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
To understand the effects of natural and
anthropogenically altered landscapes on gene ﬂow among
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
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
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,
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
Department of Energy Idaho Operations Ofﬁce
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:
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.