Abstract
BackgroundPrey DNA from diet samples can be used as a dietary marker; yet current methods for prey detection require a priori diet knowledge and/or are designed ad hoc, limiting their scope. I present a general approach to detect diverse prey in the feces or gut contents of predators.Methodology/Principal FindingsIn the example outlined, I take advantage of the restriction site for the endonuclease Pac I which is present in 16S mtDNA of most Odontoceti mammals, but absent from most other relevant non-mammalian chordates and invertebrates. Thus in DNA extracted from feces of these mammalian predators Pac I will cleave and exclude predator DNA from a small region targeted by novel universal primers, while most prey DNA remain intact allowing prey selective PCR. The method was optimized using scat samples from captive bottlenose dolphins (Tursiops truncatus) fed a diet of 6–10 prey species from three phlya. Up to five prey from two phyla were detected in a single scat and all but one minor prey item (2% of the overall diet) were detected across all samples. The same method was applied to scat samples from free-ranging bottlenose dolphins; up to seven prey taxa were detected in a single scat and 13 prey taxa from eight teleost families were identified in total.Conclusions/SignificanceData and further examples are provided to facilitate rapid transfer of this approach to any predator. This methodology should prove useful to zoologists using DNA-based diet techniques in a wide variety of study systems.
Highlights
An established field of dietary analysis is the use of prey DNA in the digestive system or feces of predators for prey identification [1,2]
Polymerase chain reaction (PCR) detection of prey DNA has proven effective when applied to both sacrificed invertebrate predators [3,4,5] and scats from vertebrate predators [6,7,8]
This is unsurprising given the uncontrolled nature of this feeding trial; : 1) Not all scats produced by the study animals were collected; 2) Only a small proportion of any single scat was collected; 3) It is unsure what prey should be present in any given scat since the specific timings of prey ingestion is unknown for specific prey species and 4) it is not known how variable prey detection is when applying DNA methods to cetacean scat
Summary
An established field of dietary analysis is the use of prey DNA in the digestive system or feces of predators for prey identification [1,2]. DNA-based methods offer the ability to identify prey where prey hard parts survive the digestion process differentially or not at all The latter being the case for many invertebrate systems [2], for feces of particular vertebrate predators such as cetaceans and sea-birds [9] and with prey items with few hard parts. Development of DNA-based prey assays can be achieved relatively rapidly, compared to techniques utilizing monoclonal antibodies [12] and multiple prey items can be screened for simultaneously [e.g. 4]. These assays offer greater taxonomic resolution of prey, though over shorter timescales, than methods such as fatty acid and stable isotope analyses [though see 13]. I present a general approach to detect diverse prey in the feces or gut contents of predators
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