Slides from Saturday 20 October Norwich Science Festival 2018. Here I outline the importance of understanding the levels of genetic diversity in a pathogen and what that can tell you about how a species can adapt to new environments. I set out the importance of determining genetic diversity in the native, as well as invasion ranges. I present evidence which suggests that the ash dieback invasion of Europe was started by just two invading fungal isolates and also that the level of genetic diversity in the native range is very large. This raises many important questions on whether to continue to invest resources to reduce invasion potential despite the fungus already being in Europe.
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
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%
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?
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
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)