title: Investigating the extent of parallelism in morphological and genomic divergence among lake trout ecotypes in Lake Superior.
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 aimed to unravel the fine genetic structure of the four lake trout ecotypes in Lake Superior. A total of 486 individuals from four sites were genotyped at 6822 filtered SNPs using RADseq technology. 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) than between ecotypes within sites (mean FST= 0.005) indicating higher level of gene flow or a more recent shared ancestor between ecotypes within each site than between populations of the same ecotype. Evidence of divergent selection was also found between ecotypes and/or in association with morphological variation. Outlier loci found in genes related to lipid metabolism and visual acuity were of particular interest in this context of ecotypic divergence. However, we did not find clear indication of parallelism at the genomic level, despite the presence of phenotypic parallelism among some ecotypes from different sampling sites. Overall, the occurrence of different levels of both genomic and phenotypic differentiation between ecotypes within each site with several differentiated loci linked to relevant biological functions supports the presence of a continuum of divergence in lake trout.
authors.affiliation: Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 avenue de la Médecine, Québec, Quebec, Canada G1V 0A6, Canada.
authors.forename: Alysse
authors.initials: A
authors.lastname: Perreault-Payette
authors.affiliation: Department of Fisheries and Wildlife, Michigan State University, 13 Natural Resources Building, East Lansing, MI, 48824, USA.|Great Lakes Fishery Commission, 2100 Commonwealth Boulevard, Suite 100, Ann Arbor, MI, 48105, USA.
authors.forename: Andrew M
authors.initials: AM
authors.lastname: Muir
authors.affiliation: Northwest Fisheries Science Center, Port Orchard, WA, 98366, USA.
authors.forename: Frederick
authors.initials: F
authors.lastname: Goetz
authors.affiliation: Centre d'Écologie Fonctionnelle et Évolutive (UMR CEFE CNRS 5175), 1919, route de Mende, 34293, Montpellier, France.
authors.forename: Charles
authors.initials: C
authors.lastname: Perrier
authors.affiliation: Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 avenue de la Médecine, Québec, Quebec, Canada G1V 0A6, Canada.
authors.forename: Eric
authors.initials: E
authors.lastname: Normandeau
authors.affiliation: Chaire de recherche sur les espèces aquatiques exploitées, Laboratoire des sciences aquatiques, Département des sciences fondamentales, Université du Québec à Chicoutimi, 555 boulevard de l'Université, Chicoutimi, Quebec, Canada G7H 2B1.
authors.forename: Pascal
authors.initials: P
authors.lastname: Sirois
authors.affiliation: Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 avenue de la Médecine, Québec, Quebec, Canada G1V 0A6, Canada.
authors.forename: Louis
authors.initials: L
authors.lastname: Bernatchez
mesh_terms: D000818:Animals; D060146:Ecotype; D051456:Gene Flow; D023281:Genomics; D060106:Lakes; D009656:North America; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D014337:Trout / Q000235:genetics*
keywords: RADseq; ecological speciation; local adaptation; morphometrics; population genomics; salmonid