Use of a Molecular Assay to Detect Predation on an Endangered Fish Species

Abstract

Mastication, digestion, and rapid evacuation rates make visual identification of larval fish remains in the digestive tracts of predatory fishes problematic. Recent advances in molecular technology, however, have increased the likelihood of identifying remnants of partially digested larval prey, thereby enabling assessment of predator impacts on local populations. Conducting controlled laboratory experiments, we evaluated the utility of quantitative polymerase chain reaction (qPCR) for identification of Razorback Sucker Xyrauchen texanus larvae in the digestive tracts of Green Sunfish Lepomis cyanellus and Western Mosquitofish Gambusia affinis. Primers and a probe were developed to amplify a fragment from Razorback Sucker mtDNA. Tests using a suite of potential predators and prey indicated that these primers and probes amplified only mtDNA from Razorback Sucker and Flannelmouth Sucker Catostomus latipinnis, an allopatric and allochronic species in the lower Colorado River. Amplification with primers for Razorback Sucker-specific DNA fragments identified Razorback Sucker DNA in the digestive tracts of 87.5% of Green Sunfish and Western Mosquitofish at 2 h postfeeding. After 12 h, DNA fragments were identified in 75.0% of Green Sunfish but in only 28.6% of Western Mosquitofish. No Razorback Sucker DNA was found in 24-h postfeeding samples, though it was detected in 12.5% of both Western Mosquitofish and Green Sunfish at 48 h postingestion. The sensitivity of qPCR provides a useful tool for extending the time period in which Razorback Sucker larvae can be identified beyond that of traditional visual analyses of stomach contents.

18S rRNA metabarcoding diet analysis of a predatory fish community across seasonal changes in prey availability

“…Diet items could be identified to similar taxonomic levels as morphological diet analyses, with the potential for metabarcoding to have even higher taxonomic resolution as more sequences and longer reads become available. Metabarcoding also revealed that predator diets were more diverse than previously thought, detecting predation on taxa such as larval fishes and rotifers that are unlikely to be accounted for using morphological diet analysis (Carreon‐Martinez et al, ; Hunter, Taylor, Fox, Maillard, & Taylor, ; Ley et al, ).…”

“…Metabarcoding also revealed that predator diets were more diverse than previously thought, detecting predation on taxa such as larval fishes and rotifers that are unlikely to be accounted for using morphological diet analysis (Carreon-Martinez et al, 2011;Hunter, Taylor, Fox, Maillard, & Taylor, 2012;Ley et al, 2014).…”

“…The greater diet breadth and taxonomic resolution that can be achieved through metabarcoding diet analysis can allow characterization of the degree of niche partitioning among species, revealing how predators can partition resources to reduce interspecific competition (Albaina, Aguirre, Abad, Santos, & Estonba, 2016;Katzinel et al, 2015;Leray, Meyer, & Mills, 2015). Dietary overlap estimated by molecular methods could also be significantly different than nonmolecular studies estimated depending on the prevalence of soft-bodied prey items in predator diets (Gebremedhin et al, 2016;Soininen et al, 2015), which are often difficult to detect in morphological diet studies due to rapid digestion times (Carreon-Martinez et al, 2011;Ley et al, 2014).…”

Fish Assemblage Associations with Floodplain Connectivity Following Restoration to Benefit an Endangered Catostomid

“…Larval sucker survival in Klamath Lake was negatively associated with Fathead Minnow density and interactions with water depth and percent vegetation (Markle and Dunsmoor 2007). Both Mosquitofish and Green Sunfish readily consumed larval Razorback Suckers Xyrauchen texanus in a controlled environment (Ley et al 2014). Interactions of larval June Sucker with the littoral species of Utah Lake need to be further explored.…”

Use of Molecular Techniques to Confirm Nonnative Fish Predation on Razorback Sucker Larvae in Lake Mohave, Arizona and Nevada

“…Advances in molecular techniques have enabled the successful identification of DNA from prey contained in the gut contents of predatory fishes after the prey are no longer visually identifiable (Rosel and Kocher 2002;Carreon-Martinez et al 2011;Hunter et al 2012;Ley et al 2014;Brandl et al 2016). Utilizing quantitative PCR (qPCR), Ley et al (2014) identified Razorback Sucker DNA in the gut contents of 87.5% of Green Sunfish Lepomis cyanellus at 2 h postconsumption and 75% of Green Sunfish at 12 h postconsumption. The Ley et al (2014) study validated the use of qPCR for identifying Razorback Sucker larvae in the gut contents of nonnative fishes and demonstrated a greatly extended timeline over which larvae could be positively identified in fish stomachs.…”