CONTRASTING POPULATION-STRUCTURE FROM NUCLEAR INTRON SEQUENCES AND MTDNA OF HUMPBACK WHALES

Powerful analyses of population structure require information from mul tiple genetic loci. To help develop a molecular toolbox for obtaining this information, we have designed universal oligonucleotide primers t hat span conserved intron-exon junctions in a wide variety of animal p hyla. We test the utility of exon-primed, intron-crossing amplificatio ns by analyzing the variability of actin intron sequences from humpbac k, blue, and bowhead whales and comparing the results with mitochondri al DNA (mtDNA) haplotype data. Humpback actin introns fall into two ma jor clades that exist in different frequencies in different oceanic po pulations. It is surprising that Hawaii and California populations, wh ich are very distinct in mtDNAs, are similar in actin intron alleles. This discrepancy between mtDNA and nuclear DNA results may be due eith er to differences in genetic drift in mitochondrial and nuclear genes or to preferential movement of males, which do not transmit mtDNA to o ffspring, between separate breeding grounds. Opposing mtDNA and nuclea r DNA results can help clarify otherwise hidden patterns of structure in natural populations.