Use of Genomic Resources to Assess Adaptive Divergence and Introgression in Oaks

Abstract

Adaptive divergence is widely accepted as a contributor to speciation and the maintenance of species integrity. However, the mechanisms leading to reproductive isolation, the genes involved in adaptive divergence, and the traits that shape the adaptation of wild species to changes in climate are still largely unknown. In studying the role of ecological interactions and environment-driven selection, trees have emerged as potential model organisms because of their longevity and large genetic diversity, especially in natural habitats. Due to recurrent gene flow among species with different ecological preferences, oaks arose as early as the 1970s as a model for understanding how speciation can occur in the face of interspecific gene flow, and what we mean by “species” when geographically and genomically heterogeneous introgression seems to undermine species’ genetic coherence. In this review, we provide an overview of recent research into the genomic underpinnings of adaptive divergence and maintenance of species integrity in oaks in the face of gene flow. We review genomic and analytical tools instrumental to better understanding mechanisms leading to reproductive isolation and environment-driven adaptive introgression in oaks. We review evidence that oak species are genomically coherent entities, focusing on sympatric populations with ongoing gene flow, and discuss evidence for and hypotheses regarding genetic mechanisms linking adaptive divergence and reproductive isolation. As the evolution of drought- and freezing-tolerance have been key to the parallel diversification of oaks, we investigate the question of whether the same or a similar set of genes are involved in adaptive divergence for drought and stress tolerance across different taxa and sections. Finally, we propose potential future research directions on the role of hybridization and adaptive introgression in adaptation to climate change.

Abiotic factors predict taxonomic composition and genetic admixture in populations of hybridizing white oak species (Quercus sect. Quercus) on regional scale

“…Because different oak species have different ecological requirements and tolerances, taxonomically diverse oak stands should be well equipped for adaptation to environmental changes through natural selection and adaptive introgression (Lazic et al 2021) and be more resilient to extreme events. Here, we hypothesized that variation in micro-environmental conditions promotes such high taxonomic diversity, and that certain environmental factors are driving this pattern.…”

Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How

“…DNA-based markers were employed in a study of a large number of species within the genus Quercus , as reviewed by Simeone et al [ 50 ], Backs and Ashley [ 51 ], Lazic et al [ 51 ], and Liang et al [ 52 ], and are summarized in Table S1 . In general, data from DNA marker techniques clearly show a high level of genetic variation within the genus, especially in Q. ilex [ 53 ].…”

From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees

“…Even though the biological concerns over possible gene drive are negligible, more attention should be paid to the detection of off-target mutations in trees due to the long generation time and preponderance of out-crossing in wind-pollinated species, such as oaks [216]. Evidence for extremely low rates of off-target mutations as well as measuring outcomes of CRISPR-mediated on-target damage in trees [15] has typically been assayed by using 1kb-range methods such as Sanger or short-read amplicon sequencing.…”