RESEARCH ARTICLE Effective size and genetic composition of two exploited, migratory whitefish (Coregonus lavaretus lavaretus) populations R. J. Scott McCairns • Anna Kuparinen • Bineet Panda • Erkki Jokikokko • Juha Merila ¨ Received: 26 March 2012 / Accepted: 23 July 2012 / Published online: 31 July 2012 Ó Springer Science+Business Media B.V. 2012 Abstract Large scale harvesting and other anthropogenic activities have caused severe population declines in many commercially important fish populations, but accurate information about census and effective population size is often hard to come by. Available evidence suggests that in marine fishes, effective population size (N e ) is often several orders of magnitude smaller than census size, such that intensively harvested populations may be particularly vul- nerable to loss of genetic diversity. The European whitefish (Coregonus lavaretus) has a long history of heavy exploi- tation in the Baltic Sea, and the Finnish commercial catch of the species has been substantially reduced, despite high fishing effort. We investigated the temporal genetic stability of migratory whitefish populations from two Finnish rivers (Tornionjoki and Kiiminkijoki), sampled at least twice between 1981 and 2006, by assaying variability in 21 microsatellite loci. Our results suggest a small, albeit sig- nificant (F ST = 0.004; p = 0.008) and temporally stable, degree of differentiation between rivers. However, in contrast to earlier reports, heterochronous runs (ascending groups) from Tornionjoki did not exhibit significant genetic divergence. Bayesian estimates of N e suggest substantial declines from historic levels dating to ca 250 years. Yet despite a probable decrease in census population size over the study period, we detected no significant change in contemporary N e . Within group genetic diversity appeared largely unchanged over this time frame; however, we detected a trend towards decreased differentiation between spawning groups (rivers) since the 1980s. These results are discussed in light of stocking programs and conservation of genetic diversity of natural populations. Keywords Fisheries stock assessment Á Genetic monitoring Á Effective population size (N e ) Á Population bottleneck Á Supplemental breeding Á Stocking Introduction Over the past few decades, several commercially important fish stocks have declined as a result of anthropogenic activities such as overexploitation, population translocation and habitat degradation. The collapse of Northern cod (Gadus morhua) provides one of the most dramatic examples of the consequence of overfishing (Hutchings 2000; Hutchings and Baum 2005), whilst Atlantic salmon (Salmo salar) has suffered worldwide from habitat destruction and fragmentation, such as effects from river damming (Thorstad et al. 2008). In 1997 it was estimated that 60 % of major marine fisheries were either overex- ploited, depleted, or in a state of collapse (FAO 1997), and more recent estimates suggest that this figure has increased to approximately 80 % (FAO 2009), leading to a prediction of total collapse of all current fisheries by the year 2048 if Electronic supplementary material The online version of this article (doi:10.1007/s10592-012-0394-2) contains supplementary material, which is available to authorized users. R. J. S. McCairns (&) Á A. Kuparinen Á B. Panda Á J. Merila ¨ Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland e-mail: scott.mccairns@helsinki.fi Present Address: B. Panda Division of Genetics and Physiology, Department of Biology, University of Turku, 20014 Turku, Finland E. Jokikokko Finnish Game and Fisheries Research Institute, Laivurintie 6, 94450 Keminmaa, Finland 123 Conserv Genet (2012) 13:1509–1520 DOI 10.1007/s10592-012-0394-2