**ABSTRACT NOT FOR CITATION WITHOUT AUTHOR PERMISSION. The title, authors, and abstract for this completion report are provided below.  For a copy of the full completion report, please contact the author via e-mail at louis.bernatchez@bio.laval.ca or via telephone at 418-656-3402. Questions? Contact the GLFC via email at frp@glfc.org or via telephone at 734-662-3209.**

Population genomics of Lake Superior lake trout in high definition

Alysse Perreault-Payette¹, Andrew M. Muir², Frederick Goetz³, Pascal Sirois⁴, Charles Perrier⁵, Eric Normandeau¹, Louis Bernatchez¹

¹Département de Biologie, Université Laval, 1030 avenue de la Médecine,

Québec, Canada G1V 0A6

²Great Lakes Fishery Commission, 2100 Commonwealth Boulevard, Suite 100,

Ann Arbor, Michigan 48105, USA

³NOAA Northwest Fisheries Science Center, Manchester Research Station,

7305 Beach Dr. East, Port Orchard, WA 98366, USA

⁴Chaire de recherche sur les espèces aquatiques exploitées, Laboratoire des sciences aquatiques, Département des sciences fondamentales,

Université du Québec à Chicoutimi, Chicoutimi, Québec, Canada

⁵Centre d’Écologie Fonctionnelle et Évolutive (UMR 5175 CNRS), 1919, route de Mende F34293 Montpellier Cedex 5, France

March 2016

ABSTRACT:

Understanding the emergence of species through the process of ecological speciation is a central question in evolutionary biology which also has implications for conservation and management. Lake Trout (Salvelinus namaycush) is renowned for the occurrence of different ecotypes linked to resource and habitat use throughout North America. We used next generation sequencing to unravel the fine genetic structure of the four Lake Trout ecotypes described in Lake Superior, the largest North American lake. A total of 486 individuals from four sites where the four ecotypes occur in sympatry were genotyped at 6822 filtered SNPs using RADseq technology. Phenotypic traits of all sequenced fish were documented using a combination of morphometric analyses of head shape, body shape and visual identification. Our results revealed different extent of morphological and genetic differentiation within the different sites. Overall, genetic differentiation was weak but significant and was on average three times higher between sites (Mean FST = 0.016 [0.012; 0.021]) than between ecotypes within sites (Mean FST = 0.005 [0.004; 0.007]) indicating higher level of gene flow and/or a more recent shared ancestor between ecotypes within each site than between populations of the same ecotype. Thus, individuals matching the different ecotype descriptions occurred within each site suggesting convergence in phenotypic traits, as we found little evidence for a shared genetic origin of the different populations belonging to a given ecotype. Evidence of divergent selection was also found between ecotypes and/or in association with morphological variation. Four outlier loci related to lipid metabolism and to visual acuity were of particular interest in this context of ecotypes divergence. Overall, the occurrence of different levels of genomic differentiation between ecotypes within each site with further differentiated loci linked to relavant biological functions support a scenario of repeated divergence of the different sympatric ecotypes within each location.