Bulletin of Entomological Research

Research Paper

Pseudogenes and DNA-based diet analyses: a cautionary tale from a relatively well sampled predator-prey system

G. Dunsheaa1a2 c1, N.B. Barrosa3, R.S. Wellsa4, N.J. Galesa2, M.A. Hindella1 and S.N. Jarmana2

a1 Antarctic Wildlife Research Unit, School of Zoology, University of Tasmania, PO Box 252-05, Hobart, Tasmania 7005, Australia

a2 Applied Marine Mammal Ecology Group, Australian Antarctic Division, 203 Channel Highway, Kingston, Tasmania, Australia, 7050

a3 Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL 34236, USA

a4 Chicago Zoological Society c/o Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL 34236, USA

Abstract

Mitochondrial ribosomal DNA is commonly used in DNA-based dietary analyses. In such studies, these sequences are generally assumed to be the only version present in DNA of the organism of interest. However, nuclear pseudogenes that display variable similarity to the mitochondrial versions are common in many taxa. The presence of nuclear pseudogenes that co-amplify with their mitochondrial paralogues can lead to several possible confounding interpretations when applied to estimating animal diet. Here, we investigate the occurrence of nuclear pseudogenes in fecal samples taken from bottlenose dolphins (Tursiops truncatus) that were assayed for prey DNA with a universal primer technique. We found pseudogenes in 13 of 15 samples and 1–5 pseudogene haplotypes per sample representing 5–100% of all amplicons produced. The proportion of amplicons that were pseudogenes and the diversity of prey DNA recovered per sample were highly variable and appear to be related to PCR cycling characteristics. This is a well-sampled system where we can reliably identify the putative pseudogenes and separate them from their mitochondrial paralogues using a number of recommended means. In many other cases, it would be virtually impossible to determine whether a putative prey sequence is actually a pseudogene derived from either the predator or prey DNA. The implications of this for DNA-based dietary studies, in general, are discussed.

(Accepted December 12 2007)

(Online publication April 28 2008)

Correspondence:

c1 Author for correspondence Fax: (+61) 36 232 3449 E-mail: glenn.dunshea@aad.gov.au