Genomic Variation and Climate Vulnerability of Grassland Species in Seed Zone-Based Restoration
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Höfner, Johannes
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Abstract
Semi-natural grasslands are among the most species-rich terrestrial ecosystems in Central Europe and have been lost at large scales to agricultural intensification and abandonment over the past two centuries. Their restoration, including that of their genetic diversity, is a legislative priority under global biodiversity commitments. Grassland restoration requires large quantities of seeds, whose genetic composition influences the fitness, local adaptation, and long-term viability of the resulting populations. In Germany, 22 legally binding, generalised seed transfer zones regulate the sourcing, production, and application of regional seeds for common and widespread grassland plant species. These zones are based on ecoregions and are expected to reflect the spatial structure of genetic variation in the common and widespread species they cover. In this context, three questions remain largely unaddressed: how well the zones actually reflect empirical patterns of genetic differentiation across species, how species exhibiting ploidy variation should be managed within the seed zone system, and how the system can accommodate adaptive lags imposed by climate change where those are present. Together, these questions define three non-exhaustive dimensions of spatial genomic variation that the seed zones should reflect. This thesis addresses all three dimensions through three empirical studies in population genomics (chapters 2–4), drawing on the unprecedented genome-wide SNP dataset generated by the RegioDiv project for more than 30 grassland species across all of Germany.
Chapter 2 (“Genetic Diversity of Seed Zones”) presents a comprehensive analysis of genetic differentiation across Germany’s 22 seed transfer zones for 33 grassland species. Genomic differentiation between seed zones was analysed using genome-wide SNP markers generated from systematic sampling across all zones. For Agrostis capillaris as a case study, five spatially coherent genetic groups were identified that did not align with zone boundaries, yet differentiation among zones was significant, with 1.17 % of genomic variation residing among zones. Both isolation by distance and isolation by environment were detected. Across all 33 species of the RegioDiv project, differentiation among zones was higher in self-compatible than in outcrossing species, while grasses and herbs did not differ significantly. These findings confirm that the zone system captures consistent but limited genetic differentiation, with its effectiveness varying with the species’ biology.
Chapter 3 (“Polyploid Complexity”) addresses the challenge of polyploid complexes in zone-based seed transfer. Six common grassland species with intraspecific ploidy variation each exhibited strong genetic differentiation between cytotypes. The genetic differentiation between cytotypes consistently exceeded differentiation among seed zones within cytotypes, highlighting the genomically differentiating effect of ploidy variation. Cytotype distributions were often parapatric, rarely aligned with zone boundaries, and were significantly associated with environmental gradients in four of six species. Taken together, these observations warrant separate and specific treatment of cytotypes in zone-based seed transfer. Based on the findings of this chapter, a management decision framework was developed that translates cytotype distribution data into zone-level management recommendations, classifying each species-zone combination according to cytotype presence, frequency, and spatial distribution. The framework provides the first practical tool for managing polyploid complexity within an existing system of generalised seed zones.
Chapter 4 (“Genomic Variation and Climate Vulnerability”) examines spatial patterns of genomic variation and climate change vulnerability in Galium album, a widespread grassland herb. Four spatially coherent genetic groups were identified, explaining 2.43 % of genomic variation, while the 22 seed zones explained 1.92 %. Environment accounted for more genomic variation than geography alone, suggesting that adaptive differentiation contributes substantially to spatial genetic structure. Climate vulnerability was assessed using genomic offsets, quantifying the expected disruption of genotype-environment associations under projected future climate by the end of the 21st century. Offsets were generally low across Germany even under the most pessimistic scenario, with only a few, isolated locations in seed Zone 10 slightly exceeding a previously suggested ad hoc genomic offset threshold. Potentially pre-adapted source populations for these locations were identified within Zone 10 itself, demonstrating that the existing zones can, at least in some of the milder cases, accommodate climate adaptation without transzonal seed transfer.
The general discussion (Chapter 5) integrates these findings and evaluates the utility and limitations of Germany’s seed zone system across all three dimensions of spatial genomic variation. Across the full RegioDiv dataset, significant isolation by distance was found in almost all species, and the 22 zones capture a meaningful proportion of the variation that a species-specific optimisation would achieve, qualifying them as a reasonable and practical compromise between biological precision and operational feasibility. Beyond general spatial variation, this thesis characterises two additional dimensions of genomic variation that are not explicitly incorporated in the current generalised zones. The results suggest that both dimensions can be addressed while largely maintaining the integrity of the established seed zones. An integrated seed source selection framework synthesises all three dimensions into a decision tool, combining cytotype filtering, climate vulnerability assessment, and genetic proximity as sequential criteria for seed source selection. As global restoration commitments drive increasing demand for genomically informed management, this thesis contributes to an empirical and practical foundation for seed transfer that accounts for specific complexities of genomic variation.
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German Federal Agency for Nature Conservation (BfN)
German Federal Ministry for the Environment (BMUV)
Flexpool mechanism of iDiv funded by the German Research Foundation
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
Czech Academy of Sciences, Institue of Botany
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Except where otherwise noted, this item's license is described as Attribution 4.0 International