Detecting genomic signatures of ecological speciation and parallel evolution in oaks

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Even though Darwin’s central idea that natural selection drives speciation is widely accepted, the mechanisms by which it may lead to reproductive isolation and the origin and maintenance of species integrity in the face of ongoing gene flow are still largely unknown. This project addresses this central question in evolutionary biology to provide additional evidence that divergent selection towards different optima can maintain species integrity in the face of gene flow and could have resulted in the evolution of new species (ecological speciation). Sympatric, multispecies oak (Fagaceae: Quercus) communities are model systems to study processes of ecological speciation with gene flow at the genome level. Thus, hybridization is common among oaks, and species boundaries in European white oaks (Quercus section Quercus) and in the North American red oaks (Quercus section Lobatae) are notoriously weak. However, recurrent gene flow among these species has not led to a loss of genetic cohesiveness or adaptive distinctness, and there is evidence that ecologically-driven selection plays an important role in limiting effective interspecific gene flow. Screening of gene-based microsatellite markers and genome scans revealed genes under strong divergent selection with potential effect on both adaptive divergence and reproductive isolation between species. This project will focus on the two hybridizing sister species of the white oak group, Quercus robur and Quercus petraea, and of the red oak group, Q. ellipsoidalis and Q. rubra, that have distinct and varied adaptations to drought. The project will be generating genome-wide data data across multiple population pairs using Whole Genome Resequencing (1) to characterize genome-wide patterns of divergent selection and (2) to identify candidate genes for adaptive divergence and reproductive isolation between species the shaped lineage divergence across the oak tree of life. Studies identifying genes involved in speciation and maintenance of species integrity are rare, but ongoing gene flow in our Quercus model system, coupled with divergent selection, allows for the identification of genes under selection (outlier loci) and of linked genomic regions that resist the homogenizing force of interspecific gene flow. Integrating genome-wide outlier screens with high density genetic linkage maps that are currently constructed in Q. robur and in Q. rubra we will characterize the genome-wide distribution of outlier loci. For this purpose, both Q. robur and Q. rubra linkage maps will be anchored to scaffolds of the sequenced and annotated Q. robur genome to identify the genomic location of outlier genes and of physically linked candidate genes with putative role in reproductive isolation between species. The proposed project forms the foundation for the identification of genes involved in adaptive divergence and reproductive isolation in oaks and for understanding adaptive divergence across the oak tree of life.