A novel synthesis of two decades of microsatellite studies on European beech reveals decreasing genetic diversity from glacial refugia

Abstract

Genetic diversity influences the evolutionary potential of forest trees under changing environmental conditions, thus indirectly the ecosystem services that forests provide. European beech (Fagus sylvatica L.) is a dominant European forest tree species that increasingly suffers from climate change-related die-back. Here, we conducted a systematic literature review of neutral genetic diversity in European beech and created a meta-data set of expected heterozygosity (He) from all past studies providing nuclear microsatellite data. We propose a novel approach, based on population genetic theory and a min–max scaling to make past studies comparable. Using a new microsatellite data set with unprecedented geographic coverage and various re-sampling schemes to mimic common sampling biases, we show the potential and limitations of the scaling approach. The scaled meta-dataset reveals the expected trend of decreasing genetic diversity from glacial refugia across the species range and also supports the hypothesis that different lineages met and admixed north of the European mountain ranges. As a result, we present a map of genetic diversity across the range of European beech which could help to identify seed source populations harboring greater diversity and guide sampling strategies for future genome-wide and functional investigations of genetic variation. Our approach illustrates how to combine information from several nuclear microsatellite data sets to describe patterns of genetic diversity extending beyond the geographic scale or mean number of loci used in each individual study, and thus is a proof-of-concept for synthesizing knowledge from existing studies also in other species.

Inferring genetic structure of European beech from observations of spectral phenotypes

“…This resulted in 1,380,310 SNPs across all sampled individuals used in further analyses. To date, patterns of F. sylvatica genetic diversity and structure have been studied with marker-based approaches including allozymes (Gallois et al 1998), AFLP (Pluess and Weber 2012, Guevara et al 2022), microsatellites and, more recently, SNPs in candidate genes (Csilléry et al 2014, Pfenninger et al 2020, Meger et al 2021, Cuervo-Alarcon et al 2021) and whole-genome sequences from limited area of the specie range (Stefanini et al 2023). We are not aware of another study so far that used whole-genome sequences from across the range of F. sylvatica .…”

First genome-wide data from Italian European beech (Fagus sylvatica L.): Strong and ancient differentiation between Alps and Apennines

“…We deliberately refrain from discussing the differentiation between the German (BHAGA and FASYL29) and Polish (JAMY) samples, their relationships with the Italian populations and the apparent incongruence between nuclear and organellar trees for BHAGA (see Results). These European areas were not covered here, being out of the scope of the present study, and only a few genomes were publicly available (considering the nuclear genome, only for the BHAGA and JAMY individuals); these regions are, moreover, characterized by supposedly complex evolutionary history, with a potential distinct glacial refugium hypothesized for Central-Eastern Europe and evidence for admixture among different lineages north of the Alps [7][8][9][10].…”

“…The broad ecological niche of this tree species reflects a complex past evolutionary history, shaped by the multiple glacial-interglacial cycles. Specifically, the integration of palaeobotanical and genetic data revealed the long-term survival of the European beech in different Quaternary glacial refugia and different routes of postglacial spread, where the Mediterranean refuge areas (Southern Balkan, Italian and Iberian Peninsula) did not contribute to the recolonization of central and northern Europe [7], although more recent studies highlighted a contact zone among different lineages in this area, indicating a potential additional refugium located in Central-Eastern Europe [8][9][10]. In the Italian peninsula, the complex orography of Alps and Apennines gave rise to local microrefugia [11]: as a consequence, Italian populations display high genetic diversity with a strong geographical structure.…”

“…In fact, a clear differentiation was shown between northern Italian populations along the Alps and central-southern Italian populations [12]. Although several studies have already been carried out, until recently, inferences on beech genetic variability and population structure were limited by the number of markers used: genetic data were based on polymorphisms of few chloroplast [7,12,13] and neutral nuclear markers [7,14,15]; see [10] for a recent meta-analysis on microsatellite data. Only in recent times the discovery of single nucleotide polymorphisms (SNPs) in coding regions has allowed the investigation of adaptation to specific environmental conditions [2,3,8,[16][17][18][19].…”

“…However, these studies have been conducted on a limited set of polymorphisms within selected genes; moreover, the geographic coverage does not embrace the whole distributional range of the species, being concentrated in the French Alps and Switzerland. Genomic information from the marginal part of the species distribution is therefore still lacking, although these geographic areas might be of particular importance for understanding the legacy of evolutionary history on the genetic diversity of the European beech [10] and assessing its adaptation potential to climate change [20][21][22].…”