Genomics of Adaptation in European Pines (GAP)
Lead Research Organisation:
NERC CEH (Up to 30.11.2019)
Department Name: Watt
Abstract
Natural selection is a geographically variable force, determined in part by local environmental conditions. As phenotype is a product of a genotype and its environment, and phenotype determines fitness, then spatial environmental variability should produce differently adapted populations, with phenotypes optimised to local conditions. This process of divergent selection is an important mechanism for maintaining genetic diversity within species, and is particularly critical for long-lived sedentary organisms like trees, where adaptation to local conditions is crucial, as they will be in one place for life and that lifetime may be centuries long. If we are to form reasonable predictions of the likely impacts of environmental change on tree species, then we must begin to understand the process of local adaptation at a genomic level and identify the genes, and the mutations in those genes, that are involved in control of tree phenotype. However, several evolutionary forces act to counter divergent selection, of which gene flow is the most significant, and demographic processes such as extinction and recolonisation may confound local adaptation. Therefore, successful detection of the molecular signature of local adaptation requires parallel evaluation of evolutionary and demographic processes, as both shape genetic variation in natural populations. This project will integrate data from the gene to phenotype to population scale and apply this to a specially selected group of European tree species, in which clear adaptive divergence is present and where post-glacial colonisation dynamics have played a strong role. The project will take advantage of a large new genomic resource to study links between phenotypic variation and nucleotide polymorphism in nuclear genes related to environmental stress, phenology and wood formation, and in the mitochondrial genome in natural populations of four pine species. The species include a generalist, Pinus sylvestris (Scots pine), and three habitat specialist species from the P. mugo complex i.e. P. mugo (dwarf mountain pine), P. uncinata (mountain pine) and P. uliginosa (peat-bog pine). The species form an excellent system for study of neutral and adaptive variation due to close phylogenetic relationships but strong contrasts in geographic distribution, biology and ecology. Fundamentally, the project will integrate genomic and phenotypic data and statistics to make a unique and ground-breaking contribution to a developing field of biodiversity research. The application of genomic approaches to the study of local adaptation is in its infancy and this project will make two major new contributions to the science: the largest analysis of genomic data in natural pine populations, and deployment of a unique experimental design, placing intraspecific adaptive divergence in the context of recent evolutionary history. In addition, the information generated by the project, on adaptive loci, will be of direct application in gene conservation and breeding programs. This will enhance management of forest genetic resources and tree production quality, particularly under the climate change scenarios currently affecting adaptive optima of most forest tree species. Project outputs will also be of direct application in science-based conservation, for example, in conserving genetic resources in the remnant Scots Pine forest fragments in Scotland. CEH's strong links with statutory bodies responsible for management of the UK forest resource and experience in communicating scientific outputs to end users will facilitate effective delivery of results. In summary, the project is an excellent opportunity to take immediate advantage of new genomic data, a ready-made collection and the skills of highly qualified and experienced researchers. All of these key project components are in place and available now, so the project promises high impact for low risk and with significant potential for downstream research.
Organisations
- NERC CEH (Up to 30.11.2019) (Lead Research Organisation)
- ROYAL BOTANIC GARDENS, KEW (Collaboration)
- Woodland Trust (Collaboration)
- Earth Trust (Collaboration)
- FOREST RESEARCH (Collaboration)
- Future Trees Trust (Collaboration)
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (Project Partner)
- University of Edinburgh (Project Partner)
Publications
Zaborowska J
(2021)
Candidate Genes for the High-Altitude Adaptations of Two Mountain Pine Taxa.
in International journal of molecular sciences
Wójkiewicz B
(2016)
Current Approaches and Perspectives in Population Genetics of Scots Pine ( Pinus sylvestris L.)
in Forest Science
Wachowiak W
(2022)
Phylogeography of Scots pine in Europe and Asia based on mtDNA polymorphisms
in Journal of Systematics and Evolution
Wachowiak W
(2014)
Interspecific gene flow and ecological selection in a pine (Pinus sp.) contact zone
in Plant Systematics and Evolution
Wachowiak W
(2022)
Admixture and selection patterns across the European distribution of Scots pine, Pinus sylvestris (Pinaceae)
in Botanical Journal of the Linnean Society
Wachowiak W
(2015)
Comparative transcriptomics of a complex of four European pine species.
in BMC genomics
Wachowiak W
(2018)
Molecular signatures of divergence and selection in closely related pine taxa.
in Tree genetics & genomes
Wachowiak W
(2018)
Early phenology and growth trait variation in closely related European pine species.
in Ecology and evolution
Description | 1. Genetic variation shared among Scots pine and species of the mugo complex. 2. Little genetic structure in pines across Europe. 3. Some gene sets show a common divergence among populations within species and among species suggesting some of the same processes are involved in local adaptation and in speciation. |
Exploitation Route | The data will be used to design faster & larger genotyping methods for pines, with a view to accelerating the process of tree breeding. |
Sectors | Agriculture Food and Drink Environment |
Description | New genomic resources for pines were developed and made available open-access. The resource will enable advances in many areas of study of this economically and ecologically important group of tree species. The associated publication as been accessed more than 700 times since being made available. |
First Year Of Impact | 2015 |
Sector | Agriculture, Food and Drink |
Impact Types | Economic |
Description | Inclusion of Forest Genetic Resources as key part of UK government's Tree Health Resilience Strategy (DEFRA, May 2018) |
Geographic Reach | National |
Policy Influence Type | Citation in other policy documents |
Impact | Research outputs on genetic diversity in trees and their value for the resilience of species underpinned the development of the UK FGR Strategy, which led to the recognition in national Tree Health Resilience policy that genetic diversity is essential to the long term sustainability of our trees and forests. |
URL | https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/7107... |
Description | (B4EST) - Adaptive BREEDING for productive, sustainable and resilient FORESTs under climate change |
Amount | € 6,478,663 (EUR) |
Funding ID | 773383 |
Organisation | European Commission |
Sector | Public |
Country | European Union (EU) |
Start | 04/2018 |
End | 04/2022 |
Description | (GenTree) - Optimising the management and sustainable use of forest genetic resources in Europe |
Amount | € 8,000,000 (EUR) |
Funding ID | 676876 |
Organisation | European Commission |
Sector | Public |
Country | European Union (EU) |
Start | 03/2016 |
End | 02/2020 |
Description | Learning to adapt to an uncertain future: linking genes, trees, people and processes for more resilient treescapes (newLEAF) |
Amount | £1,002,489 (GBP) |
Funding ID | NE/V019813/1 |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 07/2021 |
End | 07/2025 |
Title | Data from whole transcriptome sequencing of four European pine species |
Description | Sequence data from transcriptome sequencing of four pine species |
Type Of Material | Database/Collection of data |
Provided To Others? | No |
Impact | new manuscripts |
URL | http://doi.org/10.5285/b6900166-ded6-4f7a-8734-484b6f77b2f1 |
Description | Formation of the Steering Group for the UK's Forest Genetic Resources Strategy. |
Organisation | Earth Trust |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | Jontly with RBGE Kew, led the formation of the collaboration. |
Collaborator Contribution | The other partners participated actively in the formation and initiation of the collaboration and have committed to involvement in the future. |
Impact | Publication of the Strategy for the UK's Forest Genetic Resources |
Start Year | 2017 |
Description | Formation of the Steering Group for the UK's Forest Genetic Resources Strategy. |
Organisation | Forest Research |
Country | United Kingdom |
Sector | Public |
PI Contribution | Jontly with RBGE Kew, led the formation of the collaboration. |
Collaborator Contribution | The other partners participated actively in the formation and initiation of the collaboration and have committed to involvement in the future. |
Impact | Publication of the Strategy for the UK's Forest Genetic Resources |
Start Year | 2017 |
Description | Formation of the Steering Group for the UK's Forest Genetic Resources Strategy. |
Organisation | Royal Botanic Gardens, Kew |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | Jontly with RBGE Kew, led the formation of the collaboration. |
Collaborator Contribution | The other partners participated actively in the formation and initiation of the collaboration and have committed to involvement in the future. |
Impact | Publication of the Strategy for the UK's Forest Genetic Resources |
Start Year | 2017 |
Description | Formation of the Steering Group for the UK's Forest Genetic Resources Strategy. |
Organisation | Woodland Trust |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | Jontly with RBGE Kew, led the formation of the collaboration. |
Collaborator Contribution | The other partners participated actively in the formation and initiation of the collaboration and have committed to involvement in the future. |
Impact | Publication of the Strategy for the UK's Forest Genetic Resources |
Start Year | 2017 |
Description | UK Forest Genetic Resources Strategy |
Organisation | Forest Research |
Country | United Kingdom |
Sector | Public |
PI Contribution | Co-led, with RBG Kew, formation of a group to coordinate synthesis, protection and communication of knowledge regarding UK forest genetic resources. |
Collaborator Contribution | Group formed to coordinate synthesis, protection and communication of knowledge regarding UK forest genetic resources. Held stakeholder workshops to highlight initiative, to gather input and inform drafting of a national strategy. Published UK Forest Genetic Resources Strategy. |
Impact | Trivedi, Cavers, Atkinson, Clark Cottrell (2019) A Strategy for UK Forest Genetic Resources: protecting the UK's unique diversity of trees and shrubs. Royal Botanic Garden, Kew. |
Start Year | 2017 |
Description | UK Forest Genetic Resources Strategy |
Organisation | Future Trees Trust |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | Co-led, with RBG Kew, formation of a group to coordinate synthesis, protection and communication of knowledge regarding UK forest genetic resources. |
Collaborator Contribution | Group formed to coordinate synthesis, protection and communication of knowledge regarding UK forest genetic resources. Held stakeholder workshops to highlight initiative, to gather input and inform drafting of a national strategy. Published UK Forest Genetic Resources Strategy. |
Impact | Trivedi, Cavers, Atkinson, Clark Cottrell (2019) A Strategy for UK Forest Genetic Resources: protecting the UK's unique diversity of trees and shrubs. Royal Botanic Garden, Kew. |
Start Year | 2017 |
Description | UK Forest Genetic Resources Strategy |
Organisation | Royal Botanic Gardens, Kew |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | Co-led, with RBG Kew, formation of a group to coordinate synthesis, protection and communication of knowledge regarding UK forest genetic resources. |
Collaborator Contribution | Group formed to coordinate synthesis, protection and communication of knowledge regarding UK forest genetic resources. Held stakeholder workshops to highlight initiative, to gather input and inform drafting of a national strategy. Published UK Forest Genetic Resources Strategy. |
Impact | Trivedi, Cavers, Atkinson, Clark Cottrell (2019) A Strategy for UK Forest Genetic Resources: protecting the UK's unique diversity of trees and shrubs. Royal Botanic Garden, Kew. |
Start Year | 2017 |
Description | UK Forest Genetic Resources Strategy |
Organisation | Woodland Trust |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | Co-led, with RBG Kew, formation of a group to coordinate synthesis, protection and communication of knowledge regarding UK forest genetic resources. |
Collaborator Contribution | Group formed to coordinate synthesis, protection and communication of knowledge regarding UK forest genetic resources. Held stakeholder workshops to highlight initiative, to gather input and inform drafting of a national strategy. Published UK Forest Genetic Resources Strategy. |
Impact | Trivedi, Cavers, Atkinson, Clark Cottrell (2019) A Strategy for UK Forest Genetic Resources: protecting the UK's unique diversity of trees and shrubs. Royal Botanic Garden, Kew. |
Start Year | 2017 |
Description | Cavers S, Wachowiak W, et al (2018) Pursuing the genetics of local adaptation in Scots pine, Pinus sylvestris L. Keynote Talk at the conference 'Biology and ecology of woody plants', held in celebration of the 85th anniversary of the Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Keynote speech at an international conference. |
Year(s) Of Engagement Activity | 2018 |
Description | Cavers et al (2015) Genomics tools and genetic conservation. Invited talk, PROCOGEN final conference, Orleans, France. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited talk to open conference, summarising the outcomes of the international Conifer Genome sequencing project. Cavers presented summary of genomic data applied in the context of conserving forest genetic resources. |
Year(s) Of Engagement Activity | 2015 |
URL | http://bfw.ac.at/rz/bfwcms2.web?dok=9676 |
Description | Development of a Strategy for the UK's Forest Genetic Resources |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | 50 delegates attended a workshop or submitted contributions towards development of a national strategy for Forest Genetic Resources. |
Year(s) Of Engagement Activity | 2018 |
URL | https://www.ceh.ac.uk/our-science/projects/uk-forest-genetic-resources-strategy |
Description | Lecture to the Botanical Society of Scotland |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | I presented a talk, titled 'how and why do trees vary?' to the Botanical Society of Scotland as part of their lecture series. The talk (held online) was attended by 50 people and has since been uploaded to YouTube. Following the presentation there were detailed questions from the audience and I have since had several constructive discussions which may inform future research in this area and new collaborations. |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.youtube.com/watch?v=v-5wlJckGgw&t=5s |
Description | Meeting with DEFRA staff on UK Forest Genetic Resources strategy, London, 21/1/2020 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Policymakers/politicians |
Results and Impact | Representatives of groups within DEFRA, including Tree Health, Forestry / Agroforestry, Wildlife & Genetic Resources, attended for a briefing and discussion of the new UK Forest Genetic Resources Strategy and its integration with other areas of DEFRA policy. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.ceh.ac.uk/our-science/projects/uk-forest-genetic-resources-strategy |
Description | Membership of the Scientific Advisory and Response Team (SART) of Scotland's Plant Health Centre |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Professional Practitioners |
Results and Impact | The Plant Health Centre is a virtual centre of expertise funded by Scottish Government through RESAS (Rural and Environment Science and Analytical Services Division) to help tackle plant health challenges for Scotland. |
Year(s) Of Engagement Activity | 2018 |
URL | https://www.planthealthcentre.scot/about-us |
Description | POSTER: Kevin Donnelly, Joan Cottrell, Richard Ennos, Guiseppe Giovanni Vendramin, Stuart A'Hara, Sarah King, Annika Perry, Witold Wachowiak, Stephen Cavers (2016) Mitochondrial variants in Pinus sylvestris and the P. mugo complex. IUFRO Genomics and Forest Tree Genetics, Arcachon, 30 May-3 June 2016. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Poster at international conference. |
Year(s) Of Engagement Activity | 2016 |
URL | https://colloque.inra.fr/iufro2016/Programme |
Description | POSTER: Wachowiak, Perry, Donnelly, Cavers (2016) Quantitative and molecular genetic variation in closely related European pine species. IUFRO Genomics and Forest Tree Genetics, Arcachon, 30 May- 3 June 2016. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Poster at international conference. |
Year(s) Of Engagement Activity | 2016 |
URL | https://colloque.inra.fr/iufro2016/Programme |
Description | Paper given at IUFRO Forest Tree Breeding conference, Prague, Czech Republic |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other academic audiences (collaborators, peers etc.) |
Results and Impact | Talk and discussion Offers for new collaborations |
Year(s) Of Engagement Activity | 2014 |
URL | http://www.iufrobreeding2014.org/ |
Description | Poster at conference: Wachowiak W., Zaborowska J., Labiszak B., Perry A., Donnelly K., Cavers S. New genomic resources for population history and adaptive variation studies in closely related pine species. 2nd Conference of the ID PAS - Biology and Ecology of Woody Plants. Kórnik-Poznan, Poland 11-15.06.2018 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Wachowiak W., Zaborowska J., Labiszak B., Perry A., Donnelly K., Cavers S. New genomic resources for population history and adaptive variation studies in closely related pine species. Poster at 2nd Conference of the ID PAS - Biology and Ecology of Woody Plants. Kórnik-Poznan, Poland 11-15.06.2018 |
Year(s) Of Engagement Activity | 2018 |
Description | Talk at 3rd Research-Teaching Conference of the Faculty of Biology A. Mickiewicz University, Poznan, Poland |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other academic audiences (collaborators, peers etc.) |
Results and Impact | Talk and discussion Plans for future work with the University emerged. |
Year(s) Of Engagement Activity | 2014 |
Description | Talk at Ancient Tree Forum annual meeting (Aviemore) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | Talk and discussion Strong discussion about right and wrong ways to deal with tree pests / pathogens. |
Year(s) Of Engagement Activity | 2014 |
URL | http://www.ancient-tree-forum.org.uk/ancient-tree-forum/atfevents/archive/archive.htm |
Description | Talk at Ecological Genetics Group meeting, Newcastle |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | Talk and questions Good suggestions for other analytical approaches |
Year(s) Of Engagement Activity | 2014 |
Description | Talk at Procogen Dissemination Workshop, Szombathely, Hungary |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other academic audiences (collaborators, peers etc.) |
Results and Impact | Talk, discussion and planning Strong post-talk discussion and numerous requests for presentation after the meeting indicated the level of interest |
Year(s) Of Engagement Activity | 2014 |
URL | http://www.procogen.eu |
Description | Wachowiak W., Cavers S, Zukowska WB, Wójkiewicz B (2015) The use of DNA polymorphisms in population history and adaptive variation studies in pines. International Conference on "Genetic resources conservation - scientific and social challenges", 25 June, Karpacz, Poland. |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Communication with scientific community |
Year(s) Of Engagement Activity | 2015 |
Description | Wachowiak W., Zukowska WB., Cavers S., Wójkiewicz B. Evolutionary studies of adaptive variation in pines. Polish Evolutionary Conference, 2015. 24-26 Sept 2015, Poznan, Poland. p.18 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Communication with scientific community |
Year(s) Of Engagement Activity | 2015 |