The science behind MyGardenOfTrees
MyGardenOfTrees involves a range-wide transplant experiment using participatory science. Observations from this experiment are combined with genomic data to build a prediction tool for foresters across Europe.
Rationale
Foresters have been performing provenance trials (see Glossary) for centuries. The aim of these trials has been to test and compare the growth performance of species and provenances at a given location. Foresters have used the findings from these trials to guide their choices in planting and reforestation. In these trials, however, species and provenances are only assessed under the specific (often ideal) conditions of the trial site, and cannot be transferred to actual forest conditions. In addition, provenance trials are carried out with seedlings grown in a nursery, and therefore cannot inform foresters about natural regeneration.
MyGardenOfTrees attempts to provide a solution to these shortcomings by establishing a network of hundreds of small provenance trials, called micro-gardens (see Glossary). The main advantage of this approach is that many combinations of provenances (genetic origins) and site conditions (environments) can be tested. Since the performance of various provenances is evaluated across a wide range of environments, findings can be generalized across large spatial scales.
The "distributed provenance trial" design of MyGardenOfTrees. Seeds will be collected from several sites across species' ranges (seed sources) and distributed to hundreds of small test sites. Note that this figure is a schematic illustration for beech species (Fagus spp.) and not the actual location of seed sources and test sites.
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Why do we need a novel species-range-wide transplant approach?
How organisms adapt to their environments is the most fundamental question in evolutionary biology and is of utmost importance given climate change threats. Identifying key traits involved in adaptations and understanding how they interact with each other, and with the environment, is a particularly urgent task for foundation and resource-production species, such as forest trees. Existing experiments assessing local adaptation lack scalability and predictability in natural environments, especially at species range margins. Landscape genomics studies could reveal adaptive loci across environmental gradients, but they are hindered by the assumptions of a neutral model and the highly polygenic nature of most traits. To address these shortcomings, MyGardenOfTrees will be the first species-range-wide transplant experiment using participatory science and genomics to: (i) reveal major patterns and drivers of adaptation and (ii) build a predictive model for selecting optimal seed sources for a given location that accounts for gene–environment interactions and demography. The participatory network of foresters is establishing a large number (approximately 500 across three years) of small provenance trials, called micro-gardens. To evaluate plant performance in novel climate conditions, garden locations will also cover locations beyond the species’ current distribution range, especially towards higher elevations and latitudes. Participants accept an engagement for 5 years; this project thus will principally focus on monitoring and analysing early survival and growth traits, which are under the highest selection pressure in trees. Nevertheless, participants will be encouraged to keep and follow their trees beyond the time frame of this project.
What does a micro-garden look like?
Micro-gardens will be established from seeds directly in the forest, an approach called direct seeding (see Glossary). Each micro-garden contains 100 so-called "seeding spots" that contain 10 seeds from a carefully selected provenance based on a factorial experimental design. Seeds are protected with purpose-designed seed protectors to avoid seed predation, thus protecting our trials, and to avoid contaminating the forest where the trials are established wth foreign seeds.
A micro-garden in France.
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Schematic view of a micro-garden
Why participatory science?
Managing a network of hundreds of micro-gardens is beyond the capacity of any scientific team. MyGardenOfTrees uses a participatory science approach to overcome this difficulty, while also giving foresters the opportunity to observe the germination, survival, and growth of various provenances and to join an unprecedented research effort to find suitable provenances for reforestation at sites that are vulnerable to climate change. Data are collected by participants using forms, implemented with the free tool ODK Collect/Enketo, that are connected to our databases.
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Can participatory science provide sufficiently rigorous observations?
The key to successful participatory science is finding the right match between the target participatory group and the objective. A similar participatory science approach has already been successfully used in agriculture, where farmers have tested the climate resilience of crop and vegetable varieties. Farmers have been asked to run test trials of crops to breed for climate change scenarios, thus capitalizing on the knowledge and motivation of a particular target group. Forest trees share characteristics of crops and wild species, which makes them ideal study organisms for an evolutionary participatory science project. While many forests are managed or planted, most forest tree populations can be considered natural from an evolutionary and ecological perspective. There are numerous knowledgeable foresters working across Europe who are concerned about the future of our forests, and likely motivated to participate in an experimental project.
Another aspect of successful participatory science is standard data collection. Thanks to the survey forms created by our team of scientists and available in a user-friendly app (ODK Collect [Android] / Enketo [all platforms]), all data have the same format and are stored in databases ready to be used.
Further reading:
van Etten, J. et al. 2019. Crop variety management for climate adaptation supported by citizen science. Proceedings of the National Academy of Sciences of the United States of America 116, 4194–4199.
Isaac, M. E. & Martin, A. R. 2019. Accumulating crop functional trait data with citizen science. Scientific Reports 9, 1–8.
Why these species?
MyGardenOfTrees is studying several provenances of silver fir (Abies alba Mill.) and European beech (Fagus sylvatica L.). Both species are native to Europe and are ecologically and economically key for European forest ecosystems. MyGardenOfTrees is also investigating Mediterranean and Oriental sister species, such as Oriental beech (Fagus sylvatica subsp. orientalis (Lipsky) Greuter & Burdet) and Nordmann fir (Abies nordmanniana). If their performance is found to be superior, foresters may consider importing these species in a management strategy called assisted migration (see Glossary).
The distribution area of fir and beech species across Europe and the Middle East.
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Why is MyGardenOfTrees studying these two species?
Both fir and beech have recently attracted interest in the context of climate change because they are more drought tolerant than other dominant forest tree species, such as Norway spruce (Picea abies). However, both species have several Mediterranean and Oriental sister species and subspecies that harbour higher genetic diversity than our European species. Genetic diversity is the basis of adaptation and resilience, so including these sister species in our trials will bring precious knowledge to the design of assisted migration programmes in Europe. In particular, we will study Oriental beech (Fagus sylvatica subsp. orientalis (Lipsky) Greuter & Burdet), which commonly hybridizes with European beech in their multiple contact zones, such as in Bulgaria and Greece, but also in planted Oriental beech sites in Western European countries. See more.
Further reading:
Vitali, V., Büntgen, U. & Bauhus, J. Silver fir and Douglas fir are more tolerant to extreme droughts than Norway spruce in south-western Germany. Global Change Biology 23, 5108–5119 (2017).
Vitasse, Y. et al. Contrasting resistance and resilience to extreme drought and late spring frost in five major European tree species. Global Change Biology 25, 3781–3792 (2019).
Why do we complement the trait observations with genomic data?
Different provenances, or populations, across the species range share a common history: they are all descendants of an ancestral population that lived some time in the past. During the process of colonizing their current habitats, populations have become different from one another, which have left a signature in their genomes. Some of these differences between populations are neutral (or random) due to the fact that only a finite number of individuals reproduce at each generation, while other differences are the result of natural selection. MyGardenOfTrees collects genomic data to tease apart these two processes, which will be necessary to interpret the observations from the micro-garden.
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Genomic data
MyGardenOfTrees will generate homogeneous genomic data for the two study species. European beech has a moderate genome size of 542 Mb, and quality of the assembly is high. Silver fir has a giga-genome of 18.16 Gb and, accordingly, the quality of the assembly is low. Taken into account these differences, different approaches will be used for the two species. For European beech, we will perform whole genome sequencing of a selection of mother trees. For silver fir, the full transcriptome of 10 bio-geographically representative individuals will be sequenced, and followed by the design of 80K capture probes and tested on a bio-geographically representative subset of 100-150 individuals per species groups. Then, approximately 40K target regions containing SNPs range-wide will be selected for genotyping a selection of mother trees.
Further reading:
Mishra, B. et al. A reference genome of the European beech (Fagus sylvatica L.) Gigascience 7, giy063 (2018)
Mosca, E. et al. A Reference Genome Sequence for the European Silver Fir (Abies alba Mill.): A Community-Generated Genomic Resource. G3: Genes, Genomes, Genetics 9, 2039–2049 (2019)
Observations from hundreds of gardens across Europe will be combined together and with genomic data to draw general conclusions about the climate adaptedness of provenances. MyGardenOfTrees will also create a prediction tool, presented as a web-based app, for foresters to help them choose the best seeds to sow in their local environment. It is essential for the MyGardenOfTrees team to provide its participants with the benefits of the project as a whole.
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Integrating gene–environment interactions in a prediction tool
The unprecedented transplant data with a nearly full factorial design obtained from the trials of MyGardenOfTrees will be used in a genomic prediction (GP) model that exploits the genetic similarity between populations and the environmental similarity between garden locations. The new tool can be used to predict the performance of populations in untested, including future, environments, and to predict the performance of new (but genotyped) populations that have not been tested in any environment. The new tool will overcome two major limitations of existing models. First, existing prediction frameworks for evaluating climate-change-related risks for forest trees are based on climate data, and thus assume local adaptation (species distribution models or climate transfer functions). The role of historical contingency is often ignored, even though it has been commonly observed that different lineages have different phenotypes, for example growth patterns. Second, existing models are based on production traits and ignore early traits. Thus, the new tool will be suitable for deciding if assisted migration should be considered or if natural regeneration will be sufficient, and it will help guide forest restoration decisions using direct seeding. Direct seeding could gain importance in the future, given the increasing lack of natural regeneration. Direct seeding can also be an efficient tool for mitigating risks related to extreme events by converting pure stands into mixed stands, thereby increasing their diversity and resilience.
Further reading:
Crossa, J. et al. 2017. Genomic selection in plant breeding: methods, models, and perspectives. Trends in Plant Science 22, 961–975.
Resende, R.T. et al. 2021. Enviromics in breeding: applications and perspectives on envirotypic-assisted selection. Theoretical and Applied Genetics 134, 95–112.
Funding
