David M Lodge

Cornell University | CU · Department of Ecology and Evolutionary Biology

1. Invasive species often experience phenotypic change during the invasion process. For example, many invasive species are larger in their non-native than native ranges, but some invasive species experience body size declines with time since invasion. Mechanisms of these phenotypic changes are poorly known, likely due to a paucity of long-term data...

Environmental DNA (eDNA) has been established as a noninvasive and efficient approach to sample genetic material from aquatic environments. Although most commonly used to determine species presence and measure biodiversity, eDNA approaches also hold great potential to obtain population-level genetic information from water samples. In this study, we...

Advancements in environmental DNA (eDNA) approaches have allowed for rapid and efficient species detections in diverse environments. Although most eDNA research is focused on leveraging genetic diversity to identify taxa, some recent studies have explored the potential for these approaches to detect within-species genetic variation, allowing for po...

A central focus of invasive species research has been on human efforts to eradicate invaders or reduce their abundance to mitigate the worst of their impacts. In some cases, however, populations of invasive species decline without human intervention, which may inform management responses to these invaders. Such is the case of the invasive rusty cra...

Spread of nonindigenous species by shipping is a large and growing global problem that harms coastal ecosystems and economies and may blur coastal biogeographic patterns. This study coupled eukaryotic environmental DNA (eDNA) metabarcoding with dissimilarity regression to test the hypothesis that ship-borne species spread homogenizes port communiti...

Spread of nonindigenous organisms by shipping is one of the largest threats to coastal ecosystems. Limited monitoring and understanding of this phenomenon currently hinder development of effective prevention policies. Surveying ports in North America, South America, Europe, Southeast Asia, and Australia we explored environmental DNA community profi...

Environmental DNA (eDNA) analysis methods permit broad yet detailed biodiversity sampling to be performed with minimal field effort. However, considerable uncertainty remains regarding the spatial resolution necessary for effective sampling, especially in aquatic environments. Also, contemporary plant communities are under-investigated with eDNA me...

Bigheaded carps (BHCs; Silver Carp Hypophthalmichthys molitrix and Bighead Carp H. nobilis) are economically and culturally important in Asia and Europe but are considered highly invasive throughout the Mississippi River watershed and pose a threat to the food web and fisheries of the Laurentian Great Lakes. We used the Ecopath with Ecosim model fr...

Invasive nonindigenous species cause massive impacts to freshwater biodiversity and to the provisioning of ecosystem services from lakes, rivers, and wetlands. These impacts affect whole ecosystems, economies, human health, and recreational opportunities. The number and total impacts of invasive species will likely continue to increase despite incr...

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 a...

Knowledge about the size of environmental DNA (eDNA) and eDNA-bearing particles in aquatic environments is integral to efficient and sensitive analyses. To explore the influence of environmental factors on eDNA particle size distribution (PSD), we manipulated fish communities across nine experimental ponds, which led to differences in a suite of en...

Effective engagement among scientists, government agency staff, and policymakers is necessary for solving fisheries challenges, but remains challenging for a variety of reasons. We present seven practices learned from a collaborative project focused on invasive species in the Great Lakes region (USA‐CAN). These practices were based on a researcher–...

Rapid climate change has wide-ranging implications for the Arctic region, including sea ice loss, increased geopolitical attention, and expanding economic activity, including 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...

The ability to properly identify species present in a landscape is foundational to ecology and essential for natural resource management and conservation. However, many species are often unaccounted for due to ineffective direct capture and visual surveys, especially in aquatic environments. Environmental DNA metabarcoding is an approach that overc...

The introduction and establishment of nonindigenous species (NIS) through global ship movements poses a significant threat to marine ecosystems and economies. While ballast-vectored invasions have been partly addressed by some national policies and an international agreement regulating the concentrations of organisms in ballast water, biofouling-ve...

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

The introduction and establishment of non-indigenous species (NIS) through global ship movements is a significant threat to marine ecosystems and economies. While ballast-vectored invasions have been partly addressed by some national policies and an international agreement regulating the concentrations of organisms in ballast water, biofouling-vect...

Assessing the potential for aquatic invasive species (AIS) to impact ecosystem function and services is an important component of ecological risk assessment. This study focuses on quantifying changes in biomass of food web groups in response to changes in AIS biomass as a function of variable AIS prey vulnerabilities (i.e. food availability) and AI...

Invasive nonindigenous species are defined by their impacts: they substantially change native communities or ecosystems. Accordingly, invasive species might transform their habitats in ways that eventually become unfavorable to them, causing population declines or even extirpations. Here we use over 40 yr of systematically collected data on the abu...

The analysis of environmental DNA (eDNA) using metabarcoding has increased in use as a method for tracking biodiversity of ecosystems. Little is known about eDNA in marine human-modified environments, such as commercial ports, which are key sites to monitor for anthropogenic impacts on coastal ecosystems. To optimise an eDNA metabarcoding protocol...

Aquatic invasive plant species cause negative impacts to economies and ecosystems worldwide. Traditional survey methods, while necessary, often do not result in timely detections of aquatic invaders, which can be cryptic, difficult to identify, and exhibit very rapid growth and reproduction rates. Environmental DNA (eDNA) is a relatively new method...

Because significant global changes are currently underway in the Arctic, creating a large‐scale standardized database for Arctic marine biodiversity is particularly pressing. This study evaluates the potential of aquatic environmental DNA (eDNA) metabarcoding to detect Arctic coastal biodiversity changes and characterizes the local spatio‐temporal...

Bighead and Silver Carp (collectively, bigheaded carps ‘BHC’) are highly invasive planktivorous fish that threaten to invade and impact Great Lakes food webs. We used the Ecopath with Ecosim food web model to simulate potential BHC biomass and food web impacts across Great Lakes habitats that vary in productivity, prey and predator biomass, and spe...

Environmental DNA (eDNA) metabarcoding can greatly enhance our understanding of global biodiversity and our ability to detect rare or cryptic species. However, sampling effort must be considered when interpreting results from these surveys. We explored how sampling effort influenced biodiversity patterns and nonindigenous species (NIS) detection in...

Environmental DNA (eDNA) metabarcoding has been increasingly applied to biodiversity surveys in stream ecosystems. In stream networks, the accuracy of eDNA-based biodiversity assessment depends on whether the upstream eDNA influx affects downstream detection. Biodiversity assessment in low-discharge streams should be less influenced by eDNA transpo...

Early detection is imperative for successful control or eradication of invasive species, but many organisms are difficult to detect at the low abundances characteristic of recently introduced populations. Environmental DNA (eDNA) has emerged as a promising invasive species surveillance tool for freshwaters, owing to its high sensitivity to detect a...

The African Great Lakes system has high aquatic biodiversity but is increasingly threatened by anthropogenic stressors including the introduction of potentially invasive nonindigenous plant and animal species. Quantitative risk assessment models can be used to predict the potential impact of introduced species in a specific geographic region. We ad...

We report results of a study that made reciprocal comparisons of environmental DNA (eDNA) assays for two major invasive crayfishes between their disparate invasive ranges in North America. Specifically, we tested for range expansions of the signal crayfish Pacifastacus leniusculus (Dana, 1852) into the Laurentian Great Lakes region known to be inva...

The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing (‘HTS’) platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed ‘environmental DNA’ or ‘eDNA’). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called ‘...

As environmental DNA ( eDNA ) from macro‐organisms is often assumed to be highly degraded, current eDNA assays target small DNA fragments to estimate species richness by metabarcoding. A limitation of this approach is the inherent lack of unique species‐specific single‐nucleotide polymorphisms available for unequivocal species identification. We de...

Efficient management and prevention of species invasions requires accurate prediction of where species of concern can arrive and persist. Species distribution models provide one way to identify potentially suitable habitat by developing the relationship between climate variables and species occurrence data. However, these models when applied to fre...

Invasion success can be enhanced by evolution and behavioral plasticity, but the importance of these processes for most invasions is not well understood. Previous research suggests there is a genetic basis for differences in growth rate between native and invaded range rusty crayfish (Orconectes rusticus). We hypothesized that invaded range O. rust...

Knowledge of aquatic invasive species (AIS) dispersal is important to inform surveillance and management efforts to slow the spread of established invaders. We studied potential dispersal of invasive Eurasian ruffe Gymnocephalus cernua and golden mussel Limnoperna fortunei larvae in Lakes Michigan and Erie using a three-dimensional particle transpo...

Grass Carp (Ctenopharyngodon idella), is a large, herbivorous fish that was first introduced to North America in 1963 for aquatic macrophyte control. It has since escaped from where it was stocked and entered rivers of the central United States and has dispersed through the Mississippi River basin towards the Great Lakes. Commerce is also another s...

Species richness is a metric of biodiversity that represents the number of species present in a community. Traditional fisheries assessments that rely on capture of organisms often underestimate true species richness. Environmental DNA (eDNA) metabarcoding is an alternative tool that infers species richness by collecting and sequencing DNA present...

Forecasts of the locations of species invasions can improve by integrating species-specific climate and habitat variables and the effects of other invaders into predictive models of species distribution. We developed two species distribution models (SDMs) using a new algorithm to predict the global distributions of two nonindigenous species, grass...

Detection of invasive species before or soon after they establish in novel environments is critical to prevent widespread ecological and economic impacts. Environmental DNA (eDNA) surveillance and monitoring is an approach to improve early detection efforts. Here we describe a large-scale conservation application of a quantitative polymerase chain...

Risk analysis of species invasions links biology and economics, is increasingly mandated by international and national policies, and enables improved management of invasive species. Biological invasions proceed through a series of transition probabilities (i.e., introduction, establishment, spread, and impact), and each of these presents opportunit...

1.Early detection is invaluable for the cost-effective control and eradication of invasive species, yet many traditional sampling techniques are ineffective at the low population abundances found at the onset of the invasion process. Environmental DNA (eDNA) is a promising and sensitive tool for early detection of some invasive species, but its eff...

Parasites can alter communities by reducing densities of keystone hosts, but few studies have examined how trait-mediated indirect effects of parasites can alter ecological communities. We test how trematode parasites (Microphallus spp.) that affect invasive crayfish (Orconectes rusticus) behavior alter how crayfish impact lake littoral communities...

The foundation for any ecological study and the for effective management of biodiversity in natural systems requires knowing what species are present in an ecosystem. We assessed fish communities in a stream using two methods, depletion-based electrofishing and environmental DNA metabarcoding (eDNA) from water samples, to test the hypothesis that e...

Table S7. Number of raw reads assigned to each species in control samples. Species considered present after all bioinformatic filtering and species assignment thresholds applied in negative controls. The eDNA column shows the species detected in the actual Juday Creek samples from Table S6. The P/A columns shows presence (1) or absence (0) given ou...

Appendix S1. Estimating contamination rates and assessing false positives. Table S1. Parameter estimates (λ) and associated probabilities that the observed number of Johnny Darter sequences in field samples came from the distribution of errant DNA. Table S2. Detection of species as a result of presence of DNA in samples and consideration of conta...

Table S4. Number of reads from each sample (i.e. library) run on the Illumina MiSeq platform for each step of the bioinformatic pipeline. Samples are ordered from the most downstream sample (R1) to the most upstream sample (R8).

Table S5. Results for all species identified with OTU species assignment. Values of P1 – P7 represent the pathway taken to arrive at species assignment using SAP and USearch (Fig. S1).

Table S6. Raw read counts of each species identified, for each sample and all four markers. Samples are ordered from the most downstream sample (R1) to the most upstream sample (R8). Rows idenitfied in red were dropped from further analysis.

Previous publications have reached different conclusions about the balance between the socioeconomic benefits of tilapia introduction for aquaculture and capture fisheries, and the potential negative impacts of these species on ecosystem services such as the provisioning of food, habitat, and water quality. This review (1) provides a new estimate o...

Linkages between habitats can strongly affect ecosystem function through exchange of energy and materials. In lake food webs, large piscivorous fishes integrate littoral and pelagic energy sources through the consumption of smaller fishes and macroinvertebrates. We tested the hypothesis that the introduction of the invasive rusty crayfish (Orconect...

Species distribution models are valuable tools in studies of biogeography, ecology, and climate change and have been used to inform conservation and ecosystem management. However, species distribution models typically incorporate only climatic variables and species presence data. Model development or validation rarely considers functional component...

Appendix S2. Grass Carp growth rate occurrences, growth rate occurrence descriptive table and associated references.

Appendix S1. Detailed methods of Maxent implementation.

Nonindigenous bigheaded carps (Bighead Carp Hypophthalmichthys nobilis and Silver Carp H. molitrix; hereafter, “Asian carps” [AC]) threaten to invade and disrupt food webs and fisheries in the Laurentian Great Lakes through their high consumption of plankton. To quantify the potential effects of AC on the food web in Lake Erie, we developed an Ecop...

Fig. S1 Iteratively reweighted least square regressions of cumulative biomass of all species combined (g) and read abundance of all species combined (number of mapped reads) for each of the six primer sets. Fig. S2 Iteratively reweighted least square regressions of standing stock biomass (g) and read abundance (number of mapped reads) for each spe...

Table S1 Potential mismatches between the six metabarcoding primer pairs and the nine species in the current study. Table S2 Number of species detected (species with at least one mapped read) in each mesocosm using each of the six genetic primers at a mapping specificity of 99% match to reference sequence at 100% of sequence length. Table S3 Numb...

The order Decapoda includes about 15,000 species of shrimps, crayfish, lobsters, and crabs that belong to four out of the 10 infraorders of Malacostracan crustaceans. This chapter focuses on the approximately 3,000 species of freshwater decapods worldwide that includes over 760 species of caridean freshwater shrimps, 644 species of freshwater crayf...

Aim Impacts of non‐native species have motivated development of risk assessment tools for identifying introduced species likely to become invasive. Here, we develop trait‐based models for the establishment and impact stages of freshwater fish invasion, and use them to screen non‐native species common in international trade. We also determine which...

Trait-based risk assessments of invasive species focus on identifying intrinsic biological or ecological traits associated with invasion success, which allows for a new species’ invasion risk to be assessed a priori, thus facilitating cost-effective prevention strategies. However, human preferences for species traits—preferences that might affect w...

Pope Francis has found a meeting place for those with extreme religious and environmentalist stances, says David M. Lodge.

Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture of organisms via nets, traps, and electrofishing...

Risk assessment tools for non-native species can avert ecological and economic harm when they inform regulatory or voluntary management actions that seek to reduce the probability of introducing high-risk species. The Laurentian Great Lakes region contains many aquatic invasive plants, non-native species whose introduction causes economic or enviro...

Invasive species introduced via the ballast water of commercial ships cause enormous environmental and economic damage worldwide. Accurate monitoring for these often microscopic and morphologically indistinguishable species is challenging, but critical for mitigating damages. We apply eDNA sampling, which involves the filtering and subsequent DNA e...

Structured expert judgment (SEJ) is used to quantify the uncertainty of nonindigenous fish (bighead carp [Hypophthalmichthys nobilis] and silver carp [H. molitrix]) establishment in Lake Erie. The classical model for structured expert judgment model is applied. Forming a weighted combination (called a decision maker) of experts' distributions, with...

The unintentional transport of invasive species (i.e., non-native and harmful species that adversely affect habitats and native species) through the Global Shipping Network (GSN) causes substantial losses to social and economic welfare (e.g., annual losses due to ship-borne invasions in the Laurentian Great Lakes is estimated to be as high as USD 8...

Over the last 40 years, as Rusty Crayfish have invaded many inland lakes in Wisconsin and Michigan, USA, some lakes have experienced long-term low abundance of crayfish and little ecosystem change, while in other lakes, high abundance of crayfish and many undesirable ecosystem changes have occurred. Intermediate abundances of crayfish have been tra...

An inherent tradeoff between filter pore size (=captured particle size) and maximum filterable water volume makes understanding the size of eDNA-bearing particles in aquatic environments essential for efficient sample collection. Nevertheless, the particle size distribution (PSD) of eDNA represents a conspicuous gap in the growing literature on eDN...

Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a means to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture or observation of organisms via nets, traps, an...

Environmental DNA (eDNA) offers a technological solution to one of the persistent impediments to improved management and policy regarding imperiled or invasive species: unlike traditional capture methods, eDNA methods are increasingly portable and affordable for frequent sampling within geographically broad surveillance programs. Recent results fro...