DNA Profiling in Ecology

Abstract

Deoxyribonucleic acid (DNA) profiling uses various molecular biological techniques to identify, classify, and study the ecology and evolution of organisms based on differences in DNA sequence. These differences in DNA sequence are known as polymorphisms, which may be as simple as a single nucleotide at a given nucleotide position within the genome or as complex as variant numbers of tandem repeat sequences or the presence of an interspersed repetitive element. Individuals, populations or species‐specific DNA polymorphisms are used as targets to generate fingerprint patterns suitable for the differentiation of individuals and populations. Data generated by DNA profiling methods are used to provide quantitative or qualitative information for population genetics, human diseases, diversity, phylogeny, epidemiological, forensics and conservation management purposes.

Key Concepts:

  • DNA profiling methodologies allow for the classification of organisms based on polymorphisms in DNA sequences at a given loci.

  • DNA profiling methods that can be used to detect single nucleotide and repetitive element polymorphisms include: amplified and restriction fragment length polymorphisms (AFLP/RFLP), multilocus fingerprinting using hybridisation, random amplified polymorphic DNA and denaturing gradient and pulse field gel electrophoresis (DGGE/PFGE).

  • DNA profiling patterns can be used to identify individuals, determine kinship and genealogy, examine inbreeding, and bottlenecks and differentiate populations.

Keywords: DNA profiling; DNA fingerprinting; ecology; repetitive DNA; microsatellite; minisatellite; VNTR; RAPD; AFLP; Rep‐PCR

Figure 1.

Horizontal flourophore‐enhanced repetitive element PCR (HFERP) DNA profile analysis of environmental E. coli strains using primers directed at the BOX repetitive element. The DNA profiles of individual strains are shown in red, due to 6‐FAM labelling of the primer. Internal size standards are labelled with ROX and appear green in the image.

Figure 2.

(a) Microsatellite analysis of four isolated populations (UH, VC, AF and HJ) of plains zebra, Equus quagga antiquorum, in southern Africa, using a primer pair, HGT9, isolated from the horse. Microsatellite banding patterns from six representative individuals in each of the four populations after gel electrophoresis; the values at the left are the sizes in base pairs of the corresponding bands. (b) Histogram of relative allele frequencies from the full data set.

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Further Reading

Avise JC (2004) Molecular Markers, Natural History, and Evolution. Sunderland, MA: Sinauer Associates, Inc.

Baker A (ed.) (2000) Molecular Methods in Ecology. Oxford, UK: Wiley‐Blackwell.

Osborn M and Smith C (eds) (2005) Molecular Microbial Ecology. Oxford, UK: Taylor and Francis Group, Ltd.

Weising K, Nybom H, Wolff K and Kahl G (2005) DNA Fingerprinting in Plants: Principles, Methods, and Applications. Boca Raton, FL: CRC Press.

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How to Cite close
Hamilton, Matthew J, and Sadowsky, Michael J(Nov 2010) DNA Profiling in Ecology. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005454.pub2]