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Understanding the relative contribution of genetic drift, natural selection, and mutation to genetic variation, and quantifying adaptive evolution and the effects of natural selection in species are enduring goals of evolutionary genetics. Norway spruce (Picea abies) is one of the most important conifer species that dominates from both an ecological and economical point of view in many boreal ecosystems. Recently published reference genome of Norway spruce makes it possible to perform population genomic studies to understand the basis of genetic variation and evolutionary effects of natural selection in P. abies by using next-generation sequencing (NGS) data. 

We create an ultra-dense genetic linkage map for Norway spruce using sequence capture data. The consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups (LGs). We also demonstrate, however, that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors. By performing population genetic analyses using the genomic regions anchored to LGs, our genetic linkage map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.

In order to understand how different evolutionary forces have shaped patterns of nucleotide diversity in Norway spruce, we perform population genomic analyses using whole-genome resequencing data. We find that genetic diversity is low across a number of populations in spite of a very wide geographic distribution of P. abies. The demographic history of several reoccurring bottlenecks with concomitant decreases in effective population size, the recurrent natural selection (both purifying and positive selection), and the low overall mutation rates seen in conifers, together make contribute to the loss of genome-wide nucleotide diversity in Norway spruce.

We quantify adaptive evolution and the effects of natural selection across the Norway spruce whole genome. The results show that negative selection is very limited in coding regions, while positive selection is rare in coding regions but very strong in non-coding regions, suggesting the great importance of regulatory changes in evolutionary history of P. abies. We further find a positive correlation between adaptive rate with recombination rate and a negative correlation between adaptive rate and gene density, suggesting a widespread influence from Hill-Robertson interference to efficiency of protein adaptation in P. abies. The distinct population statistics between genomic regions under either positive or balancing selection with that under neutral regions indicate impact from natural selection to genomic architecture of Norway spruce.

Being one of Sweden’s most important tree species, both as a keystone species and for the forest industry, it is important that we keep our stands of Norway spruce (Picea abies (L.) Karst.) as healthy as possible. With an unclear starting point of existing genetic diversity in natural forests we need to both evaluate what levels of natural diversity we have to begin with and how modern forestry practices might affect this. Previous studies have used relatively few markers to study this or similar situation before. We proved that both capture probes and genotyping by sequencing (GBS) show similar results in common diversity measurements and offers many SNPs, although capture probes showed slightly more diversity in the results, we choose to use PoolSeq and GBS together to examine a large number of planted and natural stands of Norwegian spruce in northern Sweden. In line with previous results on the subject we did not find any large differences between our young, planted forests and our old forests, suggesting that today’s re-planting methods have not affected the general diversity in different stands. However, we did find a difference in the variance of our summary statistics on a stand level between planted and old stands, an indicator that there is a possibility that forestry can cause long-term effects. This becomes even more important in the light of possible clonal deployment of Norway spruce. I believe that more research is needed over both larger geographical areas and with a focus on within stand variation. Using mitochondrial and chloroplast DNA to discern finer details of spatial distribution within stands and looking closer at the genotypic diversity within natural and planted stands. An effort should also be put into examine how these possible differences are affecting the rest of the ecosystem, living with and among Norway spruce.