White Papers
Want to learn more about eDNA and Jonah Ventures? Click on any of the images below to read more. If you have additional questions please contact us!
Helpful Primers
Introduction to eDNA
Introduction to Environmental DNA is a primer that explains how environmental DNA (eDNA) is collected, analyzed, and used to detect species in aquatic ecosystems. It covers key concepts such as metabarcoding, qPCR, and sequencing workflows, helping clients understand how eDNA data supports ecological monitoring and research.
Aquatic eDNA Sampling and Processing
Aquatic eDNA Sampling and Processing outlines best practices for collecting, storing, and submitting aquatic environmental DNA samples to Jonah Ventures. It guides clients through the full workflow—from ordering sampling kits and field collection to sample preservation, submission, and data interpretation—ensuring high-quality eDNA results and reliable ecological insights.
Source Tracking
Source Tracking White Paper explains how Jonah Ventures uses environmental DNA (eDNA) and quantitative PCR (qPCR) to identify the sources of fecal contamination in water. The paper outlines the scientific theory, laboratory process, and available assays for host-specific detection, helping clients understand how molecular source tracking supports accurate water quality assessment and decision-making.
Low Template Metabarcoding
Environmental DNA (eDNA) metabarcoding enables powerful aquatic biodiversity monitoring, but detecting rare and low-abundance taxa remains difficult due to DNA degradation, stochastic sampling, PCR bias, and sequencing artifacts. This white paper presents Jonah Ventures’ end-to-end aquatic eDNA workflow, developed over more than a decade to maximize sensitivity, minimize bias, and support absolute DNA quantification near the limits of detection. The approach integrates high-efficiency filtration, open-source DNA preservation, contamination-controlled laboratory workflows, high-replicate two-step PCR, quantitative metabarcoding, Oxford Nanopore sequencing, and exact sequence variant–based bioinformatics. Together, these system-level design choices reduce false negatives, improve reproducibility, and generate transparent, future-proof data for ecological research, long-term monitoring, and regulatory decision-making.
Introduction to Targeted Capture
Accurate identification of species from environmental DNA (eDNA) is central to applications ranging from biodiversity monitoring to diet analysis to pathogen detection. Although existing methods—shotgun sequencing, qPCR, and metabarcoding—have enabled major advances in species detection, each technique is constrained by fundamental limitations. Targeted capture utilizes RNA baits to hybridize with target sequences, offering a powerful alternative that combines sensitivity, taxonomic resolution, and quantitative robustness.
Additional White Papers
This white paper compares Illumina MiSeq and Oxford Nanopore Technologies (ONT) MinION sequencing for DNA metabarcoding using identical sample pools spanning multiple taxonomic groups. The results show an extremely strong correlation in relative read abundance of exact sequence variants between platforms, with only minor differences primarily in low-abundance variants. These findings demonstrate that ONT now produces metabarcoding results that are functionally comparable to Illumina, and reflect Jonah Ventures’ transition to ONT sequencing to deliver faster turnaround, greater operational flexibility, and expanded future capabilities. You can download the full white paper here.
This white paper describes how Jonah Ventures enables quantitative DNA metabarcoding by adding known quantities of synthetic “spike-in” DNA to samples prior to PCR. The approach overcomes a key limitation of traditional metabarcoding by allowing read counts to be converted into copy-number estimates. Results show that spike-ins preserve relative abundance patterns, closely match qPCR-based quantification across dilution series, and can be tuned to balance sensitivity and accuracy. This method allows metabarcoding data to move beyond presence and relative abundance toward robust, scalable quantification of eDNA. You can download the full paper here.
This white paper explores the use of RNA-bait hybridization capture to identify feral pig diet from fecal DNA, overcoming a major limitation of traditional metabarcoding where host DNA overwhelms prey detection. Using custom-designed RNA baits targeting vertebrate prey, Jonah Ventures successfully recovered long mitochondrial sequences that improved taxonomic certainty and revealed prey species that were undetectable with standard metabarcoding primers. The results demonstrate that hybridization capture is a powerful approach for resolving complex diets, enabling more sensitive and confident prey identification in challenging, host-dominated samples. You can download the full white paper here.