The objective of the study was to validate and apply DNA-based approaches to describe fish diets. Laboratory experiments were performed to determine the number of hours after ingestion that DNA could be reliably isolated from stomach content residues, particularly with small prey fishes (c. 1 cm, <0·75 g). Additionally, experiments were conducted at different temperatures to resolve temperature effects on digestion rate and DNA viability. The molecular protocol of cloning and sequencing was then applied to the analysis of stomach contents of wild fishes collected from the western basin of Lake Erie, Canada-U.S.A. The results showed that molecular techniques were more precise than traditional visual inspection and could provide insight into diet preferences for even highly digested prey that have lost all physical characteristics.

Characterization of energy flow in ecosystems is one of the primary goals of ecology, and the analysis of trophic interactions and food web dynamics is key to quantifying energy flow. Predator-prey interactions define the majority of trophic interactions and food web dynamics, and visual analysis of stomach, gut or fecal content composition is the technique traditionally used to quantify predator-prey interactions. Unfortunately such techniques may be biased and inaccurate due to variation in digestion rates (Sheppard & Hardwood 2005); however, those limitations can be largely overcome with new technology. In the last 20 years, the use of molecular genetic techniques in ecology has exploded (King et al. 2008). The growing availability of molecular genetic methods and data has fostered the use of PCR-based techniques to accurately distinguish and identify prey items in stomach, gut and fecal samples. In this month's issue of Molecular Ecology Resources, Corse et al. (2010) describe and apply a new approach to quantifying predator-prey relationships using an ecosystem-level genetic characterization of available and consumed prey in European freshwater habitats (Fig. 1a). In this issue of Molecular Ecology, Hardy et al. (2010) marry the molecular genetic analysis of prey with a stable isotope (SI) analysis of trophic interactions in an Australian reservoir community (Fig. 1b). Both papers demonstrate novel and innovative approaches to an old problem -how do we effectively explore food webs and energy movement in ecosystems?Keywords: Community ecology, DNA barcoding, ecological genetics, predator-prey interactions Alternative and imaginative methods for diet analysis have been used since 1946, starting with immunological techniques and continuing with sophisticated DNA-based methods, paralleling technological advances in molecular ecology (Fig. 2). Immunological techniques used to identify prey are diverse and include antigen-antibody interactions in solution (e.g. agglutination, precipitation reactions, immuno-electrophoresis) as well as solid-phase techniques (e.g. ELISA, radio-immune assays; Boreham & Ohiagu 1978). Indeed, immunological techniques are still used and are extremely helpful (Fig. 2) Fig. 1 The aquatic habitats used for two studies of diet and trophic interactions that employed molecular genetic and stable isotope analyses. Panel a: Example of Rhone basin habitat (France) where fish diet was determined using PCR to classify prey to a series of ecological clades (photo by Emmanuel Corse). Panel b: A weir pool on the lower Murray River (Australia) where food web and prey use was evaluated using a combination of advanced molecular genetic and stable isotope analyses (photo credit: CSIRO).

Turbidity associated with river plumes is known to affect the search ability of visual predators and thus can drive 'top-down' impacts on prey populations in complex ecosystems; however, traditional quantification of predator-prey relationships (i.e. stomach content analysis) often fails with larval fish due to rapid digestion rates. Herein, we use novel molecular genetic methods to quantify larval yellow perch (YP) in predator stomachs in western Lake Erie to test the hypothesis that turbidity drives variation in larval predation. We characterize predator stomach content DNA to first identify YP DNA (single nucleotide polymorphism) and then quantify larval YP predation (microsatellite allele counting) in two river plumes differing in turbidity. Our results showed elevated larval YP predation in the less turbid river plume, consistent with a top-down impact of turbidity on larval survival. Our analyses highlight novel ecological hypothesis testing using the power of innovative molecular genetic approaches.

Nutrient-rich, turbid river plumes that are common to large lakes and coastal marine ecosystems have been hypothesized to benefit survival of fish during early life stages by increasing food availability and (or) reducing vulnerability to visual predators. However, evidence that river plumes truly benefit the recruitment process remains meager for both freshwater and marine fishes. Here, we use genotype assignment between juvenile and larval yellow perch (Perca flavescens) from western Lake Erie to estimate and compare recruitment to the age-0 juvenile stage for larvae residing inside the highly turbid, south-shore Maumee River plume versus those occupying the less turbid, more northerly Detroit River plume. Bayesian genotype assignment of a mixed assemblage of juvenile (age-0) yellow perch to putative larval source populations established that recruitment of larvae was higher from the turbid Maumee River plume than for the less turbid Detroit River plume during 2006 and 2007, but not in 2008. Our findings add to the growing evidence that turbid river plumes can indeed enhance survival of fish larvae to recruited life stages, and also demonstrate how novel population genetic analyses of early life stages can contribute to determining critical early life stage processes in the fish recruitment process.

We provide a novel method to improve the use of natural tagging approaches for subpopulation discrimination and source-origin identification in aquatic and terrestrial animals with a passive dispersive phase. Our method integrates observed site-referenced biological information on individuals in mixed populations with a particle-tracking model to retrace likely dispersal histories prior to capture (i.e., particle backtracking). To illustrate and test our approach, we focus on western Lake Erie’s yellow perch (Perca flavescens) population during 2006–2007, using microsatellite DNA and otolith microchemistry from larvae and juveniles as natural tags. Particle backtracking showed that not all larvae collected near a presumed hatching location may have originated there, owing to passive drift during the larval stage that was influenced by strong river- and wind-driven water circulation. Re-assigning larvae to their most probable hatching site (based on probabilistic dispersal trajectories from the particle backtracking model) improved the use of genetics and otolith microchemistry to discriminate among local breeding subpopulations. This enhancement, in turn, altered (and likely improved) the estimated contributions of each breeding subpopulation to the mixed population of juvenile recruits. Our findings indicate that particle backtracking can complement existing tools used to identify the origin of individuals in mixed populations, especially in flow-dominated systems.

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Ability to quantify connectivity among spawning subpopulations and their relative contribution of recruits to the broader population is a critical fisheries management need. By combining microsatellite and age information from larval yellow perch (Perca flavescens) collected in the Lake St. Clair – Detroit River system (SC-DRS) and western Lake Erie with a hydrodynamic backtracking approach, we quantified subpopulation structure, connectivity, and contributions of recruits to the juvenile stage in western Lake Erie during 2006–2007. After finding weak (yet stable) genetic structure between the SC-DRS and two western Lake Erie subpopulations, microsatellites also revealed measurable recruitment of SC-DRS larvae to the juvenile stage in western Lake Erie (17%–21% during 2006–2007). Consideration of precollection larval dispersal trajectories, using hydrodynamic backtracking, increased estimated contributions to 65% in 2006 and 57% in 2007. Our findings highlight the value of complementing subpopulation discrimination methods with hydrodynamic predictions of larval dispersal by revealing the SC-DRS as a source of recruits to western Lake Erie and also showing that connectivity through larval dispersal can affect the structure and dynamics of large lake fish populations.