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


Dunshea, GJ and Barros, NB and Wells, RS and Gales, NJ and Hindell, MA and Jarman, SN, Pseudogenes and DNA-based diet analyses: a cautionary tale from a relatively well sampled predator-prey system, Bulletin of Entomological Research, 98, (3) pp. 239-248. ISSN 0007-4853 (2008) [Refereed Article]

DOI: doi:10.1017/S0007485308005993


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. Copyright © 2008 Cambridge University Press.

Item Details

Item Type:Refereed Article
Research Division:Biological Sciences
Research Group:Zoology
Research Field:Animal cell and molecular biology
Objective Division:Environmental Management
Objective Group:Marine systems and management
Objective Field:Marine biodiversity
UTAS Author:Dunshea, GJ (Mr Glenn Dunshea)
UTAS Author:Hindell, MA (Professor Mark Hindell)
ID Code:53157
Year Published:2008
Web of Science® Times Cited:21
Deposited By:Zoology
Deposited On:2008-11-05
Last Modified:2011-09-27

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