Biology subjects

Brandao-Dias, P. F. P.

Publications and source records attributed to Brandao-Dias, P. F. P..

4 recordsLinked to original sources

bioRxiv2026

Multi-omic Environmental Monitoring Reveals When Molecular Signals Reflect Living Biology

Environmental molecular monitoring has transformed biodiversity detection, yet most methods capture only species presence through amplified DNA fragments, missing the biological information encoded in native nucleic acids. Here we show that a single shotgun Oxford Nanopore sequencing library from water can be read through several independent biological lenses, and that each class of molecule (environmental RNA, CpG methylation, and bulk DNA) differs in its environmental persistence, which sets the window over which signal can be trusted. Sampling Pacific salmon spawning runs, we simultaneously recovered environmental RNA indicating fresh biological input, CpG methylation profiles reflecting age demographics, and pathogen signatures reflecting health. Environmental RNA tracked spawning phenology, qPCR corroborated the timing of fresh biological input over the weeks sampled, and methylation-based age inference held only while fresh DNA dominated, a condition we term the 'Freshness Gate.' Because environmental water is not a tissue sample, we detect functional transcripts as evidence of biological input but do not infer differential gene expression, and we read methylation state but do not infer biological age outside the Freshness Gate. Variance partitioning is consistent with biological freshness, rather than technical factors such as fragment length or sequencing depth, structuring environmental methylation, though these comparisons did not reach significance at nine time points. Comparable dynamics were observed in Chinook salmon, with timing offsets following their distinct spawning season. By defining when environmental molecules faithfully encode living biology and when degradation decouples signal from current state, our framework sets practical and theoretical boundaries for multi-omic environmental monitoring.

ecology↗

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

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↗

bioRxiv2020

Invertebrate Community Associated with the Asexual Generation of Bassettia pallida Ashmead (Hymenoptera: Cynipidae)

Cynipid gall wasps play an important role in structuring oak invertebrate communities. Wasps in the Cynipini tribe typically lay their eggs in oaks (Quercus L.), and induce the formation of a "gall", which is a tumor-like growth of plant material that surrounds the developing wasp. As the wasp develops, the cynipid and its gall are attacked by a diverse community of natural enemies, including parasitoids, hyperparasitoids, and inquilines. Determining what structures these species-rich natural enemy communities across cynipid gall wasp species is a major question in gall wasp biology. Additionally, gall wasps are ecosystem engineers, as the abandoned gall is used by other invertebrates. The gall-associated insect communities residing on live oaks (Quercus geminata Small and Q. virginiana Mill.) are emerging as a model system for answering ecological and evolutionary questions ranging from community ecology to the evolution of new species. Documenting the invertebrates associated with cynipids in this system will expand our understanding of the mechanisms influencing eco-evolutionary processes, record underexplored axes of biodiversity, and facilitate future work. Here, we present the community of natural enemies and other associates of the asexual generation of the crypt gall wasp, Bassettia pallida Ashmead. We compare the composition of this community to communities recently documented from two other cynipid gall wasps specializing on live oaks along the U.S. Gulf coast, Disholcaspis quercusvirens Ashmead and Belonocnema treatae Mayr. B. pallida and their crypts support a diverse arthropod community, including over 25 parasitoids, inquilines, and other associated invertebrates spanning 5 orders and 16 families.

ecology↗