bridging species niche modeling and multispecies ecological modeling and analysis jeffery cavner,...
TRANSCRIPT
![Page 1: Bridging Species Niche Modeling and Multispecies Ecological Modeling and Analysis Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ Grady jcavner@ku.edu, beach@ku.edu,astewart@ku.edu,](https://reader030.vdocuments.us/reader030/viewer/2022032804/56649e4a5503460f94b3ef46/html5/thumbnails/1.jpg)
Bridging Species Niche Modeling and Multispecies Ecological Modeling and Analysis
Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ [email protected], [email protected] ,[email protected], [email protected]
Biodiversity Institute University of Kansas
![Page 2: Bridging Species Niche Modeling and Multispecies Ecological Modeling and Analysis Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ Grady jcavner@ku.edu, beach@ku.edu,astewart@ku.edu,](https://reader030.vdocuments.us/reader030/viewer/2022032804/56649e4a5503460f94b3ef46/html5/thumbnails/2.jpg)
Species DiversityLmRAD (Lifemapper Range and Diversity)
Biodiversity - describe, visualize and analyze different aspects of the numbers and abundances of taxa in time and space.
Patterns of species richness - constituent species ranges sizes and spatial locations of those ranges.
Patterns related to species associations, co-occurrence, and species interactions requires testing against randomized distributions.
Species richness and species range can be summarized and linked by one basic analytical tool, the presence/absence matrix (PAM).
![Page 3: Bridging Species Niche Modeling and Multispecies Ecological Modeling and Analysis Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ Grady jcavner@ku.edu, beach@ku.edu,astewart@ku.edu,](https://reader030.vdocuments.us/reader030/viewer/2022032804/56649e4a5503460f94b3ef46/html5/thumbnails/3.jpg)
Lifemapper as an overarching architecture
• LmRAD is built on top of the existing Lifemapper architecture
• Lifemapper is an archival and species distribution modeling platform consisting of a computational pipeline, specimen data archive, predicted species distribution model archive
• Distribution models are built on-demand using openModeller.
• Inputs: climate scenario data and aggregated specimen occurrences from GBIF and user provided occurrence points.
![Page 4: Bridging Species Niche Modeling and Multispecies Ecological Modeling and Analysis Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ Grady jcavner@ku.edu, beach@ku.edu,astewart@ku.edu,](https://reader030.vdocuments.us/reader030/viewer/2022032804/56649e4a5503460f94b3ef46/html5/thumbnails/4.jpg)
The Presence Absence Matrix (PAM)
Data Matrix Grid
![Page 5: Bridging Species Niche Modeling and Multispecies Ecological Modeling and Analysis Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ Grady jcavner@ku.edu, beach@ku.edu,astewart@ku.edu,](https://reader030.vdocuments.us/reader030/viewer/2022032804/56649e4a5503460f94b3ef46/html5/thumbnails/5.jpg)
Most existingindices of biodiversityare simple combinations of :oVectors:
species richnesssizes of distributions“dispersion fields”“diversity fields”
oWhitaker’s beta diversityoThe dimensions of the PAM
![Page 6: Bridging Species Niche Modeling and Multispecies Ecological Modeling and Analysis Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ Grady jcavner@ku.edu, beach@ku.edu,astewart@ku.edu,](https://reader030.vdocuments.us/reader030/viewer/2022032804/56649e4a5503460f94b3ef46/html5/thumbnails/6.jpg)
Constraints
• Construction of PAMs can be an extremely time consuming data management task
• Current methods for working with these matrices can be computationally slow
![Page 7: Bridging Species Niche Modeling and Multispecies Ecological Modeling and Analysis Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ Grady jcavner@ku.edu, beach@ku.edu,astewart@ku.edu,](https://reader030.vdocuments.us/reader030/viewer/2022032804/56649e4a5503460f94b3ef46/html5/thumbnails/7.jpg)
Approach
• To overcome computational restraints we use a Python implementation of the Web Processing Service standard on a compute cluster, exposing spatial and statistical algorithms.
• Allows a variety of species inputs
• Extendable clients including Quantum GIS (QGIS) and VisTrails that share a common client library
![Page 8: Bridging Species Niche Modeling and Multispecies Ecological Modeling and Analysis Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ Grady jcavner@ku.edu, beach@ku.edu,astewart@ku.edu,](https://reader030.vdocuments.us/reader030/viewer/2022032804/56649e4a5503460f94b3ef46/html5/thumbnails/8.jpg)
Clients
![Page 9: Bridging Species Niche Modeling and Multispecies Ecological Modeling and Analysis Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ Grady jcavner@ku.edu, beach@ku.edu,astewart@ku.edu,](https://reader030.vdocuments.us/reader030/viewer/2022032804/56649e4a5503460f94b3ef46/html5/thumbnails/9.jpg)
Randomizing the PAM• To test the null hypothesis
• By producing the same richness and range patterns while ignoring realistic species combinations
• Two Types of Randomization: Swap and Dye Dispersion– Swap : keeps species richness and range size totals intact.
![Page 10: Bridging Species Niche Modeling and Multispecies Ecological Modeling and Analysis Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ Grady jcavner@ku.edu, beach@ku.edu,astewart@ku.edu,](https://reader030.vdocuments.us/reader030/viewer/2022032804/56649e4a5503460f94b3ef46/html5/thumbnails/10.jpg)
Additional Randomization methods
Dye Dispersion
– Geometric constraints model
– Assumes range continuity
– Reassembles ranges
– Keeps range size intact
![Page 11: Bridging Species Niche Modeling and Multispecies Ecological Modeling and Analysis Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ Grady jcavner@ku.edu, beach@ku.edu,astewart@ku.edu,](https://reader030.vdocuments.us/reader030/viewer/2022032804/56649e4a5503460f94b3ef46/html5/thumbnails/11.jpg)
QGIS is used as a WPS client
![Page 12: Bridging Species Niche Modeling and Multispecies Ecological Modeling and Analysis Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ Grady jcavner@ku.edu, beach@ku.edu,astewart@ku.edu,](https://reader030.vdocuments.us/reader030/viewer/2022032804/56649e4a5503460f94b3ef46/html5/thumbnails/12.jpg)
Using QGIS and WPS to construct a grid
![Page 13: Bridging Species Niche Modeling and Multispecies Ecological Modeling and Analysis Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ Grady jcavner@ku.edu, beach@ku.edu,astewart@ku.edu,](https://reader030.vdocuments.us/reader030/viewer/2022032804/56649e4a5503460f94b3ef46/html5/thumbnails/13.jpg)
The asynchronous nature of WPS combined with a computational pipeline and compute cluster allow a user to intersect hundreds of species layers at a time with the data grid to populate the PAM.
![Page 14: Bridging Species Niche Modeling and Multispecies Ecological Modeling and Analysis Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ Grady jcavner@ku.edu, beach@ku.edu,astewart@ku.edu,](https://reader030.vdocuments.us/reader030/viewer/2022032804/56649e4a5503460f94b3ef46/html5/thumbnails/14.jpg)
Terrestrial Mammals
Proportional Species Richness
Per-site Range Size
High YellowModerate RedLow Blue
![Page 15: Bridging Species Niche Modeling and Multispecies Ecological Modeling and Analysis Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ Grady jcavner@ku.edu, beach@ku.edu,astewart@ku.edu,](https://reader030.vdocuments.us/reader030/viewer/2022032804/56649e4a5503460f94b3ef46/html5/thumbnails/15.jpg)
Statistical services provide diversity indices and plots using WPS
![Page 16: Bridging Species Niche Modeling and Multispecies Ecological Modeling and Analysis Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ Grady jcavner@ku.edu, beach@ku.edu,astewart@ku.edu,](https://reader030.vdocuments.us/reader030/viewer/2022032804/56649e4a5503460f94b3ef46/html5/thumbnails/16.jpg)
By-species range-diversity plot
![Page 17: Bridging Species Niche Modeling and Multispecies Ecological Modeling and Analysis Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ Grady jcavner@ku.edu, beach@ku.edu,astewart@ku.edu,](https://reader030.vdocuments.us/reader030/viewer/2022032804/56649e4a5503460f94b3ef46/html5/thumbnails/17.jpg)
The plug-ins use a simple MVC pattern with QT threads for asynchronous WPS requests and a client library for the communication layer
![Page 18: Bridging Species Niche Modeling and Multispecies Ecological Modeling and Analysis Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ Grady jcavner@ku.edu, beach@ku.edu,astewart@ku.edu,](https://reader030.vdocuments.us/reader030/viewer/2022032804/56649e4a5503460f94b3ef46/html5/thumbnails/18.jpg)
Conclusion
![Page 19: Bridging Species Niche Modeling and Multispecies Ecological Modeling and Analysis Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ Grady jcavner@ku.edu, beach@ku.edu,astewart@ku.edu,](https://reader030.vdocuments.us/reader030/viewer/2022032804/56649e4a5503460f94b3ef46/html5/thumbnails/19.jpg)
Jeffery Cavner, J.H. Beach, Aimee Stewart, CJ Grady [email protected], [email protected], [email protected],
[email protected] Institute University of Kansas