Early Detection Of Invasive Species Research Articles

New dockside eDNA based protocol to detect the seaweed Asparagopsis armata evaluated by stakeholders

Early detection of invasive species is crucial to deal effectively with biological invasions in ports, which are hotspots of species introductions. In this study, a simplified end-time PCR methodology conducted on eDNA from water samples was developed for rapid detection of the invasive seaweed Asparagopsis armata (four hours from water collection to result visualization). It was tested dockside in four international Spanish ports in presence of stakeholders, whose feedback was obtained to explore the real applicability of this biotechnology. Although biological invasions were not a main concern for them, results indicate a unanimous approval of the methodology by the stakeholders, having detected the presence of A. armata in three of the ports. Stakeholders suggested further developments for easier application of the tool and multiple species detection, to be adopted for the control of invasive species in ports.

Distribution of the Cannabis sativa L. in the Western Himalayas: A tale of the ecological factors behind its continuous invasiveness

The invasion of species in new regions depends on multiple factors, especially, the prevailing environmental factors. The environmental conditions are essential to understand for planning effective management strategies related to invasive species. Little is known about Cannabis as an established invasive weed. We hypothesized that the successful establishment of this invading species is influenced by the environmental variables; however, some of them have a much stronger influence than the others. Quantitative ecological methods were adopted for sampling the habitats invaded by Cannabis sativa, in a total of 165 quadrats. Soil samples were collected for soil analyses from each of those quadrat. Ecological and statistical approaches including Structure Equation Modeling (SEM) procedures were applied to evaluate the impact of environmental factors, ecological interrelationships, and the resultant invasiveness of the C. sativa. Our findings indicate that elevation, temperature, humidity, anthropogenic pressure, physio-chemical prperties of soil and habitat degradation play significant roles in determining the distribution and abundance of C. sativa. Principal Component Analysis (PCA) of the parameters further clarifies that elevation is the most important driver in explaining the successful establishment of the invader species with a 30.1% variance. Structural equation modeling further confirms the significant role played by elevation, which not only directly affects the abundance of Cannabis but also indirectly influences other variables such as anthropogenic pressure, temperature, and humidity etc. However, the invasion of C. sativa is less affected by soil saturation pH, electrical conductivity, phosphorous, potassium, and CaCO3. Our study provides valuable scientific information that could be used for the early detection of invasive species at the early stage of invasion and in devising policies for their management and control.

Incursion Preparedness, Citizen Science and Early Detection of Invasive Insects: The Case of Aleurocanthus spiniferus (Hemiptera, Aleyrodidae) in France.

We describe the process by which the quarantine whitefly, Aleurocanthus spiniferus (Hemiptera, Aleyrodidae), was detected in France. The initial observation was made by a volunteer who reported a picture of an adult in the Inventaire National du Patrimoine Naturel (INPN Espèces), a citizen science resource developed by l'Office Français de la Biodiversité and the French Muséum National d'Histoire Naturelle. The specimen was suspected to be A. spiniferus from this picture by one of the expert entomologists in charge of the Hemiptera group validation. Once the species was identified, it was mounted on a slide and the information was officially passed on to the ministry in charge of agriculture via a communication channel set up in advance for this type of situation. The ministry then triggered the regulatory actions planned in the event of the suspected detection of quarantine organisms. Sampling was quickly carried out and the specimens collected on this occasion were formally identified as belonging to the species A. spiniferus. This led to the formalization of an outbreak in France. This sequence of decisions took just two months from the first observation to the implementation of a management plan. This case presents how incursion preparedness contributes to a rapid response. Furthermore, this case exemplifies how citizen science can contribute to the early detection of invasive species and highlights the importance of informing both the general public and professionals about major environmental issues.

Predicting the spatio-temporal pattern of range expansion under lack of equilibrium with climate

Early detection of invasive species in regions under threat is key for biodiversity conservation. Here we conduct a retrospective study to assess whether correlative Species Distribution Models (SDMs) can predict the spatio-temporal range of expansion in an invasive species, the Asian hornet. Given that modelling invasive species distributions defies one of the main assumptions of SDMs, the equilibrium with climate, we also introduce a quantitative assessment of climatic disequilibrium in the invaded area based on hypervolume comparison between the native and invaded areas (both unoccupied and occupied territories). We evaluate the ability of three different modelling approaches (presence-only, presence-background and presence-absence) calibrated with data until 2013 to predict the species distribution observed the following years (2015, 2017, 2019, and 2021). Our results show that presence-only models based on the BIOCLIM algorithm can effectively predict the spatio-temporal pattern of invasion when predictions are rescaled based on percentiles (i.e. ranked suitability) and the model is calibrated with data from both native and invaded areas. These models predicted higher suitability values for sites that were invaded earlier in time and, importantly, they did not predict low suitability values for sites that were eventually occupied years later. Thus, they can be very useful for decision-makers and managers, as they provide a probabilistic prediction of both (i) the temporal dimension of species range expansion, and (ii) the potential distribution range in the long term. Such information would allow prioritizing monitoring efforts in the short term without losing sight of the potential risks in the long term.

Combining multiple markers significantly increases the sensitivity and precision of eDNA‐based single‐species analyses

AbstractThe analysis of environmental DNA (eDNA) is becoming integrated as an established biomonitoring tool, often characterized by detection limits exceeding those of conventional counterparts. However, further improving the sensitivity of these methods may be invaluable for the early detection of invasive species, or for locating remnant populations of endangered species, and the adequate quantification of their abundances. In this study, we provide empirical evidence showing that the implementation of multiple genetic markers targeting different loci is a surprisingly overlooked strategy to increase the sensitivity of single‐species detections and quantification of their abundance, particularly at the lower end of the species abundance range. We analyzed 45 natural eDNA samples obtained from a wide range of water bodies in Belgium, in which either the invasive American bullfrog (Lithobates catesbeianus) or the rare European weather loach (Misgurnus fossilis) occurred under variable abundances, and compared detection success and precision of quantification of simplex (single locus) versus multiplex (multilocus) droplet digital PCR (ddPCR) analyses. Multiplexing different primer/probe assays targeting independent loci resulted in a significantly enhanced detection probability compared to the simplex analyses, gaining a twofold reduction in the limit of detection (LOD). Also the precision of eDNA quantification significantly improved in multiplex reactions, especially in low concentration samples. This was reflected in a significant reduction in the coefficient of variation (CV) among technical replicates, resulting in an associated decrease of the limit of quantification (LOQ). We conclude that the use of multiple markers can significantly improve the analytical sensitivity of eDNA‐based single‐species detections and precision of absolute abundance quantifications.

Incidental invertebrate‐derived DNA detection of invasive and threatened species in temperate dry Southeast Australian forest

AbstractWell‐informed biodiversity conservation practice can often be precluded by poor species detectability. For example, populations being missed during surveys can lead to them being omitted from species lists or area management plans. iDNA (invertebrate‐derived DNA) is a recently developed set of techniques for improving the detectability of elusive vertebrates by exploiting their associated invertebrates. Parasitic and scavenging invertebrates can be readily collected, and their gut contents DNA barcoded to detect local vertebrate diversity. However, most iDNA surveys have targeted mammals and have been carried out in tropical areas and/or rainforests. We carried out iDNA surveys targeting frogs in temperate dry sclerophyll forests in south‐eastern Australia. We set mosquito traps broadcasting recorded frog calls with the aim of collecting frog‐biting flies, which are attracted to frog calls. We collected 156 fly specimens, although none were of frog‐biting species, and no frogs were detected via iDNA, despite many being observed in the field. However, two mammal and one reptile species were detected via iDNA: the feral cat (Felis catus: Felidae), domestic dog or dingo (Canis lupus: Canidae) and the threatened Rosenberg's monitor (Varanus rosenbergi: Varanidae). Vertebrate‐sampling flies are likely highly abundant in the area since they were collected apparently incidentally in traps lacking appropriate attractants; a promising result for further surveys is different attractants are employed. This study is one of the few in which an invasive species has been detected through iDNA, and highlights its potential for improved detectability of threatened species outside of the tropics and early detection of invasive species.

Undetected but Widespread: the Cryptic Invasion of Non-Native Cattail (Typha) in a Pacific Northwest Estuary

The early detection of invasive species is an important predictor of management success. Non-native narrow-leaved cattail (Typha angustifolia) has been detected in the Fraser River Estuary (FRE) in recent decades, but questions around their degree of establishment, and the potential emergence of hybrid cattail (Typha × glauca), remain unanswered. This study models the current and potential future distribution of non-native cattail in the FRE using a combination of spectral imagery analysis and species distribution modeling. Contrary to our expectation, we find that non-native cattails are widespread, currently occupying approximately 4 or 50 ha of FRE tidal marshes. Though never formally recorded in the estuary previously, T. × glauca appears to be the more abundant taxon, suggesting heterosis may be facilitating this invasion. We describe these taxa as cryptic invasive species, as their resemblance to native cattail (Typha latifolia) likely inhibited their detection. In our species distribution model, we distinguish between site suitability (ability to establish and persist) and susceptibility (risk of colonization when suitable). Our model predicts the scale of this invasion may increase over time, as 29% and 20% of the estuary has moderate or high suitability and susceptibility probabilities, respectively, while 16% and 24% of these habitats are currently occupied. Estuary-wide containment and eradication are unlikely given the extent of this invasion. Consequently, we recommend management prioritize monitoring and early eradication in areas of high conservation and cultural value. This study highlights the vulnerability of estuaries to cryptic invasions and the invasibility of Pacific Northwest estuaries by non-native cattail.

Assessing the Efficacy of Phenological Spectral Differences to Detect Invasive Alien Acacia dealbata Using Sentinel-2 Data in Southern Europe

Invasive alien plants are transforming the landscapes, threatening the most vulnerable elements of local biodiversity across the globe. The monitoring of invasive species is paramount for minimizing the impact on biodiversity. In this study, we aim to discriminate and identify the spatial extent of Acacia dealbata Link from other species using RGB-NIR Sentinel-2 data based on phenological spectral peak differences. Time series were processed using the Earth Engine platform and random forest importance was used to select the most suitable Sentinel-2 derived metrics. Thereafter, a random forest machine learning algorithm was trained to discriminate between A. dealbata and native species. A flowering period was detected in March and metrics based on the spectral difference between blooming and the pre flowering (January) or post flowering (May) months were highly suitable for A. dealbata discrimination. The best-fitted classification model shows an overall accuracy of 94%, including six Sentinel-2 derived metrics. We find that 55% of A. dealbata presences were widely widespread in patches replacing Pinus pinaster Ait. stands. This invasive alien species also creates continuous monospecific stands representing 33% of the presences. This approach demonstrates its value for detecting and mapping A. dealbata based on RGB-NIR bands and phenological peak differences between blooming and pre or post flowering months providing suitable information for an early detection of invasive species to improve sustainable forest management.

Round Goby Detection in Lakes Huron and Michigan—An Evaluation of eDNA and Fish Catches

Aquatic surveys for fish in large water bodies (e.g., Laurentian Great Lakes of North America) often require a flexible approach using multiple methods, surveying different depths, and sampling across seasons, especially when the target species is elusive in its natural habitat. The round goby (Neogobius melanostomus) is an invasive, bottom-dwelling fish inhabiting rocky areas of all five Great Lakes. While trawl surveys are typically used for abundance assessments, angling has been demonstrated as a means of supplementing surveys with additional data. Yet, round goby abundance and distribution is still not well described. Recently, with considerable success, scientists have explored sampling environmental DNA (eDNA) to complement traditional monitoring techniques for population abundance estimates, early detection of invasive species, and spawning or migration events. Therefore, we collected eDNA from water samples alongside bottom trawls and hook and line angling in Lakes Huron and Michigan to detect round goby. eDNA samples were analyzed by both droplet digital PCR (ddPCR) and quantitative PCR (qPCR) to maximize the likelihood of detection. Overall, round goby was captured in 23% of the trawls, but the eDNA based methods detected round goby in 74% and 66% of samples by ddPCR and qPCR, respectively, mostly in samples collected at <30 m depths, and mostly in the fall. More studies comparing eDNA based methods to traditional monitoring, especially trawls in large open waters, may contribute to a better understanding of using eDNA in population assessments.

Integrating invasive species risk assessment into environmental DNA metabarcoding reference libraries.

Environmental DNA (eDNA) metabarcoding has shown promise as a tool for estimating biodiversity and early detection of invasive species. In aquatic systems, advantages of this method include the ability to concurrently monitor biodiversity and detect incipient invasions simply through the collection and analysis of water samples. However, depending on the molecular markers chosen for a given study, reference libraries containing target sequences from present species may limit the usefulness of eDNA metabarcoding. To explore the extent of this issue and how it may be resolved to aid biodiversity and invasive species early detection goals, we focus on fishes in the well-studied Laurentian Great Lakes region. First, we provide a synthesis of species currently known from the region and of non-indigenous species identified as threats by international, national, regional, and introduction pathway-specific fish risk assessments. With these species lists, we then evaluate 23 primer pairs commonly used in fish eDNA metabarcoding with available databases of sequence coverage and species specificity. Finally, we identify established and potentially invasive non-indigenous fish that should be prioritized for genetic sequencing to ensure robust eDNA metabarcoding for the region. Our results should increase confidence in using eDNA metabarcoding for fisheries conservation and management in the Great Lakes region and help prioritize reference sequencing efforts. The ultimate utility of eDNA metabarcoding approaches will come when conservation management of existing fish communities is integrated with early detection efforts for invasive species surveillance to assess total fish biodiversity.

Policy action needed to unlock eDNA potential

The technological innovation of environmental DNA (eDNA) began about 14 years ago with the detection of DNA from American bullfrogs (Lithobates catesbeianus, formerly Rana catesbeiana) in water samples from French ponds (Ficetola et al. 2008). Hundreds of journal publications later, many research groups have continued to innovate, expanding the genetic information derived from field samples. What started with the detection of a single target species now extends to detecting hundreds of species simultaneously (Deiner et al. 2017), and to quantifying genetic diversity and population size (Andres et al. 2021). Terrestrial animals and plants are now also targeted from eDNA in water, soil, and air samples (Clare et al. 2022). The rapid pace of research has fueled many studies of management relevance, including detection of incipient invasions to guide control efforts (Jerde et al. 2011); detection of imperiled species to facilitate habitat protection; quantification of biodiversity trends over large spatial scales; and, in Europe, monitoring of indicator species or entire biological communities to establish baselines for environmental impacts (Lanzén et al. 2021). Deployment of eDNA technology improves measurements of biodiversity, which could enable better management. Unfortunately, US government policies have lagged behind this scientific innovation, and consequently the eDNA economy has not boomed. Federal agencies have generally regarded eDNA as unreliable for decision making, so far largely failing to establish a potentially virtuous cycle between innovations in eDNA technology and management (Figure 1). The scientific and policy communities now have a crucial opportunity to establish a positive technology–policy feedback using eDNA for biodiversity surveillance, monitoring, and protection as well as for ecosystem management. My collaborators and I are familiar with the challenges at the eDNA technology–management nexus. We took our first water samples for eDNA in 2009 and produced one of the first publications (Jerde et al. 2011) demonstrating eDNA’s potential usefulness to natural resource management at a large geographic scale – the invasion of silver carp (Hypophthalmichthys molitrix) and bighead carp (H nobilis) in Chicago area waterways that connect the watersheds of the Mississippi River and the Laurentian Great Lakes. We discovered invasive carp eDNA far closer to Lake Michigan than expected. After much controversy, many briefings, and actions involving multiple state and federal agencies, the genetic findings that I presented in a 2010 Chicago federal court were admitted as evidence, enabling future uses of eDNA by agencies in litigation. Over a decade later, doubts about the usefulness of eDNA results are long gone, while the need for standard protocols and decision support for management uptake remains (Sepulveda et al. 2020). Multiple federal agencies have built their own eDNA research laboratories (Morisette et al. 2021), providing opportunities for federal scientists and decision makers to gain confidence in the potential applications of eDNA. In addition, established companies in field equipment and environmental consulting, along with many start-ups, now sell specialized eDNA field and lab products and offer limited eDNA services. However, for eDNA use to transition – quickly and at scale – from the research laboratory to the management arena, government agencies should take the next step to base regulatory decisions on eDNA. Thus far, federal agencies have largely avoided doing so, despite the precedent of the admissibility of eDNA in federal court. Greater government reliance on eDNA would incentivize market demand for environmental consulting firms, universities, and other potential service providers. Government agencies could establish processes to certify eDNA labs as reliable sources of data. Without such steps, the potential for improved environmental protection and economic growth continues to be unrealized. There are signs of progress. The National Oceanic and Atmospheric Administration (NOAA) recently proposed to operationalize eDNA to detect harmful marine species, identify mislabeled seafood, monitor aquaculture impacts, manage marine fisheries and food webs, and search for biodiversity of commercial value – all to support the US Department of Commerce’s efforts to grow the “Blue Economy” (https://bit.ly/3T5y4uh) (Morisette et al. 2021). Also part of the Blue Economy initiative, offshore wind development has been dramatically accelerated by the Biden administration. This acceleration necessitates learning how to design, site, and operate vast offshore wind farms while minimizing adverse environmental impacts. The US Department of Interior’s Bureau of Ocean Energy Management (BOEM) has funded research in preparation for using eDNA to monitor the distribution and abundance of offshore species, as already performed at European offshore energy installations (Lanzén et al. 2021). Ørsted recently announced a US$13 million fisheries study, including eDNA surveys, in association with their proposed 1000-megawatt Ocean Wind 1 project off the New Jersey coast. The need for fast and inexpensive methods to collect baseline biodiversity data continues to grow as the Inflation Reduction Act of 2022 extends BOEM’s responsibilities to explore feasibility of offshore wind in US territories including Puerto Rico, Guam, and American Samoa. The US Environmental Protection Agency (EPA) is exploring the use of eDNA or eRNA for assessing risks associated with ballast-water discharge under the Clean Water Act (CWA). EPA could also consider accepting eDNA for pre- and post-project biodiversity monitoring for CWA compliance for inland water discharges, aquaculture facilities, and other installations under EPA purview. Likewise, the White House Council on Environmental Quality and partner federal agencies could encourage the use of eDNA in environmental impact assessments mandated by the US National Environmental Policy Act. In efforts to prevent the importation of harmful species into the US, the US Fish and Wildlife Service (USFWS) started using eDNA in 2021, as one component of inspection for importations of aquarium moss balls, many of which were contaminated with a prohibited species: zebra mussels (Dreissena polymorpha). However, eDNA has so far been neither used as the sole basis for regulatory interdiction nor expanded to other target species for several reasons, including the lack of approved protocols, resistance from states, and industry opposition. To align with inspection, forensic, and other enforcement standards, broader rules or standards for eDNA must accommodate the best available technology as eDNA innovations continue. The Bipartisan Infrastructure Law of 2022 provides opportunities for federal agencies to build better biodiversity surveillance and monitoring capacities, including eDNA, to make more efficient management possible, especially early detection of invasive species. NOAA, BOEM, EPA, and the USFWS aspire to use eDNA because no traditional tool for monitoring biodiversity satisfies the need for large-scale, repeatable, fast, and affordable measurements. Aspirations to realize the Blue Economy, and protect the US from invasive species, illustrate the urgent need to incorporate eDNA into agency decision making. At the global scale, unmet policy imperatives could also be better satisfied using eDNA. More than half of the 20 Aichi Biodiversity Targets under the UN Convention on Biological Diversity (CBD) require metrics of biodiversity. To realize the potential of eDNA in this context, however, implementation of another part of the CBD, the Nagoya Protocol, must be clarified. In the permitting processes of many countries, it is unclear whether or which stages of eDNA samples and data (eg water sample filtrate, eDNA extracts, digital sequence information) are governed by the Nagoya Protocol. This murkiness has inhibited the application of eDNA in international contexts. The adoption of eDNA for regulatory decisions by US federal agencies and international bodies would enable faster commercialization of eDNA products and services, more affordable quantification of biodiversity, and accelerated energy transitions in response to climate change.

Challenges in eDNA detection of the invasive European green crab, Carcinus maenas

The early detection of invasive species is essential to cease the spread of the species before it can cause irreversible damage to the environment. The analysis of environmental DNA (eDNA) has emerged as a non-harmful method to detect the presence of a species before visual detection and is a promising approach to monitor invasive species. Few studies have investigated the use of eDNA for arthropods, as their exoskeleton is expected to limit the release of eDNA into the environment. We tested published primers for the invasive European green crab, Carcinus maenas, in the Gulf of Maine and found them not species-specific enough for reliable use outside of the area for which they were designed for. We then designed new primers, tested them against a broad range of local faunal species, and validated these primers in a field study. We demonstrate that eDNA analyses can be used for crustaceans with an exoskeleton and suggest that primers and probe sequences must be tested on local fauna at each location of use to ensure no positive amplification of these other species.

Reinforcement of Environmental DNA Based Methods (Sensu Stricto) in Biodiversity Monitoring and Conservation: A Review.

Simple SummaryWorldwide biodiversity loss points to a necessity of upgrading to a fast and effective monitoring method that can provide quick conservation action. Newly developed environmental DNA (eDNA) based method found to be more cost-effective, non-invasive, quick, and accurate than traditional monitoring (spot identification, camera trapping). Although the eDNA based methods are proliferating rapidly, as a newly developed branch, it needs more standardization and practitioner adaptation. The present study aims to evaluate the eDNA based methods, and their potential achievements in biodiversity monitoring, and conservation for quick practitioners’ adaption. The investigation shows that the eDNA technique is applicable largely in (i) early detection of invasive species, (ii) species detection for conservation, (iii) community-level biodiversity monitoring, (iv) ecosystem health monitoring, (v) study on trophic interactions, etc. Thus, the eDNA technique shows a great promise with its high accuracy and authenticity, and will be applicable alone or alongside other methods in the near future.Recently developed non-invasive environmental DNA-based (eDNA) techniques have enlightened modern conservation biology, propelling the monitoring/management of natural populations to a more effective and efficient approach, compared to traditional surveys. However, due to rapid-expansion of eDNA, confusion in terminology and collection/analytical pipelines can potentially jeopardize research progression, methodological standardization, and practitioner adoption in several ways. Present investigation reflects the developmental progress of eDNA (sensu stricto) including highlighting the successful case studies in conservation management. The eDNA technique is successfully relevant in several areas of conservation research (invasive/conserve species detection) with a high accuracy and authentication, which gradually upgrading modern conservation approaches. The eDNA technique related bioinformatics (e.g., taxon-specific-primers MiFish, MiBird, etc.), sample-dependent methodology, and advancement of sequencing technology (e.g., oxford-nanopore-sequencing) are helping in research progress. The investigation shows that the eDNA technique is applicable largely in (i) early detection of invasive species, (ii) species detection for conservation, (iii) community level biodiversity monitoring, (iv) ecosystem health monitoring, (v) study on trophic interactions, etc. Thus, the eDNA technique with a high accuracy and authentication can be applicable alone or coupled with traditional surveys in conservation biology. However, a comprehensive eDNA-based monitoring program (ecosystem modeling and function) is essential on a global scale for future management decisions.

Mapping the Extent of Invasive Phragmites australis subsp. australis From Airborne Hyperspectral Imagery

Invasive species pose one of the greatest threats to global biodiversity. Early detection of invasive species is critical in order to prevent or manage their spread before they exceed the ability of land management groups to control them. Optical remote sensing has been established as a useful technology for the early detection and mapping of invasive vegetation populations. Through the use of airborne hyperspectral imagery (HSI), this study establishes a target detection methodology used to identify and map the invasive reed Phragmites australis subsp. australis within the entire extent of Îles-de-Boucherville National Park (Quebec, ON, Canada). We applied the Spectral Angle Mapper (SAM) target detection algorithm trained with a high accuracy GNSS ground truth data set to produce a park-wide map illustrating the extent of detected Phragmites. The total coverage of detected Phragmites was 26.74 ha (0.267 km2), which represents 3.28% of the total park area of 814 ha (8.14 km2). The inherent spatial uncertainty of the airborne HSI (∼2.25 m) was accounted for with uncertainty buffers, which, when included in the measurement of detected Phragmites, lead to a total area of 59.17 ha (0.591 km2), or 7.26% of the park. The overall accuracy of the Phragmites map was 84.28%, with a sensitivity of 76.32% and a specificity of 91.57%. Additionally, visual interpretation of the validation ground truth dataset was performed by 10 individuals, in order to compare their performance to that of the target detection algorithm. The overall accuracy of the visual interpretation was lower than the target detection (i.e., 69.18%, with a sensitivity of 59.21% and a specificity of 78.31%). Overall, this study is one of the first to utilize airborne HSI and target detection to map the extent of Phragmites over a moderately large extent. The uses and limitations of such an approach are established, and the methodology described here in detail could be adapted for future remote sensing studies of Phragmites or other vegetation species, native or invasive, at study sites around the world.

Recent advances in environmental DNA‐based biodiversity assessment and conservation

Knowledge of species distribution across space and time is critical to ecological conservation and environmental management at the local, regional and global scales (Albert et al., 2021). Traditional morphology-based surveys on either single-celled protists or larger animals and plants are time-consuming and largely expert-dependent (Baird & Hajibabaei, 2012; Liu et al., 2017; Yang et al., 2017). Recently, there has been considerable interest in the detection of environmental DNA (eDNA) fragments to allow species identification and monitoring within different environments, including soil, sediment, water, snow or air (Abdullah et al., 2021; Rees et al., 2014; Xie et al., 2018). The eDNA analysis can be used to detect common, endangered, invasive or rare species (Liu et al., 2019; Sepulveda et al., 2020), and provide a potent tool for elucidating mechanistic insights into ecological and evolutionary processes (Baird & Hajibabaei, 2012; Bohmann et al., 2014; Pawlowski et al., 2021). In past decades, eDNA metabarcoding has been increasingly used to study the present and past biodiversity from population to community levels, and eDNA-based surveys have revolutionized studies in ecology and biodiversity sciences, particularly in aquatic ecosystems (Euclide et al., 2021; Valentini et al., 2016). The significance of various human activities has resulted in multiple interacting environmental stressors in all types of ecosystems (Pukk et al., 2021; Yang et al., 2022). Such stressors, including global climate change, invasive species, chemical pollution and habitat loss, have led to biodiversity crises and threatened the human sustainability and ecosystem health (Osathanunkul & Minamoto, 2021; Yang et al., 2017). Comprehensive biodiversity assessment and conservation management are prerequisites for addressing these significant challenges in the Anthropocene (Mace et al., 2012; Sepulveda et al., 2020). Indeed, effective biodiversity assessment and conservation management require a deep understanding of organisms’ geographical distributions and their respective roles in ecosystem processes and services (Mo et al., 2021; West et al., 2021). However, researchers and conservation managers have encountered numerous obstacles in answering these fundamental and applied research questions at the local, regional and global scales. The aim of this special issue—Environmental DNA-based biodiversity assessment and conservation—was to provide a selection of studies that highlight the utility and diversity of eDNA-based research for biodiversity assessment and conservation management within marine and freshwater ecosystems. This special issue includes 12 articles that advance our knowledge of eDNA. Together, these studies deliver compelling evidence for successful applications of eDNA-based surveys in aquatic ecosystems in the Anthropocene. Six papers in this issue are focused on different technological aspects of environmental DNA, including sampling, sequence reference libraries and DNA markers. Sampling and DNA extraction are key steps in the analysis of environmental DNA (Liu et al., 2019). Curtis et al. (2021) investigated the role of water flow on eDNA concentrations and subsequent effects on the detectability of an invasive freshwater clam (Corbicula fluminea) in streams across seasons. Their results indicated that higher stream flows decreased eDNA concentrations and that stream floods increased the rate of false negatives (i.e. non-detections) at locations where the target organism was relatively common in autumn. These results also highlight that eDNA applications for environmental management and conservation can be highly sensitive to the abiotic and biotic context of field sampling in lotic ecosystems. Wang et al. (2021) compared eDNA metabarcoding results between classical kick-net-based samples and water samples. Interestingly, they found that water eDNA-based sampling exhibited more exact sequence variants (ESVs) than kick-net-ethanol-based sampling (2,866 vs. 2,406), but fewer macroinvertebrate ESVs (381 vs. 481). Further, kick-net-based metabarcoding was more consistent with morphological identification compared with water eDNA-based metabarcoding (24.24% vs. 17.63%). Reliable DNA barcode reference libraries are critical for accurate species identification and biodiversity monitoring based on eDNA. Lin et al. (2021) analysed the cytochrome c oxidase subunit 1 (COI) DNA barcodes from 298 individuals of Tanytarsus non-biting midges, representing 56 morphospecies including several cryptic species from China. This study was an important step to build a comprehensive DNA barcode library for chironomids, which are an important group for biomonitoring. In another article, Marques et al. (2021) developed a user-friendly web interface (i.e. GAPeDNA) that provides a global overview of genetic database completeness for a given fish taxon, based on different metabarcoding primer pairs across space and conservation status. This tool is flexible and can be expanded to other taxa and primers upon data availability. Vieira et al. (2021) evaluated the gaps in the availability of DNA sequences, including cytochrome c oxidase subunit I (COI) and 18S rRNA (18S) gene sequences, and their accuracy for macroinvertebrates inhabiting Macaronesia's shallow marine habitats. They demonstrated the reference DNA sequence libraries are still highly incomplete, non-indigenous species have higher levels of sequence completion than native species, and that native morphospecies have a high proportion of hidden or cryptic diversity. More than one-third of the species exhibited discordant records, with higher percentages in non-indigenous species than native species. These results suggest careful compilation, verification and annotation of available sequences are fundamental to assembling large curated and reliable reference libraries with rigorous species identifications by taxonomic experts. The eDNA-based methods are becoming technically mature and have acceptable reliabilities in many cases; however, the lack of standardized efforts in method development and validation represents a critical obstacle of eDNA applications (Pawlowski et al., 2021). Xia et al. (2021) conducted a meta-analysis to test DNA marker sensitivity and found most studies used newly designed DNA markers, but researchers did not report the marker sensitivity and the limit of detection of non-indigenous or endangered species. These results may guide researchers in experimental design choices for environmental DNA-based studies in the near future. Six papers in this issue are focused on the biodiversity assessment and conservation management. Environmental DNA metabarcoding provides a valuable and complementary survey technique in conservation and management (Sepulveda et al., 2020). One study indicated that a simple eDNA metabarcoding assessment using a high number of low-volume (50-ml) samples, centrifugation and a single gene (mitochondrial 12S gene) can describe the coarse fish community structure of freshwater lakes and rivers (Euclide et al., 2021). The authors also suggested that additional conventional sampling and environmental DNA sampling may be necessary for a complete diversity census. Osathanunkul and Minamoto (2021) used eDNA-based approaches to qualitatively and quantitatively track the crocodile newt in Thailand. They found Tylototriton uyenoi is severely declining due to anthropogenic factors, thereby suggesting that eDNA-based methods could help in designing an effective conservation plan. In north-western Australia, West et al. (2021) applied metabarcoding of the mitochondrial 16S rRNA and CO1 genes to detect bony fish, elasmobranchs and aquatic reptiles from 71 mid-shelf, inshore, coastal and nearshore estuarine sites. Their eDNA metabarcoding was a highly sensitive detection tool that was able to discern fine-scale patterns of marine fishes across the large-scale oceanic region. Pukk et al. (2021) collected eDNA samples from 22 Michigan lakes and sequenced two mitochondrial gene regions (12S and 16S rRNA) to quantify influences of drainage connectivity and human activity on aquatic invasive species prevalence. The detection probabilities were generally higher with eDNA than traditional fisheries gear. More importantly, incorporating eDNA metabarcoding as a supplement to traditional fisheries surveys will permit managers to identify greater numbers of taxa, including early detection of invasive species, with less field effort and fish mortality. Further, eDNA methods may facilitate management activities of aquatic invasive species. Recently, with the rapid development of sequencing technology DNA-based experiments have become routinely used to study the microbial community in various ecosystems (Abdullah et al., 2021; Liu et al., 2019). Based on high-throughput sequencing and qPCR of anammox 16S rRNA gene, Liu et al. (2021) found diverse anammox bacteria in the aerobic water columns of the South China Sea, and Ca. Brocadia was the most dominant genus. This finding has improved our understanding of the distribution and survival strategies of anammox communities in an aerobic marine environment. In another study, Wu et al. (2021) investigated free-living (FL), nanoparticle-associated (NA) and microparticle-associated (MA) bacterial communities in the coastal South China Sea. They found the number of amplicon sequence variants (ASVs) increased from FL, NA to MA communities, and the majority of core ASVs was potential hydrocarbonoclastic bacteria. Interestingly, the homogeneous selection was most prominent in shaping FL communities, followed by NA and MA communities, whereas the stochastic processes exhibited the reverse pattern. In the past two decades, publication titles with “environmental DNA” have increased dramatically from 3 in 2000 to 16 in 2010 and to 223 in 2020 (Web of Science, accessed on 1 September 2021). Therefore, by no means will this special issue provide a full picture of environmental DNA (eDNA)-based studies; rather, it can serve as a window to showcase the recent and global developments in environmental DNA-based biodiversity assessment and conservation management. We believe further substantial advance is foreseeable in the fields of eDNA-based studies because they are entering an exciting and rapidly accelerating era. This work was supported by the National Natural Science Foundation of China (91851104) and the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA23040302). Over the past several decades, a key scientist in the study of urban ecology and sustainable development has been Prof. Jingzhu Zhao (1958–2021)—sadly, he died of cancer on 4 August 2021, and we dedicate this paper to him.

INVASION OF SAVANNAS BY PROSOPIS TREES IN EASTERN AFRICA: EXPLORING THEIR IMPACTS ON LULC DYNAMICS, LIVELIHOODS AND IMPLICATIONS ON SOIL ORGANIC CARBON STOCKS

Abstract. Trees of the genus Prosopis from the Americas, were introduced in Eastern Africa in the 1970s to mitigate land degradation and its associated disservices. However, over time these trees have spread and invaded valuable grasslands and croplands and consequently led to significant land use and land cover (LULC) changes and livelihood stress. Early detection of invasive species is essential for formulating effective management strategies to prevent further spread into non-invaded lands and for monitoring the outcome of management interventions. We mapped the spatio-temporal evolution and dynamics of Prosopis invasion, its impacts on LULC and livelihoods in Baringo, Kenya by applying a Random Forest classifier on Landsat satellite data over seven-year intervals from 1988 – 2016. We then linked the LULC changes to soil organic carbon (SOC) stocks that we had measured for the different LULCs and also to socio-economic data on annual costs of clearing Prosopis from farmlands. By 2016, Prosopis had invaded 18,792 ha of land, spreading at a rate of 640 ha/yr, while all other land uses and land cover declined, each by over 40% of its original coverage in 1988. Through LULC specific SOC measurements, and relating the changes to annual costs of clearing Prosopis, we found that Prosopis removal and restoration to grassland is more effective for climate change mitigation compared to Prosopis “cultivation” while also avoiding trade-offs with other ecosystem services and livelihoods. Therefore, future management of this species in Kenya and Eastern Africa should be based on a more collaborative and integrated approach.

Matching a snail's pace: successful use of environmental DNA techniques to detect early stages of invasion by the destructive New Zealand mud snail.

Early detection of invasive species allows for a more rapid and effective response. Restoration of the native ecosystem after an invasive population has established is expensive and difficult but more likely to succeed when invasions are detected early in the invasion process. Containment efforts to prevent the spread of known invasions also benefit from earlier knowledge of invaded sites. Environmental DNA (eDNA) techniques have emerged as a tool that can identify invasive species at a distinctly earlier time point than traditional methods of detection. Here, we focus on whether eDNA techniques can be successfully applied to detect new invasions by the destructive New Zealand Mud Snail Potamopyrgus antipodarum (NZMS). It is an opportune time to apply eDNA-based detection in P. antipodarum, which is currently expanding its invasive range across eastern North America. We collected water samples from eight sites in central Pennsylvania that prior evidence indicated were not yet invaded by the NZMS but were part of the same watershed as other previously documented invaded sites. We found evidence for NZMS invasion at five of the eight sites, with subsequent physical confirmation of mud snails at one of these sites. This study is the first example of successful application of eDNA to detect a previously unidentified invasive population of NZMS, setting the stage for further monitoring of at-risk sites to detect and control new invasions of this destructive snail. This study also shows potential opportunities for invasion monitoring offered by using low-cost efforts and methods that are adaptable for citizen science.

Outreach increases detections of an invasive species in a crowdsourced monitoring program

Crowdsourcing can be a useful tool for the early detection of invasive species. Invasive wild pigs (Sus scrofa) have been reported in Ontario, Canada. We compared trends in reporting frequency of wild pig sightings to trends in media events that included directions for the public on where to submit their wild pig sightings. We found that media events occurring on the same week, and in up to two weeks before the sighting was reported significantly increased the number of wild pig reports we received. Our findings suggest that media can be used to increase participation by the public. Because of this relationship, our findings also imply that reporting frequency alone cannot accurately index real changes in wild pig numbers—participants were more likely to report sightings after they had been exposed to relevant media, and spikes in the number of reports tracked our outreach efforts. Despite this limitation, reports of wild pig sightings from community members remain a cost-effective tool to detect low-density invasive species across large regions, and participation in the program can be increased with periodic news media and social media blitzes.

The first detection of the fungal pathogen batrachochytrium dendrobatidis in Norway with no evidence of population declines for great crested and smooth newts based on modeling on traditional trapping data

AbstractThe pathogenic fungus Batrachochytrium dendrobatidis (Bd) causes chytridiomycosis in amphibians across the world, often leading to population declines and species extinctions. Here, we present the first detection of Bd in Norway, diagnosed using environmental DNA (eDNA) in water samples. In a genetic screening of 31 ponds in southeastern Norway for Bd, great crested newt (Triturus cristatus) and smooth newt (Lissotriton vulgaris), we detected Bd in five different localities. Resampling in one location revealed that time of sampling seemingly had a strong effect on the concentration of Bd eDNA in the water, which increased from May till June. In contrast, eDNA concentration of great crested newt decreased during the same period. Following a traditional sampling approach with traps, newts in the investigated ponds have been sampled for population estimates since 2012. We imposed a model on the catch data and contrasted the Bd‐positive ponds to the Bd‐negative ponds, finding no signs of population declines in the Bd‐positive ponds. This could suggest either recent infection events, with animals still having low prevalence of Bd and with little time for Bd to affect the present breeding generations of newts, and/or that the two newt species are infection‐tolerant. This study further highlights eDNA as a tool for early detection of invasive species.

Morphology of the early larval stages of Lysmata lipkei Okuno amp; Fiedler, 2010 (Caridea: Lysmatidae): an invasive shrimp in the Western Atlantic.

Considering the importance of establishing different approaches to the early detection of invasive species, the present study aimed to describe and illustrate the morphology of the early larval stages of the shrimp Lysmata lipkei, an invasive species in the Western Atlantic. Additionally, we did a morphological comparison and a review of the other Lysmata species from the Western Atlantic Ocean with a known larvae description. The larvae used in this study were obtained by the maintenance, under laboratory conditions, of ovigerous hermaphrodites of L. lipkei, collected in the wild. Then, larvae were dissected under a stereo microscope and illustrated using a microscope equipped with a camera lucida. The first three larval stages (zoeae) of L. lipkei were illustrated, described, and compared to other species of Lysmata previously described of the Western Atlantic. Some features of the larval morphology of L. lipkei are very similar when compared to other Lysmata species with previous larval descriptions, such as a rostrum long and simple, the eyes stalked with a long peduncle from the second zoeae, one pterygostomian spine and several denticles along the anterior ventral margin of the carapace, similarities in the segmentation of the maxillipeds, and the presence of dorsolateral spines on the posterior margin of the 5th pleomere, among other features. Also, unique features were observed for L. lipkei, such as differences in the setation of some structures, including the antennule, antenna, maxillule, and maxillipeds. Using the morphological descriptions, we expect to identify species from the plankton, especially invaders, that might be present in the Western Atlantic, as well as assist in several areas in which the larval morphology is relevant.