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Using the DCode System to Identify DNA Sequence Variation for Studies of Population Structure in Marine Organisms

Patrick M. Gaffney, Elizabeth A. Orbacz, and Ziniu Yu, College of Marine Studies, University of Delaware, Lewes, Delaware.


Introduction
DNA polymorphisms are useful tools for ecological and evolutionary studies of both terrestrial and marine organisms, with applications ranging from species identification to delineation of population structure to monitoring genetic change in wild or domesticated populations. Denaturing gradient gel electrophoresis using the DCode system provides a convenient means of identifying genes with useful levels of polymorphism, and subsequently screening populations for variation at selected loci.

Unlike biomedical model organisms, most species of interest in ecological or evolutionary studies are not genetically wellcharacterized. Genes of interest are amplified by polymerase chain reaction* using universal primers targeting highly conserved regions.1 Mitochondrial genes are popular candidates because of their typically rapid evolution, easy amplification, and sensitivity to reduced effective population size.2 For DGGE, the haploid state of mtDNA offers two advantages. First, except for heteroplasmic individuals, the electrophoretic pattern of homoduplex DNA is simple. Secondly, the deliberate construction of heteroduplex molecules by pooling homoduplex PCR products often yields unique heteroduplex electrophoresis patterns, enabling identification of different haplotypes that cannot be separated on the basis of homoduplex mobility. We use DGGE to locate and score both nuclear and mitochondrial DNA polymorphisms in a variety of marine finfish and invertebrates, and describe a few examples here.



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