Restoration genetics: Applying population genetics to plant restoration projects at local and regional levels

A shortcourse offered under the auspices of the
Society for Conservation Biology at its
20th Annual Meeting, 24–28 June 2006
San Jose, California

Instructors: Deborah Rogers (1), Kevin Rice (2),
and P.E. McGuire (1)

(1) Genetic Resources Conservation Program, Division of Agriculture and Natural Resources, University of California
(2) Dept. of Plant Sciences, University of California, Davis

Resources for Restoration Genetics

Books | Research articles and chapters | Policies & guidelines | Links


Avise, J.C. 2004. Molecular markers, natural history, and evolution, 2nd edition. Sinauer Associates, Inc. Sunderland MA USA.

Cropper, S.C. 1993. Management of endangered plants. CSIRO, Australia.

Donovan, T.M. and C.W. Welden. 2002. Spreadsheet exercises in conservation biology and landscape ecology. Sinauer Associates, Inc. Sunderland MA USA.

Falk, D.A., C.I. Millar, and M. Olwell (eds.) 1996. Restoring diversity: Strategies for reintroduction of endangered plants. Island Press. Covelo CA USA.

Frankham, R., J.D. Ballou, and D.A. Briscoe. 2004. A primer of conservation genetics. Cambridge University Press. Cambridge UK.
Good review of population genetics and molecular genetic diversity measurement tools in a context of conservation applications.

Frankham, R., J.D. Ballou, and D.A. Briscoe. 2002. Introduction to conservation genetics. Cambridge University Press. Cambridge UK.

Guarino, L., V. Ramanatha Rao, and R. Reid (eds.) 1995. Collecting plant genetic diversity, technical guidelines. CAB International, Oxon UK.

Guerrant, E.O. Jr., K. Havens, and M. Maunder (eds.) 2004. Ex situ plant conservation: Supporting species survival in the wild. Island Press. Covelo CA USA. Presentation of the principles of ex situ plant conservation as an adjunct to in situ conservation. Has updated genetic sampling guidelines.

Hartl, D.L. 2000. A primer of population genetics, 3rd edition. Sinauer Associates, Inc. Sunderland MA USA.

Hedrick, P.W. 2005. Genetics of populations, 3rd edition. Jones & Bartlett. Sudbury MA USA.

Lowe, A., S. Harris, and P. Ashton. 2004. Ecological genetics: Design, analysis, and application. Blackwell Publishing. Oxford UK.
Good review of population genetics and molecular genetic diversity measurement tools in a context of ecological applications.

McCullough, D.R. (ed.) 1996. Metapopulations and wildlife conservation. Island Press. Covelo CA USA.

Morris, W.F. and D.F. Doak. 2002. Quantitative conservation biology: Theory and practice of population viability analysis. Sinauer Associates, Inc. Sunderland MA USA.

Wilson, E.O. and W.H. Bossert. 1971. A primer of population biology. Sinauer Associates, Inc. Sunderland MA USA.Classic presentation with strong focus on quantitative population genetics and models.

Young, A., D. Boshier, and T. Boyle (eds.). 2000. Forest conservation genetics, principles and practice. CSIRO Publishing, Collingwood VIC Australia.

Research articles and chapters

Top | Policies & guidelines | Links

Bangert, R.K., R.J. Turek, G.D. Martinsen, G.M. Wimp, J.K. Bailey, and T.G. Whitham. 2005. Benefits of conservation of plant genetic diversity to arthropod diversity. Conservation Biology 19:379-390.

Bangert, R.K., R.J. Turek, B. Rehill, G.M. Wimp, J.A. Schweitzer, G.J. Allan, J.K. Bailey, G.D. Martinsen, P. Keim, R.L. Lindroth, and T.G. Whitham. 2006. A genetic similarity rule determines arthropod community structure. Molecular Ecology 15:1379-1391.

Booth, H. 2006. Helping endangered species to keep their footing on the slippery slope of the genetic bottleneck. Transect 24(1):1-10. Available online.

Booy, G., R.J.J. Hendricks, M.J.M. Smulders, J.M. VanGroenendael, and B. Vosman. 2000. Genetic diversity and the survival of populations. Plant Biology 2(4):379-395.

Buis, S. 2000. Writing woody plant specifications for restoration and mitigation practices. Native Plants Journal 1:116-119.

Buza, L., A. Young, and P. Thrall. 2000. Genetic erosion, inbreeding, and reduced fitness in fragmented populations of the endangered tetraploid pea Swainsona recta. Biological Conservation 93:177-186.

Campbell, R.K. 1992. Genotype x environment interaction: A case study for Douglas-fir in western Oregon. Research Paper PNW-RP-455. USDA, Forest Service, Pacific Northwest Research Station.

Cruden, RW. 1977. Pollen-ovule ratios: A conservative indicator of breeding systems in plants. Evolution 31:32-46.

DeWald, L.E. and M.F. Mahalovich. 1997. The role of forest genetics in managing ecosystems. Journal of Forestry 95(4):12-16.

Dow, B.D. and M.V. Ashley. 1996. Microsatellite analysis of seed dispersal and parentage of saplings in bur oak, Quercus macrocarpa. Molecular Ecology 5:615-627.

Fryxell, P.A. 1957. Mode of reproduction of higher plants. The Botanical Review 23:135-233.
A catalog of taxa (about 1,500 species) for which something is known about breeding system, obviously dated, but a good first step. There haven’t been any updates that we know of.

Galloway, L.F. 2001. Parental environmental effects on life history in the herbaceous plant Campanula americana. Ecology 82:2781-2789.

Galloway, L.F. 2001. The effect of maternal and paternal environments on seed characters in the herbaceous plant Campanula americana (Campanulaceae). American Journal of Botany 88:832-840.

Gouesnard, B., T.M. Bataillon, G. Decoux, C. Rozale, D.J. Schoen, and J.L. David. 2001. MSTRAT: An algorithm for building germ plasm core collections by maximizing allelic or phenotypic richness. Journal of Heredity 92:93-94.

Guerrant, E.O. Jr. 1992. Genetic and demographic considerations in the sampling and reintroduction of rare plants. p 321-344 in P.L. Fiedler and S.K. Jain (eds.). Conservation biology: The theory and practice of nature conservation, preservation, and management. Routledge, Chapman and Hall, Inc. New York NY USA.

Hamrick, J.L., and M.J.W. Godt. 1990. Allozyme diversity in plant species. p 43-63 in A.D.H. Brown, M.T. Clegg, A.L. Kahler, and B.S. Weir (eds.) Plant population genetics, breeding and genetic resources. Sinauer Associates, Inc. Sunderland MA USA.

Hamrick, J.L., and M.J.W. Godt. 1996. Effects of life history traits on genetic diversity in plant species. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 351:1291-1298.

Hancock, T.E. and P.E. Hosier. 2003. Ecology of the threatened species Amaranthus pumilus Rafinesque. Castanea 68:236-244.

Harrison, S. and A. Hastings. 1996. Genetic and evolutionary consequences of metapopulation structure. Trends in Ecology & Evolution 11:180-183.

Hedrick, P.W. 2004. Recent developments in conservation genetics. Forest Management and Ecology 197:3-19.

Hedrick, P. 2005. ‘Genetic restoration:’ A more comprehensive perspective than ‘genetic rescue’. Trends in Ecology & Evolution 20:109.

Hufford, K.M. and S.J. Mazer. 2003. Plant ecotypes: Genetic differentiation in the age of ecological restoration. Trends in Ecology & Evolution 18:147-155.

Hunter, K.L., J. Murfree, and H. Davis. 2002. Genetic variability of the threatened seabeach amaranth (Amaranthus pumilus) on Assateague and Fenwick Islands. Unpublished report to the National Park Service.

Husband, B.C., D.W. Schemske, T.L. Burton, and C. Goodwillie. 2002. Pollen competition as a unilateral reproductive barrier between sympatric diploid and tetraploid Chamerion angustifolium. Proceedings of the Royal Society of London. Series B 269:2565-2571.

Kawecki, T.J. and D. Ebert. 2004. Conceptual issues in local adaptation. Ecology Letters 7:1225-1241.

Keim, P., K.N. Paige, T.G. Whitham, and K.G. Lark. 1989. Genetic analysis of an interspecific hybrid swarm of Populus occurrence of unidirectional introgression. Genetics 123:557-566.

Kimura, M. and G.H. Weiss. 1964. The stepping stone model of population structure and the decrease of genetic correlation with distance. Genetics 49:561-576.

Kingsolver, J.G., H.E. Hoekstra, J.M. Hoekstra, D. Berrigan, S.N. Vignieri, C.E. Hill, A. Hoang, P. Gibert, and P. Beerli. 2001. The strength of phenotypic selection in natural populations. American Naturalist 157:245-261.

Knapp, E.E., M.A. Goedde, and K.J. Rice. 2001. Pollen-limited reproduction in blue oak: Implications for wind pollination in fragmented populations. Oecologia 128(1):48-55.

Knapp, E.E. and K.J. Rice. 1998. Comparison of isozymes and quantitative traits for evaluating patterns of genetic variation in purple needlegrass (Nassella pulchra). Conservation Biology 12:1031-1041.

Lacy, R.C. 1987. Loss of genetic diversity from managed populations: interacting effects of drift, mutation, immigration, selection, and population subdivision. Conservation Biology 1:143-158.

Langlet, O. 1971. Two hundred years of genecology. Taxon 20:653-722.

Lawrence, M.J., D.F. Marshall, and P. Davies. 1995a. Genetics of genetic conservation. I. Sample size when collecting germplasm. Euphytica 84:89-99.

Lawrence, M.J., D.F. Marshall, and P. Davies. 1995b. Genetics of genetic conservation. II. Sample size when collecting seed of cross-pollinating species and the information that can be obtained from the evaluation of material held in gene banks. Euphytica 84:101-107.

Linhart, Y.B. 1995. Restoration, revegetation, and the importance of genetic and evolutionary perspectives. in B.A. Rotundy, E.D. McArthur, J.S. Haley, and D.K. Mann, comps. Proceedings: Wildland shrub and arid land restoration symposium October 19-21, 1993. Las Vegas, NV. Gen. Technical Report INT-GTR-315, Ogden ,UT, U.S. Department of Agriculture, Forest Service, Intermountain Research Station.

Linhart, Y.B. and M.C. Grant. 1996. Evolutionary significance of local genetic differentiation in plants. Annual Reviews of Ecology and Systematics 27:237-278.

Lockwood, D.R., C.M. Richards, and G.M. Volk. 2006. A review of wild plant sampling strategies: The roles of ecology and evolution. Horticultural Science In press.

Lockwood, D.R., C.M. Richards, and G.M. Volk. 2006. Probabilistic models for collecting genetic diversity: comparisons, caveats and limitations. Crop Science In press.

Marshall, D.R. and A.H.D. Brown. 1975. Optimum sampling strategies in genetic conservation. p 53-80. in O.H. Frankel and J.G. Hawkes (eds.) Crop genetic resources for today and tomorrow. International Biological Programme No. 2. Cambridge University Press, Cambridge UK.

McKay, J.K., C.E. Christian, S. Harrison, and K.J. Rice. 2005. "How local is local?"-A review of practical and conceptual issues in the genetics of restoration. Restoration Ecology 13:432-440.

McKay, J.K. and R.G. Latta. 2002. Adaptive population divergence: Markers, QTL and traits. Trends in Ecology & Evolution 17(6):285-291.

Merila, J. and P. Crnokrak. 2001. Comparison of genetic differentiation at marker loci and quantitative traits. Journal of Evolutionary Biology 14:892-903.

Montalvo, A.M. and N.C. Ellstrand. 2000. Transplantation of the subshrub Lotus scoparius: Testing the home-site advantage hypothesis. Conservation Biology 14(4):1034-1045.

Moritz, C. 2002. Strategies to protect biological diversity and the evolutionary processes that maintain it. Systematic Biology 51:238-254.

Nei, M., T. Maruyama, and R. Chakraborty. 1975. The bottleneck effect and genetic variability in populations. Evolution 29:1-10.

Neigel, J.E. 2002. Is Fst obsolete? Conservation Genetics 3:167-173.

Newman, D., and D. Pilson. 1997. Increased probability of extinction due to decreased genetic effective population size: Experimental populations of Clarkia pulchella. Evolution 51:354-362.

Pearse, D.E. and K.A. Crandall. 2004 Beyond Fst: Analysis of population genetic data for conservation. Conservation Genetics 5:585-602.

Reed, D.H. and R. Frankham. 2001. How closely correlated are molecular and quantitative measures of genetic variation? A meta-analysis. Evolution 55: 1095-1103.

Reed, D.H. and R. Frankham. 2003. Correlation between fitness and genetic diversity. Conservation Biology 17:230-236.

Reusch, T.B.H., A. Ehlers, A. Hämmerli, and B. Worm. 2005. Ecosystem recovery after climatic extremes enhanced by genotypic diversity. Proceedings of the National Academy of Science (USA) 102:2826-2831.

Rhymer, J.M. and D. Simberloff. 1996. Extinction by hybridization and introgression. Annual Reviews of Ecology and Systematics 27:83-110.

Rice, K.J. and N.C. Emery. 2003. Managing microevolution: Restoration in the face of global climate change. Frontiers in Ecology and the Environment 1:469-478.

Richards, C.M. 2000. Inbreeding depression and genetic rescue in a plant metapopulation. American Naturalist 155:383-394.

Richards, C.M., M.F. Antolin, A. Reilley, J. Poole, and C. Walters. 2006. Capturing genetic diversity of wild populations for ex situ conservation: Texas wild rice as a model. Genetic Resources and Crop Evolution In press.

Rogers, D.L. 2004. Genetic erosion: No longer just an agricultural issue. Native Plants Journal 5:112-122.

Rogers, D.L., C.I. Millar, and R.D. Westfall. 1999. Fine-scale genetic structure of whitebark pine (Pinus albicaulis) associated with elevation in the eastern Sierra Nevada. Evolution 53(1):74-90.

Rogers, D.L. and A.M. Montalvo. 2004. Genetically appropriate choices for plant materials to maintain biological diversity. Report to the USDA Forest Service, Rocky Mountain Region, Lakewood, CO. Available online.

Shaw, R.G. and D. L. Byers. 1998. Genetics of maternal and paternal effects. p 97-111 in T.A. Mousseau and C. W. Fox (eds.). Maternal effects as adaptations. Oxford University Press, New York NY USA.

Sherwin, W.B. and C. Moritz. 2000. Managing and monitoring genetic erosion. p 9-34 in A.G. Young and G.M. Clarke (eds.) Genetics, demography and viability of fragmented populations. Conservation Biology Series, Vol. 4. Cambridge University Press, Cambridge UK.

Spielman, D., B.W. Brook, and R. Frankham. 2004. Most species are not driven to extinction before genetic factors impact them. Proceedings of the National Academy of Science (USA) 101(4):15261-15264.

Slatkin, M. and N.H. Barton. 1989. A comparison of three indirect methods of estimating average levels of gene flow. Evolution 43:1349-1368.

Squillace, A.E. and R.R. Silen. 1962. Racial variation in ponderosa pine. Forest Science 2:1-27.

Storfer, A. 1996. Quantitative genetics: A promising approach for the assessment of genetic variation in endangered species. Trends in Ecology & Evolution 11:343-348.

Van Gaal, T.M., S.M. Galatowitsch, and M.S. Strefeler. 1998. Ecological
consequences of hybridization between a wild species (Echinacea purpurea) and related cultivar (E. purpurea ‘White Swan’). Scientia Horticulturae 76:73-88.

Vekemans, X. and O.J. Hardy. 2004. New insights from fine-scale spatial genetic structure analyses in plant populations. Theoretical Applied Genetics 13:921-935.

Whitham, T.G., W.P. Young, G.D. Martinsen, C.A. Gehring, J.A. Schweitzer, S.M. Shuster, G.M. Wimp, D.G. Fischer, J.K. Bailey, R.L. Lindroth, S. Woolbright, and C.R. Kuske. 2003. Community and ecosystem genetics: A consequence of the extended phenotype. Ecology 84:559-573.

Whitlock, M.C. and D.E. McCauley. 1999. Indirect measures of gene flow and migration: Fst ? 1/(4Nm+1). Heredity 82:117-125.

Williams, S.L. and C.A. Davis. 1996. Population genetic analyses of transplanted eelgrass (Zostera marina) beds reveal reduced genetic diversity in southern California. Restoration Ecology 4:163-180.

Williams, S.L. and C.A. Davis. 2001. Reduced genetic diversity in eelgrass transplantations affects both population growth and individual fitness. Ecological Applications 11:1472-1488.

Wimp, G.M., G.D. Martinsen, K.D. Floate, R.K. Bangert, and T.G. Whitham. 2005. Plant genetic determinants of arthropod community structure and diversity. Evolution 59:61-69.

Wu, J., K.B. Krutovskii, and S.H. Strauss. 1999. Nuclear DNA diversity, population differentiation, and phylogenetic relationships in the California closed-cone pines based on RAPD and allozyme markers. Genome 42:893-908.

Young, A., T. Boyle, and T. Brown. 1996. The population genetic consequences of habitat fragmentation for plants. Trends in Ecology & Evolution 11(10):413-418.

Policies and guidelines pertaining to genetic restoration

Top | Research articles & chapters | Links

BLM. 2001. 1745-Native plant material manual, BLM manual supplement. RE: No. 1-242, September 13, 2001, California State Office, US Bureau of Land Management, Sacramento CA USA.

California Native Plant Society (CNPS): The document archive at the CNPS website offers pdf and html versions of their policies and bibliographies, several of which contain genetic recommendations and bibliographies:
* Guidelines for landscaping to protect native vegetation from genetic degradation;
* Policy on sowing of wildflowers;
* Policy on oak hardwoods.

California State Park and Recreation Commission. 2005. Statements of Policy
Preservation of vegetative entities. II.4 (Amended May 4, 1994). p 25 at

Center for Plant Conservation. 1991. Genetic sampling guidelines for conservation collections of endangered plants. p 225-238 in D.A. Falk and K.E. Holsinger (eds.). Genetics and conservation of rare plants. Center for Plant Conservation. Oxford University Press. New York NY USA.

CONPS. no date. Policy and guidelines for use of native plants. Colorado Native Plant Society. Available online.

CONPS. 2001. Guidelines for collection of native plants for use in restoration, horticulture, medicinal preparations and scientific research. Colorado Native Plant Society. Available online

Gordon, D.R. 1994. Translocation of species into conservation areas: A key for natural resource managers. Natural Areas Journal 14:31-37.

Guerrant, E.O. Jr., P.L. Fiedler, K. Havens, and M. Maunder. 2004. Revised genetic sampling guidelines for conservation collections of rare and endangered plants. p 419-441 in E.O. Guerrant Jr., K. Havens, and M. Maunder (eds.) Ex situ plant conservation: Supporting species survival in the wild. Island Press. Covelo, CA USA.

Guidelines for selecting native plants: The importance of local ecotype. Wild Ones Journal May/June 2002. Available online.

Mahalovich, M.F. and E.D. McArthur. 2004. Sagebrush (Artemisia spp.) seed and plant transfer guidelines. Native Plants Journal 5:141-148.
Example of attempt to establish transfer guidelines for several species in one genus, based on forest tree species guidelines.

Millennium Seed Bank Project. no date. A field manual for seed collectors. Royal Botanic Gardens, Kew, UK. Available online:
Has section on sampling strategy and Annex 5 has guidelines for collecting seed from rare and threatened plant species.

National Park Service Management Policies. 2001. Chapter 4 Natural Resource Management Genetic resource management principles Restoration of native plant and animal species Management of threatened or endangered plants and animals

Richards, R.T., J.C. Chambers, and C. Ross. 1998. Use of native plants on federal lands: Policy and practice. Journal of Range Management 51:625-632.

USDI and USDA. 2002. Interagency program to supply and manage native plant materials for restoration and rehabilitation on federal lands. Report to Congress, April 2002.

Wagenius, S., M. Dudash, M. Cotter, K. Holsinger, and K. Kennedy. 2006. Conservation checklist: Should you worry about genetics? Available online.

Woodward, R., and W. Harrison. 1989. The importance of using "local" plant genetic resources for rehabilitation in California State Parks. The California Ranger 5(5):5-10.

Website links

Top | Research articles & chapters | Policies & guidelines

Molecular marker glossary

IUCN Red List of Threatened Species

US Fish and Wildlife Service Species listings

PLANTS database, USDA Natural Resources Conservation Service

USDA-NRCS Plant Materials Program

California Native Plant Society’s Inventory of Rare and Endangered Plants

Native Plant Information Network, hosted at the Lady Bird Johnson Wildflower Center website, has a native plant suppliers directory.

Wild Ones: a not-for-profit environmental education and advocacy organization promoting environmentally sound landscaping practices to preserve biodiversity through the preservation, restoration, and establishment of native plant communities

Population biology Java simulations from Kent Holsinger, Dept. of Ecology and Evolutionary Biology, University of Connecticut.

National Center for Biotechnological Information (NCBI), a National Institutes of Health clearinghouse and databases for nucleotide sequence information by species for genomes or fragments of genomes (genes, ESTs, markers, etc.) as well as source of tools for sequence analysis.

This page last updated October 7, 2006. Copyright UC Regents. All rights reserved.