Genetic structure in alpine brown trout Salmo trutta L. shows that indirect stocking affects native lake populations J. H. SØNSTEBØ, R. BORGSTRØM AND M. HEUN* Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, P. O. Box 5003, NO-1432 A ˚ s, Norway (Received 30 August 2007, Accepted 2 January 2008) Genetic variation of brown trout inhabiting six connected lakes (Krokavatn, Skavatn, Kollsvatn, Litlosvatn, Kvennsjøen and Øvre Krokavatn) of the Hardangervidda mountain plateau was analysed by 11 microsatellites covering a period of 24–35 years. Temporal changes were found and are deemed to be mostly related to stocking in the headwater lakes Krokavatn and Skavatn. A pronounced change was evident in one population (Kollsvatn) and was the result of downstream migration of stocked fish from these headwater lakes. This indirect stocking accounted for up to 50% in the STRUCTURE analysis of Kollsvatn fish and was less pronounced in the other downstream populations of Litlosvatn (c. 28%), Kvennsjøen (c. 17%) and Øvre Krokavatn (c. 13%). Since significant downstream migration of stocked fish affecting native populations occurs, nature management efforts must respond accordingly. # 2008 The Authors Journal compilation # 2008 The Fisheries Society of the British Isles Key words: freshwater fish; genetic change; indirect stocking; microsatellite; migration. INTRODUCTION The management of natural populations based on conservation genetics de- pends on an understanding of population structure over time and space. Al- though spatial genetic differentiation has been reported for brown trout (Ryman et al., 1979; Ferguson & Mason, 1981; Skaala & Nævdal, 1989; Hansen & Loeschcke, 1996; Estoup et al., 1998; Heggenes et al., 2002), only recently has temporal population structure been studied (Hansen, 2002; Campos et al., 2007). Both temporally stable (i.e. no strong or significant changes over time) and unstable populations have been found (Laikre et al., 2002; Palm et al., 2003; Østergaard et al., 2003; Jensen et al., 2005). Temporal instability may be especially pronounced in small populations inhabiting variable environ- ments, where small effective population sizes might lead to high levels of genetic drift (Østergaard et al., 2003; Jensen et al., 2005). Alpine populations of brown trout on the Hardangervidda mountain plateau in Norway experience unpredictable environments. Growth rate and survival of *Author to whom correspondence should be addressed: Tel.: þ47 64 96 57 91; Fax: þ47 64 96 58 01; email: manfred.heun@umb.no Journal of Fish Biology (2008) 72, 1990–2001 doi:10.1111/j.1095-8649.2008.01815.x, available online at http://www.blackwell-synergy.com 1990 # 2008 The Authors Journal compilation # 2008 The Fisheries Society of the British Isles