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.
Highlights
IntroductionBased on a limited number of nuclear DNA markers, previous studies indicated extensive shared ancestral polymorphisms, suggesting a relatively recent divergence time measured on an effective population size timescale, as well as weak but significant effect of migration (Heuertz et al 2006; Chen et al 2010; Li et al 2010a; Chen et al 2016; Tsuda et al 2016). Chen et al (2016) concluded that the Fennoscandian domain split from the two southern domains of P. abies around 5 million years ago (mya), i.e. before the Pliocene-Quaternary glaciation, which is consistent with estimates of dating based on the molecular clock (~6 mya, (Lockwood et al 2013))
Genetic diversity and population divergence Genetic diversity was calculated at 0-fold and 4-fold sites (π0 and π4) and their ratio calculated for protein coding sequences of P. omorika, P. obovata, and the three main domains of P. abies (Alpine, Carpathian and Fennoscandian)
This led to large π0/π4 ratios in all three species but especially in P. omorika (0.44 compared to 0.39 and 0.4, for P. obovata and P. abies, respectively, Table 1)
Summary
Based on a limited number of nuclear DNA markers, previous studies indicated extensive shared ancestral polymorphisms, suggesting a relatively recent divergence time measured on an effective population size timescale, as well as weak but significant effect of migration (Heuertz et al 2006; Chen et al 2010; Li et al 2010a; Chen et al 2016; Tsuda et al 2016). Chen et al (2016) concluded that the Fennoscandian domain split from the two southern domains of P. abies around 5 million years ago (mya), i.e. before the Pliocene-Quaternary glaciation, which is consistent with estimates of dating based on the molecular clock (~6 mya, (Lockwood et al 2013)). In this paper we investigated past demographics and recent translocations in Norway spruce using genome-wide SNP data from > 1,600 individuals sampled from: i) populations from southern Sweden that were used to establish the Swedish Norway spruce breeding program, ii) natural populations of P. abies across its natural range and iii) two close relatives, the Siberian spruce (P. obovata) and the Serbian spruce (P. omorika). We collected needles from 1,499 individuals that were initially used to create the Swedish breeding program, i.e. were selected as “plus trees” (trees of outstanding phenotype) in 20-40 years old production forestry stands or selected as “superior” 3-4 years old seedling genotypes in commercial nurseries This was done across central and Southern Sweden. 448,698 SNPs are in introns and 192,010 fall in intergenic regions
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