Genomics of speciation in lake whitefish (Coregonus spp.)
During ecological speciation, reproductive isolation arises as a consequence of 
divergent natural selection. The lake whitefish complex offers an excellent opportunity to study the genetic basis of reproductive isolation and adaptive divergence. Two ecologically and morphologically distinct young species are present in sympatry in many North American lakes: the normal and dwarf whitefish (Bernatchez et al. 2010).
For my PhD project, we have made pure and hybrid whitefish crosses and compared gene expression profiles using microarrays at different developmental stages. We have identified little expression divergence early compared to late in ontogeny (Nolte et al. 2009). Following this, we also documented patterns of gene expression in hybrids and identified several key developmental genes showing highly transgressive patterns of expression (Renaut et al. 2009). Finally, we contrasted gene expression in normally and abnormally developing backcross embryos (Renaut & Bernatchez 2011).
In the second part of my project, we sequenced candidate genes to develop Single Nucleotide Polymorphism (SNP) markers and demonstrated that little sequence divergence existed between normal and dwarf whitefish. Furthermore, using next generation sequencing technology (454 pyrosequencing), several thousands SNPs were discovered. By combining our sequencing results to previous studies, we identified key metabolic genes involved in the adaptive divergence of lake whitefish (Renaut et al. 2010). Finally, by genotyping SNP markers both in natural populations and in an association family, we identified several genes under the effect or natural selection and also responsible for adaptive phenotypic traits (Renaut et al. 2010).