Landscape Genetics of Great Basin Rattlesnakes, Crotalus Oreganus Lutosus, on the Upper Snake River Plain


This project will model how landscape characteristics affect gene flow and population structure in Great Basin rattlesnakes, Crotalus oreganus lutosus. Over the last three decades, a signifi cant body of baseline data has been amassed addressing various aspects of Great Basin rattlesnake ecology on the INL Site, through efforts of an 18 year reptile monitoring project funded by the Department of Energy, and various theses completed by students of Idaho State University’s Herpetology Laboratory. Although data exists on population size dynamics, reproduction, neonate survivorship, and disturbance effects, there has yet to be genetic component to this ongoing research. Genetic distance data can effectively ascertain landscape features influencing movement patterns and gene flow among sampling locations of animals (Bushar et al. 1998). The field of landscape genetics, made possible by GIS and microsatellite DNA imaging technologies, attempts to correlate habitat heterogeneity with patterns of gene flow and population structure (Manel et al., 2003, Storfer et al., 2006). This type of analysis is valuable for understanding the interplay between rattlesnake ecology and their physical environment, as well as lending insights to ways of avoiding the deleterious effects of habitat fragmentation, reproductive isolation, and genetic drift on genetic variability and population viability of snake species (Bushar et al. 1998).


  • To understand how landscape characteristics influence genetic connectivity among populations of Great Basin rattlesnakes from over-wintering sites (dens) in the shrub-steppe ecosystem of the Upper Snake River Plain in eastern Idaho.
  • To understand the effects of natural and anthropogenically altered landscapes on gene flow among rattlesnake populations.

Accomplishments Through 2007

  • 243 rattlesnakes from 13 geographically distinct denning locations have been captured and had a tissue sample collected for subsequent DNA analysis.

  • DNA has been extracted from individuals captured at 10 geographically distinct denning locations.

  • Of 17 potential microsatellite loci developed for genotyping use in other species of rattlesnake, six loci have been successfully amplified and used to genotype 180 Great Basin rattlesnakes.

  • Digital geospatial data files for cover type, soils, geology, elevation, grazing, infrastructure, landownership, and burn status on the INL Site and surrounding BLM managed lands have been compiled and incorporated into a GIS.


Initial results have shown that population genetic sub-structuring is highly likely among the rattlesnake dens on the INL Site, but are not reported due to insufficient sample size used in this preliminary analysis.

Plans for Continuation

  • In-depth statistical analysis of genotype data will be performed.

  • ArcMap will be used to make correlations between molecular and geospatial data to determine how landscape attributes affect gene flow and population connectively among the Great Basin rattlesnake dens on the INL Site.

Publications, Theses, Reports, etc.

Thesis research will be completed December 2008, and submitted for publication early 2009.

Investigators and Affiliations

Susan B. Parsons, Graduate Student, Herpetology and Molecular Ecology Laboratories, Department of Biological Sciences, Idaho State University, Pocatello, Idaho

Dr. Charles R. Peterson, Professor , Herpetology Laboratory, Department of Biological Sciences Idaho State University, Pocatello, Idaho

Dr. Marjorie D. Matocq, Professor, Molecular Ecology Laboratory, Department of Biological Sciences, Idaho State University, Pocatello, Idaho

Funding Sources

U.S. Department of Energy Idaho Operations Office

Idaho State University Molecular Core Research Facility Seed Grant


Bushar, L.M., Reinert, H.K., and L. Gelbert. 1998. Genetic variation and gene flow within and between local populations of the timber rattlesnake, Crotalus horridus. Copeia. 1998(2): 411-422.

Manel, S., M.K. Schwartz, G. Luikart, and P. Taberlet. 2003. Landscape genetics: combining
landscape ecology and population genetics. Trends in Ecology & Evolution 18, 189-197.

Storfer, A., M.A. Murphy, J.S. Evans, C.S. Goldberg, S. Robinson, S. F. Spear, R. Dezzani, E. Delmelle, L. Vierling, and L.P. Waits. 2006. Putting the ‘landscape’ in landscape genetics. Heredity. 1-15.

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