Convergent transcriptomic landscapes under polygenic selection accompany inter-continental parallel evolution within a Nearctic Coregonus (Salmonidae) sister-species complex.

In contrast to the plethora of studies focusing on the genomic basis of adaptive phenotypic divergence, the role of gene expression during speciation has been much less investigated and consequently, less understood. Yet, the convergence of differential gene expression patterns between closely related species-pairs might reflect the role of natural selection during the process of ecological speciation. Here, we test for intercontinental convergence in differential transcriptional signatures between limnetic and benthic sympatric species-pairs of Lake Whitefish (Coregonus clupeaformis) and its sister-species, the European Whitefish (C. lavaretus). We analysed six replicated sympatric species-pairs from North America, Norway and Switzerland. Following de novo transcriptome assembly based on RNAseq data, we characterized genomic variation and differential gene expression between sympatric limnetic and benthic species but also across regions and continents. We found significantly differentially expressed genes (DEG) between limnetic and benthic whitefish by analyzing orthologous genes. DEG were enriched in shared polymorphism among sister-species, supporting the idea that some ancestral polymorphisms involved in parallel phenotypic divergence between sympatric species-pairs are maintained over long-term by the interaction of selection and gene flow. Using both and genotypes to infer polygenic selection and co-variation of genes expression involved in the same metabolic pathways, we identified parallel outliers and DEG with genes primarily over-expressed in limnetic species relative to the benthic species. Finally, we discovered a cis-eQTL associated with variable level of gene expression related to a trait involved in limnetic-benthic species divergence, which is shared in parallel across continents despite 500,000 years of geographic isolation. Overall, comparative transcriptomics across continents allowed identifying biological functions and candidate genes enriched in shared polymorphism associated with parallel phenotypic divergence across species-pairs of the sister-species complex from different continents, consistent with a fundamental role of longstanding natural selection on phenotypic traits involved in the ecological speciation of limnetic/benthic whitefish species-pairs.