Conservation Genetics

, Volume 8, Issue 5, pp 1043–1050 | Cite as

Genetic diversity and structure in the rare Colorado endemic plant Physaria bellii Mulligan (Brassicaceae)

  • Linda KotheraEmail author
  • Christopher M. Richards
  • Shanna E. Carney
Original Paper


Physaria bellii (Brassicaceae) is a rare, outcrossing perennial endemic to shale and sandstone outcrops along the Front Range of northern Colorado, USA. This species is locally abundant, but ranked G2/S2—imperiled because of threats to its habitat and a small number of populations—according to NatureServe’s standardized ranking system. Leaf tissue from ten populations was analyzed with ISSR (Inter-Simple Sequence Repeat) markers to discern the amount of genetic diversity and degree of population subdivision in P. bellii. Genetic diversity was moderate (0.22) and a moderately high degree of population structure was found (F ST calculated using two algorithms ranged from 0.17 to 0.24). An AMOVA partitioned most of the variation among individuals within populations (76%), and the remainder among populations (24%). Results from a Principal Coordinates analysis were consistent with the geographic distribution of populations. A Mantel test of the correlation between genetic and geographic distances was highly significant (P < 0.001). The pattern of variation thus appears to be distributed along a gradient, and efforts to conserve this species should involve preserving enough populations so that gene flow between populations is not interrupted.


ISSR Physaria Naturally rare plant Dominant markers 



This work was supported by grants to LK from the City of Boulder Open Space and Mountain Parks (OSMP) Small Grants Program and the Colorado Native Plant Society’s Steinkamp Fund, and start up funds to SEC. Lynn Riedel from OSMP, the staff of the Colorado Natural Heritage Program, Meegan Fleniken from the Larimer County Parks and Open Lands department, Claire DeLeo of the Boulder County Open Space Department and the City of Fort Collins Natural Areas department are gratefully acknowledged for providing location information and/or permits to work with Physaria bellii.


  1. Bassam BJ, Caetano-Anollés G (1993) Silver staining of DNA in polyacrylamide gels. Appl Biochem Biotechnol 42:181–188Google Scholar
  2. Carpenter A (1997) Ecological studies of the rare plant Physaria bellii (Bell’s Twinpod) on City of Boulder Open Space Lands. Unpublished report, Boulder (Colorado, USA) Open Space and Mountain Parks DepartmentGoogle Scholar
  3. Charlesworth D (2003) Effects of inbreeding on the genetic diversity of populations. Philos Trans R Soc Lond B Biol Sci 358:1051–1070PubMedCrossRefGoogle Scholar
  4. Colorado Natural Heritage Program. Natural Heritage Methodology. Scholar
  5. de Lange PJ, Norton DA (2004) The ecology and conservation of Kunzea sinclairii (Myrtaceae), a naturally rare plant of rhyolitic rock outcrops. Biol Conserv 117:49–59CrossRefGoogle Scholar
  6. Donahue RL, Miller RW, Shickluna JC (1983) Soils: an introduction to soils and plant growth. 5th edn. Prentice-Hall, Upper Saddle River, New JerseyGoogle Scholar
  7. Doyle GA, Neid SL, Rondeau RJ (2004) Survey of Critical Biological Resources, Larimer County, Colorado. Unpublished report, Colorado Natural Heritage ProgramGoogle Scholar
  8. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Cited 10 Oct 2005Google Scholar
  9. Fleishman E, Launer AE, Switky KR et al (2001) Rules and exceptions in conservation genetics: genetic assessment of the endangered plant Cordylanthus palmatus and its implications for management planning. Biol Conserv 98:45–53CrossRefGoogle Scholar
  10. Frankham R, Ballou JD, Briscoe DA (2002) Population fragmentation. In: An Introduction to Conservation Genetics, pp 309–335. Cambridge University Press, CambridgeGoogle Scholar
  11. Gaston KJ (1994) Abundances and range sizes: measuring rarity. In:Gaston KJ, (ed.) Rarity. Population and Community Biology Series 13. Chapman Hall, New York, pp 22–56Google Scholar
  12. Gupta M, Chyi YS, Romeroseverson J et al (1994) Amplification of DNA markers from evolutionarily diverse genomes using single primers of simple-sequence repeats. Theor Appl Genet 89:998–1006CrossRefGoogle Scholar
  13. Hardy OJ (2003) Estimation of pairwise relatedness between individuals and characterization of isolation-by-distance processes using dominant genetic markers. Mol Ecol 12:1577–1588PubMedCrossRefGoogle Scholar
  14. Hartl DL, Clark AG (1997) Organization of genetic variation. In: Principles of Population Genetics, pp 74–107. Sinauer Associates, Sunderland, MassachusettsGoogle Scholar
  15. Hensen I, Oberprieler C (2005) Effects of population size on genetic diversity and seed production in the rare Dictamnus albus (Rutaceae) in central Germany. Conserv Genet 6:63–73CrossRefGoogle Scholar
  16. Holsinger KE, Lewis PO, Dey DK (2002) A Bayesian approach to inferring population structure from dominant markers. Mol Ecol 11:1157–1164PubMedCrossRefGoogle Scholar
  17. Holsinger KE, Lewis PO (2003) HICKORY: a package for analysis of population genetic data V1.0. Cited 15 Oct 2005Google Scholar
  18. Huenneke LF (1991) Ecological implications of genetic variation in plant populations. In: Falk DA, Holsinger KE (eds) Genetics and conservation of rare plants, Oxford University Press, New York, pp 31–44Google Scholar
  19. Jacquemyn H, Honnay O, Galbusera P et al (2004) Genetic structure of the forest herb Primula elatior in a changing landscape. Mol Ecol 13:211–219PubMedCrossRefGoogle Scholar
  20. Juan A, Crespo MB, Cowan RS et al (2004) Patterns of variability and gene flow in Medicago citrina, an endangered endemic of islands in the western Mediterranean, as revealed by amplified fragment length polymorphism (AFLP). Mol Ecol 13:2679–2690PubMedCrossRefGoogle Scholar
  21. Kunin WE, Gaston KJ (1997) Concluding comments. In: Kunin WE, Gaston KJ (eds) The biology of rarity. Chapman & Hall, London, pp 262–272Google Scholar
  22. Llorens TM, Ayre DJ, Whelan RJ (2004) Evidence for ancient genetic subdivision among recently fragmented populations of the endangered shrub Grevillea caleyi (Proteaceae). Heredity 92:519–526PubMedCrossRefGoogle Scholar
  23. Lynch M, Milligan BG (1994) Analysis of population genetic structure with RAPD markers. Mol Ecol 3:91–99PubMedGoogle Scholar
  24. Mace GM, Kershaw M (1997) Extinction risk and rarity on an ecological timescale. In: Kunin WE, Gaston KJ (eds) The biology of rarity: the causes and consequences of rare-common differences. Chapman & Hall, London, pp 131–149Google Scholar
  25. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220PubMedGoogle Scholar
  26. Mateu-Andres I, Segarra-Moragues JG (2000) Population subdivision and genetic diversity in two narrow endemics of Antirrhinum L. Mol Ecol 9:2081–2087PubMedCrossRefGoogle Scholar
  27. Mattner J, Zawko G, Rossetto M et al (2002) Conservation genetics and implications for restoration after mining of the Western Australian serpentine endemic Hemiginea exilis. Biol Conserv 107:37–45CrossRefGoogle Scholar
  28. Miller MP (2000) Tools For Population Genetic Analyses. A Windows program for the analysis of allozyme and molecular population genetic data. http:// Cited 8 Oct 2005Google Scholar
  29. Miyashita NT, Kawabe A, Innan H (1999) DNA variation in the wild plant Arabidopsis thaliana revealed by amplified fragment length polymorphism analysis. Genetics 152:1723–1731PubMedGoogle Scholar
  30. Morse LE (1986) The network of state natural heritage inventory programs – information management for environmental review and conservation planning. Am J Bot 73:776Google Scholar
  31. Mulligan GA (1966) Two new species of Physaria (Cruciferae) in Colorado. Can J Bot 44:1661–1665CrossRefGoogle Scholar
  32. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590Google Scholar
  33. Owuor ED, Beharav A, Fahima T et al (2003) Microscale ecological stress causes RAPD molecular selection in wild barley, Neve Yaar microsite, Israel. Genet Resour Crop Evol 50:213–223CrossRefGoogle Scholar
  34. Peakall R, Smouse PE (2001) GenAlEx V5: Genetic Analysis in Excel. Cited 12 Oct 2005Google Scholar
  35. Pepper AE, Norwood LE (2001) Evolution of Caulanthus amplexicaulis var. barbarae (Brassicaceae), a rare serpentine endemic plant: a molecular phylogenetic perspective. Am J Bot 88:1479–1489CrossRefGoogle Scholar
  36. Rabinowitz D (1981) Seven forms of rarity. In: Synge H (ed) The biological aspects of rare plant conservation. John Wiley & Sons, New York, pp 205–217Google Scholar
  37. Rosenzweig ML, Lomolino MV (1997) Rarity and community ecology: who gets the tiny bits of the broken stick. In: Kunin WE, Gaston KJ (eds) The biology of rarity: the causes and consequences of rare-common differences. Chapman & Hall, London, pp 63–90Google Scholar
  38. Sales E, Nebauer SG, Mus M et al (2001) Population genetic study in the Balearic endemic plant species Digitalis minor (Scrophulariaceae) using RAPD markers. Am J Bot 88:1750–1759CrossRefGoogle Scholar
  39. SAS (2003) SAS/STAT software: changes and enhancements through release 9.1. SAS Institute, Cary, North Carolina, USAGoogle Scholar
  40. Segarra-Moragues JG, Palop-Esteban M, Gonzalez-Candelas F et al (2005) On the verge of extinction: genetics of the critically endangered Iberian plant species, Borderea chouardii (Dioscoreaceae) and implications for conservation management. Mol Ecol 14:969–982PubMedCrossRefGoogle Scholar
  41. Spackman S, Jennings B, Coles J et al (1997) Colorado Rare Plant Field Guide. Prepared for the Bureau of Land Management, USDA Forest Service, and U.S. Fish and Wildlife Service by the Colorado Natural Heritage ProgramGoogle Scholar
  42. Spiegelhalter DJ, Best NG, Carlin BP et al (2002) Bayesian measures of model complexity and fit. J R Statist Soc B 64:583–640Google Scholar
  43. Supples C (2001) Differences in canopy cover, density, and reproductive activity, with respect to aspect, of Physaria bellii populations within Fort Collins Natural Areas. Unpublished BS Honors Thesis, Colorado State University Google Scholar
  44. Tero N, Aspi J, Siikamaki P et al (2003). Genetic structure and gene flow in a metapopulation of an endangered plant species, Silene tatarica. Mol Ecol 12:2073–2085PubMedCrossRefGoogle Scholar
  45. Vos P, Hogers R, Bleeker M et al (1995) AFLP – A new technique for DNA-fingerprinting. Nucleic Acids Res 23:4407–4414PubMedCrossRefGoogle Scholar
  46. Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213–7218PubMedCrossRefGoogle Scholar
  47. Williams JGK, Kubelik AR, Livak KJ et al (1990) DNA polymorphism amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535PubMedCrossRefGoogle Scholar
  48. Wolfe AD, Xiang Q, Kephart SR (1998) Assessing hybridization in natural populations of Penstemon (Scrophulariaceae) using hypervariable intersimple sequence repeat (ISSR) bands. Mol Ecol 7:1107–1125PubMedCrossRefGoogle Scholar
  49. Xiao LQ, Ge XJ, Gong X et al (2004) ISSR variation in the endemic and endangered plant Cycas guizhouensis (Cycadaceae). Ann Bot 94:133–138PubMedCrossRefGoogle Scholar
  50. Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR) – anchored polymerase chain-reaction amplification. Genomics 20:176–183PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2007

Authors and Affiliations

  • Linda Kothera
    • 1
    • 3
    Email author
  • Christopher M. Richards
    • 2
  • Shanna E. Carney
    • 1
    • 2
  1. 1.Department of Biology Colorado State UniversityFort CollinsUSA
  2. 2.USDA-ARS National Center for Genetic Resources PreservationFort CollinsUSA
  3. 3.Division of Vector-Borne Infectious DiseasesCenters for Disease Control and PreventionFort CollinsUSA

Personalised recommendations