( ngle common haplotype (frequency 90%) ...)Using the DCode System to Identify DNA Sequence Variation for Studies of Population Structure in Marine Organisms

ngle common haplotype (frequency >90%) plus a number of rare variants. To identify new or questionable haplotypes with more certainty, a standard heteroduplex panel of 56 known variants was used. If an individual in question did not show banding patterns identical to that of a previously characterized variant for all heteroduplex combinations, it was classified as a new haplotype. For the total data set, three extremely common haplotypes (Gulf Coast, South Atlantic, North Atlantic), three moderately common variants (Long Island Sound, two from Prince Edward Island) and eight rare variants were found (Figure 2). All were further characterized by direct sequencing.

Discussion
DGGE analysis of PCR products amplified using universal primers may be coupled with heteroduplex analysis to yield a powerful and versatile tool for both the detection of genetic polymorphisms and subsequent haplotype identification. This approach, applicable to temperature gradient gel electrophoresis (TGGE)⁵ as well as the related constant denaturant gel electrophoresis (CDGE), is gaining popularity in population genetics and phylogenetic studies as an alternative to direct sequencing of population samples. Although identification of haplotypes by denaturing gel electrophoresis does not yield the same type of information that DNA sequencing does, it has two particular advantages: 1) it allows the investigator to identify amplified regions with desirable levels of polymorphism, which may vary depending on the purpose of the study; 2) large population samples typically collapse into a much smaller set of haplotypes, which may be sequenced, avoiding repetitive sequencing of common haploty
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