Search for: All records

Environmental DNA (eDNA) data make it possible to measure and monitor biodiversity at unprecedented resolution and scale. As use‐cases multiply and scientific consensus grows regarding the value of eDNA analysis, public agencies have an opportunity to decide how and where eDNA data fit into their mandates. Within the United States, many federal and state agencies are individually using eDNA data in various applications and developing relevant scientific expertise. A national strategy for eDNA implementation would capitalize on recent scientific developments, providing a common set of next‐generation tools for natural resource management and public health protection. Such a strategy would avoid patchwork and possibly inconsistent guidelines in different agencies, smoothing the way for efficient uptake of eDNA data in management. Because eDNA analysis is already in widespread use in both ocean and freshwater settings, we focus here on applications in these environments. However, we foresee the broad adoption of eDNA analysis to meet many resource management issues across the nation because the same tools have immediate terrestrial and aerial applications.

 

Data accompanying the paper Szydlowski et al. "Macrophyte and snail community responses to 30 years of population declines of invasive rusty crayfish (Faxonius rusticus)." Macrophytes and snails were sampled in ten lakes in Vilas County, Wisconsin, USA during summer sampling events in 1987, 2002, 2011, and 2020. Lakes had varying levels of invasion by F. rusticus, which affected measures of macrophytes and snails. Macrophytes were sampled using a point-intercept transect method and snails were sampled using different sampler types which were dependent on substrate. Macrophytes were sampled at 6-14 sites per lake and snails were sampled at 16-31 sites per lake. Crayfish were regularly sampled at either 24 or 36 sites per lake between 1987 and 2020. Overall, this dataset provides abundance and richness data for over 25 species of snails and over 40 species of macrophytes in 10 north temperate lakes. 

Biodiversity surveys may require the use of multiple types of sampling gear to maximize the efficiency of species detections, yet few studies have investigated how to optimally distribute effort among gear. In this study, we conducted eDNA metabarcoding and capture‐based sampling surveys (electrofishing, fyke netting, gillnetting, and seining) to sample fish species richness in a large northern temperate lake. We evaluated the success of the sampling methods individually and in combination to determine the allocation of effort and cost across sampling gear that provides the optimal approach for lake‐wide species inventories. We found that eDNA metabarcoding detected more species than any other sampling method, including 11 species that were not detected with any capture‐based approach. Optimal gear combination analyses revealed that detected species richness is maximized when most of the effort or budget is allocated to eDNA metabarcoding, with smaller allocations to seining and fyke netting. eDNA metabarcoding and capture sampling gear showed similar patterns of spatial heterogeneity in the fish community across habitat types, with pelagic samples forming a group that was distinct from nearshore samples. Our results indicate that eDNA metabarcoding is a rapid and cost‐efficient tool for biodiversity monitoring and that assessing the complementarity of multiple sampling types can inform the development of optimal approaches for measuring fish species richness.

 

Rapid climate change has wide-ranging implications for the Arctic region, including sea ice loss, increased geopolitical attention, and expanding economic activity resulting in a dramatic increase in shipping activity. As a result, the risk of harmful non-native marine species being introduced into this critical region will increase unless policy and management steps are implemented in response. Using data about shipping, ecoregions, and environmental conditions, we leverage network analysis and data mining techniques to assess, visualize, and project ballast water-mediated species introductions into the Arctic and dispersal of non-native species within the Arctic. We first identify high-risk connections between the Arctic and non-Arctic ports that could be sources of non-native species over 15 years (1997–2012) and observe the emergence of shipping hubs in the Arctic where the cumulative risk of non-native species introduction is increasing. We then consider how environmental conditions can constrain this Arctic introduction network for species with different physiological limits, thus providing a tool that will allow decision-makers to evaluate the relative risk of different shipping routes. Next, we focus on within-Arctic ballast-mediated species dispersal where we use higher-order network analysis to identify critical shipping routes that may facilitate species dispersal within the Arctic. The risk assessment and projection framework we propose could inform risk-based assessment and management of ship-borne invasive species in the Arctic.

 

Advances in environmental DNA (eDNA) methodologies have led to improvements in the ability to detect species and communities in aquatic environments, yet the majority of studies emphasize biological diversity at the species level by targeting variable sites within the mitochondrial genome. Here, we demonstrate that eDNA approaches also have the capacity to detect intraspecific diversity in the nuclear genome, allowing for assessments of population‐level allele frequencies and estimates of the number of genetic contributors in an eDNA sample. Using a panel of microsatellite loci developed for the round goby (Neogobius melanostomus), we tested the similarity between eDNA‐based and individual tissue‐based estimates of allele frequencies from experimental mesocosms and in a field‐based trial. Subsequently, we used a likelihood‐based DNA mixture framework to estimate the number of unique genetic contributors in eDNA samples and in simulated mixtures of alleles. In both mesocosm and field samples, allele frequencies from eDNA were highly correlated with allele frequencies from genotyped round goby tissue samples, indicating nuclear markers can be reliably amplified from water samples. DNA mixture analyses were able to estimate the number of genetic contributors from mesocosm eDNA samples and simulated mixtures of DNA from up to 58 individuals, with the degree of positive or negative bias dependent on the filtering scheme of low‐frequency alleles. With this study we document the application of eDNA and multiple amplicon‐based methods to obtain intraspecific nuclear genetic information and estimate the absolute abundance of a species in eDNA samples. With proper validation, this approach has the potential to advance noninvasive survey methods to characterize populations and detect population‐level genetic diversity.

 

The spread of nonindigenous species by shipping is a large and growing global problem that harms coastal ecosystems and economies and may blur coastal biogeographical patterns. This study coupled eukaryotic environmental DNA (eDNA) metabarcoding with dissimilarity regression to test the hypothesis that ship‐borne species spread homogenizes port communities. We first collected and metabarcoded water samples from ports in Europe, Asia, Australia and the Americas. We then calculated community dissimilarities between port pairs and tested for effects of environmental dissimilarity, biogeographical region and four alternative measures of ship‐borne species transport risk. We predicted that higher shipping between ports would decrease community dissimilarity, that the effect of shipping would be small compared to that of environment dissimilarity and shared biogeography, and that more complex shipping risk metrics (which account for ballast water and stepping‐stone spread) would perform better. Consistent with our hypotheses, community dissimilarities increased significantly with environmental dissimilarity and, to a lesser extent, decreased with ship‐borne species transport risks, particularly if the ports had similar environments and stepping‐stone risks were considered. Unexpectedly, we found no clear effect of shared biogeography, and that risk metrics incorporating estimates of ballast discharge did not offer more explanatory power than simpler traffic‐based risks. Overall, we found that shipping homogenizes eukaryotic communities between ports in predictable ways, which could inform improvements in invasive species policy and management. We demonstrated the usefulness of eDNA metabarcoding and dissimilarity regression for disentangling the drivers of large‐scale biodiversity patterns. We conclude by outlining logistical considerations and recommendations for future studies using this approach.

 

Synthesis research in ecology and environmental science improves understanding, advances theory, identifies research priorities, and supports management strategies by linking data, ideas, and tools. Accelerating environmental challenges increases the need to focus synthesis science on the most pressing questions. To leverage input from the broader research community, we convened a virtual workshop with participants from many countries and disciplines to examine how and where synthesis can address key questions and themes in ecology and environmental science in the coming decade. Seven priority research topics emerged: (1) diversity, equity, inclusion, and justice (DEIJ), (2) human and natural systems, (3) actionable and use‐inspired science, (4) scale, (5) generality, (6) complexity and resilience, and (7) predictability. Additionally, two issues regarding the general practice of synthesis emerged: the need for increased participant diversity and inclusive research practices; and increased and improved data flow, access, and skill‐building. These topics and practices provide a strategic vision for future synthesis in ecology and environmental science.

 

The genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“HTS”) platforms now enable the rapid sequencing ofDNAfrom diverse kinds of environmental samples (termed “environmentalDNA” or “eDNA”). CouplingHTSwith our ability to associate sequences fromeDNAwith a taxonomic name is called “eDNAmetabarcoding” and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use ofeDNAmetabarcoding for surveying animal and plant richness, and the challenges in usingeDNAapproaches to estimate relative abundance. We highlighteDNAapplications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of differenteDNAsample types to approximate richness in space and across time. We provide guiding questions for study design and discuss theeDNAmetabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications ofeDNAmetabarcoding in ecology, conservation, invasion biology, biomonitoring, and howeDNAmetabarcoding can empower citizen science and biodiversity education.