Genetically appropriate choices for plant materials to maintain biological diversity

343 Pages·2004·3.09 MB·English

by  Deborah L Rogers

Genetically Appropriate Choices
for Plant Materials
to Maintain Biological Diversity

Deborah L. Rogers Arlee M. Montalvo
Genetic Resources Conservation Program Department of Botany and Plant Sciences
University of California and Center for Conservation Biology
Davis, CA1 University of California
Riverside, CA
and
Riverside–Corona Resource Conservation District
Riverside, CA2

1 Genetic Resources Conservation Program, University of California, One Shields Avenue, Davis, CA 95616.
email: [email protected]
2 Riverside-Corona Resource Conservation District, 4500 Glenwood Drive, Riverside, CA 92501.
email: [email protected]
Prepared for:

USDA Forest Service
Rocky Mountain Region
Lakewood, CO

December 31, 2004

Citation: Rogers, D.L. and A.M. Montalvo. 2004. Genetically appropriate choices for plant materials to
maintain biological diversity. University of California. Report to the USDA Forest Service, Rocky
Mountain Region, Lakewood, CO. Online: http://www.fs.fed.us/r2/publications/botany/plantgenetics.pdf
Copyright © 2004 The Regents of the University of California
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ii
Table of Contents
vi Foreword
vii Preface
viii Acknowledgements
1 Chapter 1 Introduction
18 Chapter 2 Context for making genetically appropriate plant material
choices on USDA Forest Service lands
32 Chapter 3 Genetic impacts of natural versus artificial regeneration
56 Chapter 4 Description of genetic diversity
77 Chapter 5 Genetic diversity and its relationship with evolution, ecology,
and life history characteristics
103 Chapter 6 What is genetically local?
130 Chapter 7 Fitness consequences of poor genetic matching
151 Chapter 8 Purchased plant materials for wildland revegetation projects
197 Chapter 9 Choosing appropriate genetic sources
217 Chapter 10 Information on Region 2 native plants
310 Chapter 11 Demonstration of using the guidelines to choose appropriate
genetic materials
316 Chapter 12 Concluding remarks
320 Glossary
List of Boxes
Page Number Title
12 1 The significance of in situ genetic reserves
15 2 Genetic policies: A sample from US agencies and organizations
25 3 USDA Forest Service Directives related to genetically appropriate use
of native plants
28 4 Federal acts, presidential directives, and executive orders related to the
use of native plants
44 5 The recurring question: To seed or not to seed
48 6 Ecological genetic considerations in species selection
53 7 Some ecological resources available for guiding species selection
145 8 Making the best use of limited and valuable genetic collections
148 9 Genetic monitoring for signs of genetic erosion or genetic shifts
191 10 Wildland seed certification programs
195 11 Conventions for classification and naming of native plant materials
209 12 Native plant species in FS Region 2 that are listed under the Federal or a
State Endangered Species Act
211 13 Genetic considerations in restoring clonal species
214 14 Polyploidy in native plant species: implications for revegetation projects
iii
List of Figures
Page Number Title
8 1.1 Elements of a natural area revegetation project
9 1.2 A representation of the four levels of biodiversity as viewed by the
Forest Service and others
23 2.1 Examples of how the spatial scale of genetic diversity within a species
may relate to the spatial scale of the revegetation project
120 6.1 Comparison of historic and revised southwestern ponderosa pine
seed transfer rules for Colorado in Region 2
121 6.2 Example of species-specific seed zones for ponderosa pine (var. scopulorum)
in Regions 1 and 2
122 6.3 USDA plant hardiness zones for central US showing range in average
annual minimum temperature
123 6.4 Ecoregion maps for United States and South Dakota
124 6.5 Four of the possible fitness outcomes of population hybridization
following mixing of a resident and genetically non-local population
141 7.1 The three subspecies of Artemisia tridentata in relation to the habitats to
which they are adapted
185 8.1 AOSCA seed certification guidelines and nomenclature for release types
in the genetically manipulated versus natural development tracks
205 9.1 Forest Service Seed Collection Zones for the State of Colorado
206 9.2 Forest Service Seed Collection Zones for the State of South Dakota
206 9.3 Forest Service Seed Collection Zones for the State of Wyoming
207 9.4 Basic steps for informing choices on genetically appropriate source
for each species involved in a revegetation project
311 11.1 Rocky Mountain sedge (Carex scopulorum)
313 11.2 Poverty oat grass (Danthonia spicata)
314 11.3 Scarlet globemallow (Sphaeralcea coccinea)

List of Tables*
Page Number Title
10 1.1 Some basic differences between plants and animals in some genetic
characteristics
24 2.1 Spatial and temporal scales relevant to plant introductions in
revegetation projects
40 3.1 A classification for plant growth following a disturbance
41 3.2 Risks and opportunities associated with natural (or unassisted)
regeneration and assisted regeneration of native plant species on sites
where fires or harvests have occurred
iv
List of Tables continued*
Page Number Title
73 4.1 Summary of common statistical measures of genetic diversity within
and among populations
74 4.2 Some values for allozyme diversity for western conifer species
93 5.1 Contrasts and comparisons among various DNA markers that can be
useful in genetic monitoring
95 5.2 Groups of species in the Great Plains and Intermountain West floras
with high frequencies of hybridization and no reported hybridization
95 5.3 Evidence of cytoplasmic (cpDNA) genomic capture in plant species.
96 5.4 Correlates between life-history traits and spatial genetic structure
(differences among populations) in plant species.
96 5.5 Average levels of among-population genetic differentiation (spatial
genetic structure) for several plant families
97 5.6 Effect of life-history characteristics of plant species on the ‘Sp statistic’
measuring spatial genetic structure (SGS)
147 B8.1 Spectrum of value to be applied to research projects that requests use
of limited collection of plant genetic resources
167 8.1 Specifications for the different classes of native plant germplasm made
available for release by USDA Plant Materials Centers
168 8.2 Information about releases of plants native to Region 2
182 8.3 Example of conservation plant releases from USDA NRCS Manhattan
Plant Materials Center, KS
183 8.4 Example of procedures that could minimize genetic bottlenecks and
unintended genetic shifts in native plant collections and releases
184 8.5 Questions relating to commercial plant materials
209 B12.1 Native plant species in FS Region 2 that are listed (or Candidates for
Listing) under the Federal or a State Endangered Species Act
220 10.1 General species life-history information for a sample of species from
Region 2 that have some genetic information available
245 10.2 Characteristics of some Region 2 native plant species that are known to
reproduce vegetatively or re-sprout after disturbance
250 10.3 Information on local adaptation or genetic differentiation in a sample of
plant species native to at least one of the five states in Forest Service
Region 2
267 10.4 Region 2 native plant species that have variable ploidy levels (cytotypes)
274 10.5 Species from Region 2 studied for inbreeding or outbreeding effects
282 10.6 Ecological genetic details for Populus tremuloides
285 10.7 Ecological genetic details for Linum lewisii
287 10.8 Ecological genetic details for Bouteloua gracilis
* ‘B’ in the table number indicates that this table is associated with the box of that number, rather than the chapter.
v
Foreword
Native plant material use in revegetation or restoration efforts has increased nationally over the
past couple of decades, replacing to some extent our past reliance on European grasses. This shift
to natives has raised questions about the selection of appropriate genetic stocks, similar to the
issues involved in using native trees for reforestation. There is a need and an opportunity for dia-
log between land managers choosing native plant materials for wildland use, and geneticists who
can provide counsel on relevant (but often complicated) details. This guide is intended to foster
such a dialog. It synthesizes important genetic principles and provides many examples to better
inform land managers, and help them understand the context for advice from geneticists. It fo-
cuses on details relevant to the USDA Forest Service’s Rocky Mountain Region, but contains a
wealth of information that is relevant elsewhere, as well.
Revegetation, restoration, or emergency rehabilitation efforts are conducted at the local
level, but assistance can be provided from regional or national levels. Tools are needed to help
local land managers make informed decisions when native materials suitable for the site are not
commercially available (or feasible), and when seed transfer guidelines or seed zones have not
been developed for the particular plant species of interest. Regional strategies can help provide
guidance, and lead to economies of scale. Development of this Guide was the top priority in a
strategic effort in the Rocky Mountain Region in 2002, to assist our National Forests and Grass-
lands in addressing their needs for native plant materials. The other products (for example, pri-
oritized lists of species, seed procurement plans, native seed collections from the Forests and
Grasslands, common garden studies) remain unfunded at this time.
A tremendous amount of scientific study, policy, and infrastructure support the use of mer-
chantable native tree species for reforestation following timber harvest, fire, disease or insect
epidemics, and other disturbances. But we are in the early stages of developing and incorporating
genetic information into our selection of other native plant materials in public land management.
There is also a significant need to understand the interplay between our choices of germplasm
and its ecological interaction in the landscape (for example, competitive interactions, pollination
ecology, herbivory, etc.). It is hoped that this Guide will be further developed over time or lead
to the production of other documents, workshops, policies or procedures, and serve as a catalyst
to elevate the need (increase the awareness) for native seed collections and common garden stud-
ies.

Andrew Kratz
Regional Botanist
USDA Forest Service
Rocky Mountain Region

Mary Frances Mahalovich
Regional Geneticist
USDA Forest Service
Northern, Rocky Mountain, Southwestern and Intermountain Regions

December 30, 2004
vi
Preface
This document was prepared as a guide to making genetically appropriate choices for native
plant materials in revegetation projects. This being its most appropriate identity, ‘the Guide’ or
‘this Guide’ are used when referring to this document rather than the longer document title. In
general, the flow of this Guide is from principles to specific decisions and case studies. The first
several chapters provide information on why genetic diversity and integrity are important for na-
tive plant species and why they are worth conserving and considering in management decisions.
Information is provided about the nature of genetic diversity, how it is shaped by natural proc-
esses such as selection and migration, and how we measure it. In Chapter 5, we place genetic di-
versity within the context of long-term evolutionary processes, ecology, and life-history charac-
teristics of plant species. Through this review, we emphasize the relationships between genetics
and ecology—important for two reasons. First, it underscores the consistency in natural features
and processes: when we conserve genetic diversity and integrity, we are concomitantly conserv-
ing other ecological and ecosystem processes and values. Second, more often than not, sufficient
and direct genetic information for a particular species is not available. Hence, understanding the
relationships and correlations with life-history traits can help make an informed decision in the
absence of direct genetic information. We consider these chapters to be important in strengthen-
ing the decision-making ability of Guide users, as well as providing the rationale and context for
the guidelines we present later.
In Chapters 6 and 7, the information becomes more applied and focused on revegetation is-
sues. Chapter 6 addresses the concepts of what are genetically local and genetically appropriate
in the context of revegetation projects. In the following chapter the consequences of poor genetic
decisions (or failure to consider genetic source) in selecting revegetation materials for a site are
presented. At this point in the Guide, a foundation for making genetically appropriate decisions:
explaining the genetic principles about the importance of maintaining genetic integrity, empha-
sizing the relationships between genetic diversity and ecological processes, and providing some
sense of the risk involved when genetic decisions are not well made.
The information in chapters 8 through 11 directly address the decisions involved in genetic
selections of plant revegetation materials. Chapter 8 covers the issue of what to consider when
purchasing plant materials. Chapter 9 provides guidelines for how to make genetic decisions in a
specific project. This chapter is no doubt an attractive, and hopefully useful, one for readers. But
again, we emphasize that it is best used in the context of the information presented in other chap-
ters. Chapter 10 is a resource of genetic information for some of the native plant species in Re-
gion 2 of the Forest Service, presented here as a convenient reference, but recognizing that new
information is constantly available and Readers should not assume this chapter is comprehen-
sive. Chapter 11 provides an opportunity for Readers to practice the guidelines presented in
Chapter 9. We present here some real and theoretical examples and illustrate how the decision of
what is genetically appropriate would be made, using our guidelines. A brief summary of the ma-
jor messages in the Guide and some concluding comments are provided in Chapter 12. The
Guide concludes with a glossary that contains some of the more technical words used in the
chapters and boxes. The intent is to provide a brief definition that provides sufficient clarity for
the reader to understand the term in the context in which it was provided in the text.
vii
Some additional information is included as sidebars or boxes about topics that are mentioned
in the text, for example, genetic policies of other organizations or agencies. This structure was
chosen for additional information to allow Readers the opportunity to delve more deeply into
some topics, without compromising the general flow of the main narrative.
We strongly recommend that Readers visit the introductory chapters before making use of
the information in Chapters 8 through 11. The best use of our guidelines requires both an under-
standing of genetic principles which we have tried to effectively convey here, as well as the
knowledge of site conditions and objectives and the valuable management experience that the
reader possesses. Our objective is to better support with science the Readers’ discretion, not re-
place it.
The PLANTS Database (http://plants.usda.gov/) of the USDA’s Natural Resource Conserva-
tion Service has been used as the source of taxonomic information throughout the Guide.
Acknowledgements
This Guide was made possible by funding from the USDA Forest Service's Rocky Mountain Re-
gion and the University of California under a Joint Venture Agreement between the Forest Ser-
vice and the Regents of the University of California (FS Agreement No. 03-JV-11020000-051;
UC Proposal No. 03101065). It was designed to fill a gap seen by Andrew Kratz, Regional Bota-
nist, Rocky Mountain Region. His interest in using the best available science in resource man-
agement, and in particular, making genetic information more accessible, was the impetus for cre-
ating this Guide. In addition to his initiative that led to the Guide’s development, he has provided
liberal amounts of materials to inform the Guide and has provided thoughtful reviews of earlier
drafts.
Mary Frances Mahalovich, Regional Geneticist for the USDA Forest Service’s Northern,
Rocky Mountain, Southwestern, and Intermountain Regions, has been a strong source of support
and wealth of genetic information in the preparation of this Guide. Her reviews of earlier drafts
have assisted in keeping the utility of the Guide focused on the Forest Service mission, and in
maintaining a strong scientific basis for the narrative.
Gay Austin provided considerable information and suggestions, reviewed an earlier draft of
the Guide, and supported the development of this Guide with enthusiasm. Kat Anderson,
Gay Austin, Richard Cronn, Norman Ellstrand, Vicky Erickson, James Hensen, Valerie Hipkins,
Randy Johnson, Scott Peterson, Chuck Quimby, John Randall, Leslie Stewart, and Nancy Warren
have reviewed and provided helpful comments on all or particular sections of this Guide. We are
very grateful for their interest and their contributions.
Many other individuals—including Norm Ellstrand, Laura Galloway, Subray Hegde,
Keli Kuykendall, E. Durant McArthur, Patrick McGuire, Steven Monsen, Leonard Nunney,
Chris Richards, and Ken Vogel—have contributed information generously: sharing their expert
synthesis on bodies of work, offering recent insights on work in progress, or providing guidance
on other aspects of preparing this Guide.
This is certainly a collaborative effort.

viii
Chapter 1
Introduction

“The history of plant and animal introductions is littered with catastrophes.
[Reports] concerning the implications of moving genes between populations sug-
gest that caution is needed here also.”
Moore 2000
Context and Objectives
Two trends have made revegetation and restoration projects on public lands increasingly sophis-
ticated and information-demanding: i) changes in public values require that more attention be
given to supporting biodiversity and maintaining natural processes (Richards et al. 1998); and ii)
an explosion in restoration-related research and publications has heightened concern about the
negative impacts of translocating plant materials and has created a myriad of information sources
(Hufford and Mazer 2003, Manel et al. 2003). For public lands managers, the decision-making
process for revegetation projects goes beyond selecting the species. The lesson of “plant natives”
is now broadly accepted and often required by law or policy. Exclusive planting of native plant
species and removal of exotic species is now common practice in parks, forests, and natural ar-
eas, and increasingly common and encouraged in roadside treatments (for example, Harper-Lore
and Wilson 2000). However, the second and equally important step is selecting the genetically
appropriate population or seed source. The USDA Forest Service has long recognized the impor-
tance of this decision for commercially significant forest tree species and has made large re-
search investments in understanding the local adaptations and tolerances of those trees, translat-
ing that information into seed transfer zones. The biological principles and issues are relevant to
all native plant species, and not only the trees. The decision about appropriate genetic source for
plant species is critical to both the success of the restoration or revegetation project and the long-
term environmental value of the restored site. Furthermore, this genetic decision-making step is
essential whether wild seeds, plants propagated from wild-collected seed (such as rooted cuttings
or seedlings), direct transplants from a source population, or selected agricultural lines of native
seeds are used.
Chapter 1 Introduction 2
Genetically appropriate choices regarding the introduction of plant materials consider both
the quality and quantity of genetic diversity. The appropriate amount of genetic diversity is de-
termined in relation to the species and the project area, and is addressed by appropriate sampling.
The quality of genetic diversity refers to the issue of matching the diversity appropriately to the
site to address local adaptations and the natural patterns in the species’ genetic diversity.
Planting projects are opportunities to have positive or negative impacts on preserving the
genetic diversity of native plant species. Indeed, some view the genetic source decision as being
on par with species selection in that bad genetic choices can have consequences that could rival
those of bad species choices such as introducing exotic invasive species (Moore 2000). The con-
sequences of bad genetic choices, though, may be slower to be manifest, often are less well re-
corded, and may be more difficult to diagnose.
A rationale for this Guide is that the genetic principles that have informed decisions con-
cerning appropriate seed sources for commercially important forest tree species can also be ap-
plied to such decisions for other native plant species. Some land-managing public agencies and
organizations do have policies that strive to protect genetic diversity by recommending or requir-
ing the planting of genetically local material (Box 1). However, even when there is such a policy
there may not be guidelines that are sufficiently specific or flexible to guide individual planting
projects. And in many other situations, there is no such policy in place or the most appropriate
genetic materials may not be available.
The overall objective of this Guide is to increase awareness about the implications of man-
aging for genetic diversity in native plant species and to provide decision-making support and
tools for choosing genetically appropriate sources for planting projects. Towards meeting this
objective, the importance of genetic diversity in native plant populations is explained, the genetic
principles underlying the concepts of genetically local and genetically appropriate seed sources
for native plants are described, tools for assessing biological value and risk in using non-local or
mass-produced plant materials for large projects are provided, and illustrations of these concepts
are offered with case studies involving native (US) plant species. In preparing these descriptions
and tools, we have incorporated the most recently developed patterns of genetic diversity and
understanding of its role in long-term plant population viability and species interactions.
Scope of Guide
In this Guide, the focus is the under-serviced area of the genetic aspects of choosing different
sources of plant materials. This is only one aspect of the spectrum of decisions involved in
revegetation projects (Figure 1.1). In general, decisions for site preparation, species selection,
seral stage considerations, or most of the establishment, management, and monitoring activities
are beyond the scope of this Guide. Many of these decisions are informed by the rapidly expand-
ing field of restoration science, and much literature and large compendia of information are
available (for example, CNAP 1998; Gobster and Hull 2000; Perrow and Davy 2002a, 2002b).
Furthermore, the Guide does not cover all the genetic considerations or consequences of every
type of planting (or seeding) project, but focuses on the large-scale revegetation projects that are
considered after fires or mechanical overstory removal. However, the genetic principles pre-
sented here also apply to other—smaller-scale or alternative objective—situations, but there may
also be additional considerations in those projects that have not been covered here. For example,
rehabilitation on a former mine site may require selection of plant materials that tolerate the de-
graded site status, or may require several stages of planting—using different species to achieve