Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales

Powerful analyses of population structure require information from multiplegenetic loci. To help develop a molecular toolbox for obtaining thisinformation, we have designed universal oligonucleotide primers that spanconserved intron-exon junctions in a wide variety of animal phyla. We testthe utility of exon-primed, intron-crossing amplifications by analyzing thevariability of actin intron sequences from humpback, blue, and bowheadwhales and comparing the results with mitochondrial DNA (mtDNA) haplotypedata. Humpback actin introns fall into two major clades that exist indifferent frequencies in different oceanic populations. It is surprisingthat Hawaii and California populations, which are very distinct in mtDNAs,are similar in actin intron alleles. This discrepancy between mtDNA andnuclear DNA results may be due either to differences in genetic drift inmitochondrial and nuclear genes or to preferential movement of males, whichdo not transmit mtDNA to offspring, between separate breeding grounds.Opposing mtDNA and nuclear DNA results can help clarify otherwise hiddenpatterns of structure in natural populations.