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
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
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
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.
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 51:625-632.
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
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.
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