Environmental DNA methods for biosecurity and invasion biology in terrestrial ecosystems: Progress, pitfalls, and prospects

Analysis of environmental DNA (eDNA) enables indirect detection of species without the need to directly observe and sample them. For biosecurity and invasion biology, eDNA-based methods are useful to address biological invasions at all phases, from detecting arrivals to confirming eradication of past invasions. We conducted a systematic review of the literature and found that in biosecurity and invasion biology, eDNA has primarily been used to detect new incursions and monitor spread in marine and freshwater ecosystems, with much slower uptake in terrestrial ecosystems, reflecting a broader trend common to the usage of eDNA tools. In terrestrial ecosystems, eDNA research has mostly focussed on the use of eDNA metabarcoding to characterise biodiversity, rather than targeting biosecurity threats or non-native populations. We discuss how eDNA-based methods are being applied to terrestrial ecosystems for biosecurity and managing non-native populations at each phase of the invasion continuum: transport, introduction, establishment, and spread; across different management options: containment, control, and eradication; and for detecting the impact of non-native organisms. Finally, we address some of the current technical issues and caveats of eDNA-based methods, particularly for terrestrial ecosystems, and how these might be solved. As eDNA-based methods improve, they will play an increasingly important role in the early detection and adaptive management of biological invasions, and the implementation of effective biosecurity controls.

The genome of the toxic invasive species Heracleum sosnowskyi carries an increased number of genes despite absence of recent whole-genome duplications

Heracleum sosnowskyi, belonging to a group of giant hogweeds, is a plant with large effects on ecosystems and human health. It is an invasive species that contributes to the deterioration of grassland ecosystems. The ability of H. sosnowskyi to produce linear furanocoumarins (FCs), photosensitizing compounds, makes it very dangerous. At the same time, linear FCs are compounds with high pharmaceutical value used in skin disease therapies. Despite this high importance, it has not been the focus of genetic and genomic studies. Here, we report a chromosome-scale assembly of Sosnowsky's hogweed genome. Genomic analysis revealed an unusually high number of genes (55106) in the hogweed genome, in contrast to the 25-35 thousand found in most plants. However, we did not find any traces of recent whole-genome duplications not shared with its confamiliar, Daucus carota (carrot), which has approximately thirty thousand genes. The analysis of the genomic proximity of duplicated genes indicates on tandem duplications as a main reason for this increase. We performed a genome-wide search of the genes of the FC biosynthesis pathway and surveyed their expression in aboveground plant parts. Using a combination of expression data and phylogenetic analysis, we found candidate genes for psoralen synthase and experimentally showed the activity of one of them using a heterologous yeast expression system. These findings expand our knowledge on the evolution of gene space in plants and lay a foundation for further analysis of hogweed as an invasive plant and as a source of FCs.

Appraising the Genetic Makeup of an Allochthonous Southern Pike Population: An Opportunity to Predict the Evolution of Introgressive Hybridization in Isolated Populations?

Biological invasions are a major threat to the conservation of biodiversity, as invasive species affect native biota through competition, predation, pathogen introduction, habitat alteration, and hybridisation. The present study focuses on a southern pike population, Esox cisalpinus (Teleostei: Esocidae), that has been introduced outside the species' native range. Using microsatellite markers, this study's objective was to gather baseline genetic information and assess the presence of hybrids between this species and E. lucius in the introduced population. The resulting estimates of genetic diversity and effective population size are comparable to those observed in the species' native range. Although different methods yield contrasting and uncertain evidence regarding introgressive hybridization, the presence of late-generation hybrids cannot be completely ruled out. Large numbers of breeders as well as multiple introductions of genetically divergent cohorts and introgressive hybridisation may explain the high genetic diversity of this recently introduced southern pike population. The present study issues a warning that the conservation of southern pike' introgressive hybridisation between northern and southern pike might be underestimated. The genetic information gathered herein may unravel the origin, number of introduction events, and evolutionary trajectory of the introduced population. This information may help us understand the evolution of introgressive hybridisation in the southern pike's native areas.

Advancing the protection of marine life through genomics

The rapid growth in genomic techniques provides the potential to transform how we protect, manage, and conserve marine life. Further, solutions to boost the resilience of marine species to climate change and other disturbances that characterize the Anthropocene require transformative approaches, made more effective if guided by genomic data. Although genetic techniques have been employed in marine conservation for decades and the availability of genomic data is rapidly expanding, widespread application still lags behind other data types. This Essay reviews how genetics and genomics have been utilized in management initiatives for ocean conservation and restoration, highlights success stories, and presents a pathway forward to enhance the uptake of genomic data for protecting our oceans.

Genomic data is missing for many highly invasive species, restricting our preparedness for escalating incursion rates

Biological invasions drive environmental change, potentially threatening native biodiversity, human health, and global economies. Population genomics is an increasingly popular tool in invasion biology, improving accuracy and providing new insights into the genetic factors that underpin invasion success compared to research based on a small number of genetic loci. We examine the extent to which population genomic resources, including reference genomes, have been used or are available for invasive species research. We find that 82% of species on the International Union for Conservation of Nature “100 Worst Invasive Alien Species” list have been studied using some form of population genetic data, but just 32% of these species have been studied using population genomic data. Further, 55% of the list’s species lack a reference genome. With incursion rates escalating globally, understanding how genome-driven processes facilitate invasion is critical, but despite a promising trend of increasing uptake, “invasion genomics” is still in its infancy. We discuss how population genomic data can enhance our understanding of biological invasion and inform proactive detection and management of invasive species, and we call for more research that specifically targets this area.

A genotyping‐in‐thousands by sequencing panel to inform invasive deer management using noninvasive fecal and hair samples

Studies in ecology, evolution, and conservation often rely on noninvasive samples, making it challenging to generate large amounts of high‐quality genetic data for many elusive and at‐risk species. We developed and optimized a Genotyping‐in‐Thousands by sequencing (GT‐seq) panel using noninvasive samples to inform the management of invasive Sitka black‐tailed deer (Odocoileus hemionus sitkensis) in Haida Gwaii (Canada). We validated our panel using paired high‐quality tissue and noninvasive fecal and hair samples to simultaneously distinguish individuals, identify sex, and reconstruct kinship among deer sampled across the archipelago, then provided a proof‐of‐concept application using field‐collected feces on SGang Gwaay, an island of high ecological and cultural value. Genotyping success across 244 loci was high (90.3%) and comparable to that of high‐quality tissue samples genotyped using restriction‐site associated DNA sequencing (92.4%), while genotyping discordance between paired high‐quality tissue and noninvasive samples was low (0.50%). The panel will be used to inform future invasive species operations in Haida Gwaii by providing individual and population information to inform management. More broadly, our GT‐seq workflow that includes quality control analyses for targeted SNP selection and a modified protocol may be of wider utility for other studies and systems where noninvasive genetic sampling is employed.

Population genomics of Sitka black-tailed deer supports invasive species management and ecological restoration on islands

Invasive mammals represent a critical threat to island biodiversity; eradications can result in ecological restoration yet may fail in the absence of key population parameters. Over-browsing by invasive Sitka black-tailed deer (Odocoileus hemionus sitkensis) is causing severe ecological and cultural impacts across the Haida Gwaii archipelago (Canada). Previous eradication attempts demonstrate forest regeneration upon deer removal, but reinvasion reverses conservation gains. Here we use restriction-site associated DNA sequencing (12,947 SNPs) to investigate connectivity and gene flow of invasive deer (n = 181) across 15 islands, revealing little structure throughout Haida Gwaii and identifying the large, central island of Moresby (>2600 km²) as the greatest source of migrants. As a result, the archipelago itself should be considered the primary eradication unit, with the exception of geographically isolated islands like SGang Gwaay. Thus, limiting eradications to isolated islands combined with controlled culling and enhanced biosecurity may be the most effective strategies for achieving ecological restoration goals.

Genomic data presented in this study provide clues about why previous attempts to eradicate the invasive Sitka black-tailed deer from the Haida Gwaii archipelago in Canada have been incomplete. The authors find substantial gene flow between islands, with the exception of the remote island of SGang Gwaay, which they argue is a viable option for near-term eradication efforts.