What is CDPOP?

CDPOP (Cost Distance POPulations) is a spatially-explicit simulator of gene-flow in complex landscapes to explain observed population responses and provide a foundation for landscape genetics.  The program implements individual-based population modeling with Mendelian inheritance on a resistant landscape.  Simulation begins with an initial homogeneous population and followed by divergence through time as functions of individual based movement, breeding and dispersal on a continuous cost surface.

Solving problems with CDPOP:

This program is used in the study of landscape genetics by increasing our understanding about the effects of life-history and differential models of landscape resistance on the genetic structure of populations in complex landscapes.· Example simulations have included:

1. Quantifying the time to detect barriers.
2. Correlating migration rates to landscape resistance barriers.
3. Testing for the effects of sample size and number of markers.

Example Simulation:

See the CDPOP example simulation page.

What's new in Version 1.0?

1. Sex-specific dispersal.
2. A graphical user interface.
3. Genetic output provided in optional formats (GENALEX, GENEPOP, etc.).
4. Significant computational simulation time speed-up.
5. Additional movement function options: negative exponential movement.
6. Natural selection.
7. Dynamic landscapes.
8. Mating and dispersal landscapes.
9. Vertical transmission.
10. mtDNA option.
    

What's new in v1.1?

1. v1.1 is way faster - significant computational simulation time speed-up.
2. More population tracking numbers added to output.csv. Including tracking variance in reproductive success, mean and standard deviations of mate and dispersal distances traveled, subpopulation immigration numbers.

What's new in v1.2?

1. Demographics! User specifies carrying capacity of spatially-explicit x-y locations. Population dynamics is then controlled by birth rate, death rate, and ability for offspring to disperse to a open habitat location as function of your resistance landscape surface.

What's coming next?

1. Module-Driver plug-in architecture.
2. More genetic distance matrix calculation options (with time speed-ups).
3. User input organized in Stanza format for the package RipMgr (J. Glassy 2010).
4. Hdf5 file formats.
5. Recombination.
   
6. Linkage disequilibrium.
   
7. Parallel processing.
   
8. Optional cost distance matrix calculation using UNICOR (give a resistance surface as input).
   
9. Additional mutation models.
   

Disclaimer

The software is in the public domain, and the recipient may not assert any proprietary rights thereto nor represent it to anyone as other than a University of Montana-produced program (version 1.x).  CDPOP is provided "as is" without warranty of any kind, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose.  The user assumes all responsibility for the accuracy and suitability of this program for a specific application.  In no event will the authors or the University be liable for any damages, including lost profits, lost savings, or other incidental or consequential damages arising form the use of or the inability to use this program.

We strongly urge you to read the entire documentation before ever running CDPOP.  We wish to remind users that we are not in the commercial software marketing business.  We are scientists who recognized the need for a tool like CDPOP to assist us in our research on landscape genetic issues.  Therefore, we do not wish to spend a great deal of time consulting on trivial matters concerning the use of CDPOP.  However, we do recognize an obligation to provide some level of information support.  Of course, we welcome and encourage your criticisms and suggestions about the program at all times.  We will welcome questions about how to run CDPOP or interpret the output only after you have read the entire documentation.  This is only fair and will eliminate many trivial questions.  Finally, we are always interested in learning about how others have applied CDPOP in ecological investigation and management application.  Therefore, we encourage you to contact us and describe your application after using CDPOP.

We hope that CDPOP is of great assistance in your work and we look forward to hearing about your applications.

Download: ·

CDPOP can be obtained from the downloads page

Questions? A user manual can be downloaded here

Acknowledgements

This program was originally developed by Erin Landguth and Sam Cushman. Refactoring is currently underway with the involvement of Brian Hand and Tyler Julian. To cite CDPOP or acknowledge its use, cite this note as follows, substituting the version of the application that you used:

• Landguth EL, Cushman, SA (2010) CDPOP: A spatially-explicit cost distance population genetics program. Molecular Ecology Resources 10, 156-161. PDF