Hostname: page-component-cd9895bd7-q99xh Total loading time: 0 Render date: 2024-12-31T15:57:48.208Z Has data issue: false hasContentIssue false
  • English
  • Français

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

Published online by Cambridge University Press:  28 April 2008

G. Dunshea ,
N.B. Barros ,
R.S. Wells ,
N.J. Gales ,
M.A. Hindell  and
S.N. Jarman
G. Dunshea*
Affiliation:
Antarctic Wildlife Research Unit, School of Zoology, University of Tasmania, PO Box 252-05, Hobart, Tasmania 7005, Australia Applied Marine Mammal Ecology Group, Australian Antarctic Division, 203 Channel Highway, Kingston, Tasmania, Australia, 7050
N.B. Barros
Affiliation:
Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL 34236, USA
R.S. Wells
Affiliation:
Chicago Zoological Society c/o Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL 34236, USA
N.J. Gales
Affiliation:
Applied Marine Mammal Ecology Group, Australian Antarctic Division, 203 Channel Highway, Kingston, Tasmania, Australia, 7050
M.A. Hindell
Affiliation:
Antarctic Wildlife Research Unit, School of Zoology, University of Tasmania, PO Box 252-05, Hobart, Tasmania 7005, Australia
S.N. Jarman
Affiliation:
Applied Marine Mammal Ecology Group, Australian Antarctic Division, 203 Channel Highway, Kingston, Tasmania, Australia, 7050
*
*Author for correspondence Fax: (+61) 36 232 3449 E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

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.

Keywords

fecal analysisNUMTPCRprey detectionTursiops truncatus
Type
Research Paper
Information
Bulletin of Entomological Research , Volume 98 , Issue 3 , June 2008 , pp. 239 - 248
Copyright
Copyright © 2008 Cambridge University Press

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Bensasson, D., Zhang, D., Hartl, D.L. & Hewitt, G.M. (2001) Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends in Ecology and Evolution 16(6), 314–321.CrossRefGoogle ScholarPubMed
Blankenship, L.E. & Yayanos, A.A. (2005) Universal primers and PCR of gut contents to study marine invertebrate diets. Molecular Ecology 14(3), 891–899.CrossRefGoogle ScholarPubMed
Burk, A., Douzery, J.P. & Springer, M.S. (2002) The secondary structure of mammalian mitochondrial 16S rRNA molecules: refinements based on a comparative phylogenetic approach. Journal of Mammalian Evolution 9(3), 225–252.CrossRefGoogle Scholar
Casper, R.M., Jarman, S.N., Gales, N.J. & Hindell, M.A. (2007) Combining DNA and morphological analyses of fecal samples improves insight into trophic interactions: a case study using a generalist predator. Marine Biology 152(4), 815–825.Google Scholar
Collura, R.V. & Stewart, C. (1995) Insertions and duplications of mtDNA in the nuclear genomes of Old World monkeys and hominoids. Nature 378, 485–489.CrossRefGoogle ScholarPubMed
Deagle, B.E., Eveson, J.P. & Jarman, S.N. (2006) Quantification of damage in DNA recovered from highly degraded samples − a case study on DNA in faeces. Frontiers in Zoology 3 (11), 10.1186/1742-9994-3-11.Google Scholar
Dunshea, G. (in review) DNA-based diet analysis for any predator. Marine Ecology Resources.Google Scholar
Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5), 1792–1797.CrossRefGoogle ScholarPubMed
Gonzalez, J.M., Zimmermann, J. & Saiz-Jimenez, C. (2004) Evaluating putative chimeric sequences from PCR amplified products. Bioinformatics 21(3), 333–337.CrossRefGoogle ScholarPubMed
Hajibabaei, M., Smith, A., Janzen, D.H., Rodriguez, J., Whitfield, J.B. & Hebert, P.D.N. (2006) A minimalist barcode can identify a specimen whose DNA is degraded. Molecular Ecology Notes 6, 959–964.Google Scholar
Harper, G.L., King, R.A., Dodd, C.S., Harwood, J.D., Glen, D.M., Bruford, M.W. & Symondson, W.O.C. (2005) Rapid screening of invertebrate predators for multiple prey DNA targets. Molecular Ecology 14(3), 819–827.Google Scholar
Huber, J.A., Butterfield, D.A. & Baross, J.A. (2002) Temporal changes in archaeal diversity and chemistry in a mid-ocean ridge subseafloor habitat. Applied and Environmental Microbiology 68(4), 1585–1594.Google Scholar
Jarman, S.N., Deagle, B.E. & Gales, N.J. (2004) Group-specific polymerase chain reaction for DNA-based analysis of species diversity and identity in dietary samples. Molecular Ecology 13, 1313–1322.CrossRefGoogle ScholarPubMed
Juen, A. & Traugott, M. (2005) Detecting predation and scavenging by DNA gut-content analysis: a case study using a soil insect predator-prey system. Oecologia 142(3), 344–352.CrossRefGoogle ScholarPubMed
Kumar, S., Tamura, K. & Nei, M. (2004) MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics 5, 150–163.Google Scholar
Lopez, J.V., Yuhki, N., Masuda, R., Modi, W. & O'brien, S.J. (1994) Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. Journal of Molecular Evolution 39(2), 174–190.Google Scholar
Mirol, P.M., Mascheretti, S. & Searle, J.B. (2000) Multiple nuclear pseudogenes of mitochondrial cytochrome b in Ctenomys (Caviomorpha, Rodentia) with either great similarity to or high divergence from the true mitochondrial sequence. Heredity 84, 538–547.Google Scholar
Olsen, L.E. & Yoder, A.D. (2002) Using secondary structure to identify ribosomal numts: cautionary examples from the human genome. Molecular Biology and Evolution 19(1), 93–100.Google Scholar
Pereira, S.L. & Baker, A.J. (2004) Low number of mitochondrial pseudogenes in the chicken (Gallus gallus) nuclear genome: implications for molecular inference of population history and phylogenetics. BMC Evolutionary Biology 4(17), doi: 10.1186/1471-2148-4-17.CrossRefGoogle ScholarPubMed
Perna, N.T. & Kocher, T.D. (1996) Mitochondrial DNA: Molecular fossils in the nucleus. Current Biology 6(2), 128–129.CrossRefGoogle ScholarPubMed
Poulakakis, N., Lymberakis, P., Paragamian, K. & Mylonas, M. (2005) Isolation and amplification of shrew DNA from barn owl pellets. Biological Journal of the Linnean Society 85(3), 331–340.CrossRefGoogle Scholar
Purcell, M., Mackey, G., LaHood, E., Huber, H. & Park, L. (2004) Molecular methods for the genetic identification of salmonid prey from Pacific harbor seal (Phoca vitulina richardsi) scat. Fishery Bulletin 102(1), 213–220.Google Scholar
R Development Core Team (2006) R: A language and environment for statistical computing. Vienna, Austria, R Foundation for Statistical Computing. ISBN 3-900051-7-0. URL http://www.R-project.org.Google Scholar
Richly, E. & Leister, D. (2004) NUMTs in Sequenced Eukaryotic Genomes. Molecular Biology and Evolution 21(6), 1081–1084.Google Scholar
Rubinoff, D., Cameron, S. & Will, K. (2006) A genomic perspective on the shortcomings of mitochondrial DNA for “barcoding” identification. Journal of Heredity 97(6), 581–594.Google Scholar
Sambrook, J., Fritsch, E.F. & Maniatis, T. (1989) Molecular Cloning: A laboratory Manual. 1659 pp. Cold Spring Harbor, NY, Cold Spring Harbor Laboratory Press.Google Scholar
Sorenson, M.D. & Fleischer, R.C. (1996) Multiple independent trans-positions of mitochondrial DNA control region sequences to the nucleus. Proceedings of the National Academy of Sciences of the United States of America 93, 15239–15243.Google Scholar
Symondson, W.O.C. (2002) Molecular identification of prey in predator diets. Molecular Ecology 11(4), 627–641.CrossRefGoogle ScholarPubMed
Thalmann, O., Hebler, J., Poinar, H.N., Paabo, S. & Vigilant, L. (2004) Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes. Molecular Ecology 13, 321–335.CrossRefGoogle ScholarPubMed
Wells, R.S., Rhinehart, H.L., Hansen, L.J., Sweeny, J.C., Townsend, F.I., Stone, R., Casper, D.R., Scott, M.D., Hohn, A.A. & Rowles, T.K. (2004) Bottlenose dolphins as marine ecosystem sentinels: developing a health monitoring system. EcoHealth 1, 246–254.Google Scholar
Woischnick, M. & Moraes, C.T. (2002) Pattern of Organization of Human Mitochondrial Pseudogenes in the Nuclear Genome. Genome Research 12, 885–893.Google Scholar
Zischler, H. (2000) Nulcear integrations of mitochondrial DNA in primates: inferences of associated mutational events. Electrophoresis 21, 531–536.3.0.CO;2-P>CrossRefGoogle Scholar