by Beth Purse and Dan Chapman

1. Beth Purse beth@ceh.ac.uk
WP3 Team: Dan Chapman, Ana Perez-Sierra, Beatrice
Henricot, Mariella Marzano, Michael Dunn
Phytothreats:
WP 3 overview

2. Talk Outline
• WP3 Objectives and approach
• Team members and responsibilities
• Approach
• WP3.1 Risk of introduction
• WP3.2 Risk of establishment and spread
• WP3.3 Scoping knowledge gaps
• Potential policy impact
• Milestones and plan for next 12 months

3. WP3 Team and roles
Ana
Perez-Sierra
Beatrice
Henricot
PATHOGEN TRAITS,
EPIDEMIOLOGY AND
OCCURRENCE DATA
Mariella
Marzano
Mike Dunn
SCOPING
KNOWLEDGE GAPS
TOURISM, TRADE &
BIOSECURITY
Beth Purse
Dan Chapman
RISK MODELS
OCCURRENCE
DATA

4. WP3 objective –identify and rank global Phytophthora
threats to the UK
WP3.1 Risk of introduction
WP3.3 Horizon-scanning for emerging
pathogens: scoping of knowledge gaps
WP3.2 Risk of establishment and spread
Trait-based
frameworks to
inform risk
register
• Identify the most important trade and
recreational pathways
• Link introduction risk to ecological
traits
• Map global environmental niches of
Phytophthora species
• Link establishment in Europe to social
factors and ecological traits
• Map risk areas in the UK
• identify research priorities for horizon
scanning for emerging pathogens (supply
chains, tourism pathways)

5. WP3.1 - Risk of introduction
Aims:
• Identify the most important trade and recreational pathways
linking Phytophthora source regions to the UK
• Model introduction risk statistically based on position in
transport networks and intersection with sources of
Phytophthora
• Test links between introduction risk and pathogen traits

6. Existing modelling
• 422 non-native EPPO-categorised plant pests
(invertebrates, pathogens, plants)
• Models for presence in EPPO countries (GLMM)
Probability of presence of pest p in country j ~
network connectivity for p to j +
pest characteristics +
destination country characteristics +
(1|destination country) + (1|species)
• Compare different connectivity measures, multiple
networks, assignment of specie to known pathways, etc.

7. Network connectivity indices
Agricultural tradeBilateral
network
Species
presence
Source country characteristics
Climatic similarity
GDP per capita
Sum columns  index of
connectivity to all sources

8. Results
• Best model uses climate-
weighted connectivity through
multiple pathways and
assignment of species to known
pathways
• Host breadth increases pathogen
invasiveness
Relative invasion source risk

9. For Phytophthora
• More refined analysis:
• Better temporal resolution of arrivals and spread(?)
• Air transport as well as trade
• More traits in the analysis
• Relevant socio-economic drivers (e.g. nursery density?)

10. WP3.2 - Risk of establishment and spread
Aims:
• Identify known Phytophthora species worldwide with
greatest capacity for establishment and spread under UK
conditions
• Quantify global environmental niches of Phytophthora
species
• Map areas of the UK landscape most at risk of invasion
• Link patterns of establishment/spread in Europe to
pathogen traits

11. Existing approaches to mapping pathogen niches
Pattern Process
Statistical models Biological models
Oospore
Chlamydospore
Matching disease patterns with
patterns in environmental drivers
Applicable, given occurrence data, in
absence of detailed ecological
knowledge
Mathematical descriptions of life cycle
processes
Require detailed ecological knowledge
Hourlyrateofinfection
Temperature
Pr
Pk
Data from P. Jennings APHA

12. Particular challenges of mapping pathogen niches
Potential distribution of sudden oak death
pathogen Phytophthora ramorum in Oregon
Vaclavik & Meentemeyer 2012
•Occurrence data may be patchy,
clustered and incomplete
•Species not yet spread to every
where that they can persist
• May capture only a small
proportion of potential
environmental niche
•Models developed early in
invasion may underestimate
environmental niche
•Biology may be poorly known
EARLY
LATE

13. Mapping pathogen niches – statistical approaches, integrating
some ecology
•US distribution used to predict global distribution
•Eco-climatic index defined by known occurrence, tweaked by known laboratory
temperature and moisture responses
•But which areas of the UK are more suitable than others?
•Habitat suitability also defined by other factors e.g. disturbance, host availability
Global climate suitability map for Phytophthora ramorum, Ireland et al. 2013 PLoS ONE

14. Mapping pathogen niches – biological models
• Temperature and humidity requirements for infection process
• Hourly temperature and relative humidity for each 4km grid cell (Met Office)
• Number of days suitable for Pr or Pk infection
Hourlyrateofinfection
Temperature
Pr
Pk
Infection data from P. Jennings APHA
Model funding from Scottish
Government and Forestry Commission Match between onward Pr spread in England and
modelled suitability (2007-2010)

15. Mapping pathogen niches – biological models
• Temperature and humidity requirements for infection process
• Hourly temperature and relative humidity for each 4km grid cell
• Number of days suitable for Pr or Pk infection
Hourlyrateofinfection
Temperature
Pr
Pk
Infection data from P. Jennings APHA
Model funding from Scottish
Government and Forestry Commission
0
50
100
150
200
250
300
2006 2008 2010 2012 2014
No.suitabledays
Year
Scotland
England
Wales
N. Ireland
Annual variation in number of days suitable for
Pr infection

16. Phytothreats approach to mapping pathogen niches
• Test out approaches on well-described Phytophthoras
already found in the UK (yr 1-2)
• Can the UK distribution be reproduced from the global occurrence?
• Evidence of niche shifts?
• Environmental drivers - literature review of drivers
explaining patterns in Phytophthora, different scales (yr 1)
• e.g. disturbance, climatic predictors, host and landscape predictors
(fragmentation, host density)
• Roll out best-performing methods across 40 focal species
to predict global environmental niches (yr 3)
• Relate global spread and niches to traits (yr 3)

17. Relating pathogen establishment in countries in
Europe to social and ecological factors
• Escape from nursery and horticulture sectors
• biological and social factors associated with escape
e.g. GDP, human population density, forestry production
• Santini et al. 2012, invasive forest pathogens more likely to
establish in countries with a wider range of environments,
higher human impact and international trade volumes.
Rainfall influenced the diffusion rates between countries.

18. Ecological traits affecting arrival and establishment
• Substrate
• Host range
• Disease
symptoms
•Survival - oospore and
chlamydospore stages
•Aerial spread
•Oospore wall index
•Temperature optima/range
•Homothallic/heterothallic
Oospore
Chlamydospore Caducous sporangia enables
dispersal in running water /
wind
Species limited to one or two hosts spread
less than species with wide host range
e.g P. austrocedri versus P. kernoviae
P. austrocedrae on juniper P. kernoviae on Rhododendron,
beech, Vaccinium

19. Focal species for modelling
• 10-15 species already present in the UK (validate approach)
• 25-30 species outside Europe that pose threats
• E.g. Species listed on the UK Plant Health Risk Register
Species here already Species yet to arrive
• P. alni P. acerina
• P. austrocedri P. pinifolia
• P. fragariae P. pluvialis
• P. infestans P. polonica
• P. kernoviae
• P. lateralis
• P. pseudosyringae
• P. ramorum
• P. rubi
• P. siskiyouensis
• Species selection criteria to be decided in July following trait database collation
• Span wide range of ecological traits, exclude crop pathogens(?), define by data
availability

20. Mapping pathogen distributions: source data
Potential global data sources on interceptions, and
occurrences
National level
• EPPO GD (155 spp)
• CABI ISC (12 spp)
• GBIF (165 spp)
• DAISIE (36 spp)
• Europhyt (no Phytophthora?)
Site to county level data
• PhytophthoraDB (isolates)
• Forest Phytophthoras of the World
• Literature (e.g. Jung et al 2015)
• Unpublished survey data
(FR, APHA, other countries)
• Other workpackages of Phytothreats
Distribution of P. ramorum isolates in
Phytophthoradb

21. WP 3.3. Horizon scanning for emerging pathogens:
scoping knowledge gaps
Aim: Building our understanding of patterns of movement in source country and
ways in which pathogens are transferred to UK
• Prioritise most likely source countries
• Literature review/Discussion with nursery partners/Contact with international
colleagues/EPPO to identify and map state of knowledge of relevant supply
chains at national and sub-national levels. Input into WP2 Consumer survey -
internet purchases
• Develop our understanding of tourism and recreational spread pathways and
implications for potential disease spread. Initially contact with tourism agents,
travel companies and international forest and recreational organisations in
source countries to map patterns of international movement (e.g. who is coming
to UK & when) for recreational purposes. Any data on reason for visits? Link
this to flight paths?
• If possible - source available data from border security on what people are
bringing into the UK

22. WP3 potential policy impact
• UK Plant Health Risk Register – can we tailor models to
needs of register?
• Publish ecological trait database (data paper and doi)
• Make collated distribution data publicly accessible
• UK/global pathogen habitat /climate suitability maps
• UK Plant and Animal Health Internet of Things?

23. Milestones: Plan for next 12 months
• Trade and environmental data extracted for country level analysis of
introduction risk. Introduction models tested on EPPO plant pathogen
data
• Met 6th April, devised strategy for compiling traits database (July target
for initial version)
• Species selection and strategy for extracting occurrence data decided
in July WP3 meeting
WP3 Milestones
• WP3 Compile European database of country level occurrence/arrival of Phytophthoras in
nursery and wider environment and associated trade and environmental data (year 1)
• WP3 Compile global database of fine scale occurrence data for ~40 target Phytophthora species
and associated environmental data (year 1)
• WP3 Compile traits database for Phytophthora species (including all species found in Europe plus
selected others worldwide) (year 2)
• WP3 Complete models relating to patterns of introduction and establishment in Europe to
species traits, trade pathways and local environmental conditions and global niche models for ~
40 target Phytophthora species worldwide (year 3)
• WP3 Develop policy brief for UK risk register board and other stakeholders on improved risk
ranking for Phytophthoras (year 3)