Genomics of Adaptation in European Pines (GAP)

Lead Research Organisation: NERC Centre for Ecology and Hydrology
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.

Publications

10 25 50
 
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 BES Scottish Policy Group response to the Scottish Government's consultation on the Forestry Strategy 2019-2029
Geographic Reach Local/Municipal/Regional 
Policy Influence Type Participation in a national consultation
Impact Highlighted need for genetic diversity to secure resilient trees and forests.
URL https://www.britishecologicalsociety.org/policy/reports-publications/consultation-inquiry-responses/
 
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 05/2018 
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
 
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 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 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 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