A Rapid Screening Procedure for Detecting mtDNA Haplotypes in Humpback Whales (<i style="box-sizing: inherit;">Megaptera novaeangliae</i>)

The highly polymorphic control region of mitochondrial (mt) DNA is used extensively in population genetic studies (1, 2). Variation in the control region is usually detected by sequencing. We have studied the variation in the first 288 base-pairs of the mt control region of the North Atlantic humpback whale by direct sequencing. Based upon previous studies (3) and samples collected in connection with the YoNAH project (Years of the North Atlantic Humpback whale) (4), 545 samples representing all known feeding aggregations in the North Atlantic were analysed. From these studies a total of 32 unique haplotypes were identified. Among the first 41 samples, 23 haplotypes were scored, after which the frequency of new haplotypes decreased dramatically. Furthermore, new haplotypes were represented by only one or a few individuals.