Widespread amplification of amplified fragment length polymorphisms (AFLPs) in marine Antarctic animals

Hoffman J, Clark MS, Amos W, Peck LS (2012)
Polar Biology 35(6): 919-929.

Journal Article | Published | English

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Abstract
Although recent years have witnessed a rapid growth in the number of genetic studies of Antarctic organisms, relatively few studies have so far used nuclear markers, possibly due to the perceived cost and difficulty of isolating markers such as microsatellites. However, an often overlooked alternative is to use amplified fragment length polymorphisms (AFLPs), a versatile and low-cost method capable of generating large numbers of predominantly nuclear loci in virtually any organism. We conducted a literature review of population genetic studies of Antarctic organisms, finding that fewer than 10% used AFLPs. Moreover, a strong taxonomic bias was found, with studies employing mitochondrial DNA or microsatellites focussing predominantly on animals, while those using AFLPs were mostly of plants or lower organisms. Consequently, we explored the extent to which AFLPs amplify across a range of Antarctic marine animal taxa by genotyping eight individuals each of twelve different species, ranging from echinoderms through soft corals to pelagic fish, at four selective primer combinations. AFLPs readily amplified across all of the taxa, generating between 32 and 84 loci per species, with on average 56.5% of these being polymorphic. In general, levels of polymorphism bore little relationship with expectations based on larger populations of broadcast-spawning species being more variable, though we did find a tentative positive correlation between the number of AFLP bands amplified and a measure of effective population size. Our study lends further support for the utility and ease of use of AFLPs and their suitability for studies of Antarctic species across a wide range of taxa.
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Hoffman J, Clark MS, Amos W, Peck LS. Widespread amplification of amplified fragment length polymorphisms (AFLPs) in marine Antarctic animals. Polar Biology. 2012;35(6):919-929.
Hoffman, J., Clark, M. S., Amos, W., & Peck, L. S. (2012). Widespread amplification of amplified fragment length polymorphisms (AFLPs) in marine Antarctic animals. Polar Biology, 35(6), 919-929.
Hoffman, J., Clark, M. S., Amos, W., and Peck, L. S. (2012). Widespread amplification of amplified fragment length polymorphisms (AFLPs) in marine Antarctic animals. Polar Biology 35, 919-929.
Hoffman, J., et al., 2012. Widespread amplification of amplified fragment length polymorphisms (AFLPs) in marine Antarctic animals. Polar Biology, 35(6), p 919-929.
J. Hoffman, et al., “Widespread amplification of amplified fragment length polymorphisms (AFLPs) in marine Antarctic animals”, Polar Biology, vol. 35, 2012, pp. 919-929.
Hoffman, J., Clark, M.S., Amos, W., Peck, L.S.: Widespread amplification of amplified fragment length polymorphisms (AFLPs) in marine Antarctic animals. Polar Biology. 35, 919-929 (2012).
Hoffman, Joseph, Clark, M. S., Amos, W., and Peck, L. S. “Widespread amplification of amplified fragment length polymorphisms (AFLPs) in marine Antarctic animals”. Polar Biology 35.6 (2012): 919-929.
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