Skip to main content

Advertisement

SpringerLink
Log in

Fine scale population genetic structure of pumas in the Intermountain West

  • Research Article
  • Published:
Conservation Genetics Aims and scope Submit manuscript

Abstract

In this study, I examined the population genetic structure of subpopulations of pumas (Puma concolor) in Idaho and surrounding states. Patterns of genetic diversity, population structure, levels of inbreeding, and the relationship between genetic differentiation and dispersal distance within and between 15 subpopulations of pumas were compared. Spatial analyses revealed that the Snake River plain was an important barrier to movement between northern and southern regions of Idaho. In addition, subpopulations south of the Snake River plain exhibited lower levels of genetic diversity, higher levels of inbreeding, and a stronger pattern of isolation by distance relative to subpopulations north of the Snake River plain. Lower levels of diversity and restricted gene flow are likely the result of historically lower population sizes in conjunction with more recent changes in habitat use and available dispersal corridors for movement. The subdivision of puma populations north and south of the Snake River plain, along with the patterns of genetic diversity within regions, indicate that landscape features are affecting the population genetic structure of pumas in Idaho. These results indicate that information about the effects of landscape features on the distribution of genetic diversity should be considered when designing plans for the management and conservation of pumas.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Allendorf FW, Seeb LW (2000) Concordance of genetic divergence among sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers. Evolution 54:640–651

    PubMed  CAS  Google Scholar 

  • Altendorf KB, Laundré JW, Lopez Gonzalez CA, Brown JS (2001) Assessing effects of predation risk on foraging behavior of mule deer. J Mammal 82:430–439

    Article  Google Scholar 

  • Anderson MJ (2003) DISTLM forward. a FORTRAN computer program to calculate a distance-based multivariate analysis for a linear model using forward selection. Department of Statistics, University of Aukland, New Zealand

    Google Scholar 

  • Anderson MJ, Gribble NA (1998) Partitioning the variation among spatial, temporal and environmental components in a multivariate data set. Aust J Ecol 23:158–167

    Article  Google Scholar 

  • Anderson CR, Lindzey FG, McDonald DB (2004) Genetic structure of cougar populations across the Wyoming Basin: metapopulations or megapopulation. J Mammal 85:1207–1214

    Article  Google Scholar 

  • Avise JC, Hamrick JL (1996) Conservation genetics: case histories from nature. Chapman and Hall, New York

    Google Scholar 

  • Beier P (1993) Determining minimum habitat areas and habitat corridors for cougars. Conserv Biol 7:94–108

    Article  Google Scholar 

  • Beier P (1995) Dispersal of cougars in fragmented habitat. J Wild Manage 59:228–237

    Article  Google Scholar 

  • Bowcock AM, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd JR, Cavalli-Sforza LL (1994) High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368:455–457

    Article  PubMed  CAS  Google Scholar 

  • Busch JD, Waser PM, DeWoody JA (2007) Recent bottlenecks are not accompanied by a genetic signature in banner-tailed kangaroo rats (Dipodomys spectabilis). Mol Ecol 16:2450–2462

    Article  PubMed  CAS  Google Scholar 

  • Chen C, Durand E, Forbes F, Francois O (2007) Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study. Mol Ecol 7:747–756

    Article  Google Scholar 

  • Cornuet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001–2014

    PubMed  CAS  Google Scholar 

  • Culver M (1999) Molecular genetic variation, population structure, and natural history of free-ranging pumas (Puma concolor). Dissertation, University of Maryland

  • Culver M, Johnson I, Pecon-Slattery J, O’Brien SJ (2000) Genomic ancestry of the American puma (Puma concolor). J Hered 91:186–197

    Article  PubMed  CAS  Google Scholar 

  • Dieringer D, Schlötterer C (2003) Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Mol Ecol Notes 3:167–169

    Article  CAS  Google Scholar 

  • Driscoll CA, Menotti-Raymond M, Nelson G, Goldstein D, O’Brien SJ (2002) Genomic microsatellites as evolutionary chronometers: a test in wild cats. Genome Res 12:414–423

    Article  PubMed  CAS  Google Scholar 

  • Earl DA (2009) Structure Harvester v0.3. http://users.soe.ucsc.edu/~dearl/software/struct_harvest/

  • Ernest HB, Boyce WM, Bleich VC, May B, Stiver SJ, Torres SG (2003) Genetic structure of mountain lion (Puma concolor) populations in California. Conserv Genet 4:353–366

    Article  CAS  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  PubMed  CAS  Google Scholar 

  • Felsenstein J (1993) PHYLIP—phylogeny inference package (version 3.5). University of Washington, Seattle

    Google Scholar 

  • Francois O, Ancelet S, Guillot G (2006) Bayesian clustering using a hidden Markov random fields in spatial population genetics. Genetics 174:805–816

    Article  PubMed  CAS  Google Scholar 

  • Frankham R (2006) Genetics and landscape connectivity. In: Crooks KR, Sanjayan W (eds) Connectivity conservation. Cambridge University Press, Cambridge, pp 72–96

    Chapter  Google Scholar 

  • Frankham R, Ballou JD, Briscoe DA (2002) Introduction to conservation genetics. Cambridge University Press, Cambridge

    Google Scholar 

  • Garza JC, Williamson EG (2001) Detection and reduction in population size using data from microsatellite loci. Mol Ecol 10:305–318

    Article  PubMed  CAS  Google Scholar 

  • Goldstein DB, Pollock DD (1997) Launching microsatellites: a review of mutation processes and methods of phylogenetic inference. J Hered 88:335–342

    PubMed  CAS  Google Scholar 

  • Gottelli D, Sillero-Zubiri C, Applebaum GD, Roy MS, Girman DJ, Garcia-Moreno J, Ostrander EA, Wayne RK (1994) Molecular genetics of the most endangered canid: the Ethiopian wolf Canis simensis. Mol Ecol 3:301–312

    Article  PubMed  CAS  Google Scholar 

  • Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). http://www.unil.ch/izea/softwares/fstat.html

  • Gutiérrez-Espeleta GA, Kalinowski ST, Boyce WM, Hedrick PW (2000) Genetic variation and population structure in desert bighorn sheep: implication for conservation. Conserv Genet 1:3–15

    Article  Google Scholar 

  • Hedrick PW (1995) Gene flow and genetic restoration: the Florida panther as a case study. Conserv Biol 9:996–1007

    Article  Google Scholar 

  • Hundertmark KJ, Van Daele LJ (2009) Founder effect and bottleneck signatures in an introduced, insular population of elk. Conserv Genet 11:139–147

    Article  Google Scholar 

  • Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806

    Article  PubMed  CAS  Google Scholar 

  • Kalinowski ST (2004) Counting alleles with rarefaction: private alleles and hierarchical sampling designs. Conserv Genet 5:539–543

    Article  CAS  Google Scholar 

  • Kalinowski ST (2005) HP-RARE-1.0: a computer program for performing rarefaction on measures of allelic richness. Mol Ecol Notes 5:187–189

    Article  CAS  Google Scholar 

  • Leberg PL (2002) Estimating allelic richness: effects of sample size and bottlenecks. Mol Ecol 11:2445–2449

    Article  PubMed  CAS  Google Scholar 

  • Legendre P, Anderson MJ (1999) Distance-based redundancy analysis: testing multispecies responses in multifactorial ecological experiments. Ecol Monogr 69:1–24

    Article  Google Scholar 

  • Logan KA, Sweanor LL (2000) Puma. In: Demarais S, Krausman PR (eds) Ecology and management of large mammals in North America. Prentice-Hall, New Jersey, pp 347–377

    Google Scholar 

  • Logan KA, Sweanor LL (2001) Desert Puma: evolutionary ecology and conservation of an enduring carnivore. Island Press, Washington DC

    Google Scholar 

  • Luikart G, Cornuet JM (1998) Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conserv Biol 12:228–237

    Article  Google Scholar 

  • Maehr DS, Darnell-Land E, Roof JC (1991) Social ecology of Florida panthers. Natl Geogr Res Explor 7:414–431

    Google Scholar 

  • Mantel N (1967) The detection of disease clustering and a generalised regression approach. Cancer Res 27:209–220

    PubMed  CAS  Google Scholar 

  • McCauley DE (1995) Effects of population dynamics on genetics in mosaic landscapes. In: Hansson L, Fahrig L, Merriam G (eds) Mosaic landscapes and ecological processes. Chapman and Hall, New York, pp 179–198

    Google Scholar 

  • McRae BH, Beier P, Dewald LE, Huynh Y, Keim P (2005) Habitat barriers limit gene flow and illuminate historical events in a wide-ranging carnivore, the American puma. Mol Ecol 14:1965–1977

    Article  PubMed  CAS  Google Scholar 

  • Menotti-Raymond M, O’Brien SJ (1995) Evolutionary conservation of ten microsatellite loci in four species of felidae. J Hered 86:319–322

    PubMed  CAS  Google Scholar 

  • Menotti-Raymond M, David V, Stephens JC, Lyons LA, O’Brien SJ (1997) Genetic individualization of domestic cats using feline STR loci for forensic applications. J Forensic Sci 42:1037–1050

    Google Scholar 

  • Menotti-Raymond M, David VA, Lyons LA, Schaffer AA, Tomlin JF, Hutton MK, O’Brien SJ (1999) A genetic linkage map of microsatellites in the domestic cat (Felis catus). Genomics 57:9–23

    Article  PubMed  CAS  Google Scholar 

  • Nadeau S (ed) (2004) Mountain lion report. Project W-170-R-28. Idaho Department of Fish and Game, Idaho

  • Nowell K, Jackson P (1996) Wild Cats: status, survey and conservation action plan. IUCN/SSC Cat Specialist Group, Gland

    Google Scholar 

  • Paetkau D, Waits LP, Clarkson PL, Craighead L, Strobeck C (1997) An empirical evaluation of genetic distance statistics using microsatellite data from bear (Ursidae) populations. Genetics 147:1943–1957

    PubMed  CAS  Google Scholar 

  • Paetkau D, Shields GF, Strobeck C (1998) Gene flow between insular, coastal and interior populations of brown bears in Alaska. Mol Ecol 7:1282–1283

    Article  Google Scholar 

  • Paetkau D, Amstrup C, Born EW, Calvert W, Derocher AE, Garner GW, Messier F, Stirling I, Taylor MK, Wiig Ø, Strobeck C (1999) Genetic structure of the world’s polar bear populations. Mol Ecol 8:1571–1584

    Article  PubMed  CAS  Google Scholar 

  • Peacock MM, Smith AT (1997) The effect of habitat fragmentation of dispersal patterns, mating behaviour, and genetic variation in a pika (Ochotona princeps) metapopulation. Oecologica 112:524–533

    Article  Google Scholar 

  • Pierce BM, Bleich VC, Wehausen JD, Bowyer RT (1999) Migratory patterns of mountain lions: implications for social regulation and conservation. J Mammal 80:986–992

    Article  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 105:945–959

    Google Scholar 

  • Quigley TM, Gravenmier RA, Graham RT (tech. eds) (2001) The interior Columbia Basin ecosystem management project: project data. U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station, Portland

  • Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249

    Google Scholar 

  • Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223–225

    Article  Google Scholar 

  • Riley SJ, Malecki RA (2001) A landscape analysis of cougar distribution and abundance in Montana, USA. Environ Manag 28:317–323

    Article  CAS  Google Scholar 

  • Roelke ME, Martenson JS, O’Brien SJ (1993) The consequences of demographic reduction and genetic depletion in the endangered Florida panther. Curr Biol 3:340–350

    Article  PubMed  CAS  Google Scholar 

  • Ross PI, Jalkotzy MG (1992) Characteristics of a hunter population of cougars in southwester Alberta. J Wild Manag 6:417–426

    Article  Google Scholar 

  • Roy MS, Geffen E, Smith D, Ostrander EA (1994) Patterns of differentiation and hybridization in North American wolflike canids, revealed by analysis of microsatellite loci. Mol Biol Evol 11:553–570

    PubMed  CAS  Google Scholar 

  • Schneider S, Kueffer JM, Roessli D, Excoffier L (2000) Arlequin version 2.000: a software for population genetic data analysis. Genetics and Biometry Laboratory, University of Geneva, Geneva

    Google Scholar 

  • Schonewald-Cox C, Azari R, Blume S (1991) Scale, variable density, and conservation planning for mammalian carnivores. Conserv Biol 5:491–495

    Article  Google Scholar 

  • Seidensticker JC, Hornocker MG, Wiles WV, Messick JP (1973) Mountain lion social organization in the Idaho Primitive Area. Wildl Monogr 35:1–60

    Google Scholar 

  • Sinclair EA, Swenson EL, Wolfe ML, Choate D, Wolf M, Crandall KA (2001) Gene flow estimates in Utah’s cougars imply management beyond Utah. Anim Conserv 4:257–264

    Article  Google Scholar 

  • Slatkin M (1993) Isolation by distance in equilibrium and non-equilibrium populations. Evolution 46:264–279

    Article  Google Scholar 

  • Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457–462

    PubMed  CAS  Google Scholar 

  • Stow AJ, Sunnucks P, Briscoe DA, Gardner MG (2001) The impact of habitat fragmentation on dispersal of Cunningham’s skink (Egernia cunninghami): evidence from allelic and genotypic analyses of microsatellites. Mol Ecol 10:867–878

    Article  PubMed  CAS  Google Scholar 

  • Sweanor LL, Logan KA, Hornocker MG (2000) Cougar dispersal patterns, metapopulation dynamics, and conservation. Conserv Biol 14:798–808

    Article  Google Scholar 

  • Thompson DJ, Jenks JA (2005) Long-distance dispersal by a subadult male cougar from the Black Hills, South Dakota. J Wild Manag 69:818–820

    Article  Google Scholar 

  • Van Dyke FG, Brocke RH, Shaw HG, Ackerman BB, Hemker TP, Lindzey FG (1986) Reactions of mountain lions to logging and human activity. J Wild Manage 50:95–102

    Article  Google Scholar 

  • Walker CW, Harveson LA, Pittman MT, Tewes ME, Honeycutt RL (2000) Microsatellite variation in two populations of mountain lions (Puma concolor) in Texas. Southwest Nat 45:196–203

    Article  Google Scholar 

  • Wayne RK, Lehman N, Girman D, Gogan PJP, Gilbert DA, Hansen K, Peterson RO, Seal US, Eisenhawer A, Mech LD, Krumenaker RJ (1991) Conservation genetics of the Isle Royale gray wolf. Conserv Biol 1:41–51

    Article  Google Scholar 

  • Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370

    Article  Google Scholar 

  • Wilson GA, Rannala B (2003) Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163:1177–1191

    PubMed  Google Scholar 

  • Wright S (1951) The genetical structure of populations. Ann Eugen 15:323–354

    Article  Google Scholar 

  • Young AC, Clarke GM (2000) Genetics, demography and viability of fragmented populations. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Young SP, Goldman EA (1946) The puma, mysterious American cat. The American Wildlife Institute, Washington

    Google Scholar 

Download references

Acknowledgments

This work was supported by the National Science Foundation-Idaho EPSCoR Program (EPS-9720634) and National Science Foundation grants (IBN-0091735) to Margaret B. Ptacek and by grants from the Department of Biological Sciences and the Graduate Student Research and Scholarship Committee at Idaho State University to JLL. I would like to thank Margaret Ptacek for providing funding and advice on data analysis and manuscript preparation. The Idaho Department of Fish and Game (IDFG), Nevada Division of Wildlife, Utah Division of Wildlife Resources, W. Glenn, and J. Laundré provided the samples included in this study. I also thank C. Anderson, J. Crenshaw, T. Ferguson, J. Hayden, M. Scott, and R. Smith from IDFG and J. Laundré for information on dispersal corridors and habitat use by pumas throughout the state. I am grateful to E. Keeley for advice on statistical analyses, K. Barr for assistance with the cluster analysis, and to M. Culver, V. David, and E. O’Leary-Jepsen for providing advice on microsatellite techniques. S. Blum, D. Oldham, G. Pearce, M. Whitmore, J. Wiklund, and H. Rosa Worley assisted with the data collection. Earlier versions of this manuscript were greatly improved by the comments of C. Baer, E. Keeley, B. Sacks, M. Small, and R. Wayne.

Author information

Authors and Affiliations

  1. Department of Biological Sciences, Stop 8007, Idaho State University, Pocatello, ID, 83209, USA

    Janet L. Loxterman

Authors
  1. Janet L. Loxterman
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Janet L. Loxterman.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Loxterman, J.L. Fine scale population genetic structure of pumas in the Intermountain West. Conserv Genet 12, 1049–1059 (2011). https://doi.org/10.1007/s10592-011-0208-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10592-011-0208-y

Keywords

Search

Navigation