Genomic Diversity and Phylogeography of Oak Species

Oaks (genus Quercus) stand among the most widespread and ecologically important tree groups in the Northern Hemisphere, exhibiting exceptional genetic variation and a complex history of population divergence. Advances in sequencing technologies have yielded draft nuclear and chloroplast genomes for multiple oak species, revealing high heterozygosity, extensive gene families and lineage‐specific duplications. Genome‐wide surveys of single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) have elucidated patterns of local adaptation and identified genomic regions under selection, while comparative linkage maps have demonstrated strong collinearity among species. Phylogeographic analyses, integrating both plastid and nuclear markers, have reconstructed oak dispersal from glacial refugia, post‐glacial colonisation routes and the establishment of contact zones. These studies highlight the role of hybridisation and introgression in shaping species boundaries, often resulting in cytonuclear discordance between chloroplast and nuclear genealogies. Observations of long‐distance pollen and seed flow further underscore the permeable nature of oak genomes, informing conservation strategies and the design of seed transfer guidelines under climate change.

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Genomic Diversity and Phylogeography of Oak Species publication trend

The graph below shows the total number of articles in genomic diversity and phylogeography of oak species across all publications each year (not limited to Nature Index journals).

Technical terms

Single nucleotide polymorphism (SNP): A variation at a single DNA base position among individuals in a population, used as a marker for genetic diversity and association studies.

Phylogeography: The discipline that examines the historical processes responsible for the geographic distributions of genetic lineages, typically using molecular markers.

ddRAD-seq: Double digest restriction‐site associated DNA sequencing, a method for sampling genome‐wide SNPs by sequencing fragments adjacent to restriction enzyme cut sites.

Chloroplast genome (plastome): The circular DNA molecule within plant chloroplasts, inherited uniparentally and commonly used in studies of maternal lineage and biogeography.

References

1. First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Née (Fagaceae). G3: Genes, Genomes, Genetics (2016).
2. A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study. BMC Genomics (2010).
3. Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data. Heredity (2023).
4. Genetic Structure and Evolutionary History of Three Alpine Sclerophyllous Oaks in East Himalaya-Hengduan Mountains and Adjacent Regions. Frontiers in Plant Science (2016).
5. Comparative systematics and phylogeography of Quercus Section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation. PeerJ (2018).
6. High Rates of Gene Flow by Pollen and Seed in Oak Populations across Europe. PLOS ONE (2014).
7. Comparative mapping in the Fagaceae and beyond with EST-SSRs. BMC Plant Biology (2012).
8. Evidence for hybridization and introgression within a species-rich oak (Quercus spp.) community. BMC Ecology and Evolution (2007).