updating ecological niche modeling methodologies
TRANSCRIPT
![Page 1: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/1.jpg)
ECOLOGICAL NICHE MODELING METHODS UPDATETown Peterson, University of Kansas
![Page 2: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/2.jpg)
It Is A Bit Too Easy …
• Very easy access to lots of occurrence data
• Very easy access to rich geospatial data
• Easy-to-use modeling tools• Lots of literature setting out
the examples
![Page 3: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/3.jpg)
Ecological Niche Modeling
1. Accumulate Input Data2. Integrate Occurrence and Environmental Data3. Model Calibration4. Model Evaluation5. Summary and Interpretation
![Page 4: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/4.jpg)
Accumulate Input Data
Collate primary biodiversity data documenting occurrences
Process environmental layers to be maximally relevant to distributional ecology of species in question
Collate GIS database of relevant data layers
Assess spatial precision of occurrence data; adjust inclusion of data accordingly
Data subsetting for model evaluation
Occurrence andenvironmental data
Assess spatial autocorrelation
![Page 5: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/5.jpg)
Occurrence Data in Niche Modeling
• Goal is to represent the full diversity of situations under which a particular species maintains populations
• Spatial biases (i.e., non-random or non-uniform distribution within G) is not damning
• Biases within E are catastrophic, and will translate directly into biases in any niche estimate
• More is usually better, but not always…
![Page 6: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/6.jpg)
speciesLink Network
![Page 7: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/7.jpg)
Uncertainty in Direction and Distance
![Page 8: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/8.jpg)
Georeferencing should …
• Represent the place at which the species was found
• Represent the certainty and uncertainty with which that place is characterized
• Summarize the methods used to establish that place
• Preserve all of the original information for possible reinterpretation
![Page 9: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/9.jpg)
![Page 10: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/10.jpg)
![Page 11: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/11.jpg)
Internal Consistency Testing
![Page 12: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/12.jpg)
Data Cleaning• Attempt to detect meaningfully erroneous records, so
that they can be treated with caution in analysis• Use internal consistency to detect initial problems– Species names consistent?– Terrestrial species on land, marine species in the ocean?– Latlong matches country, state, district, etc.
• Use external consistency to go deeper– Occurrence data match known distribution spatially?– Occurrence data match known distribution environmentally?
• If precision data are available, filter to retain only records that are precise enough for the study
• Iterative process with important consequences
![Page 13: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/13.jpg)
![Page 14: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/14.jpg)
Data Subsetting
• Must respond to the question at hand … why are you doing the study?
• Ideally completely independent data streams• Failing that, can be – Macrospatial– Microspatial (but see spatial autocorrelation)– Random
• Will return to this point later…
![Page 15: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/15.jpg)
Generalities: Environmental Data
• Raster format: i.e., information exists across entire region of interest
• Relevant information as regards the distributional potential of the species of interest
• More dimensions = better (generally), BUT – collinearity is bad– too many dimensions is bad
![Page 16: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/16.jpg)
Major Sources
• Climate data – long time span, but low temporal resolution
• Remote-sensing data – high temporal resolution, diverse products, short time span
• Topographic data – high temporal resolution, uncertain connection to species’ distributional ecology
• Soils data – uneven global coverage, categorical data
• Others
![Page 17: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/17.jpg)
Spatial Autocorrelation
![Page 18: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/18.jpg)
Two Major Implications• Non-independence in model evaluation– Available data are often split into data sets for calibration and
evaluation– Data points that are not independent of one another may end
up in different data sets, thereby compromising the robustness of the test
• Inflation of sample sizes– Because individual data points may be non-independent of one
another, sample sizes may appear larger than they actually are– This inflation may create opportunity for Type 1 errors in model
evaluation and model comparisons
![Page 19: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/19.jpg)
![Page 20: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/20.jpg)
Process for Maximum Relevancy
![Page 21: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/21.jpg)
Integrate Occurrence and Environmental Data
Assess BAM scenario for species in question; avoid M-limited situations
Saupe et al. 2012. Variation in niche and distribution model performance: The need for a priori assessment of key causal factors. Ecological Modelling, 237–238, 11-22.
Estimate M and S as area of analysis in study
Barve et al. 2011. The crucial role of the accessible area in ecological niche modeling and species distribution modeling. Ecological Modelling, 222, 1810-1819.
Reduce dimensionality (PCA or correlation analysis)
Occurrence andenvironmental data
Occurrence andenvironmental data ready for analysis
![Page 22: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/22.jpg)
Assess BAM Scenario
![Page 23: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/23.jpg)
BAM I: Eltonian Noise Hypothesis
A
M
B A
M
![Page 24: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/24.jpg)
BAM II
ClassicBAM
Hutchinson’sDream
Wallace’sDream
All OK
![Page 25: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/25.jpg)
Project onto Geography
![Page 26: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/26.jpg)
Effect of BAM Scenarios
![Page 27: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/27.jpg)
BAM Conclusions
• Some situations are not amenable to fitting ecological niche models that will have predictive power
• Models tend much more to good fitting of the potential distribution, rather than the actual distribution
• Must ponder carefully the BAM configuration in a particular study situation to avoid configurations that will not yield usable models
![Page 28: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/28.jpg)
M and S as Study Area
![Page 29: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/29.jpg)
Test Arena: The Lawrence Species
![Page 30: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/30.jpg)
M and Model Training
![Page 31: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/31.jpg)
Model Evaluation
![Page 32: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/32.jpg)
M and Model Comparison
![Page 33: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/33.jpg)
Model Comparison
![Page 34: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/34.jpg)
M• When the species has no history in an area:– Use a radius related to dispersal distances
• When history is short (i.e., environment constant):– Use a radius representing compounding of
dispersal distances• When history is long (i.e., environmental
change is a factor) – Seek ways of assessing areas that the species’
distribution through time has covered…
![Page 35: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/35.jpg)
Icterus cucullatus
Sampling
![Page 36: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/36.jpg)
Reduce Dimensionality
![Page 37: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/37.jpg)
Model Calibration
Estimate ecological niche (various algorithms)
Model calibration, adjusting parameters to maximize quality
Model thresholding
Peterson et al. 2007. Transferability and model evaluation in ecological niche modeling: A comparison of GARP and Maxent. Ecography, 30, 550-560.
Occurrence andenvironmental data ready for analysis
“No Silver Bullet” paper to appear
Warren, D. L. and S. N. Seifert. 2011. Ecological niche modeling in Maxent: The importance of model complexity and the performance of model selection criteria. Ecological Applications 21:335-342.
Preliminary models
![Page 38: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/38.jpg)
Estimate Ecological Niche
![Page 39: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/39.jpg)
![Page 40: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/40.jpg)
![Page 41: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/41.jpg)
![Page 42: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/42.jpg)
![Page 43: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/43.jpg)
![Page 44: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/44.jpg)
![Page 45: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/45.jpg)
![Page 46: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/46.jpg)
![Page 47: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/47.jpg)
No Silver Bullets in ENM
• Single algorithms may perform ‘best’ on average• The best algorithm in any given situation, however,
may be other than the ‘best’• NSB thinking suggests that we should not use a
single approach• Use a suite of approaches (e.g., as implemented in
OM, BIOMOD, BIOENSEMBLES, etc.), challenge to predict, choose best for that situation
• Maxent is good, but it is not the only algorithm …
![Page 48: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/48.jpg)
Model Thresholding
![Page 49: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/49.jpg)
“Presence”
![Page 50: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/50.jpg)
Thresholding
• Use an approach that prioritizes omission error over commission error, in view of the greater reliability of presence data
• Minimum training presence thresholding seeks the highest suitability value that includes 100% of the calibration data
• Suggest (strongly) using a parallel approach that seeks that highest suitability value that includes (100-E)% of the calibration data
![Page 51: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/51.jpg)
Model Optimization and Parameter Choice
![Page 52: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/52.jpg)
Model Evaluation
Project niche model to geographic space
Model evaluation
Peterson et al. 2008. Rethinking receiver operating characteristic analysis applications in ecological niche modelling. Ecological Modelling, 213, 63-72.
Preliminarymodels
Reset data subsets based on evaluation results
Corroborated models ready for projection to
geographic times/regions of
interest
![Page 53: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/53.jpg)
![Page 54: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/54.jpg)
If predicted suitable area covers 15% of the testing area, then 15% of evaluation points are expected to fall in the predicted suitable area by chance.
• p = proportion of area predicted suitable
• s = number of successes• n = number of evaluation
points
Cumulative binomial distribution calculates the probability of obtaining s successes out of n trials in a situation in which p proportion of the testing area is predicted present. If this probability is below 0.05, we interpret the situation as indicating that the model’s predictions are significantly better than random.
Threshold-dependent Approach
![Page 55: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/55.jpg)
Threshold-independent Approaches
![Page 56: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/56.jpg)
![Page 57: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/57.jpg)
![Page 58: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/58.jpg)
http://shiny.conabio.gob.mx:3838/nichetoolb2/
![Page 59: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/59.jpg)
Significance vs Performance
• Predictions that are significantly better than random is important, and is a sine qua non for model interpretation
• BUT, it is also important to assure that the model performs sufficiently well for the intended uses of the output
• Performance measures include omission rate, correct classification rate, etc.
![Page 60: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/60.jpg)
Summary and Interpretation
Evaluation of model transfer results
Transfer to other situations (time and space)
Assess extrapolation (MESS and MOP)Owens, H. L., L. P. Campbell, L. Dornak, E. E. Saupe, N. Barve, J. Soberón, K. Ingenloff, A. Lira-Noriega, C. M. Hensz, C. E. Myers, and A. T. Peterson. 2013. Constraints on interpretation of ecological niche models by limited environmental ranges on calibration areas. Ecological Modelling 263:10-18.
Refine estimate of current distribution via land use, etc.
Compare present and “other” to assess effects of change
Models calibrated and evaluated, and transferred to present and “other” situations
![Page 61: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/61.jpg)
![Page 62: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/62.jpg)
![Page 63: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/63.jpg)
![Page 64: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/64.jpg)
![Page 65: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/65.jpg)
![Page 66: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/66.jpg)
MESS and MOP• Both have the intention of detecting extrapolative
situations• MESS is implemented within Maxent• MESS compares the area in question to the
centroid of the calibration cloud• MOP compares the area in question to the nearest
part of the calibration cloud• Agree on ‘out of range’ conditions• MOP better characterizes similarities between
calibration and transfer regions, and thus is more optimistic as regards in-range extrapolation
![Page 67: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/67.jpg)
![Page 68: Updating Ecological Niche Modeling Methodologies](https://reader036.vdocument.in/reader036/viewer/2022070511/58a25c931a28abb92b8b4bdf/html5/thumbnails/68.jpg)
Ecological Niche Modeling
1. Accumulate Input Data2. Integrate Occurrence and Environmental Data3. Model Calibration4. Model Evaluation5. Summary and Interpretation