Genetic signatures of historical bottlenecks in sympatric lake trout (Salvelinus namaycush) morphotypes in Lake Superior Bruno Guinand & Kevin S. Page & Mary K. Burnham-Curtis & Kim T. Scribner Received: 28 April 2011 / Accepted: 26 March 2012 / Published online: 13 April 2012 # Springer Science+Business Media B.V. 2012 Abstract Humans have played a significant role in reducing levels of genetic diversity and differentiation of many teleost fishes, leading to homogenization across biological entities. We compare patterns of historical and contemporary genetic structure for three sympatric Great Lake’ s lake trout (Salvelinus namaycush) morphs (lean, siscowet, and humper) that differ in patterns of habitat occupancy, susceptibility to overfishing and pre- dation by invasive sea lamprey (Petromyzon marinus). Differential susceptibilities to overfishing and predation were expected to result in different impacts to levels of genetic diversity loss for each morphotype. Genetic data was collected for samples at three points in time: 1948 (pre-collapse), 1959 (collapse) and 1990s (current), corresponding to periods of intensive fishing, mortality due to lamprey and recovery, respectively. The lean morph preferentially targeted by the fishery and recog- nized as highly preyed upon by sea lamprey was more highly impacted genetically than other morphs, as evidenced by greater loss of genetic diversity first during the period of overfishing, then during the period of high sea lamprey abundance once the fishery collapsed. The siscowet morph also experienced genetic bottlenecks during the period of overfishing (pre-collapse period). Results indicate significant levels of genetic differentia- tion among morphs historically prior to declines in Environ Biol Fish (2012) 95:323–334 DOI 10.1007/s10641-012-0005-6 Electronic supplementary material The online version of this article (doi:10.1007/s10641-012-0005-6) contains supplementary material, which is available to authorized users. B. Guinand (*) : K. S. Page : K. T. Scribner Department of Fisheries and Wildlife, Michigan State University, 13 Natural Resources Building, East Lansing, MI 48824, USA e-mail: bruno.guinand@univ-montp2.fr B. Guinand UMR-CNRS 5554 Institut des Sciences de l’Evolution de Montpellier, Département de Biologie Intégrative, Université Montpellier 2, CC63, Place E. Bataillon, 34095 Montpellier Cedex 05, France K. T. Scribner Department of Zoology, Michigan State University, 203 Natural Science Building, East Lansing, MI 48824, USA K. S. Page Inland Fisheries Research Unit, Ohio Department of Natural Resources, 10517 Canal Rd., Hebron, OH 43025, USA M. K. Burnham-Curtis National Forensics Laboratory, U.S. Fish and Wildlife Service, 1490 Main St., Ashland, OR 97520, USA