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- 1. Mark McMullan Trees on the Brink Evolution of the Ash Dieback Pathogen mcmullan0
- 2. What’s one of them? Ne = 800 Ne = 1000 Nm > 1 Nm < 1 Llaurnes et al., 2012 MBE
- 3. What’s one of them? 1 2 3 5 0 8942 4 6 Exp 2-6 Recombination event #2 Recombination event #2 Non-recombinant Recombinant T30/(NV+T30) 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 Llaurnes et al., 2012 MBE Li et al., 2014 Gen & Dev
- 4. Li et al., 2016 Nat Plants What’s one of them?
- 5. Fragilariopsis cylindrus Mock et al., 2017 Nature What’s one of them?
- 6. Invasion of Europe by the ash dieback pathogen Hymenoscyphus fraxineus Nature Ecology and Evolution
- 7. •Anne Edwards (JIC) •Volunteer woodland care and coppicing Discovery in the UK 2012 •British Empire Medal for services to the environment
- 8. •Cabinet Office Briefing Room A • Cameron government • Ministers and officials meet for major events and emergencies. • Ash imports banned COBRA crisis meeting Nov 2012
- 9. •Professor Allan Downie (JIC) •Research from 11 institutes
- 10. Disease Progression Map 4: Chalara (Hymenoscyphus fraxineus) - confirmed infection sites Based on information obtained as at midday on 4th September 2018 ±1:2,500,000 Please note that the Northern Ireland Grid uses the Irish Coordinate System and appears at an angle to the British National Grid. The OS 10km grid squares containing one or more Wider Environment infections identified: in 2012 in 2013 in 2014 in 2015 in 2016 in 2017 in 2018 OS 10km grid squares 0.00% 10.00% 20.00% 30.00% 40.00% 50.00% 60.00% 70.00% 80.00% 90.00% Scotland England Wales N Ireland Isle of Man % of all 10k squares in country -Forestry Comission Forestry Commission
- 11. The Threat How long does it take to kill a tree? • We don’t know how bad it will be • Juveniles and adults respond differently • Early estimates suggested 95% • Maybe closer to 60% • No one can rule out 100%
- 13. Woodland Trust Fraxinus excelsior European ash Joint nature conservation committee 2014 Bird 12 Bryophyte 58 Fungi 68 Invertebrate 239 Lichen 546 Mammal 55 Vascular plants 78 Over 1000 associated species
- 14. ASH (Fraxinus excelsior) MAP OF EUROPE Poland 1992 1994 2003 2003 2000 2001/02 1992 2004 2004 2005 2006 2002 2009 2008 2009 2010 2012 2007 Anne Edwards • Fungus • Invasion from Asia • Changed host • Spread unhindered with some reduced susceptibility • Sexual reproduction
- 15. The Spread How far has it come? • Asia • China, Korea, Japan, Russia • Fraxinus mandshurica • Doesn’t kill the tree
- 18. Why study pathogen population genomics? • “The fungus is here, the horse has bolted, so what?” • Dutch elm disease • The Irish potato famine pathogen
- 19. Dutch elm disease -killed billions of elm trees • Another ascomycete fungus • Europe, North America and parts of Asia • 1920s -Ophiostoma ulmi • 1960s - O. novo-ulmi & americana
- 20. Great Famine in Ireland -killed a million people • An Oomycete • 1845-1852 -Phytophthora infestans • Outbreaks continue today • West Bengal 2014 • Second largest producer of potatoes in India
- 21. Genetic diversity • Conservation biology • How adaptable is the species? • Potential to survive change? O’Brien et al., 2017 Heredity
- 22. Genetic diversity • Conservation biology • How adaptable is the species? • Potential to survive change? Agathe Jouet McMullan et al., 2015 elife O’Brien et al., 2017 Heredity • Invasion biology • How adaptable is the species? • Potential to infect many hosts?
- 23. The ash dieback invasion –the science bit • Where did the fungus come from? • How genetically diverse is the invasion? • How genetically diverse is the source? • How should we deal with further invasion? • Has the horse bolted?
- 24. Samples for genome sequencing
- 25. ers480843 ers480865 ers480854 lib6767 lib6758 lib6763 lib2570 lib6753 lib6757 lib6765 ers480863 ers480859 ers480850 ers480848 ers480856 ers480852 ers480851 ers480858 lib6754 ers480844 ers480860 lib6762 lib6756 ers480849 lib6759 lib6761 ers480845 ers480855 lib6768 ers480853 lib6760 lib6764 ers480861 lib6769 ers480864 lib6755 ers480847 lib6771 lib6770 lib6766 ers480862 ers480846 ers480857 • High divergence between EU and Japan • Japan may not be the origin • Signs of extreme founder effect in EU • No EU pattern
- 26. Genetic diversity in H. fraxineus π
- 27. Genetic diversity in H. fraxineus π • How comparable are the invasion and native ranges?
- 28. 0.0 0.2 0.4 0.6 0.8 1.0 024681012 EU pairwise relative distance Relative distance Density 0.0 0.2 0.4 0.6 0.8 1.0 0.00.51.01.52.0 Jp pairwise relative distance Relative distance Density Core genes have 2 divergent haplotypes • Two founders • Large source population
- 29. EU source as large as Jp 0.01 0.02 0.03 0.04 0.05 1e+06 2e+06 3e+06 4e+06 Ancestral EU Ne Distance(s/L95%CI) Ancestral haplotype divergence over a range of Ne
- 30. Host pathogen co-evolution -effectors Dangl et al. 2013 Science
- 31. Host pathogen co-evolution -effectors Dangl et al. 2013 Science 10% Hf genes are putative effectors
- 32. Adaptive diversity in Ash Dieback 0 0.01 0.02 0.03
- 33. The ash dieback invasion –the science bit • Where did the fungus come from? • How genetically diverse is the invasion? • How genetically diverse is the source? • How should we deal with further invasion? • Has the horse bolted?
- 34. Ash Dieback Summary • Europe was founded by two haploid individuals • The European source was a large genetically diverse population • Genetic diversity in the native range is adaptive and greater in the important effector genes • How should we deal with further invasion? • Has the horse bolted? π
- 35. How we might understand pathogen evolution and biological invasions? How can we understand the genetic ingredients of a successful pathogen invasion? 1. Unsuccessful invasions could happen all the time but we never see them 2. We must characterise the native population 3. What can we tell from the successful one? Invasion range
- 36. Agriculture delivers the largest, annually replicated experiment on Earth • Where does novel polymorphism for adaptation come from? • “Everything exists everywhere but the environment selects” • The genetic ingredients for success • Consider success against unsuccessful variation • What can wild host pathogen diversity teach us about agricultural pathogen evolution? W W W W W AgricultureW W W W W W AgricultureW
- 37. Sugar beet • Recently domesticated from sea beet • Grows in the UK and on mainland Europe • Coastal distribution applications to modelling • Questions • Can repeated invasions between wild and agricultural beets help us understand pathogen evolution and adaptation for invasion? • Can we use this understanding to better defend our crops? A tractable system to study wild agricultural pathogen evolution
- 38. Sugar beet Rust incursion • Developed leaf peel extraction/sequencing • Sampled ~500 wild and agricultural beets • Constructed rust genome • Population differentiation analysis (46 ind)
- 39. • Developed leaf peel extraction/sequencing • Sampled ~500 wild and agricultural beets • Constructed rust genome • Population differentiation analysis (46 ind) Sugar beet Rust incursion
- 40. Trees on the Brink • Genetic diversity is considered important for species to adapt to new environments • The Ash dieback pathogen has lost diversity upon entry to Europe • There is much more genetic diversity in the native range mcmullan0
- 41. Thank you Earlham Institute • Neil Hall • Matt Clark • Lawrence Percival-Alwyn • Bernardo Clavijo • Gemy Kaithakottil • David Swarbreck • Genomics Pipelines • Kew • Maryam Rafiqi • Edinburgh • Mark Blaxter • Georgios Koutsovoulos • JIC • Elizabeth Orton • Lorelei Bilham • Anne Edwards • Diane Saunders • James Brown • Allan Downie • FERA • Philip Jennings • Louisa Williamson • BBRO • Mark Stevens • Kevin Sawford • Collaborations • Eva Stukenbrock (MPI) • Mark Stevens (BBRO) • Jon Rathjen (ANU) • Jonathan Jones (TSL) • Isabel de Cauwer (Lille)