Oak genomics takes off … and enters the ecological genomics era

Abstract

‘The emerging field of ecological genomics … provides a multidisciplinary platform to understand how great oaks from little acorns grow – Parvis e glandibus quercus – and how they interact with their environment.’ The emerging field of ecological genomics (Song & Mitchell-Olds, 2011) provides a multidisciplinary platform to understand how great oaks from little acorns grow – Parvis e glandibus quercus – and how they interact with their environment. Indeed, fields and tools from ecology to genetics and genomics interact in a mutually beneficial manner, especially as sequencing and genotyping technologies show continuous declining costs (Wall et al., 2009) and become affordable for individual laboratories. Thus, ecologists are rapidly harnessing the genomic toolbox to study rules that govern processes influencing the distribution and abundance of organisms (Ekblom & Galindo, 2011). Through molecular approaches they can now easily study short-term responses of organisms to their biotic (Barakat et al., 2009) and abiotic environments (Dassanayake et al., 2009) and make inferences on how these molecular factors matter for adaptation (Hohenlohe et al., 2010). Understanding how natural selection drives evolution is a key challenge in evolutionary biology. Studies of adaptation usually focus on how a single environmental factor, either physical (i.e. water availability), or biotic (i.e. pathogen infection) affects evolution within a single species. But nature is much more complex and species are embedded within communities of thousands of species that interact with one another and with the physical environment. Experiments such as those of Tarkka et al. represent a very first step in addressing the complexity of the evolutionary significance of such ecological complexity, and in testing the evolutionary impact of interactions among multiple species during adaptation. What to expect next? Examination of naturally occurring genetic variation of molecular phenotypes and test for their relative fitness, since selection acts within species and inferences about adaptation can only be made while testing among individual differences for fitness-related traits. To this end, comparing oak transcriptome/proteome/metabolome, as well as structural genomic differences between different gene-pools in relation to biotic interaction, should help towards a better understanding of the genetic basis underlying complex interactions and adaptation: do tree-associated communities select for the dynamic of ontogeny in the regulatory landscape of plant genomes, or do they select for different allelic combinations, or both? Moving from Petri dish experiments (i.e. highly controlled laboratory settings) with limited genetic diversity to the wild with high genetic diversity and a much higher number of interactions is an obvious prerequisite to understand ecological adaptation and fitness. In this context, the European white oak species complex offers contrasted genetic resources (segregating mapping pedigrees, locally adapted populations, sister species undergoing incipient speciation, hybrids between sympatric species) to answer key questions in evolutionary ecology.