Qiujie Zhou: Drivers and Components of Genetic Diversity in Boreal Forest Trees: The Role of Hybridization and Gene Copy Number Variation in the Evolution of Norway and Siberian Spruce

Abstract

The genetic diversity that underpins biodiversity is shaped by a combination of evolutionary forces, including mutation, migration, genetic drift, and natural selection. The advent of sequencing technologies has enabled genetic studies to be scaled up, both in terms of the number of individuals and the number and types of genetic markers considered. In particular it has shown that structural variation captures more genetic diversity than single nucleotide polymorphisms. Extensive population genomics studies across species ranges have also revealed much more permissive boundaries between species than previously thought. A comprehensive understanding of the origins of genetic diversity and the factors that shape it would therefore require large-scale studies spanning a range of biological levels and scales, from individual genomes to whole populations, and from point mutations to large structural variations. We have addressed these questions in the case of Norway spruce (Picea abies) and Siberian spruce (Picea obovata), two boreal forest tree species with continental ranges.

In Paper I, we used genome-wide SNPs to show that extensive gene flow exists between Norway spruce and Siberian spruce, and we used coalescent simulations to reveal the occurrence of repeated hybridization events between the two species across glacial cycles. These events had a profound impact on the evolutionary trajectories of both species, and a large hybrid zone now extends from northwestern Europe to the southern Urals. Paper II is an eco-evolutionary study in which we demonstrated the role of hybridization in expanding both the species' ecological niche breadth and their resilience to climate change. In Paper III, we investigated patterns of adaptation at two different geographical scales (a latitudinal cline across Sweden and a longitudinal cline across both species' ranges), focusing on the role of gene copy number variations (gCNVs). We showed that a significant proportion of genes have copy number variations and that they are distributed across the genome. These gCNVs are associated with responses to abiotic and biotic stresses, including drought tolerance, temperature regulation and immune responses. Genotype-environment association also revealed that gCNVs play an important role in adaptation along environmental gradients, probably because of the quantitative response they allow. Importantly, we did not detect these candidate genes with conventional methods using SNP data. This work on gCNVs was made possible by the development of a comprehensive framework for detecting CNVs from single nucleotide polymorphism (SNP) data, presented in Paper IV. Paper V further extends the method under a composite likelihood ratio framework to be used with whole genome resequencing data.