Environmental DNA detection and quantification of invasive red-eared sliders, Trachemy scripta elegans, in ponds and the influence of water quality

Climate match is key to predict range expansion of the world's worst invasive terrestrial vertebrates

Understanding the determinants of the range expansion of invasive alien species is crucial for developing effective prevention and control strategies. Nevertheless, we still lack a global picture of the potential factors influencing the invaded range expansion across taxonomic groups, especially for the world's worst invaders with high ecological and economic impacts. Here, by extensively collecting data on 363 distributional ranges of 19 of world's worst invasive terrestrial vertebrates across 135 invaded administrative jurisdictions, we observed remarkable variations in the range expansion across species and taxonomic groups. After controlling for taxonomic and geographic pseudoreplicates, model averaging analyses based on generalized additive mixed-effect models showed that species in invaded regions having climates more similar to those of their native ranges tended to undergo a larger range expansion. In addition, as proxies of propagule pressure and human-assisted transportation, the number of introduction events and the road network density were also important predictors facilitating the range expansion. Further variance partitioning analyses validated the predominant role of climate match in explaining the range expansion. Our study demonstrated that regions with similar climates to their native ranges could still be prioritized to prevent the spread of invasive species under the sustained global change.

Rarely naturalized, but widespread and even invasive: the paradox of a popular pet terrapin expansion in Eurasia

The North American terrapin, the red-eared slider, has globally recognized invasive status. We built a new extensive database using our own original and literature data on the ecology of this reptile, representing information on 1477 water bodies throughout Eurasia over the last 50 years. The analysis reveals regions of earliest introductions and long-term spatio-temporal dynamics of the expansion covering now 68 Eurasian countries, including eight countries reported here for the first time. We established also long-term trends in terms of numbers of terrapins per aquatic site, habitat occupation, and reproduction success. Our investigation has revealed differences in the ecology of the red-eared slider in different parts of Eurasia. The most prominent expression of diverse signs of invasion success (higher portion of inhabited natural water bodies, higher number of individuals per water body, successful overwintering, occurrence of juvenile individuals, successful reproduction, and establishment of populations) are typical for Europe, West Asia and East Asia and tend to be restricted to coastal regions and islands. Reproduction records coincide well with the predicted potential range based on climatic requirements but records of successful wintering have a wider distribution. This invader provides an excellent and possibly unique (among animals) example of wide alien distribution, without the establishment of reproducing populations, but through the recruitment of new individuals to rising pseudopopulations due to additional releases. Therefore, alongside the potential reproduction range, a cost-effective strategy for population control must take in account the geographical area of successful wintering.

A review of applications of environmental DNA for reptile conservation and management

Reptile populations are in decline globally, with total reptile abundance halving in the past half century, and approximately a fifth of species currently threatened with extinction. Research on reptile distributions, population trends, and trophic interactions can greatly improve the accuracy of conservation listings and planning for species recovery, but data deficiency is an impediment for many species. Environmental DNA (eDNA) can detect species and measure community diversity at diverse spatio-temporal scales, and is especially useful for detection of elusive, cryptic, or rare species, making it potentially very valuable in herpetology. We aim to summarize the utility of eDNA as a tool for informing reptile conservation and management and discuss the benefits and limitations of this approach. A literature review was conducted to collect all studies that used eDNA and focus on reptile ecology, conservation, or management. Results of the literature search are summarized into key discussion points, and the review also draws on eDNA studies from other taxa to highlight methodological challenges and to identify future research directions. eDNA has had limited application to reptiles, relative to other vertebrate groups, and little use in regions with high species richness. eDNA techniques have been more successfully applied to aquatic reptiles than to terrestrial reptiles, and most (64%) of studies focused on aquatic habitats. Two of the four reptilian orders dominate the existing eDNA studies (56% Testudines, 49% Squamata, 5% Crocodilia, 0% Rhynchocephalia). Our review provides direction for the application of eDNA as an emerging tool in reptile ecology and conservation, especially when it can be paired with traditional monitoring approaches. Technologies associated with eDNA are rapidly advancing, and as techniques become more sensitive and accessible, we expect eDNA will be increasingly valuable for addressing key knowledge gaps for reptiles.

Water pre-filtration methods to improve environmental DNA detection by real-time PCR and metabarcoding

Environmental DNA (eDNA) analysis is a novel approach for biomonitoring and has been mostly used in clear water. It is difficult to detect eDNA in turbid water as filter clogging occurs, and environmental samples contain various substances that inhibit the polymerase chain reaction (PCR) and affect the accuracy of eDNA analysis. Therefore, we applied a pre-filtration method to better detect the fish species (particularly pale chub, Opsariichthys platypus) present in a water body by measuring eDNA in environmental samples containing PCR inhibitors. Upon conducting 12S rRNA metabarcoding analysis (MiFish), we found that pre-filtration did not affect the number or identities of fish species detected in our samples, but pre-filtration through pore sizes resulted in significantly reduced variance among replicate samples. Additionally, PCR amplification was improved by the pre-filtration of environmental samples containing PCR inhibitors such as humic substances. Although this study may appear to be a conservative and ancillary experiment, pre-filtration is a simple technique that can not only improve the physical properties of water, such as turbidity, but also the quality of eDNA biomonitoring.

Influence of landscape condition on relative abundance and body condition of two generalist freshwater turtle species

Anthropogenic land use changes have broad impacts on biological diversity, often resulting in shifts in community composition. While many studies have documented negative impacts on occurrence and abundance of species, less attention has been given to native species that potentially benefit from anthropogenic land use changes. For many species reaching high densities in human-dominated landscapes, it is unclear whether these environments represent higher quality habitat than more natural environments. We examined the influence of landscape ecological integrity on relative abundance and body condition of two native generalist freshwater turtle species that are prevalent in anthropogenic systems, the painted turtle (Chrysemys picta) and red-eared slider (Trachemys scripta elegans). Relative abundance was negatively associated with ecological integrity for both species, but the relationship was not strongly supported for painted turtles. Body condition was positively associated with ecological integrity for painted turtles, with no strong association for red-eared sliders. Our study suggests that both species benefitted at the population level from reduced ecological integrity, but individual-level habitat quality was reduced for painted turtles. The differing responses between these two habitat generalists could partially explain why red-eared sliders have become a widespread exotic invasive species, while painted turtles have not.

A Model and Simulation of the Influence of Temperature and Amplicon Length on Environmental DNA Degradation Rates: A Meta-Analysis Approach

Environmental DNA (eDNA) analysis can detect aquatic organisms, including rare and endangered species, in a variety of habitats. Degradation can influence eDNA persistence, impacting eDNA-based species distribution and occurrence results. Previous studies have investigated degradation rates and associated contributing factors. It is important to integrate data from across these studies to better understand and synthesize eDNA degradation in various environments. We complied the eDNA degradation rates and related factors, especially water temperature and amplicon lengths of the measured DNA from 28 studies, and subjected the data to a meta-analysis. In agreement with previous studies, our results suggest that water temperature and amplicon length are significantly related to the eDNA degradation rate. From the 95% quantile model simulation, we predicted the maximum eDNA degradation rate in various combinations of water temperature and amplicon length. Predicting eDNA degradation could be important for evaluating species distribution and inducing innovation (e.g., sampling, extraction, and analysis) of eDNA methods, especially for rare and endangered species with small population size.

Comparing the efficiency of open and enclosed filtration systems in environmental DNA quantification for fish and jellyfish

Water sampling and filtration of environmental DNA (eDNA) analysis have been performed by several different methods, and each method may yield a different species composition or eDNA concentration. Here, we investigated the eDNA of seawater samples directly collected by SCUBA to compare two widely used filtration methods: open filtration with a glass filter (GF/F) and enclosed filtration (Sterivex). We referred to biomass based on visual observation data collected simultaneously to clarify the difference between organism groups. Water samples were collected at two points in the Sea of Japan in May, September and December 2018. The respective samples were filtered through GF/F and Sterivex for eDNA extraction. We quantified the eDNA concentration of five fish and two cnidarian species by quantitative polymerase chain reaction (qPCR) using species-specific primers/probe sets. A strong correlation of eDNA concentration was obtained between GF/F and Sterivex; the intercepts and slopes of the linear regression lines were slightly different in fish and jellyfish. The amount of eDNA detected using the GF/F filtration method was higher than that detected using Sterivex when the eDNA concentration was high; the opposite trend was observed when the eDNA concentration was relatively low. The concentration of eDNA correlated with visually estimated biomass; eDNA concentration per biomass in jellyfish was approximately 700 times greater than that in fish. We conclude that GF/F provides an advantage in collecting a large amount of eDNA, whereas Sterivex offers superior eDNA sensitivity. Both filtration methods are effective in estimating the spatiotemporal biomass size of target marine species.