Week 6: Species Distribution Modeling

Icebreaker

What is a good icebreaker question?

Paper discussion

Drew will be leading the discussion this week of Rzeszowski et al 2026 "Divergent Environmental Niches and Climate Vulnerabilities of Jonah Crab (Cancer borealis) and Atlantic Rock Crab (Cancer irroratus)"

A tour of Github features

A quick tour through some of githubs more useful features for biologists

Lab Exercise: A simple species distribution model from first principles

First, a brief lecture on simple-as-possible species distribution modeling
Next, the usual intro update exercise: Go to your JupyterHub and pull the latest version of the class github repository.

Commands to pull the latest version of the class repository

Change directory to your local copy of the course repo
Pull the latest copy of 'upstream' which is my copy of the class website

Push the changes to your own github repo

cd ~/BIO597-SpatialBiodiversity/`
git upstream
git push

Core Questions

What is the basic logic behind a species distribution model?
How can occurrence records be connected to environmental conditions?
What is the difference between the environment where a species is observed and the environment that is available in the study area?
How can a simple suitability rule be projected back into geographic space?

Concepts

Occurrence records as samples of used environments
Background environments as samples of available conditions
One-variable species-environment relationships
Suitability curves
Projection from environmental space to geographic space

Applied Lab

Students build a simple species distribution model from first principles. Using one amphibian species and one environmental raster, they extract environmental values at occurrence records, compare those values with background conditions across Maine, create a hand-built suitability curve, and project that curve back onto the landscape as a continuous suitability map.

Assignment

Submit a completed first-principles SDM notebook with occurrence and background comparisons, a suitability curve, a projected suitability map, a thresholded map, and short interpretations of the assumptions and limitations of the approach.

docs/labs/Lab06-FirstPrinciplesSDM.ipynb
docs/assignments/Assignment-06-FirstPrinciplesSDM.ipynb

Paper discussion leader next week: Allie! Please select a paper for the group to discuss before Sunday 10/11 6pm and send it around to the class email list: bio597-fall2026-group@maine.edu