| Summary: | Study of the genetic population structure and the demographic history of the harbour porpoise (Phocoena phocoena) has been nearly comprehensive throughout its distribution in North Atlantic, most studies using the mitochondrial control region as a genetic marker. Although these studies have shown population structure in some parts of the North Atlantic, mitochondrial DNA is a single, maternally inherited locus and therefore insufficient to fully characterize population structure and history. Polymorphism at 11 microsatellite loci was analyzed in harbour porpoises collected throughout the range of the species in the Central and Eastern North Atlantic from the Iberian peninsula northward to Arctic waters (Portugal, Spain, bay of Biscay, Irish waters, English Channel, the southern bay of the North Sea, Norway, Faroe Islands, and Iceland) and also along the coasts of the Black Sea (Turkey, Ukraine, Bulgaria and Georgia). Multilocus tests for allele frequency differences and population structure estimates indicate complete genetic isolation between Atlantic and Black Sea porpoises. No fine population structure was observed within the Black Sea, and this population displayed a low genetic diversity compared to those of Atlantic. These results can be interpreted in the light of the demographic history of this relict population and the strong founder effect and bottleneck it may have undergone in its past evolution. In Eastern North Atlantic waters, microsatellite data revealed fine scale partitioning of the genetic variation. These results will be compared to the pattern previously reported based on the analysis of the mtDNA control region, and seem to correlate with variation in oceanographic features.
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