| Summary: | Although biological data concerning the North Atlantic fin whale ( Balaenoptera physalus) have been collected since the beginning of this century, much is still unknown regarding their biology and evolution. The aim of this study was to increase our knowledge of the evolution, population structure and molecular ecology of this species using modern molecular techniques. Fin whale samples were collected in six feeding areas from the North Atlantic Ocean, the Mediterranean Sea and the Sea of Cortez (North Pacific Ocean). To facilitate the molecular analyses, two new sexing techniques were developed, and several hyper-variable microsatellite loci were isolated from humpback whale (Megaptera novaeangliae) genomic DNA. The sex as well as the genotype at six microsatellite loci was determined and the first 288 nucleotides of the mitochondrial (mt) control region sequenced in 407 samples. Population genetic and phylogeographic analyses of mtDNA and nuclear loci supported the hypothesis that North Atlantic and North Pacific fin whales constitute separate populations. However, the degree of divergence did not correlate with the rise of the Panama Isthmus and suggested the occurrence of occasional gene flow between the two oceans. The analysis of the mtDNA indicated the existence of several separate populations in the North Atlantic Ocean and Mediterranean Sea. The mtDNA analysis identified eastern and western fin whale populations, both distinct from the Mediterranean Sea fin whales. The result of the microsatellite loci analysis revealed significant levels of heterogeneity only between the most distant areas. The observed difference in the relative level of divergence at mtDNA and nuclear loci was consistent with expanding populations not yet in "drift-mutation" equilibrium, which have diverged recently. This scenario was supported by the distribution of pairwise differences among the mtDNA nucleotide sequences. The sex ratio in the samples collected from Gulf of St. Lawr
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