Potential biodiversity impact of two new
species of Phytophthora
Stuart Ball, Chris Cheffings, James Williams
Phytophthora
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Phytophthora is a genus of plant-damaging water moulds
(Oomycetes)
For example P. infestans is the potato blight which caused
the great Irish famines of 1845 – 1849
Two new species have recently been identified in the UK:
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P. ramorum is known as “Sudden Oak Death” in the USA and
was first detected in the UK in 2002 on ornamentals, especially
Rhododendron and viburnum, within the horticultural trade
P. kernoviae was discovered in woodlands in Cornwall in 2003
and described as a new species
They are believed to be non-native and to have been
introduced via the international nursery trade
Biology
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Phytophthora may reproduce sexually or asexually.
They spread via different types of spores:
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Sporangia produce zoospores which swim in water films using
a pair of flagellae. They invade new host plants. Sporangia may
be shed in great numbers, can be spread by wind or water and
are the main dispersal mechanism. They are relatively short
lived.
Chlamydospores are usually spherical and pigmented, and may
have a thickened cell wall to aid in their role as a survival
structure. They have the potential for long term survival in the
soil.
Sexual reproduction results in Oospores which germinate to
produce sporangia
Pathology
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Both species can infect a wide range of plant species, both
native and horticultural
Three types of damage occur:
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Bleeding cankers of tree trunks
Leaf blights
Die-back of shoots and buds
Bleeding cankers can occur on a wide range of trees
especially in the Fagaceae and Magnolialaceae
They do not produce sporangia and cannot, therefore,
cause further infections
Infected trees can eventually be killed by cambial ringing
Pathology (continued)
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Plants affected by leaf blight and die-back do
produce sporangia and are referred to as
“sporulating hosts”
Rhododendron ponticum has proved to be the main sporulating
host in wild outbreaks in Britain
A range of low ericaceous shrubs have been found to be highly
susceptible. These include:
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Vaccinium myrtillus (bilberry)
Vaccinium vitis-idaea (cowberry)
Arctostaphylos uva-ursi (bearberry)
Empetrum nigrum (crowberry)
The small number of wild outbreaks affecting bilberry so far
have shown that the disease is devastating to this species
The threat
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Bilberry forms a dominant component in a range of vegetation
types, especially in the north and west:
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Moorland and bog
Lowland heath
Western Atlantic woodlands
Rhododendron ponticum is
often abundant in these
habitats
They also provide the moist
conditions that Phytophthora
needs to spread effectively
– especially the Atlantic
woodland types
Widespread loss of bilberry from these habitats would have a
devastating impact
JNCC’s role
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The agencies and JNCC responded to the 2008
consultation on management options, but the potential
impact does not appear to have been widely recognised
JNCC is attempting to produce evidence showing the
potential scale of impact on biodiversity at landscape and
habitat scale
Better understanding of the potential impact may aid the
partnership between biodiversity organisations and
management bodies in the attempt to eradicate these
diseases
It is not within JNCC’s remit to advise on operational
responses
What can JNCC contribute?
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The threat is likely to be greatest where both Vaccinium
and Rhododendron occur in abundance
Can we estimate their distributions and hence the areas
of greatest overlap?
Can we estimate the distribution of vegetation
communities in which Vaccinium is dominant? How do
these relate to the overlap areas?
What other species are strongly associated with
Vaccinium and are therefore potentially at risk?
What sites have been designated for vegetation
communities or species that may be at risk? Are they in
the overlap areas?
Estimating distributions
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Distribution data for Rhododendron ponticum and Vaccinium
myrtillus is available via the NBN Gateway
Although the coverage for Vaccinium is likely to be good
at the 10km level, it is too common to have been
recorded in greater detail
Coverage for Rhododendron is probably less consistent,
even at the 10km square level, because it is considered as
an alien weed and therefore, not necessarily recorded
consistently by botanical workers
Presence/absence at 10km square level is not sufficient
for our purposes
10km square distributions from NBN
Rhododendron ponticum
Vaccinium myrtillus
Fit a Species Distribution Model
Layers
+
Known distribution
Mean altitude
Weather
Model
Apply to
all layers
=
Potential
distribution
Land cover
Maxent models
Fitted Maxent models
to observations since
1980 with1km square
or better precision
Colours show the
predicted probability of
occurrence in a 1km square
Red = highest
Blue = lowest
Rhododendron ponticum
Vaccinium myrtillus
Testing the fit: Probability to presence/absence
Probability
Apply a threshold
Compare to
observations
Testing: Compare to observations
Observations
Model predicts
presence for a
particular threshold
Four possible outcomes:
Observed and model predicts
presence
Observed but model does not
predict presence
Not observed, but model
predicts presence
Not observed and model does not
predict presence
Testing: Matrix of confusion
Observations
Observed
Model
prediction
Not observed
Presence
a = 127
b = 1,005
Absence
c=4
d = 8,995
a +c = 131
b +d = 10,000
Totals
True positives = a / (a + c) = 96.95%
False positives = b / (b + d) = 10.04%
Testing: Receiver Operating Characteristic
ROC
1.0
Area Under the Curve
AUC = 0.947
0.9
0.8
Perfection
Rule
thumb
Alwaysofright,
never
wrong
0.85 – Acceptable
AUC = 1.0
0.90 – Good
True Positive Rate
0.7
0.6
0.5
0.4
0.95 – Very good
0.3
0.2
Random
AUC = 0.5
0.1
0.0
0.0
0.1
0.2
0.3
0.4
0.5
0.6
False Positive Rate
0.7
0.8
0.9
1.0
Testing: Independent test
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Train the model with
one half of the
available data
Test it with the other
half that was not used
for training
Assess the fit using the
Test AUC
Training AUC = 0.948
Test AUC = 0.895
How well did they fit?
Pretty well!
Available
observations
Test AUC
Rhododendron ponticum
1,722
0.941
Vaccinium myrtillus
3,653
0.932
Overlap
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1km squares where the
predicted probability of
both Rhododendron and
Vaccinium is ≥ 0.3
Needs more and better
information about wild
outbreaks to estimate
these thresholds
Unlikely to be estimated
at all accurately on the
small numbers of
outbreaks so far!
Model distribution of NVC communities
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NVC communities can be
modelled in a similar way
to species
This model is for W17:
Quercus petraea-Betula
pubescens-Dicranum majus
woodland
The observations are the
locations of quadrats
assigned to this
community
W17
Training
samples
Test
samples
Test AUC
530
529
0.9447
Species feeding on bilberry
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The Phytophagous Insect Data Bank lists 113 species as
feeding on Vaccinium, Arctostaphylos or Empetrum
42 appear to be entirely or mainly associated with the
ericaceous shrubs known to be highly susceptible
3 of these are BAP species and 2 more have British Red
Data Book statuses
Xestia alpicola, Northern Dart (BAP) mainly feeds on Empetrum
Rhopobota myrtillana only feeds on Vaccinium myrtillus
Conclusion
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Looks like we can contribute something
Its going to be rough and at a GB and landscape scale