Southern Forests: a Journal of Forest Science

ISSN: 2070-2620 (Print) 2070-2639 (Online) Journal homepage: http://www.tandfonline.com/loi/tsfs20

A tool for identifying potential Eucalyptus

nitens seed orchard sites based on climate and
topography

Ilaria Germishuizen & Robin AW Gardner

To cite this article: Ilaria Germishuizen & Robin AW Gardner (2015) A tool for identifying
potential Eucalyptus nitens seed orchard sites based on climate and topography, Southern
Forests: a Journal of Forest Science, 77:2, 123-130, DOI: 10.2989/20702620.2014.984554

To link to this article: http://dx.doi.org/10.2989/20702620.2014.984554

Published online: 18 Dec 2014.

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 Southern Forests 2015, 77(2): 123–130 Copyright © NISC (Pty) Ltd
Printed in South Africa — All rights reserved SOUTHERN FORESTS
ISSN 2070-2620 EISSN 2070-2639
http://dx.doi.org/10.2989/20702620.2014.984554

A tool for identifying potential Eucalyptus nitens seed orchard sites based
on climate and topography
Ilaria Germishuizen* and Robin AW Gardner

Institute for Commercial Forestry Research, Pietermaritzburg, South Africa

* Corresponding author, e-mail: ilaria.germishuizen@icfr.ukzn.ac.za

Shy seed production in orchards of Eucalyptus nitens is a major barrier to the deployment of genetic gain in
South African plantations. A machine learning method was used to identify optimal sites for the establishment
of E. nitens seed orchards within the plantation forestry landscape of the summer rainfall region of South
Africa. The ensemble classifier random forests (RF) was used to identify the environmental factors conducive
Downloaded by [University of California, San Diego] at 01:35 17 March 2016

to E. nitens floral bud production, and, based on these, build a predictive model deployable to the plantation
forestry landscape for identifying suitable areas for E. nitens seed orchards. The RF model predicted site
suitability likelihood for floral bud production with a high level of accuracy (area under the receiver operating
characteristic curve  0.83). Within the climatically optimal range for growing E. nitens, flower bud production
was more abundant and consistent on cold slopes, i.e. sites experiencing lower minimum air temperatures during
spring and autumn. The model was applied to the commercial plantation forestry landscape for the purpose of
indicating sites climatically optimal for floral bud production in E. nitens and the establishment of breeding and
seed production orchards of the same species.

Keywords: machine learning, predicting flowering, random forests, temperate eucalypts

Introduction

Eucalyptus nitens is an important species for cool Materials and methods

temperate sites in South Africa (Smith et al. 2005),
particularly those prone to moderate to heavy snowfalls
(Swain and Gardner 2003). Tree breeding has made
available significant growth and yield improvement
opportunities with this species (Swain et al. 2013a).
However, operational deployment is hampered by low seed
production from orchards and poor out-crossing within
orchards, which reduces realised genetic gain (Jones 2002;
Swain et al. 2013b). Although flower induction controls
are not fully understood for E. nitens, colder winters have
been observed to increase flowering and seed production
(Moncur and Hasan 1994; Moncur and Boland 2000). In
South Africa, studies have shown that floral bud production
correlates well with accumulated winter chilling, and at
higher altitude sites (1 200 m above sea level) flowering
is more abundant and consistent (Gardner and Bertling
2005; Gardner et al. 2013; Gardner et al. 2014). However,
the relationship between floral bud production and the
environment has never been geographically interpreted
and extrapolated from site to landscape. The aim of
the work reported here was, firstly, to develop a spatial
understanding of controls of E. nitens floral bud induction
based on available observations across sites and years
using the random forests (RF) classification algorithm of
Breiman (2001) and, secondly, to express the results in
the form of a suitability map highlighting areas potentially
optimal for the establishment of E. nitens production
seed orchards.
Site conditions
Sixteen E. nitens site  flowering interaction trials were
established between 1996 and 2004 across a latitudinal
(25°02′ to 30°54′ S) and altitudinal (1 473–2 000 m above
sea level [asl]) range in the summer rainfall plantation
forestry area (Figure 1). The sites were all located in
areas within the optimum growing range for E. nitens
(mean annual temperature [MAT] 14–16 °C, mean annual
precipitation [MAP] 840 mm, altitude 1 350–1 850 m asl;
Swain and Gardner 2003; Smith et al. 2005). Differences in
aspect, relief and slope were included as trial site selection
criteria. Sites with MAP above 840 mm and soils deeper
than 0.8 m were selected for the study so as to minimise
possible water supply influence on floral bud induction
(Owens 1995; Table 1).
Plant material and experimental design
The genetic material was sourced from an E. nitens clonal
seed orchard established by the Institute for Commercial
Forestry Research (ICFR) and located at Tweedie,
KwaZulu-Natal, South Africa. Two clones (scion genotypes)
differing in flowering potential were selected from each
of two provenances (Barrington Tops and Ebor, naturally
occurring in New South Wales, Australia) represented in the
South African E. nitens breeding population. Hence, a total
of four E. nitens clones were included in the investigation.
A 2  2 factorial experiment consisting of 32 grafted trees,

Southern Forests is co-published by NISC (Pty) Ltd and Taylor & Francis
 124 Germishuizen and Gardner

30° E 31° E 32° E

AFRICA LIMPOPO

South Enlarged area

Africa

25°S In Die Diepte 25°S

Blyfstaanhoogte

IQUE
SOUTH Nelspruit

MOZAMB
AFRICA
26° S 26° S

MPUMALANGA Wyntoun

28° E 29° E
SWAZILAND
Downloaded by [University of California, San Diego] at 01:35 17 March 2016

GAUTENG

27° S 27° S
Piet Retief

FREE STATE
28° S 28° S

KWAZULU-NATAL

Richards Bay

29° S 29° S
Gilboa Tweefontein
Peak

Netherby 1 Pietermaritzburg
LESOTHO
Netherby 2
Netherby 3 Gowan Brae
Willowmere Mossbank
30° S Blairathol 30° S

0 50 100 km

Tentkop
Thoresway
31° S
Chamisso E. nitens trial sites 31° S
EASTERN CAPE
Commercial forestry
Ugie

28° E 29° E 30° E 31° E 32° E

Figure 1: Locality of the Eucalyptus nitens trial sites within the South African summer rainfall commercial plantation forestry areas. Base map
supplied by the Institute for Commercial Forestry Research, Pietermaritzburg, South Africa

with treatments replicated twice, was implemented as a
split plot design (Gomez and Gomez 1984). Paclobutrazol
(PBZ) was assigned as a whole-plot factor (PBZ 0  nil PBZ
applied (control), PBZ 1  PBZ soil drench applied), and
‘Scion genotype’ (Clone 1, Clone 2, Clone 3 and Clone 4)
as a subplot factor. Each experimental unit consisted of
two trees planted at a spacing of 5 m  4 m, for a total of
32 trees assessed at each site. Experimental units were
surrounded by two buffer rows of trees of similar species.
The purpose of this work was to develop a model that would
relate site, particularly climate and topography, to floral bud
production; hence, the PBZ1 treatment was excluded from
the analysis, and only the measurements from the 16 trees
in the control plots were used for model development.
Floral crop data collection
Presence of newly emerged floral buds and magnitude
of floral bud crop were scored on an individual tree basis
annually in May/June. This is the time of the year when
swollen individual flower buds are at their most conspic-
uous. The scoring system adopted for the assessment of
floral bud production is described in Gardner and Bertling
(2005). Tree floral bud crop load was scored as follows:
0  no floral buds; 1  very light crop, 25% or less of
the secondary laterals bearing one or more floral buds
(secondary laterals defined as branches originating from
primary stems); 2  light crop, 25–50% of secondary
laterals bearing one or more floral buds; 3  moderate crop,
50–75% of secondary laterals bearing one or more floral
 Southern Forests 2015, 77(2): 123–130 125

Table 1: Site details for the Eucalyptus nitens flowering trials (ranked in order from north to south). MAP  Mean annual precipitation, MAT 
mean annual temperature, MPU  Mpumalanga, KZN  KwaZulu-Natal, EC  Eastern Cape

Altitude MAP MAT Soil form/ Soil depth Slope

Site name Province Latitude Longitude Aspect
(m) (mm)1 (°C)2 Family3 (m) (%)
In Die Diepte MPU 25°02′ S 30°44′ E 1 828 1 241 14.5 Magwa/1 100 1.0 NW 39
Wyntoun MPU 26°12′ S 30°44′ E 1 733 905 15.0 Kranskop/1 200 1.2 S 5
Gilboa KZN 29°14′ S 30°17′ E 1 595 957 15.3 Kranskop/1 200 1.2 N 10
The Peak KZN 29°15′ S 30°09′ E 1 629 929 15.5 Magwa/1 200 1.2 SE 8
Tweefontein KZN 29°15′ S 30°13′ E 1 588 842 15.1 Magwa/1 200 1.2 N 14
Netherby 1 KZN 29°39′ S 29°38′ E 1 688 948 14.1 Inanda/1 200 1.2 N 31
Netherby 2 KZN 29°38′ S 29°38′ E 1 700 948 14.1 Magwa/1 100 1.0 E 31
Netherby 3 KZN 29°38′ S 29°38′ E 1 678 948 14.1 Kranskop/1 200 1.2 SW 7
Willowmere KZN 29°51′ S 29°26′ E 1 708 914 14.1 Kranskop/1 200 1.2 E 10
Blair Athol KZN 29°52′ S 29°37′ E 1 568 843 14.6 Magwa/1 200 1.2 E 7
Thoresway EC 30°50′ S 28°13′ E 1 809 908 13.8 Kranskop/1 100 1.2 E 4
Chamisso EC 30°54′ S 28°11′ E 1 686 904 14.1 Magwa/1 200 1.2 NE 15
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Blystaanhoogte MPU 25°10′ S 30°36′ E 2 000 1 075 15.2 Magwa/1 100 1.0 NE 23
Gowan Brae KZN 29°37′ S 30°08′ E 1 473 919 15.2 Magwa/1 100 1.2 N 2
Mossbank KZN 29°49′ S 29°42′ E 1 661 970 14.2 Magwa/1 100 1.2 SW 17
Tentkop KZN 30°48′ S 28°15′ E 1 911 863 13.6 Kranskop/1 100 1.2 SW 8
1 Lynch and Schulze (2007)
2 Schulze and Maharaj (2007)
3 Soil Classification Working Group (1991)

buds; 4  heavy crop, 75–100% of secondary laterals
bearing one or more floral buds. For the purpose of this
study, ‘flowering success’ was defined by average floral
crop score (average of the four- and five-year scores)
for each experimental plot, with moderate and heavy
crop scores identifying high flowering success. The data
set utilised in the analysis consisted of 28 data points,
15 classified as high flowering and 13 as low flowering.
Environmental data
Climatic variables used as predictors were based on 1′  1′
historical climatic grids derived from more than 1 000
weather stations distributed across South Africa (Schulze
2007). The variables included MAT, monthly mean temper-
ature, monthly minimum temperature, monthly maximum
temperature, extremes of minimum temperature and
extremes of maximum temperature (Table 2). Topographic
variables used as predictors consisted of slope and aspect
that were derived from a 90 m  90 m digital elevation
model gridded data set (Jarvis et al. 2008). A total of 63
environmental variables were extracted for each data point
for input into the model.
Statistical analysis and model building
The statistical analysis was performed using the RF
classification algorithm (Breiman 2001) within the R statis-
tical computing environment (R Development Core Team
2008). The RF classifier has been widely used to predict
the potential occurrence or distribution of a phenom-
enon (Debeljak et al. 2001; Thuiller et al. 2003; Cutler
et al. 2007; Garzόn et al. 2007; Magness et al. 2008;
Bradter et al. 2013). The RF classification algorithm has
also been successfully applied to evaluate the vulner-
ability of South African plantation forests to a number
of forest pests (Ismail et al. 2010; Adam et al. 2013).
Random forests has no assumptions of normality of the
variables, and both categorical and numerical variables
Table 2: Climatic and topographic predictors used in the study
Variable Abbreviation
Aspect Aspect
Slope Slope
Mean annual temperature MAT
Mean monthly temperature Tmean01 to tmean12
Mean monthly minimum temperature Tmin01 to tmin12
Mean monthly maximum temperature Tmax01 to tmax12
Extremes of minimum temperature Tminl01 to tminl12
Extremes of maximum temperature Tmaxh01 to tmaxh12
can be included in the analysis, making it very suitable for
ecological modelling.
In the present study, the response data set consisted
of the flowering success (high and low) observed at the
trial sites and the explanatory data sets consisted of 63
environmental predictors (Table 2). Misclassification rate
and variable importance were calculated from the out-of-
bag (OOB) samples. In RF, each tree is constructed using
a different bootstrap sample of approximately two-thirds
of the original data (training data set). Each tree is then
used to predict the classification of the leftover one-third
(OOB) sample and the misclassification rate is calculated.
The overall OOB error rate is calculated from the
aggregation of the misclassification rate of each tree and
expressed in terms of percentage. Variable importance
was assessed using the mean decrease in accuracy and
the mean decrease in Gini coefficient (Breiman et al. 1984)
measures. Mean decrease in accuracy is calculated during
the OOB computation phase. The values of a particular
variable are randomly permuted in the OOB sample,
and this modified sample is used to get new classifica-
tions. The difference between the misclassification rate
for the modified and original OOB sample is the measure
of the variable importance. The mean decrease in Gini is
 126
calculated as the sum of all the decreases in Gini impurity
due to a given variable being used to form a split at a
node. A higher decrease in Gini means that a particular
variable plays a bigger role in partitioning the data set in
the defined classes.
A confusion matrix was computed to visualise the perfor-
mance of the model. Precision (p) and recall (r) were
calculated from the confusion matrix and are stated as:
TP
p (1)
TP  FP
TP
r (2)
TP  FN
where TP  true positive, FP  false positive, and FN  false
negative.
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Precision expresses the proportion of predicted positives
over observed positives, whereas recall is defined by the
proportion of observed positives over predicted positives.
The model’s predictive power was estimated using the
weighted F-measure (van Rijsbergen 1979), where F  0
indicates no predictive power and F  1 indicates perfect
predictive power (Powers 2011):
( E 2  1)pr
FE ( p,r ) (3)
E 2p  r
where F(p,r)  the weighted version of the F-measure and
  a weighting factor controlling the relative importance of
precision and recall.
In this analysis,  was set to one, so that precision and
recall were given equal importance (Peters et al. 2007). The
receiver operating characteristic (ROC) curve was used to
assess the model’s classification accuracy (Fielding and
Bell 1997). The ROC curve expresses the true positive rate
or recall (y-axis) against the false positive rate (x-axis). A
diagonal line divides the ROC space, with points above
the diagonal representing good classification (better
0.6 Out-of-bag
Low flowering
TRUE POSITIVE RATE
0.5 High flowering
0.4
ERROR
0.3
0.2
0.1
0.0
0 200 400 600 800 1000
TREES
Figure 2: Out-of-bag and test errors in relation to the number of
decision trees built. Out-of-bag error rate  total misclassification
rate, Low flowering  misclassification rate of ‘low flowering’ sites,
High flowering  misclassification rate of ‘high flowering’ sites.
All three measures of error rate are stable when the number of
classification trees is equal or greater than 300
Germishuizen and Gardner
than random). Model accuracy was measured in terms of
the area under curve (AUC). The AUC provides a single
measure of overall accuracy with the value ranging from
0.5 to 1, where 1 represents perfect classification and 0.5
a random classification (Fielding and Bell 1997). The model
was applied to all commercial plantation forests within the
summer rainfall region of South Africa where the climatic
conditions for E. nitens optimum growth were met (MAT
14–16 °C, MAP  840 mm, altitude 1 350–1 850 m asl;
Swain and Gardner 2003; Smith et al. 2005). Each 1′  1′
pixel was classified 1 000 times and a suitability score on
a scale between zero and one was assigned based on the
proportion of total votes cast. The score was interpreted
as the likelihood that climate and topography at a location
would be conducive to high floral bud production by
E. nitens. Maps highlighting areas of high and low potential
for the establishment of E. nitens seed orchards were
generated from the probability map in ArcGis 10.1 (ESRI,
Redlands, CA, USA) to facilitate interpretation. A threshold
of 0.5 was set to discriminate between suitable and unsuit-
able sites. Hence sites that were assigned a score below
0.5 were classified as unsuitable and sites with a score
equal or greater than 0.5 were classified as suitable.
Results
The RF classifier performed well in classifying high and
low flowering sites. The classification error remained
constant when the number of classification trees was
equal or greater than 300 (Figure 2). The number of classi-
fication trees was set to 1 000 to increase the stability of
variable importance estimation (Liaw and Wiener 2002).
The number of variables randomly selected at each node
was set to five. The AUC computed from the ROC curve
(Figure 3) was 0.83.
The weighted F-measure obtained was 0.85, indicating
excellent predictive power. The OOB estimate of error rate
was 15.79%. Misclassification rate was higher in the false
positives (0.18) than in the false negatives (0.12).
1.0
0.8
0.6
0.4
0.2 AUC = 0.83
0.0
0.0 0.2 0.4 0.6 0.8 1.0
FALSE POSITIVE RATE
Figure 3: Receiver operating characteristic curve showing the true
positive rate against the false positive rate. The perfect classification
is given at the upper left corner of the chart (area under the curve
[AUC] 1), while the diagonal line represents random classification
(AUC  0.5). The distance between the model curve and the
diagonal line represents how much better the model does compared
to random guess
 Southern Forests 2015, 77(2): 123–130
Aspect was rated as the most important predictor by
both the mean decrease in accuracy and mean decrease
Gini (Figure 4). Minimum temperature extremes in late
winter, spring and autumn months in order of descending
importance were also scored as highly important predictors.
The model overall showed that high flowering success is
associated with colder sites that experience frequent cold
spells during the winter months and, within those sites,
colder slopes enhanced floral bud production.
In the summer rainfall region of South Africa, the commer-
cial forestry industry manages approximately 354 000 ha
of land that meet the climatic requirements for optimum
E. nitens growth. By applying the RF model to this portion
of the forestry landscape, the area suitable for establishing
E. nitens seed orchards was quantified and mapped
(Figure 5). Fifty-six percent (approximately 200 000 ha) of
Downloaded by [University of California, San Diego] at 01:35 17 March 2016
the potential area available for E. nitens was classified as
climatically suitable for optimal flowering (Table 3).
Discussion
The high performance of RF models in predicting species’
and ecosystems’ ecological niches and envelopes has
been documented in a number of studies (Elith et al. 2006;
Garzόn et al. 2007; Marmion et al. 2009; Ismail et al. 2010;
Wang et al. 2012; Adam et al. 2013). The strength of RF
models has been attributed to the two sources of random-
ness, bagging and classification tree splitting, which
are key to the model building process (Breiman 2001).
Random forests predicted site suitability likelihood for
E. nitens floral bud production with a high level of accuracy
(AUC  0.83). Both RF variable importance measures
considered in this analysis indicated aspect as the most
Aspect
Tminl08
Tminl011
Tminl05
Tminl09
Tminl04
Slope
Tminl07
Tminl06
Tminl010
Tminl012
0 1 2 3
MEAN DECREASE ACCURACY
Figure 4: Measures of relative importance of predictive variables based on mean decrease in accuracy (MDA) and mean decrease Gini
(MDG). The MDA measures the changes in error rate when the value of the predictive variable is randomly permuted. The MDG is calculated
as the sum of all decreases in Gini impurity when a given predictive variable is used to form a split at a node. Variable abbreviations are
explained in Table 2
127
influential variable in the model, with colder, south-
facing slopes being those most associated with flowering
success. Trial sites were originally selected in areas within
the cool temperate forestry zone where climatic conditions
were favourable for optimum growth in E. nitens (Smith
et al. 2005). Therefore the relevance of aspect as a key
predictor variable further emphasises the floral-inducing
effect of colder temperatures, in accordance with what has
been observed by Moncur and Hasan (1994), Gardner and
Bertling (2005) and Gardner et al. (2014). Low minimum
temperatures in autumn and spring were also rated as
important predictors, further stressing the key regula-
tory role that low temperatures play with respect to floral
induction in E. nitens.
Due to the unavailability of consistent floral crop data
from existing production and breeding E. nitens seed
orchards, the reliability of the model in identifying optimal
sites for floral crop production in E. nitens could not be
tested against the actual performance of existing breeding
and production seed orchards.
The implementation of the RF model at the landscape
level allows for the practical use of the model in decision
making. Poor and inconsistent flowering is a major obstacle
in E. nitens genetic improvement and commercial seed
production (Moncur and Hasan 1994; Reid et al. 1995;
Swain and Gardner 2002), and the selection of sites for the
establishment of productive E. nitens seed orchards is a
challenge to forest managers. Hence, the mapping of areas
within the South African summer rainfall region’s forestry
landscape where climatic and topographic conditions are
conducive to consistent and abundant flower bud produc-
tion is a much-needed tool for both cold-tolerant eucalypt
breeders and forestry practitioners. Given adequate
Aspect
Tminl08
Tminl011
Tminl05
Tminl04
Tminl09
Tminl06
Slope
Tminl010
Tminl07
Tminl012
4 0.0 0.2 0.4 0.6 0.8 1.0
MEAN DECREASE GINI
 128 Germishuizen and Gardner

27° E 28° E 29° E 30° E 31° E 32° E (b) 30°20' E 30°40' E 31° E
Enlarged
area (a) LIMPOPO ¯
24° S

SOUTH MPUMALANGA
AFRICA
25° S
26° S
Nelspruit
!

(a) GAUTENG Enlarged

area (b) 26° S
! Johannesburg
SWAZILAND
MPUMALANGA

! Piet Retief 27° S

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26°20' S
FREE STATE
28° S
KWAZULU-NATAL

!
29° S
SWAZILAND
LESOTHO ! Pietermaritzburg

30° S

26°40' S
0 10 20 km

31° S
! Ugie
E. nitens potential seed orchard sites
E. nitens climatically suitable area
EASTERN CAPE
0 100 200 km Commercial forestry
32° S Piet Retief !

Figure 5: Predicted potential Eucalyptus nitens seed orchard sites within E. nitens climatically suitable growing areas in the summer rainfall
region of South Africa (a). Map (b) is an excerpt at a larger scale

Table 3: Available area suitable for the establishment of Conclusions

Eucalytpus nitens seed orchards within the current South African
summer rainfall commercial plantation forestry areas
Forestry areas Area (ha)
High flowering potential 198 214
Low flowering potential 155 450
Total area suitable for E. nitens 353 664
environmental and flowering data, the predictive tool may
be applicable to other important temperate eucalypt species
for similar purpose in South Africa.
The input data set was derived from a trial series that
included only four clones from two provenances. The limited
genetic variation may represent a weakness in the model
when applied for the identification of optimal sites for the
establishment of E. nitens seed orchards with a broad
genetic base. Future model enhancement by adding flower
bud production data from E. nitens seed orchards with a
broad genetic base to the original data set is recommended
for the development of a robust management tool. The
data set used in this work was not inclusive of the E. nitens
genetic variation in South Africa and results may not be fully
applicable when establishing E. nitens seed orchards with a
broad genetic base.
The modelling framework adopted in this study provided
satisfactory results and highlighted the importance of
Percentage (%) microclimate within the optimal climate range for growing
56 E. nitens when establishing breeding and production seed
44 orchards. The implementation of the model in a spatial
100
environment and the development of a mapping tool for
site selection for E. nitens seed orchards is a first step
towards a decision tool to support breeders in achieving a
successful breeding and/or seed production strategy for this
important commercial species. However, it is advisable to
further enhance the model by broadening the genetic base
of the data set used in the model development.
The model was developed based on data collected at
sites within the summer rainfall region, hence it cannot be
used to identify potential suitable sites in the forestry areas
of South Africa experiencing a winter rainfall regime. This
represents a limitation of this tool as climatic conditions
suitable for the optimum growth of E. nitens are well
represented in the southern and Western Cape regions of
South Africa. The absence of established site  flowering
interaction trials in the winter rainfall areas of South Africa
preclude further development of the tool in the near future.
Seed orchards are a long-term investment and climate
change projections for the southern Africa region foresee
 Southern Forests 2015, 77(2): 123–130
increases in MAT (IPCC 2007) up to 3.4 °C by the year
2100. Further research should investigate the potential
shifts and reduction in sites suitable for the establishment of
E. nitens seed orchards as a result of climate change.
Acknowledgements — The authors thank the ICFR Tree
Improvement funding group for providing the financial support for
the project. The ICFR technical staff are acknowledged for their
assistance with the establishment and maintenance of the field
trials. Dr Andrew Morris is thanked for his constructive comments
and suggestions. The authors thank the anonymous reviewers for
their useful suggestions on the original manuscript.
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