Oak Population Genomics

Oaks (genus Quercus) are foundation tree species significantly affecting community assembly and ecosystem functions. Their ecological importance, high diversity in adaptive traits and genes, and rapidly growing genomic resources make them model species for the integration of population, evolutionary, and ecological research. Their demonstrated replicated sympatric diversification history in the Americas and recurrent gene flow between related but ecologically divergent sympatric species make oaks a strong system for studying genomic signatures of local adaptation and adaptive trait evolution. Here, we present a summary of available genomic, transcriptomic, and experimental resources for the genus and applications of these resources to population genomic analyses such as association mapping (Genome-wide Association Analyses, GWAS), landscape genetics, population epigenomics, paleogenomics, and phylogenomics studies. High density genetic linkage maps and Quantitative Trait Locus (QTL) studies are reviewed as important tools for the detection of chromosomal regions associated with adaptive trait variation for the validation of causal associations in GWAS and of outlier loci between ecologically contrasting populations. The application of genomics tools to the study of local adaptation, adaptive divergence and interspecific hybridization and introgression is also highlighted, focusing on contemporary population genomics approaches that have addressed questions related to the genomic architecture of adaptive trait variation and local adaptation, the potential role of interspecific hybridization and epigenetic variation in rapid local adaptation, lineage divergence and speciation, and the temporal dimension of adaptive genomic changes. Future perspectives and advances in our understanding of genome-wide variation patterns such as resequencing of whole genomes at the population level, high-resolution population epigenomics, assessment of genomic vulnerability, and the conservation and sustainable management of oak populations in the face of changing environmental conditions are briefly outlined.