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Ecological Niche Modeling: Ecological Niche Modeling: A tool set to assess distributional A tool set to assess distributional
patterns in biodiversity and patterns in biodiversity and pathogenspathogens
based onbased on
Jane [email protected]
Instituto Oswaldo Cruz, FiocruzRio de Janeiro, Brasil
Townsend Peterson [email protected]
University of Kansas, Lawrence, Kansas, USA Emerging Infectious Diseases,
12, December, 2006
What is ecologic niche What is ecologic niche modelingmodeling
The idea is that known occurrences of species The idea is that known occurrences of species across landscapes can be related to digital raster across landscapes can be related to digital raster GIS coverages summarizing environmental GIS coverages summarizing environmental variation across those landscapes to develop a variation across those landscapes to develop a quantitative picture of the ecologic distribution of quantitative picture of the ecologic distribution of the species.the species.
ENM characterizes the distribution of the species ENM characterizes the distribution of the species in a space defined by environmental parameters, in a space defined by environmental parameters, which are precisely those that govern the species' which are precisely those that govern the species' geographic distribution under Grinnell's definition geographic distribution under Grinnell's definition of ecological niches. of ecological niches.
The set of environmental The set of environmental conditions, resources, conditions, resources, interactions, etc., in which a interactions, etc., in which a species is able to maintain species is able to maintain populations without populations without immigrationimmigration
Ecological Niche ConceptEcological Niche Concept
project
GarpGarp
GARP is a genetic algorithm that creates ecological niche models for species. The models describe environmental conditions under which the species should be able to maintain populations. For input, GARP uses a set of point localities where the species is known to occur and a set of geographic layers representing the environmental parameters that might limit the
species' capabilities to survive.
Geographic Space Ecological Space
occurrence points on native distribution
ecological niche modeling
Projection back onto geography
Native range prediction
Invaded range prediction
Essence of Ecological Niche Essence of Ecological Niche ModelingModeling
temperature
Model of niche in ecological dimensions
pre
cip
itatio
nNote that ENM applications such as GARP can show
excellent predictive ability for quite small samples
The applications of ENM
Here is outlined what the Here is outlined what the technique has to offer to the field.technique has to offer to the field.
The applications of ENM 1-Understanding Ecology of Diseases1-Understanding Ecology of Diseases
In many cases, the details of ecologic parameters In many cases, the details of ecologic parameters associated with occurrences of diseases or of species associated with occurrences of diseases or of species participating in disease transmission (e.g., vectors, participating in disease transmission (e.g., vectors, hosts, pathogens) may be unclear because of small hosts, pathogens) may be unclear because of small sample sizes, biased reporting, or simply lack of sample sizes, biased reporting, or simply lack of detailed geographic or ecologic analysis. detailed geographic or ecologic analysis.
ENM encompasses a suite of tools that relate known ENM encompasses a suite of tools that relate known occurrences of these species or phenomena to raster occurrences of these species or phenomena to raster geographic information system layers that geographic information system layers that summarize variation in several environmental summarize variation in several environmental dimensions.dimensions.
The applications of ENM 1-Understanding Ecology of Diseases1-Understanding Ecology of Diseases
The result is an objective, quantitative picture The result is an objective, quantitative picture of how what is known about a species or of how what is known about a species or phenomenon relates to environmental phenomenon relates to environmental variation across a landscape. variation across a landscape.
Studies using these approaches include an Studies using these approaches include an examination of ecologic differences among examination of ecologic differences among different Chagas disease vectors in Brazil and different Chagas disease vectors in Brazil and a characterization of ecologic features of a characterization of ecologic features of outbreaks of hemorrhagic fever caused by outbreaks of hemorrhagic fever caused by Ebola and Marburg virusesEbola and Marburg viruses
Am. J. Trop. Med. Hygiene 67:516-520The The Triatoma brasiliensisTriatoma brasiliensis
species complexspecies complex
Ecological similarity matrix among populations based on the ability of the model for one population to predict the distribution of another
br me ma juPredicted br 0.98 0.00 0.44 0.51
me 0.38 0.85 0.10 0.21ma 0.87 0.00 1.00 0.87ju 0.87 0.00 0.76 0.93
Predictor
The applications of ENM 2- Characterizing Distributional Areas2- Characterizing Distributional Areas
ENM is used to investigate landscapes for areas ENM is used to investigate landscapes for areas
that meet the ecologic requirements of the that meet the ecologic requirements of the
speciesspecies
The result is an interpolation between known The result is an interpolation between known
sampling locations informed by observed sampling locations informed by observed
associations between the species and associations between the species and
environmental characteristics.environmental characteristics.
The applications of ENM 2- Characterizing Distributional Areas2- Characterizing Distributional Areas
ENM produces statistically robust predictions ENM produces statistically robust predictions of geographic distributions of species or of geographic distributions of species or phenomena (even in unsampled areas), phenomena (even in unsampled areas), greatly exceeding expectations under greatly exceeding expectations under random (null) models. Numerous examples of random (null) models. Numerous examples of applications of this functionality to disease applications of this functionality to disease systems have been publishedsystems have been published. .
The applications of ENM 3- Identifying Areas of Potential Invasion in 3- Identifying Areas of Potential Invasion in other Regionsother Regions
ENMs characterize general environmental regimes ENMs characterize general environmental regimes
under which species or phenomena may occur. under which species or phenomena may occur.
To the extent that the model is appropriately and To the extent that the model is appropriately and
correctly calibrated, it may be used to seek areas of correctly calibrated, it may be used to seek areas of
potential distribution. potential distribution.
Thus, ENMs can be used to identify areas that fit the Thus, ENMs can be used to identify areas that fit the
ecologic bill for a species, even if the species is not ecologic bill for a species, even if the species is not
present there.present there.
The applications of ENM 3- Identifying Areas of Potential Invasion 3- Identifying Areas of Potential Invasion in other Regionsin other Regions
This approach has seen extensive
experimentation and testing in the
biodiversity realm, but applications to
disease transmission have as yet been have as yet been
few. few.
The applications of ENM 4- Anticipating Risk Areas with Changing 4- Anticipating Risk Areas with Changing ClimatesClimates
A logical extension of using ENMs to identify potential A logical extension of using ENMs to identify potential
distributional areas is to address the question of likely distributional areas is to address the question of likely
geographic shifts in distributional areas of species or geographic shifts in distributional areas of species or
phenomena under scenarios of climate change or changing land phenomena under scenarios of climate change or changing land
use.use.
This approach has seen considerable attention in the This approach has seen considerable attention in the
biodiversity realm, with both tests and validations, and with biodiversity realm, with both tests and validations, and with
broad applications across faunas and floras. In the disease broad applications across faunas and floras. In the disease
world, applications have been few, although 1 study used likely world, applications have been few, although 1 study used likely
climate change–mediated range shifts to hypothesize the climate change–mediated range shifts to hypothesize the
identity of identity of LutzomyiaLutzomyia vectors of recent leishmaniasis outbreaks vectors of recent leishmaniasis outbreaks
in southern Brazil.in southern Brazil.
The applications of ENM 5- Identifying Unknown Vectors or Hosts5- Identifying Unknown Vectors or Hosts
ENM approaches can be applied to various parts of disease transmission ENM approaches can be applied to various parts of disease transmission
cycles (e.g., overall case distribution, reservoir host distribution, vector cycles (e.g., overall case distribution, reservoir host distribution, vector
distribution) to identify unknown elements in systems. distribution) to identify unknown elements in systems.
The geography of overall case distributions can provide an indication of The geography of overall case distributions can provide an indication of
which clades are potential reservoirs and which are not. A first which clades are potential reservoirs and which are not. A first
application was an attempt to identify mammalian hosts of the application was an attempt to identify mammalian hosts of the Triatoma Triatoma
protractaprotracta group of Chagas disease vectors in Mexico, which succeeded group of Chagas disease vectors in Mexico, which succeeded
in anticipating the mammal hosts of 5 of 5 species for which a test was in anticipating the mammal hosts of 5 of 5 species for which a test was
possible. possible.
Further exploration of this possible application of ENM methods has Further exploration of this possible application of ENM methods has
focused on the mysterious long-term reservoir of the filoviruses (Ebola focused on the mysterious long-term reservoir of the filoviruses (Ebola
and Marburg viruses) by comparing African mammal distributions with and Marburg viruses) by comparing African mammal distributions with
those of filovirus-caused disease outbreaks.those of filovirus-caused disease outbreaks.
DiscussionDiscussion1-Current Challenges in ENM1-Current Challenges in ENM
ENM, although it has old roots, is nonetheless a relatively ENM, although it has old roots, is nonetheless a relatively new tool in distributional ecology and biogeography. As such new tool in distributional ecology and biogeography. As such numerous challenges remain in terms of refining approaches numerous challenges remain in terms of refining approaches toward a more powerful and synthetic methodology. toward a more powerful and synthetic methodology.
To improve the of ability to interpolate accurately versus To improve the of ability to interpolate accurately versus ability to extrapolate effectively remains a challenge for the ability to extrapolate effectively remains a challenge for the ENM methods. ENM methods.
A second frontier that includes yet-to-be-resolved details for A second frontier that includes yet-to-be-resolved details for ENM is that of testing and evaluating model results. Currently ENM is that of testing and evaluating model results. Currently accepted approaches center on the ability to predict accepted approaches center on the ability to predict independent test occurrence data in the smallest area independent test occurrence data in the smallest area predicted. However, efficient predictions can be poor predicted. However, efficient predictions can be poor descriptors of a species' geographic range descriptors of a species' geographic range
DiscussionDiscussion2-Current Challenges in 2-Current Challenges in Applications of ENM to Disease Applications of ENM to Disease SystemsSystems The first, and perhaps most important, is The first, and perhaps most important, is
understanding the role of scale in space and time. understanding the role of scale in space and time.
Preliminary explorations suggest that proper matching Preliminary explorations suggest that proper matching
of temporal and spatial scales in analyses may offer of temporal and spatial scales in analyses may offer
particular opportunities for precise and accurate particular opportunities for precise and accurate
prediction of the behavior of disease phenomenaprediction of the behavior of disease phenomena
Similarly, proper choice of environmental datasets Similarly, proper choice of environmental datasets
requires further exploration. requires further exploration.
DiscussionDiscussion2-Current Challenges in 2-Current Challenges in Applications of ENM to Disease Applications of ENM to Disease SystemsSystems Climate data provide longer temporal applicability, but Climate data provide longer temporal applicability, but
remotely sensed data that summarize aspects of remotely sensed data that summarize aspects of
surface reflectance can provide finer spatial surface reflectance can provide finer spatial
resolution, and may measure aspects of ecologic resolution, and may measure aspects of ecologic
landscapes that climate parameters alone may not landscapes that climate parameters alone may not
capture capture
Finally, because disease transmission systems often Finally, because disease transmission systems often
represent complex interactions among multiple represent complex interactions among multiple
species (e.g., vectors, hosts, pathogens), options exist species (e.g., vectors, hosts, pathogens), options exist
for how they should be analyzed and modeled. for how they should be analyzed and modeled.
ConclusionsConclusions
ENM can solve several problems of spatial resolution of ENM can solve several problems of spatial resolution of
summaries of geographic risk for disease. summaries of geographic risk for disease.
ENM is in the early stages of being explored for its potential ENM is in the early stages of being explored for its potential
for illuminating unknown phenomena in the world of disease for illuminating unknown phenomena in the world of disease
transmission. transmission.
The extensive explorations of ENM in the biodiversity field, The extensive explorations of ENM in the biodiversity field,
however, serve as a benchmark of quality and acceptance however, serve as a benchmark of quality and acceptance
for the technique for the technique