Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce

Abstract

Primeval forests are today exceedingly rare in Europe, and transfer of forest reproductive material for afforestation and improvement has been very common, especially over the last two centuries. This can be a serious impediment when inferring past population movements in response to past climate changes such as the last glacial maximum (LGM), some 18,000 years ago. In the present study, we genotyped 1,672 individuals from three Picea species ( P. abies , P. obovata , and P. omorika ) at 400K SNPs using exome capture to infer the past demographic history of Norway spruce ( P. abies ) and estimate the amount of recent introduction used to establish the Norway spruce breeding program in southern Sweden. Most of these trees belong to P. abies and originate from the base populations of the Swedish breeding program. Others originate from populations across the natural ranges of the three species. Of the 1,499 individuals stemming from the breeding program, a large proportion corresponds to recent introductions from mainland Europe. The split of P. omorika occurred 23 million years ago (mya), while the divergence between P. obovata and P. abies began 17.6 mya. Demographic inferences retrieved the same main clusters within P. abies than previous studies, that is, a vast northern domain ranging from Norway to central Russia, where the species is progressively replaced by Siberian spruce ( P. obovata ) and two smaller domains, an Alpine domain and a Carpathian one, but also revealed further subdivision and gene flow among clusters. The three main domains divergence was ancient (15 mya), and all three went through a bottleneck corresponding to the LGM. Approximately 17% of P. abies Nordic domain migrated from P. obovata ~103K years ago, when both species had much larger effective population sizes. Our analysis of genomewide polymorphism data thus revealed the complex demographic history of Picea genus in Western Europe and highlighted the importance of material transfer in Swedish breeding program.

Assessing the potential for assisted gene flow using past introduction of Norway spruce in southern Sweden: Local adaptation and genetic basis of quantitative traits in trees

“…Incidentally, our results also have important consequences for the estimation of trait polygenicity and more specifically for understanding the presence of a large number of false positives due to population structure. Chen et al (2019), indicated the presence of secondary contacts between these main domains (Figure 3a), and current P. abies populations are mainly structured along a latitudinal gradient as are the climatic variables influencing growth traits ( Figure 2, Figure 3b,c). In contrast, bud-burst varies along both latitudinal and longitudinal gradients (Figure 3b).…”

Quantifying adaptive evolution and the effects of natural selection across the Norway spruce genome

“…We therefore removed these individuals (Pab015 and Pab002) from further analyses and regarded remaining samples as being derived from three populations corresponding to the groupings seen in the PCA, hereafter referred to as "Central-Europe," "Finland," and "Sweden-Norway" (see also . Earlier results have shown that P. abies can be subdivided into three main domains, including the Alpine domain, the Carpathian domain, and the Fennoscandian (Baltico-Nordic) domain (Heuertz et al 2006;Chen et al 2019). Our population structure analyses suggest that our Central-Europe population is likely composed of individuals derived from the Carpathian and/or Alpine domains, and there is also substructure within the Fennoscandian (Baltico-Nordic) domain that could represent either population structure within the Fennoscandian domain or the effects of ongoing hybridization with P. obovata that is more apparent in the eastern (Finland) part of the distribution range (Tsuda et al 2016).…”

“…We calculated the effective population size (Ne) for each population based on levels of polymorphism quantified by Watterson's estimator of 4Neμ (θW) (Watterson 1975) and nucleotide diversity, π (Tajima 1983) for synonymous sites (Gossmann et al 2010). The effective population size using the level of synonymous site diversity and dividing this by an estimate of the mutation rate per generation (Ne= πsynonymous/4μ), where synonymous site diversity for each population refer to , and a mutation rate of 1.1x10 -9 per site per year and a generation time of 25 years was used for P. abies (Nystedt et al 2013;Chen et al 2019).…”

“…Based on 4-fold synonymous sites using data for 33 individuals (Pab034 was removed because it was found to be highly related with Pab033, see for more details), the PCA result clearly reflects geographic structure within P. abies (supplementary Figure S2): samples from Belarus, Poland, and Romania grouped into one cluster, most Finish samples clustered into one group, most individuals from Norway and northern Sweden clustered into one group. Two individuals, one from southern Finland (Pab015) and one from southern Sweden (Pab002), could not be grouped within any of the populations as they fell between the three main groups in the PCA plot, indicating that they represent materials that have recently been introduced in to Sweden and Finland from elsewhere in Europe (Chen et al 2019;). We therefore removed these individuals (Pab015 and Pab002) from further analyses and regarded remaining samples as being derived from three populations corresponding to the groupings seen in the PCA, hereafter referred to as "Central-Europe," "Finland," and "Sweden-Norway" (see also .…”

“…Historical population size fluctuations and reoccurring bottlenecks have sharply reduced the effective population size in Norway spruce and is one of the likely reasons for the large proportion of new amino acid mutations that we classify as effectively neutral. Human-mediated selection and the use of limited seed sources for reforestation could also have contributed to a reduction in the effective population size Chen et al (2019). showed that a large proportion of the 1,499 individuals stemming from the Norway spruce breeding program in southern Sweden corresponds to recent introductions from mainland Europe.…”