Restoration Genetics Resources

5/20/2015
Restoration genetics_resources
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, 2428 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
Books
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
http://grcp.ucdavis.edu/projects/ConBio/ConGen/RestorGen_resources.htm
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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.
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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
havent 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
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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.
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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 27:237278.
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 14:892903.
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
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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. Hmmerli, 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.
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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 42:893908.
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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
http://www.parks.ca.gov/pages/843/files/CommissionPolicies9-23-05.pdf
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.
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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
4.4.1.2 Genetic resource management principles
4.4.2.2 Restoration of native plant and animal species
4.4.2.3 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 51:625632.
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 Societys 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
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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.
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Restoration Genetics Resources

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Restoration genetics: Applying population

Resources for Restoration Genetics

CA USA. Presentation of the principles of ex situ plant conservation as an

Amaranthus pumilus Rafinesque. Castanea 68:236-244.

Lawrence, M.J., D.F. Marshall, and P. Davies. 1995a. Genetics of genetic

genetic variability in populations. Evolution 29:1-10.

Young, A., T. Boyle, and T. Brown. 1996. The population genetic

Example of attempt to establish transfer guidelines for several species in

Molecular marker glossary

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