is not contamination or stochastic noise but an expected, repeatable phenomenon. Logistic models confirm that higher abundance in one medium predicts spillover into the other. For instance, peaks in Coho and Chinook salmon eDNA align within 24 hours, demonstrating that passive air sampling reflects the temporal abundance trends of the most common aquatic species. In contrast, low-read-abundance taxa appear only sporadically, implying that rare detections are the first to drop out of cross-medium transfer and therefore demand intensified sampling in their primary habitat. Together, our findings bridge the conventional separation of aquatic and airborne eDNA and establish a unified, non-invasive framework for holistic vertebrate monitoring at the land-water interface. This approach offers transformative potential for conservation, invasive-species early warning, and One Health surveillance.

molecular biology↗

bioRxiv2025

Fish from the sky: Airborne eDNA tracks aquatic life

Water and air are generally treated as separate reservoirs of environmental DNA (eDNA) derived from the species resident in those respective environments. However, it is likely that eDNA routinely crosses the air-water boundary in both directions as a result of deposition, evaporation, or other processes. Here, we systematically tested methods of sampling eDNA at the air-water interface, showing for the first time that aquatic life can be reliably detected from passive air samples collected nearby. We deployed four simple air samplers -- three different kinds of filters and one open tray of deionized water -- alongside paired water samples and visual counts over a six-week peak run of Coho salmon (Oncorhynchus kisutch) at a local spawning stream. We then quantified eDNA concentrations in both air and water (air: copies/day/cm2; water: copies/L) using quantitative PCR, to estimate (1) the concentration of target eDNA in air vs. water, and (2) the capture performance of each filter type. Despite an approximate 25,000-times dilution versus water, passive air collectors captured quantitative airborne eDNA signals that closely paralleled salmon counts, although recovery varied with sampler design and orientation. We show the air-water interface is a quantifiable source of aquatic genetic information using simple, passive samplers that do not require electricity, making them appealing for biomonitoring in remote or resource-limited settings. This work points the way to using airborne eDNA as a robust pathway for biological information critical to conservation, resource management, and public-health protection.

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↗