WHAT IS CDFISH?
CDFISH is a landscape genetics program to simulate gene flow in complex riverscapes under a wide range of environmental scenarios for aquatic organisms. The spatially-explicit program implements individual-based population modeling with Mendelian inheritance and a k-allele mutation model on a stream network with an underlying resistance surface (e.g. partial barriers). The program simulates stochastic changes in subpopulations (demography with age structure) and genotypes frequencies through time as functions of individual-based movement, reproduction, mortality, and dispersal through migration and straying on a continuous riverscape. This program is a valuable tool for the study of landscape genetics for aquatic species living in complex stream environments.
See News Release 2011.08.09
Solving problems with CDFISH:
This program is used in the study of riverscape 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 could included:
CDFISH EXAMPLE:See the CDFISH example simulation to see how to run CDFISH with an example of 19 subpopulations and 50 individuals per subpopulation. Population genetics parameters (H, A, Fst) are computed and program performance validation is conducted through comparing simulated and theoretical estimates of parameters.
What's new in versions >0.50?
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). CDFISH 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 from the use of or the inability to use this program.
Although this program has been used by the USGS, no warranty, expressed or implied, is made by the USGS or the United States Government as to the accuracy and functioning of the program and related program material nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith.
We strongly urge you to read the entire documentation before ever running CDFISH. 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 CDFISH 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 CDFISH. 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 CDFISH 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 CDFISH in ecological investigation and management application. Therefore, we encourage you to contact us and describe your application after using CDFISH.
We hope that CDFISH is of great assistance in your work and we look forward to hearing about your applications.
CDFISH can be obtained from the downloads page
Questions? A user manual can be downloaded here
This program was originally developed by Erin L. Landguth and Clint Muhlfeld. We are grateful to Leslie Jones, Gordon Luikart, and Helen Neville for their valuable input in the model development. We thank Ross Carlson for his help creating Figures, beta testing, and website maintenance. Funding was provided by the Great Northern Landscape Conservation Cooperative (U.S. Department of Interior) through the Rocky Mountain Cooperative Ecosystem Study Unit at the University of Montana, Missoula. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. The reference to cite is:
Landguth EL, Muhlfeld CC, Luikart G (2011) CDFISH: an individual-based, spatially-explicit, landscape genetics simulator for aquatic species in complex riverscapes. Conservation Genetics Resources. DOI:10.1007/s12686-011-9492-6.
Computational Ecology Laboratory
Division of Biological Sciences (DBS)
The University of Montana
32 Campus Drive, HS 507
Missoula MT, 59812-1002
Phone: (406) 243-2393
Fax: (406) 243-4184