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

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 diYculty of isolating markers such as microsatellites. However, an often overlooked alternative is to use ampliWed 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, Wnding 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 diVerent species, ranging from echinoderms through soft corals to pelagic Wsh, at four selective primer combinations. AFLPs readily ampliWed 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 broadcastspawning species being more variable, though we did Wnd a tentative positive correlation between the number of AFLP bands ampliWed and a measure of eVective 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.

Hierarchical Population Genetic Structure in a Direct Developing Antarctic Marine Invertebrate

“…This study was made feasible through the use of AFLPs because these markers are capable of generating large numbers of genome-wide distributed bands in virtually any organism, including diverse Antarctic marine taxa [61], with little need for optimisation. Although we were able to score a large number of bands, however, the dominant nature of these markers leads to increased variance in the estimation of allele frequencies [54].…”

Evolutionary patterns in Antarctic marine invertebrates: An update on molecular studies

“…On the one hand, a study using COI demonstrated no apparent genetic structure along the South Shetland Islands and Antarctic Peninsula, supporting a single genetic unit along this area, which could be the result of past bottleneck events during the glacial maxima and further founder effects (González-Wevar et al, 2011). On the other hand, another study using AFLP markers found significant differences between one of the Southern-most areas surveyed (Anchorage Island, South to Adelaide Island) and the rest of the localities (Hoffman et al, 2012). The results for N. concinna contrast with those obtained for the bivalve Margarella antarctica.…”

“…A range of markers including ribosomal genes (18S and 28S rDNA) and internal transcribed spacers (ITS1 and ITS2), Exon-primed Intron-crossing (EPIC) markers, and microsatellites have also been applied in some Antarctic species (see Table 1). In addition, Amplified Fragment Length Polymorphism (AFLP) techniques have also been used in two studies on Antarctic organisms (Hoffman et al, 2011(Hoffman et al, , 2012; see Table 1). However, the reduced number of examples studied hinders the comprehensive comparisons among taxa.…”

Genetic structure of declining chinstrap penguin (Pygoscelis antarcticus) populations from South Shetland Islands (Antarctica)

“…The aim of this study was to explore the genetic diversity and population structure of two declining chinstrap penguin populations from the South Shetland Islands using amplified fragment length polymorphism (AFLP) analyses (Busch et al 2000;Milot et al 2008;Hoffman et al 2012). Falling population sizes can lead to loss of neutral genetic variation, fixation of mildly deleterious alleles, and thereby reduced population fitness (Kalinowski and Waples 2002;Baker 2006;Markert et al 2010).…”