Abstract
Molecular approaches to prey identification are increasingly useful in elucidating predator–prey relationships, and we aimed to investigate the feasibility of these methods to document the species identities of prey consumed by invasive Burmese pythons in Florida. We were particularly interested in the diet of young snakes, because visual identification of prey from this size class has proven difficult. We successfully extracted DNA from the gastrointestinal contents of 43 young pythons, as well as from several control samples, and attempted amplification of DNA mini-barcodes, a 130-bp region of COX1. Using a PNA clamp to exclude python DNA, we found that prey DNA was not present in sufficient quality for amplification of this locus in 86% of our samples. All samples from the GI tracts of young pythons contained only hair, and the six samples we were able to identify to species were hispid cotton rats. This suggests that young Burmese pythons prey predominantly on small mammals and that prey diversity among snakes of this size class is low. We discuss prolonged gastrointestinal transit times and extreme gastric breakdown as possible causes of DNA degradation that limit the success of a molecular approach to prey identification in Burmese pythons.
Highlights
A major impact of an invasive predator species in its non-native range is the consumption of prey and concomitant decline of prey populations (Gurevitch & Padilla, 2004; Pimentel, Zuniga & Morrison, 2005; Zavaleta, Hobbs & Mooney, 2001)
A visual approach to prey identification is potentially problematic because: (1) it relies on specialized expert analysis; (2) sufficient identifiable material may not be present in the GI contents; and (3) a reference library for all life stages of all potential prey species may not be available
Our results suggest that prey DNA in Burmese python GI contents is so degraded that a molecular approach to prey identification will only rarely be feasible
Summary
A major impact of an invasive predator species in its non-native range is the consumption of prey and concomitant decline of prey populations (Gurevitch & Padilla, 2004; Pimentel, Zuniga & Morrison, 2005; Zavaleta, Hobbs & Mooney, 2001). A DNA isolate from a sample of GI contents will almost certainly contain DNA from the predator in addition to the prey, and several enrichment methods are available to favor the sequencing of prey DNA (O’Rorke, Lavery & Jeffs, 2012; Pompanon et al, 2012). A PNA clamp is a PNA oligomer that does not prime polymerization and is designed to anneal only to the predator sequences, so only the target locus of prey DNA is available for amplification (Chow et al, 2011; Pompanon et al, 2012). The PNA clamp is highly specific and has a relatively high melting temperature, making it generally more efficient at preventing predator DNA amplification than a blocking primer (Pompanon et al, 2012)
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