Ancestry and evolution affect genetic diversity in Norway spruce

Many European trees have a long history of change associated with changes in climate. During ice ages, populations survive in local areas, called refugia, where the climate is more benign. As the ice age wanes, the trees expand to colonise, or recolonise, larger areas. As populations expand, two forces are at work on their genetics. One is a demographic effect; in each refugium the trees in the population may well have been selected by evolution. So the descendants of one population probably differ genetically from the descendants of a different population. The other is a more straightforward evolutionary effect, as natural selection favours the trees best adapted to their environment. Both forces leave their mark on the genetic make-up of the population, and for scientists trying to ensure that tree populations can survive and adapt to climate change, it is important to be able to understand how demography and evolution affect genetic diversity.Picea abies, Western Alps, Italy. Photo: B.Vinceti

In search of answers, a group of scientists in the FORGER project focused on Norway spruce (Picea abies) in south-eastern Europe. In this region there are three main groups of populations; in the Alps, in Hercynia (north of the Alps centred on Bohemia) and in the Carpathian Mountains of eastern Europe. Each of these is believed to have expanded from a different refugium, while the main population of Norway spruce in northern Europe is all descended from a single refugium and so does not help to untangle the role of demography.

The search for signals of selection and demography focussed on so-called single nucleotide polymorphisms, or SNPs. A SNP is simply a one-letter difference in the genetic code of a particular piece of DNA. Differences in SNPs often indicate differences in the function of genes. They offer a way to measure the differences between individuals and between populations, and then to associate those differences with differences among specific genes.

The researchers looked at DNA extracted from Norway spruce needles that had been sampled across two geographic scales. At two places in the Alps they sampled trees at six different altitudes going up the slope. This micro scale might be expected to reveal genetic differences that are the result of adaptation to different environmental conditions. Across Europe, at macro scale, they sampled trees from 27 different populations, where both demography and adaptation might be expected to influence genetic diversity.

Looking first at the micro scale, there were no genetic differences among the populations at different heights above sea level. This is somewhat unexpected, as the researchers expected to find that trees would have been selected by the different environmental conditions at different altitudes. They suggest that the reason they see no evidence of adaptation is that pollen travels easily up and down the slopes, eliminating the effect of local selection.

At macro scale, there were clear genetic differences among the populations, shown by differences in the frequency of different SNPs. Just looking at geography, eight SNPs distinguished different samples. Bringing demography into the picture, however, by adding information about the population structure into the analysis, reduced the number of significant genetic differences.

The researchers also looked for associations between genetic differences and climate variables, such as temperature and precipitation. Here too there were effects. At the micro scale, two SNPs correlated with climate variables, while at the macro scale 12 SNPs were closely associated with climate; two of the 12 were also significant at the micro scale. And six of the 12 SNPs were also markers of distinct geographic populations.

In other words, a lot — though not all — of the differences among populations of Norway spruce across Europe are the result of their ancestry, rather than adaptation and evolution. But not all. The study does also tell us something about the genes apparently adapted to climate.

Some SNPs map to specific genes of known function, and in the case of Norway spruce, two of the climate-associated SNPs are in genes that make intuitive sense as candidates for selection. One is believed to be involved in the synthesis of the vitamin riboflavin, which has a role in plant defence. It is highly correlated with combined temperature and precipitation and is found only in some alpine populations, so could well be adaptive. Another encodes a gene that makes sucrose, and so is responsible for energy supply. In Aleppo pine (Pinus halepensis) this gene is known to be switched on by water stress. In this study, it is strongly correlated with annual precipitation. Other SNPs, some of which reflect genes of currently unknown function, could equally well have plausible explanations for their differences among the populations.

The take-home message of this study is that genetic diversity in Norway spruce is shaped to some extent by both demography and adaptation. From the point of view of forest management, ignoring demography can inflate the differences among populations. And while there are clear associations between genetic diversity and environmental conditions, it will take more study, including transplant experiments, to understand the details of genetic adaptation.

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