Environmental Layers for HPC Maximum Entropy Species Distribution Models in Great Smoky Mountains National Park

Currently there are 10 environmental layers that were used by Simmerman et. al in the demonstration project, “Exploring similarities among many species distributions.”

  1. Bedrock geology
  2. Digital elevation model
  3. Slope measured in degrees
  4. Solar radiation data
  5. Soil organic type
  6. Terrain shape index
  7. Topographic convergence index
  8. Leaf on canopy cover
  9. Understory density classes
  10. Vegetation classes

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The contribution of environmental variables to each “Maximum Entropy” Species Distribution Model (MaxEnt SDM) environmental variables are accessible from each model under the “Environmental Layers” tab.

The help icon accompanying each model provides this text:

This is a species distribution model (SDM) produced by MaxEnt. This SDM is actually a composite from ten cross-validation runs for each species (see cross-validation results tab for more information). Original ATBI record locations are shown with black dots. The color scale goes from 0 probability of presence (dark brown) to 100% probability (dark green).

Color distribution depicting a probability between 0 (no chance of finding a species) and 1 (100% chance of finding a species)

Color distribution depicting a probability between 0 (no chance of finding a species) and 1 (100% chance of finding a species)

Below is a screen capture of the model generated for the Fraser fir (Abies fraseri). This model is based on 474 occurrence records.  The full size image is available online at <http://seelab.eecs.utk.edu/alltaxa/maps/Abies_fraseri.png>


SDM model generated by the ATBI mapping project / University of Tennessee SEElab.

Interestingly, the MaxEnt model output suggests that the “Digital Elevation Model” contributed 88.8% to the Species Distribution Model for Abies frasieri.  This makes sense, since the Fraser fir is a species of conifer favoring cold environments that inhabits only the highest elevations of the Park.  The remaining layers contribute less than 5% to the model.

I’m copying out the taxonomic classification from Wikipedia:

Scientific classification
Kingdom: Plantae
Division: Pinophyta
Class: Pinopsida
Order: Pinales
Family: Pinaceae
Genus: Abies
Species: A. fraseri

The purpose is to access the records from the ATBI database, where I don’t see the Fraser fir listed in the ATBI “plants” kingdom. From <http://tremont22.campus.utk.edu/ATBI_Query.cfm> I searched by “order’ for “pinales.”

Fraser fir is accessible: <http://tremont22.campus.utk.edu/ATBI_Species.cfm?genus=Abies&epithet=fraseri&subspecies=%7E>.  Interestingly, the number of specimens in the database is 866.  Contrast this with the 474 records that were used to generate the model.  The model may simply be older (there does not appear to be a timestamp for the model; either from “Get Info” or opening up “Properties” in GIMP for both the large 299×1302 pixel PNG file and the small 600×269 pixel png) or, not all 866 occurrence records have spatial coordinates associated (e.g., they are “references from the literature.”)


About Tanner Jessel

I am a recent M.S. in Information Science graduate from the University of Tennessee School of Information Science. I was formerly a graduate research assistant funded by DataONE (Data Observation Network for Earth). Prior, I worked for four years as a content lead and biodiversity scientist with the U.S. Geological Survey's Biodiversity Informatics Program. Building on my work experience in biodiversity and environmental informatics, my work with DataONE focused on exploring the nature of scientific collaborations necessary for scientific inquiry. I also conducted research concerning user experience and usability, and assisted in development of member nodes with an emphasis on spatial data and infrastructure. I assisted with research designed to understand sociocultural issues within collaborative research communities. Through August 1, 2014, I was based at the Center for Information and Communication Studies at the University of Tennessee School of Information Science in Knoxville, Tennessee.

Posted on February 24, 2014, in Practicum, Research, Uncategorized and tagged , , , . Bookmark the permalink. Leave a comment.

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