ECOLOGICAL NICHE
MODELING:
PRACTICAL
July 3 rd , 2014
Charlotte Germain-Aubrey
cgermain@ufl.edu
ECOLOGICAL NICHE MODELS
Occurrence data:
where the species
is present, but not
where it is absent
Distribution map:
where the species
is absent, but not
where it is present
Look at a set of conditions under which
a species occurs naturally (presence
data)
When possible, also look at conditions
under which the species does NOT
occur (absence data)
 BUILD THE MODEL
Apply the model in space (around
where it occurs naturally, or in another
area), or in time (where did it use to
occur, or where will it occur in the
future)
 PROJECT THE MODEL
Step 1:
gather points
• Occurrence points
• Specimens from
museum
• Observation
points
• Distribution map
(absence map)
http://scienceasaverb.wordpress.com/2010/10/29/introduction-to-ecological-niche-modeling-environmental-niche-modelingspecies-distribution-modeling-part-two-what-is-niche-modeling/
Step 2:
gather
environmental data
•
•
•
•
•
Climatic
Geological
Soil
Water
Chemicals
• Species interaction
• positive: obligate
host
• negative:
excluding
competitor
http://scienceasaverb.wordpress.com/2010/10/29/introduction-to-ecological-niche-modeling-environmental-niche-modelingspecies-distribution-modeling-part-two-what-is-niche-modeling/
Step 3:
Extract environmental
values at points of
occurrence
http://scienceasaverb.wordpress.com/2010/10/29/introduction-to-ecological-niche-modeling-environmental-niche-modelingspecies-distribution-modeling-part-two-what-is-niche-modeling/
Step 4: Build a
model
Here, a very simple
model: 95% of the
species distribution for
each environmental
variable
http://scienceasaverb.wordpress.com/2010/10/29/introduction-to-ecological-niche-modeling-environmental-niche-modelingspecies-distribution-modeling-part-two-what-is-niche-modeling/
Step 4: Build a
model
Here, a machine
learning model
comparing the
presence and absence
MaxEnt
http://scienceasaverb.wordpress.com/2010/10/29/introduction-to-ecological-niche-modeling-environmental-niche-modelingspecies-distribution-modeling-part-two-what-is-niche-modeling/
Step 5: project the
model
Here projection in the
space and time of
occurrence
http://scienceasaverb.wordpress.com/2010/10/29/introduction-to-ecological-niche-modeling-environmental-niche-modelingspecies-distribution-modeling-part-two-what-is-niche-modeling/
Step 5:
project the model
Here, a projection into
a new area
http://www.oceanecology.ca/species_model_data.jpg
ITIS
National biological
data
Online conservation
tools
ITIS
Environmental data
Species
occurrence
databases
Point occurrences,
Valid taxonomies
Range maps,
Validation services
Biodiversity
encyclopedias
Range maps
Species data
MAXENT
Maximum Entropy algorithm used
(machine-learning) to build and
project niche models.
25% of dataset set aside for
testing the model and giving
feedback on how well it performs
(machine learning process)
species,longitude,latitude
bradypus_variegatus,-65.4,-10.3833
bradypus_variegatus,-65.3833,-10.3833
bradypus_variegatus,-65.1333,-16.8
WHAT IS YOUR QUESTION ?
WHERE IS YOUR DATA ?