Norway spruce DNA variants show a north–south pattern

Trees across Sweden experience differing temperatures, day lengths and patterns of light. Norway spruce populations also vary in seasonal traits, including when they resume growth in spring or stop growing for winter. Could genetic variation in particular genes follow a north–south pattern too?

Sonali Sachin Ranade and María Rosario García-Gil analysed exome-capture data from 1,654 Norway spruce trees sampled in natural forests between about 55°N and 67°N. Exome capture focuses on DNA regions that code for proteins. The researchers divided the trees into six continuous populations spanning the region. They note that the groups were not formed using a specific sampling strategy. The analysis focused on missense variants: changes in coding DNA that alter an amino acid in a protein. The researchers examined how variant frequencies differed among populations and assessed genetic differentiation across the groups.

The paper distinguishes two kinds of geographic pattern. A “standard cline” means allele frequency changes consecutively, increasing or decreasing from one population to the next as latitude shifts north. A “trend cline” means there is an overall increase or decrease, but not a consecutive change in every population. The reported result of 2,935 missense variants across 2,084 annotated genes refers specifically to variants showing standard clines.

Among the steepest standard clines were variants assigned to RPL18C, a gene associated with stress and defence responses, and LAF3, involved in light responses. The paper reports a cline steepness of 0.6 for leading variants assigned to each gene. This measure is the difference in allele frequency between the southernmost and northernmost populations. Variants in ZDP, linked to DNA repair and DNA demethylation, also showed steep clines. However, the authors caution that the reference genome used in their analysis was fragmented: the sequences assigned to RPL18C and LAF3 may be gene homologues rather than definitive identifications of those genes.

Other clinal variants occurred in genes associated with flowering and reproductive development, including BAM1, VRN1, FCA and TFL1. The researchers also reported low genetic differentiation among the six populations, measured using 238,512 biallelic missense variants. This result describes differentiation in the data analysed; it does not show that the populations have identical genetic backgrounds. The paper notes that earlier work described two broad population groups, one in central and southern Sweden and another in the north.

The findings are consistent with local adaptation: some variants vary geographically in a pattern that could reflect selection under different local conditions. But a cline alone does not prove adaptation. This study did not experimentally establish that the specific variants alter protein function, improve survival, or cause differences in defence or flowering. Nor does it distinguish the possible effects of temperature, day length and light quality, which vary together across the region.

The approach also has limits. Because the analysis used exome capture and focused on missense variants, it did not survey the entire genome or every part of each gene. The authors say the reference genome was fragmented and that some sequences were incomplete. Gene functions were also informed by comparisons with Arabidopsis, a well-studied model plant; those comparisons suggest possible roles but do not establish that spruce genes function identically. The six-population analysis describes patterns across those groups, rather than providing a continuous measurement at every location.

The results identify candidates for further study, not a tested guide to moving forest seed stocks. The authors argue that breeding and assisted migration should consider more than warming: day length does not change when trees are moved, and seasonal light conditions may not match temperature-based expectations. Testing whether the variants affect traits in controlled experiments and across planting sites would help clarify their importance.

This article is based on a bioRxiv preprint posted November 12, 2026. The preprint has not been certified by peer review, so its analyses and interpretations should be considered provisional.