Biology subjects

Kroos, G. C.

Publications and source records attributed to Kroos, G. C..

4 recordsLinked to original sources

bioRxiv2026

Temporal persistence of vertebrate airborne environmental DNA in a natural open-air setting

Airborne environmental DNA (eDNA) is a promising tool for detecting a wide range of terrestrial taxa, including threatened and invasive species, from trace genetic material shed into the air. Yet, application of this technique in species management is constrained by a limited understanding of airborne eDNA ecology, including temporal persistence of signals in open-air environments. We investigated the temporal persistence of airborne eDNA in a natural outdoor setting, using the invasive Bennetts wallaby Notamacropus rufogriseus as a case study. We captured airborne eDNA from a single Bennetts wallaby carcass, deployed in an area where wallabies are otherwise not present. A total of 180 samples were collected, spanning the period before deploying the carcass, the 11 days it was on site, and for 32 days after its removal, at distances of 1, 10, and 100 metres using both active (fan-assisted) and passive (no fan) collection methods. Although overall detection rates were low, wallaby DNA was detectable up to 100 metres away shortly after the wallaby was introduced to the site and for up to three days after its removal. These findings indicate that airborne eDNA persists only briefly. Actively sampling air using battery-powered fans significantly improved detection rates relative to passive sampling. We demonstrate that airborne eDNA can detect individual organisms in outdoor environments, but reliable detection requires robust sampling and replication to capture rare, transient signals. By revealing how these signals persist over time, our findings provide a framework for optimizing field deployment and for distinguishing remnant DNA from new incursions.

molecular biology↗

bioRxiv2025

Targeted Airborne eDNA Detection of Pest Wallabies: Effects of Sampler Type and Distance

Bennetts wallabies Notamacropus rufogriseus, introduced to New Zealand from Australia in the late 1800s, strongly exemplify the detection challenges posed by invasive terrestrial species that are rare, cryptic, and highly mobile. Across their invasive range, N. rufogriseus occupy large landscapes at low densities, making their surveillance challenging. Recent research has demonstrated that airborne environmental DNA (eDNA) can rapidly identify terrestrial vertebrate diversity in an area. Leveraging these findings, we investigate the utility of airborne eDNA for the targeted monitoring of N. rufogriseus, using a novel, probe-based quantitative PCR assay. The effects of filtration material, collection method (active versus passive), distance from the source, and environmental conditions were examined for their effects on airborne detection probability, using a captive population of wallabies in a controlled park setting. A total of 110 airborne samples were collected, 55 with active (battery-powered fan) samplers and 55 passive (non-powered) samplers, across six distinct experimental periods at distances of 0, 10, 100, and 1000 metres from the closest known source of wallaby DNA. Filters designed to capture coarse particles (>10 {micro}m) significantly improved detection rates and DNA recovery for actively collected samples, compared to filters targeting finer particles (1-10 {micro}m). Active samplers significantly outperformed passive samplers in overall detection rates, particularly at shorter ranges from the target. Distance from the source had a significant negative effect on detection probability. Detection rates declined sharply beyond 10 metres but remained possible up to 1 kilometre from the source for both collection methods. These findings demonstrate that airborne eDNA can detect terrestrial vertebrate species at ecologically relevant distances, supporting its potential for landscape-scale surveillance. Notably, these results underscore the importance of optimising sampler design when applying airborne eDNA for targeted species monitoring.

genetics↗

bioRxiv2024

tombRaider - improved species and haplotype recovery from metabarcoding data through artefact and pseudogene exclusion.

Environmental DNA metabarcoding has revolutionized ecological surveys of natural systems. By amplifying and sequencing small gene fragments from environmental samples containing complex DNA mixtures, scientists are now capable of exploring biodiversity patterns across the tree of life in a time-efficient and cost-effective manner. However, the accuracy of species and haplotype identification can be compromised by sequence artefacts and pseudogenes. Despite various strategies developed over the years, effective removal of artefacts remains challenging and inconsistent data reporting standards hinder reproducibility in eDNA metabarcoding experiments. To address these issues, we introduce tombRaider, an open-source command line software program (https://github.com/gjeunen/tombRaider) and R package (https://github.com/gjeunen/tombRaider_R) to remove artefacts and pseudogenes from metabarcoding data post clustering and denoising. tombRaider features a modular algorithm capable of evaluating multiple criteria, including sequence similarity, co-occurrence patterns, taxonomic assignment, and the presence of stop codons. We validated tombRaider using various published data sets, including mock invertebrate communities, air eDNA from a zoo, and salmon haplotypes from aquatic eDNA. Our results demonstrate that tombRaider effectively removed a higher proportion of artefacts while retaining authentic sequences, thus enhancing the accuracy and reliability of eDNA-derived diversity metrics. This user-friendly software program not only improves data quality in eDNA metabarcoding studies, but also contributes to standardised reporting practices, an aspect currently lacking in this emerging research field.

bioinformatics↗

bioRxiv2022

Ebony underpins Batesian mimicry in an insect melanic polymorphism

The evolution of Batesian mimicry - whereby harmless species avoid predation through their resemblance to harmful species - has long intrigued biologists. In rare cases, such mimicry systems can be highly dynamic, being maintained via frequency-dependent selection on intraspecific polymorphisms, in which only some individuals within a population resemble a noxious model. Here, we use genomic approaches to identify the genetic basis of a striking mimicry polymorphism within a widespread New Zealand stonefly complex. Specifically, highly melanised specimens of Zelandoperla closely resemble an aposematic stonefly (Austroperla cyrene) well-known for its production of hydrogen cyanide. We assess convergence in the colour pattern of these two species, compare their relative palatability to predators, and use genome-wide association mapping to elucidate the genetic basis of this mimicry polymorphism. Our analysis reveals that melanised Zelandoperla overlap significantly with Austroperla in colour space, but are significantly more palatable to predators, indicating that they are indeed Batesian mimics. Analysis of 194,773 genome-wide SNPs reveals a strong outlier locus (ebony) differentiating melanic (mimic) versus non-melanic phenotypes. As ebony has a well-documented role in insect melanin biosynthesis, our findings highlight its conserved function across deeply divergent hexapod lineages. Distributional records suggest a link between the occurrence of Zelandoperla mimics and forested ecosystems where the model Austroperla is abundant, suggesting the potential for adaptive shifts in this system underpinned by environmental change.

evolutionary biology↗