**An introduction to restoration genetics.**

Donald A. Falk

University of Arizona and

Society for Ecological Restoration

Eric E. Knapp

U.S. Geological Survey

Edgar O. Guerrant

Berry Botanic Garden

Prepared by the

Society for Ecological Restoration

November 2001

For:

Plant Conservation Alliance

Bureau of Land Management, US Department of Interior

U.S. Environmental Protection Agency

![](media/image1.png) ![](media/image2.png)

**Acknowledgments.** Major funding for this project was provided by
Plant Conservation Alliance and the Environmental Protection Agency,
Environmental Response Team. Thanks to Peggy Olwell (Bureau of Land
Management, Plant Conservation Alliance), Sally Brown (US Department of
Agriculture and University of Washington), and Scott Fredericks (US
Environmental Protection Agency) for their encouragement and assistance
in initiating this project. Steve Gatewood (SER) gave helpful comments
on an earlier version. Steve Caicco, Jennifer Lippert, Teresa Presdusi,
and Mike Williams pointed us to relevant literature and resources. This
paper is a project of the Society for Ecological Restoration, with
support from the agencies listed above.

D.A.F., Tucson, AZ

E.E.K. Three Rivers, CA

E.O.G., Portland, OR

November 2001

**An introduction to restoration genetics.**

Donald A. Falk[^1]

Eric Knapp[^2]

Edgar O. Guerrant[^3]

17 December 2001

[1. Why is genetic diversity important?
2](#why-is-genetic-diversity-important)

[a. Genotypes partly determine organisms' physical form and function.
2](#a.-genotypes-partly-determine-organisms-physical-form-and-function.)

[b. Genetic diversity helps organisms cope with current environmental
variability.
3](#b.-genetic-diversity-helps-organisms-cope-with-current-environmental-variability.)

[c. Diversity within populations reduces potentially deleterious effects
of breeding among close relatives.
5](#c.-diversity-within-populations-reduces-potentially-deleterious-effects-of-breeding-among-close-relatives.)

[d. Genetic diversity is the primary basis for adaptation to future
environmental uncertainty.
6](#d.-genetic-diversity-is-the-primary-basis-for-adaptation-to-future-environmental-uncertainty.)

[2. How is genetic diversity distributed in natural populations?
7](#how-is-genetic-diversity-distributed-in-natural-populations)

[a. Monomorphic and polymorphic alleles.
7](#a.-monomorphic-and-polymorphic-alleles.)

[b. Diversity within and among populations of a single species.
7](#b.-diversity-within-and-among-populations-of-a-single-species.)

[c. How is genetic variation detected and measured?
10](#c.-how-is-genetic-variation-detected-and-measured)

[3. How do genetic questions enter into restoration?
12](#how-do-genetic-questions-enter-into-restoration)

[a. Accuracy and functionality of restored populations.
12](#a.-accuracy-and-functionality-of-restored-populations.)

[b. Geographic location of source material for (re)introduction.
13](#b.-geographic-location-of-source-material-for-reintroduction.)

[c. Sampling the diversity of source populations.
16](#c.-sampling-the-diversity-of-source-populations.)

[d. Genetic diversity within reintroduced populations.
19](#d.-genetic-diversity-within-reintroduced-populations.)

[e. Genetic diversity among reintroduced populations.
21](#e.-genetic-diversity-among-reintroduced-populations.)

[4. Resources. 22](#resources.)

[a. Web sites and organizations. 23](#a.-web-sites-and-organizations.)

[b. Literature cited. 24](#b.-literature-cited.)

# 1. Why is genetic diversity important?

All living organisms carry a genetic blueprint. This is so regardless of
whether they are plants, animals, or fungi, whether they are short- or
long-lived, and whether they reproduce sexually or clonally. Therefore,
to the extent that restoration deals with living organisms, genetics are
part of the picture. Although the basic principles underlying
restoration genetics may be familiar, to date surprisingly little
attention has been devoted to genetic considerations in restoration
practice. The purpose of this Restoration Science and Policy Paper is to
outline some considerations that restoration designers and managers
should be aware of, and to identify more detailed resources that may be
useful in practice.

## a. Genotypes partly determine organisms' physical form and function.

Biologists refer to two basic expressions of variation, the genotype and
the phenotype. The *genotype* is the genetic code of an organism; in
organisms with nucleated cells (most multi-cellular plants, animals, and
fungi), the essential code is found in the nucleus of each cell.
Additional genetic codes reside in other components of the cell, such as
mitochondria (in animals) and chloroplasts (in plants). An organism's
genotype consists of a large number of *genes* (50,000-100,000 in a
typical vertebrate), which can be at multiple sites (*loci*) on
chromosomes. Genes have a variety of functions, the most important of
which is to code for the production of specific amino acids, which are
ultimately used to synthesize proteins. In most higher plants and
animals (but not fungi, bryophytes, and many marine invertebrates), the
adult phase has two copies of each gene, one derived from each parent.
When the two copies are the same, the individual is *homozygous* for
that gene; if the two copies are different, the individual is
*heterozygous* for that gene. The various forms of a gene are referred
to as *alleles*; when these forms are identical across a population, the
gene is considered *monomorphic*, and if more than one allele exists the
gene is considered *polymorphic.*

*Phenotype* is the expression of these genes as a living organism in a
particular environment, and is influenced by environmental context at
every level from the cell to the whole organism. It is frequently very
difficult to separate variation in an organism\'s traits with a genetic
basis from traits that are phenotypically variable; mistakes are
commonly made both ways (assuming a genetic basis when observed
variation is really phenotypic plasticity; underestimating subtle
genetic effects on traits that are assumed to be simply "phenotype").
For example, a plant growing in a poor environment might end up having a
small and stunted phenotype, despite having "good" genes. This does not
mean that genetic variation is not important to the fitness of
individuals or populations. Both the environment and the genes will
ultimately contribute to restoration success, but steps to ensure an
optimal genetic makeup of a population are commonly overlooked.

Examples abound in the scientific literature illustrating how genetic
composition affects the form and function of organisms (Hamrick,
Linhart, and Mitton 1979; Hedrick 1985; Primack and Kang 1989; Rehfeldt
1990; Allen, Antos, and Hebda 1996; Hartl and Clark 1997). In fact, the
recognition of genetic variation among individuals was a primary insight
that led to the formulation of evolutionary theory as we know it today
(Freeman and Herron 1998). Genes regulate body size, shape,
physiological processes, behavioral traits, reproductive
characteristics, tolerance of environmental extremes, dispersal and
colonizing ability, the timing of seasonal and annual cycles
(*phenology*), disease resistance, and many other traits (Raven, Evert,
and Eichhorn 1986). Thus, to ignore genetic variation in ecology is to
ignore one of the fundamental forces that shape the biology of living
organisms. From a restoration perspective, organism and population
genetics are fundamental considerations in the design, implementation,
and expectations of any project, whether or not explicit consideration
is given to the genetic dimension.

## b. Genetic diversity helps organisms cope with current environmental variability.

Organisms exist in environments that vary in time and over space. Such
variation is often described in terms of the *natural* or *historic
range of variability* (NRV, HRV) in environmental conditions such as
weather, disturbance events, resource availability, population sizes of
competitors, etc. (White and Walker 1997). If a group of organisms (say,
a population of species X) were to live in a completely stable physical
and biological environment, then a relatively narrow range of phenotypes
might be optimally adapted to those conditions. Under these
circumstances, Species X would benefit more by maintaining a narrow
range of genotypes adapted to prevailing conditions, and allele
frequencies might eventually attain equilibrium. By contrast, if the
environment is patchy, unpredictable over time, or includes a wide and
changing variety of diseases, predators, and parasites, then subtle
differences among individuals increase the probability that some
individuals and not others will survive to reproduce \-- *i.e.*, the
traits are "exposed to selection." Since differences among individuals
are determined at least partly by genotype, population genetic theory
predicts (and empirical observation confirms) that in variable
environments a broader range of genetic variation (higher
heterozygosity) will persist (Cohen 1966; Chesson 1985; Tuljapurkar
1989; Tilman 1999).

Examples of traits with a genetic basis for tolerance of environmental
variation important in restoration work include tolerance of freezing,
drought or inundation, high or low light availability, salinity, heavy
metals, soil nutrient deficiencies, and extreme soil pH values in
plants; resilience to fluctuating temperature, dissolved oxygen, and
nutrient availability in aquatic organisms; and resistance to novel
diseases in all groups of organisms (Huenneke 1991). For example, if all
individuals in a population are the same genotype with limited drought
tolerance, then a single climatic event may destroy the entire
population. Plant populations often include individuals with a range of
flowering or emergence times. For instance, Great Basin shrub
populations include individuals that leaf out and flower over a period
of weeks, increasing the likelihood of persistence of the population
through periods of unusually early or late growing conditions. Knapp *et
al.* (2001) documented flowering periods in a population of individual
blue oak trees and found that trees initiated flowering over a period of
a month in the spring. Such variability could potentially be adaptive,
since it is more likely that at least some trees in the population will
flower during warm sunny periods when wind pollination is most
successful.

A diverse array of genotypes appears to be especially important in
disease resistance (Schoen and Brown 1993; McArdle 1996). Genetically
uniform populations (such as highly inbred crops) are famously
vulnerable to diseases and pathogens, which can (and do) decimate
populations in which all individuals are equally vulnerable. Such
uniformity also predisposes a population to transmit disease from one
individual to another: instead of having isolated diseased individuals,
nearly every individual may be exposed to disease by direct contact or
proximity. More diverse populations are more likely to include
individuals resistant to specific diseases; moreover, infected
individuals occur at lower density, and thus diseases or pathogens may
move more slowly through the population.

Finally, genetic variation is a factor in competition among individuals
in real ecological communities. Traits with a genetic basis such as
flower size are key factors in competition among individuals. Among
animals, behavioral traits may regulate interspecific competition. Since
organisms make energetic or life history tradeoffs among traits (for
example, allocating energy between growth and reproduction), genetic
variability is an important factor in how populations function (Koyama
and Kira 1956; Thompson and Plowright 1980; Fowler 1981; Gurevitch 1986;
Goldberg 1987; Manning and Barbour 1988; Welden, Slauson, and Ward 1988;
Grace and Tilman 1990; Tilman and Wedin 1991; Pantastico-Caldas and
Venable 1993; Wilson and Tilman 1993; Delph, Weinig, and Sullivan 1998).

## c. Diversity within populations reduces potentially deleterious effects of breeding among close relatives.

In addition to its adaptive value at the population level, genetic
variation (or its lack) within individuals can affect their survival and
performance. When both copies of a gene (in a diploid organism) are
identical (*i.e.*, when an individual is *homozygous* at that gene or
locus), the expression of that gene may include traits that are less
beneficial to survival or reproduction in particular circumstances. This
may lead to physiological or behavioral problems of genetic origin, such
as malformed physical structure, poor biochemical balance, improper
organ formation and function, altered social behavior, and
susceptibility to disease (Chai 1976).

Homozygosity at key gene loci is a common result of *inbreeding*, which
is sexual reproduction among closely related individuals. Small
populations and species that do not disperse well (or are constrained by
a fragmented landscape from exchanging genes with other populations) can
be particularly susceptible to *inbreeding depression*, which is reduced
overall survival and reproduction of organisms with low heterozygosity.
Inbreeding depression arises from a variety of causes, including
expression of unfavorable or deleterious alleles, and often leads to
lower survival and birth or reproductive rates (Templeton 1991; Meffe
and Carroll 1994; Husband and Schemske 1996).

Heterozygosity is not always beneficial, nor does inbreeding always have
adverse effects. In some circumstances, a population may be so well
adapted to its local circumstances that introducing alleles from other
populations actually reduces its performance (*outbreeding depression*)
(Templeton 1991). Paradoxically, organisms can experience outbreeding
depression for some traits, while suffering the effects of inbreeding
depression for other characters. Many organisms (particularly plants)
have evolved breeding strategies, such as self-pollination, that allow
successful persistence in small populations without apparent short-term
effects of inbreeding depression.

## d. Genetic diversity is the primary basis for adaptation to future environmental uncertainty.

Finally, genetic variation holds the key to the ability of populations
and species to persist over evolutionary time through changing
environments (Freeman and Herron 1998). No organism can predict the
future (and evolutionary theory does not require them to), nor can any
organism be optimally adapted for all environmental conditions.
Nonetheless, the current genetic composition of a species influences how
well its members will adapt to future physical and biotic environments.

Consider, for example, the response of a population of plant Species A
to a period of rapid climate change. Changes in climate are reflected
locally in altered annual rainfall and its seasonal distribution,
changes in annual mean maximum and minimum temperatures and their
seasonality, changes in prevailing wind direction and speed, and many
other factors. These changes cause the zone of suitable climate for
Species A to shift geographically. Populations with a diverse array of
optima for these climatic conditions (*i.e.*, some individuals that are
slightly more cold or heat tolerant, etc.) are more likely to persist,
because some individuals will survive the new conditions and reproduce.
If suitable climate zones shift across the landscape, seeds of some
individuals may be dispersed into the new location and find good
conditions for growing. In this manner, the population can "migrate"
across the landscape over generations. By contrast, populations that
have a narrower range of genotypes (and are more phenotypically uniform)
may simply fail to survive and reproduce at all as conditions become
less locally favorable. Such populations are more likely to become
*extirpated* (locally extinct), and in extreme cases the entire species
may end up at risk of extinction. For example, the Florida Yew (*Torreya
taxifolia*) is currently one of the rarest conifer species in North
America. But in the early Holocene (10,000 years ago), when conditions
in southeastern North America were cooler and wetter than today, the
species was probably widespread. For reasons that are not completely
understood, *T. taxifolia* failed to migrate northward as climate
changed during the Holocene. Today, it is restricted to a few locations
in the Apalachicola River Basin in southern Georgia and the Florida
panhandle.

As the *T. taxifolia* story illustrates, once species are pushed into
marginal habitat at the limitations of their physiological tolerance,
they may enter an "extinction vortex," a downward cycle of small
populations, reduced genetic variability, reduced ability to adapt to
novel conditions, leading to further reductions in population size, and
so on (Shaffer and Samson 1985; Gilpin and Soulé 1986). Reduced genetic
variability is a key step in the extinction vortex.

# 2. How is genetic diversity distributed in natural populations?

There are genetic differences among individuals within most (but not
all) populations of plants and animals. There are also differences among
populations across the range of each species. In this section we review
some basic patterns of how genetic diversity of species is distributed,
or *partitioned*.

## a. Monomorphic and polymorphic alleles.

By definition, individuals within a given species share some percentage
of alleles; otherwise, they would not be considered members of the same
species. This shared (or common) portion of the gene pool includes two
basic classes of genes. Genes that are monomorphic (*i.e.*, *A* = 1,
where *A* is the number of alleles per locus) within a species are
common to all populations, and indeed essentially to all individuals.
(Technically, "monomorphic" genes are defined as those for which the
frequency of the most common allele is [\>]{.underline} 99%; thus, some
variation may be present even at these loci). The monomorphic proportion
of the total genome varies among taxonomic groups, typically in the
range of 85% in animals and 50% in plants (Hedrick 1985; Hartl and Clark
1997).

The remainder of loci (on average, 15% in animals and 50% in plants) is
polymorphic (*A* \> 1), varying among individuals in a population, and
among populations within a species. These loci are of most concern to
restoration, since polymorphic loci may or may not be adequately
represented depending on the design and execution of a restoration
program.

## b. Diversity within and among populations of a single species.

The genetic profile of whole populations typically varies from place to
place across a species range. These differences may arise as the result
of chance occurrences, such as the genetic composition of dispersing
individuals that create a new population (*founder effect*), or changes
in allele frequencies that result from chance matings in very small
populations (*genetic drift*) (Primack and Kang 1989; Templeton 1991;
Meffe and Carroll 1994; Eckert, Manicacci, and Barrett 1996; Husband and
Schemske 1996). Differences among populations can also arise
systematically, especially if the environment in various places exposes
individuals to different optima for survival and reproduction
(*fitness*). For these and other reasons, populations often diverge from
one another in their genetic composition. Such divergence is especially
strong and rapid when there is little *gene flow* between populations
(*e.g.,* limited dispersal of seeds or pollen, or limited movement of
animals across physiographic barriers). Over evolutionary time, such
among-population genetic differences can accumulate and eventually
result in the development of a new species (*allopatric speciation*).
Indeed, "populations" are defined as much (or more) by patterns of
mating and gene flow as by the physical distribution of individuals,
although the two are often closely related (Hartl and Clark 1997).

Each species distributes its genetic diversity (one measure of which is
the total of all alleles at all loci) in a pattern reflecting both its
biology and its history (Wright 1965; Nei 1975). For example, nearby
populations of plants that are pollinated by bees may share many alleles
because genes (packaged in pollen grains) can flow easily between sites.
Such species may have fewer unique alleles in each population, so
populations tend to be genetically similar. By contrast, there may be
less gene flow among populations of species that are pollinated by
ground-dwelling flightless beetles, or whose heavy fruits fall to the
ground in the vicinity of the parent tree. Gene flow can also be
obstructed by physical barriers (*i.e.*, topography or habitat that a
pollinator, disperser, or migrating individual cannot cross), as well as
by disturbance (Levin 1981; Slatkin 1987).

Even if variation within a population is low, there may be considerable
variability *among* populations. Imagine Species X, a plant that lives
in high mountaintop alpine areas, in which every individual on a given
mountain is nearly identical genetically to others. In this case,
individuals in Population 1 will all be nearly identical to each other;
individuals in Population 2 will also be identical to each other, but
because populations are very isolated from one another, they may all be
very different from all the individuals in Population 1; and so on.
Under these circumstances, most of the variation in Species A is *among*
populations; within-population variation is low or nonexistent.

Now imagine a contrary example. Species B lives in tallgrass prairie,
where suitable habitats are relatively close to one another (or even
continuous), and dispersal among populations is common. Here we might
find a great deal of variation among individuals in each population
(reflecting the benefits of variation discussed above), but because gene
flow is high among sites, most populations are similar (that is, most
polymorphic alleles are widely distributed). This illustrates a species
with a high proportion of variation distributed *within* populations,
while among-population variation is relatively small.

A variety of measures are used to quantify the distribution of genetic
variation among individuals within populations, and among populations.
These measures are the basis for describing how genetic variation is
*partitioned* within species. Differences among populations are commonly
quantified by the use of one of several statistics, including Wright's
inbreeding coefficient (*F~ST~*) and Nei's coefficient of gene variation
(*G~ST~*). These indices are functions of how heterozygosity is
partitioned within and among populations, based on differences in allele
frequencies (Wright 1969; Nei 1975; Chai 1976; Wright 1978). Where
*p~i~* is the frequency of the *i*th allele, heterozygosity (*H*) = 1 -
∑ *p~i~*^2^ for {i = 1\...n} for populations within a larger sample.
Then, the proportion of total variation that is distributed among
populations (*G~ST~*) is
![](media/image3.wmf){width="0.6034722222222222in"
height="0.4166666666666667in"}, or equivalently, 1- (*H~S\ ~*/ *H~T~*),
where *H~S~* and *H~T\ ~*are the mean heterozygosity within populations
and in the entire species respectively. Values for these statistics can
often (although not often enough!) be found in the population genetic
literature, so restorationists do not have to generate them. Values of
*F~ST\ ~*and *G~ST~* vary from 0 to 1 (Nei 1975; Hedrick 1985; Crow
1986; Hartl and Clark 1997). *G~ST~* in particular has a number of
useful properties: it can be used for one or many loci, mutation rates
do not alter the statistic significantly, the exact number of
populations need not be specified, and the statistic is relatively
responsive to changes in allele frequencies in time. Although they have
important conceptual differences, in practice *F~ST\ ~*and *G~ST~* are
used in similar fashion as indices of genetic difference among
populations (Crow 1986).

Species genetic structure can be modeled in a variety of ways. The
simplest is a "finite island" conceptual model, in which alleles can
flow between any pair of populations. In this case, the key parameters
are the migration rate and *effective population size* (Crow 1986).
However, the assumption that any two populations are equally likely to
exchange alleles is probably unrealistic. Instead, a "stepping stone"
model can be used, in which alleles spread by "stepping" from one
population to an adjacent one (Wright 1969; Crow 1986).

In practical terms, *G* and *F* statistics tell us whether the majority
of genetic variation is distributed among or within populations. In
species with low *G~ST~* (approaching 0), the majority of variation is
found *within populations*; individuals within populations are likely to
be genetically different, but each population contains the same
complement of alleles in similar frequencies Where *G~ST~* is high
(approaching 1), individuals within a population are relatively similar
but *populations* are significantly different. Most species fall
somewhere in between these extremes.

The distribution of genetic variation within and among species is
strongly linked to life-history traits, particularly dispersal and
*reproductive mode* (Hamrick and Godt 1990; Hamrick et al. 1991).
Species that disperse genes (in plants, this includes both pollen and
seeds) widely and frequently will tend, other things being equal, to
have lower *G~ST\ ~*(*i.e.,* populations will be more similar). Even a
moderate rate of gene movement among populations (one individual every a
few generations) can "link" the gene pools of two populations. Mutation
and drift (chance selection of genotypes, especially likely in small
populations) can also lead to changes in allele frequencies, although in
general these forces are believed to act more slowly than dispersal and
selection.

## c. How is genetic variation detected and measured?

A variety of methods exist for the assessment of genetic variation
(Schaal, Leverich, and Rogstad 1991). Traditionally, genetic variation
was inferred by the shape (*morphology*) or growth responses of
organisms. Such approaches often use *common garden experiments* or
*reciprocal transplants* to distinguish genotypic and phenotypic
variation. In this approach, individuals that appear phenotypically
different (or that grow in different environments) are placed in a
common environment. This eliminates the environmental component of
variation; presumably, the remaining variation has a genetic basis.

While these methods can be useful, they measure higher-order effects of
genetic variation (*i.e.*, expression in the whole organism), and hence
address genetic variation only indirectly. Moreover, the confounding
effects of phenotypic variation are often difficult to separate from
underlying genetic differences among organisms. In practical terms, it
is often not possible to know whether organisms that look different are
actually different genetically, or whether their differing phenotypes
reflect the influences of environment or chance in development.

Since the 1960's the most widely applied method of estimating genetic
differences among individuals is *enzyme electrophoresis* (also referred
to as *starch gel electrophoresis*, including both *allozyme* and
*isozyme* analysis). Electrophoresis detects variation in amino acids
that are early products of gene *translation* (the process by which a
cell translates a copy of its genetic code in messenger-RNA into amino
acids). Since there may be multiple biochemical pathways leading to the
synthesis of a single amino acid or enzyme, electrophoresis is
relatively conservative in its estimates of genetic variation among
individuals (Hamrick, Linhart, and Mitton 1979). Enzyme electrophoresis
remains the most widely used method of estimating genetic variation, and
literally thousands of studies have been conducted on a wide range of
organisms. Electrophoretic analysis permits individuals to be
distinguished from one another based on enzyme variation. These
differences among individuals can be compiled to generate statistics
about the degree of variation within and among populations (§2.b), a key
consideration in restoration ecology.

In the past decade, powerful methods have developed and emerged to
detect variation in DNA itself, not simply its products (Karp, Isaac,
and Ingram 1998). While a bewildering variety of tools and techniques
may be encountered in the literature, they all have in common the
ability to reconstruct the sequence of nucleotides in the DNA molecule,
arguably the most basic level of genetic variation (Britten 1986; Clegg
1990). The conceptually simplest (although experimentally most
laborious) technique is *gene sequencing* \-- that is, the exact
reconstruction of the complete nucleotide sequence. Part of the
difficulty in interpreting DNA sequences is that "genes" in a functional
sense may be distributed over several sections of a chromosome; there
are also large sections of all chromosomes that do not code for any
known function, or that are redundant or *regulatory* (influence the
transcription, translation, or function of other genes). Thus, unlike
enzyme analysis, much of the information in a DNA sequence may be of
little relevance to understanding ecologically significant genetic
variation. Since in theory every sexually-produced individual is likely
to be unique, DNA sequences can be almost too variable to detect the
kinds of patterns required for restoration work. However, new analytical
techniques allow DNA sequence variation to be interpreted in meaningful
ways. Complete gene sequences have been complied for relatively few
organisms, and generally only a few individuals each, although these
numbers are increasing all the time.

It is important to note that isozymes and genetic markers may not
reflect traits under strong natural selection. For example, Knapp and
Rice ((1998) evaluated patterns of variation in a native grass using
both quantitative traits and isozymes, and compared these to geographic
distance and climate. They found overall that isozymes did not reflect
an adaptation to climate, whereas the quantitative traits did. In a
restoration context, this suggests that climate may in some cases serve
as more useful guide for collecting and reintroduction zones than
genetic markers *per se*.

# 3. How do genetic questions enter into restoration?

The genetic principles outlined above have a direct bearing on the
practice of ecological restoration (Falk and Holsinger 1991; Young and
Clarke 2000). In this section we summarize how restoration practitioners
and researchers can (and should) take population genetics into account.

## a. Accuracy and functionality of restored populations.

Sophisticated restoration practitioners recognize that the starting pool
of genetic variation to be used is a critical element in design and
implementation. However, opinions abound on how to select a suitable
source pool for a restoration project (Landis and Thompson 1997).

The current debate often confuses two related, but distinct issues: the
*accuracy* ("authenticity") of a restoration project, and its
*functionality* (Clewell, 2000). A reintroduction project is genetically
*accurate* ("authentic") if it replicates the original gene pool of the
population it replaces. If the original population has been destroyed,
then perfect accuracy is strictly speaking impossible, because some
alleles were probably unique to that population (*i.e.*, G~ST~ \< 1). A
restoration can be accurate and function poorly; it can also be
inaccurate but functional.

Since no reintroduction is perfectly accurate genetically, the question
then becomes: "How close is close enough?" To this there can be no
absolute ecological answer, since not all variation is of adaptive
significance. Moreover, variation among populations is a continuous
variable: two populations can differ by one allele or thousands. If the
motivation is an ethical commitment to fidelity to the historic
distribution of genotypes, the line can be drawn anywhere. The best
practice is to estimate and report the degree of genetic accuracy based
on available information, so that others studying a project can take
authenticity into account.

How well a reintroduced population [functions]{.underline} is a very
different matter. Here the concern is not so much whether specific
genotypes have been re-established, but rather how well a restored
population will work in terms of persistence, resilience, and stability.
Since many adaptive traits have a genetic basis, reintroduction material
that performs (survives, grows, reproduces) well may come from a site
with similar ecological conditions, but not necessarily close
geographically (Knapp and Rice 1998; Procaccini and Piazzi 2001).
Moreover, if functionality is the main objective, then a range of
genotypes can be introduced, allowing selection (differential survival
and reproduction) to sort out the best for the site. If this approach is
taken, there may be considerable attrition, which can be accounted for
in initial sampling (§3.c).

## b. Geographic location of source material for (re)introduction.

Perhaps no single genetic issue is more intensely debated in restoration
circles than the location of source populations: "Where should material
for restoration come from?" Interest in population genetic variation
often arises in the context of asking whence source material should
come. In other words the restorationist is concerned not only with the
degree of variability but its particular geographic distribution.

The most common approach is to specify a geographic (and often
elevation) range, within which source material can be confidently
collected. This is essentially a "space-for-genotype" substitution: we
expect that populations near one another, and growing in similar
conditions, will be more similar genetically due both to ecotypic
variation and the effects of gene flow. Geographic distance is a
reasonable first approximation of genetic distance, assuming that
genetic diversity most likely obeys the "distance decay of similarity"
in broad outline (Nekola and White 1999). In population genetic terms,
this favors the "stepping stone" model (§2.b) of gene flow. On public
lands in the western United States, commonly-applied guidelines suggest
that material for outplanting be collected from within 1,000 ft.
elevation bands and 100 miles lateral distance of the planting area
(elevation bands vary from 500-3,000 ft for different agencies) (see §
4, *Resources*). As noted above (§ 2.c), climatic zones may also offer a
better first approximation of genetic distance between populations than
simple geographic distance (Knapp and Rice 1998; ONPS 2001).

Unfortunately, there are no simple distance rules that apply equally to
all species, because species vary in gene flow among populations,
population size, and the resulting distribution of diversity (G~ST~).
For some species (*e.g.*, self-fertilizing plants in small, isolated
patches of habitat, or fishes in isolated stream reaches), each site may
reflect a unique local adaptation, and the geographic range of suitable
genotypes can be very small (a few km^2^). Other species (for example,
species with wind dispersed pollen and seeds) with higher rates of gene
flow, and those with larger effective populations, are probably less
differentiated over the landscape and can be collected from much wider
ranges. Most species have dispersal curves that are leptokurtic (*i.e.*,
with long tails), meaning that a few seeds or offspring in each
generation may travel far beyond the majority; while few in number,
these long-range dispersers may play a critical role in helping species
to adjust their ranges in periods of climate and vegetation change. For
each species, the restorationist must ask: "How widely does this species
disperse its genes under normal conditions, and what factors (distance,
geographic barriers, habitat types) influence where genes can spread?"
This uncertainty is reflected in the wide range of recommendations for
suitable collecting zones, which range over more than three orders of
magnitude from 100 meters to 100 miles.

The issue of geographic range for source material cannot be separated
from the distinction made earlier between historical accuracy and
functionality. If historical accuracy (authenticity) *sui generis* is
the primary concern, then the range of potential collecting sites is
governed most strongly by historical patterns of dispersal, and the
collecting radius will be very small. If population function is the
primary concern, on the other hand, then the net may be cast over a
wider area (although still focusing on similar ecological communities).
This is because populations that are widely separated in space may
nonetheless occupy similar ecological settings, and by selection may
have developed genotypes that are similar in key ecological traits. If
the main goal is population function, then it is probably more important
to derive source material from large, diverse populations than from
small, genetically depauperate sites, even if the latter are closer
geographically. Of course, it is always possible to mix genotypes from
different populations, and to let selection sort out the variation: this
is, after all, exactly what nature does. Mixing of genotypes may be
particularly suitable if existing "populations" are in fact isolated and
reduced remnants of formerly widespread and interconnected groups.
Re-combining fragmented populations genetically is appropriate as the
geographic scale is ecologically realistic, and should not be done
indiscriminately. Mixing too broadly (*i.e.*, combining genotypes from
very diverse ecological settings) can result in too many individuals
that are poorly adapted for the new given environment (high genetic
load). Some geneticists advocate the use of regional mixtures \--
composite collections of genotypes, all of which are at least moderately
well adapted to a given environment (Knapp and Dyer 1997; Lesica and
Allendorf 1999).

There are valid arguments on both sides of the authentic *vs.*
functionality debate. On one hand, there is little question that the
gene pools of many remnant native populations have been seriously
eroded, so that what occurs today is a small remnant of the original
diversity. Small gene pools are more prone to inbreeding, as well as
random genetic change from drift. Populations that formerly exchanged
genes regularly may have also become genetically isolated by habitat
fragmentation. In such cases, a good argument can be made to bring
together genetic material from several nearby populations, in effect
replicating the natural (but now disrupted) processes of gene flow. In
addition, some restoration sites may be so heavily disturbed (*i.e.*
mine tailing reclamation areas) that the most "local" population may no
longer be the one best adapted to the growing environment. In such
cases, a wide diversity of genotypes can increase the chances that at
least some plants will have the genetic composition to survive.

It is possible, however, that genotypes from outside the apparent
current range may perform [too]{.underline} well \-- that is, swamp the
local genotype. If remnant native populations of the species being
introduced already exist at a site, additional genetic considerations
reinforce the importance of the scale of collection. Introduced
populations may hybridize with the existing native population,
introducing new genes (genetic pollution) and potentially negatively
affecting genetic integrity (Rieseberg 1991; Glenne and Tepedino 2000).
If a few poorly adapted individuals make it into the existing native
population, it might be argued that natural selection will eventually
remove the deleterious genes. However, the issue is partly one of
numbers; with commercial seed production of many native species,
restorationists now have the tools to dump large volumes of seed into
ecosystems. If the number of poorly adapted, non-local propagules is
large in relation to the number of local native types, the chance of
matings between the well adapted and the poorly adapted plants will
increase (especially in cross-pollinating species), thereby potentially
swamping the native population and diluting the local genes. Progeny
from such matings may additionally experience outbreeding depression
(*i.e.* poor survival and growth in relation to the parents). Carefully
chosen introductions, with genotypes similar to the existing native
population, can avoid these negative impacts.

***Take-home messages:*** Since no single rule applies to all
situations, the most important recommendation is to use explicit and
reasoned criteria in selecting source populations. To summarize the
issues presented here:

1.  Species vary in their dispersal rates and distances, and hence in
    the degree of genetic differentiation among populations. These
    differences are often closely correlated with life-history
    attributes particular to each species that affect rates and patterns
    of gene flow. Therefore, guidelines are inherently species-specific.

2.  The restorationist must decide if historical accuracy or
    functionality is the primary objective. True historical accuracy can
    be difficult to determine if existing populations are remnants of a
    formerly widespread range. Moreover, most natural populations
    experience a degree of genetic change over time and space. However,
    even where the emphasis is on functionality, historical reference
    conditions are essential to "anchor" restoration work within a
    natural range of variability.

3.  Geographic distance (*i.e.*, the "space-for-genotype" substitution)
    is a reasonable, but crude, substitute for patterns of gene flow
    among populations. However, in a disrupted landscape the most local
    remnant populations may be genetically reduced, and may not have
    genotypes that correspond to the conditions under restoration.
    Moreover, if populations are strongly selected to local habitat
    conditions, then habitat similarity may outweigh distance as a
    selection criterion. Local and regional climatic and soil zones can
    be useful criteria for obtaining material for reintroduction, since
    these will often represent plants adapted to the conditions at the
    restoration site.

4.  As a source of material for reintroduction, large, genetically
    diverse source populations are generally preferable to small,
    limited populations even when the latter are closer to the
    restoration site. It may be preferable to combine material from
    several suitable sites, to capture a wider array of genotypes that
    can succeed in the new location. Such "regional mixtures" should
    draw on populations within a similar ecological zone (climate, soil)
    to the restoration site, to avoid too large a proportion of
    individuals that may not be well adapted to the new conditions.

5.  Small local populations can be "swamped" by non-native genotypes if
    a species already exists at a restoration site. If existing
    populations are to be augmented, the number of individuals
    introduced from other locations should not be so large as to
    overwhelm the local gene pool, particularly if there is evidence of
    local adaptation.

## c. Sampling the diversity of source populations.

The initial gene pool for a restoration project is inevitably limited by
the diversity of the original sample. While other genes may enter the
project area over time (for instance, by migration of individuals,
dispersal of gametes, or additional reintroduction measures), the
starting pool of genetic diversity will govern the performance of a
reintroduced population for a long time. Hence, the diversity of the
original source collection is a critical consideration in restoration.

A variety of guidelines have been developed for sampling wild
populations of plants and animals for breeding and reintroduction
(Center for Plant Conservation 1991; Guerrant 1992; BGCI 1994; Guerrant
1996; IUCN/SSC 1998). These guidelines address four fundamental sampling
issues:

1.  How many populations will be sampled to create the source pool?

2.  How many individuals will be sampled from each population?

3.  Will samples be collected all at once, or over a period of years?

4.  What is the probability of a collected sample surviving to
    establishment?

***Number of populations:*** In most species, the cumulative amount of
genetic variation captured increases as successive populations are added
to the sample. However, since populations have some measure of
similarity (0 \< G~ST~ \< 1), each additional population added to a
sample collects some alleles that are new to the sample, and some that
are already present from previous samples. As the number of populations
sampled increases, the *marginal diversity rate* decreases (that is,
fewer and fewer novel alleles are captured), and the *cumulative
diversity function* approaches an asymptote. For a pool of populations
sampled at random, there comes a point at which further sampling across
populations provides little or no additional genetic benefit (Falk 1991;
Falk and Gibbs *In prep.*).

The number of populations at which this occurs is related strongly to
the measure of differentiation among populations, G~ST~, which we have
already encountered. When G~ST~ is high, populations are markedly
different from one another, and more should be sampled to capture the
maximum total diversity. When G~ST~ is low, most populations are
similar, and sampling from only a few will capture most of the diversity
that exists(provided that the statistic was generated using populations
across the full range of the species). Of course, it is always worth
remembering that a significant fraction of most genomes is monomorphic,
and is therefore captured in the first population, if not the first
individual.

There can be no hard and fast rules for the number of populations to be
sampled across all taxa. In a recent survey of 13 plant species, the
sample for some species was saturated for common isozyme alleles after
just 3-5 populations (20% of the total), while in other species the
cumulative diversity curve was still rising after all populations (as
many as 15-30) were included in the sample (recall, however, that
isozyme loci may be less variable among populations than other loci
under strong selection) (Falk and Gibbs *In prep.*). Rare or uncommon
alleles accumulate in the sample at a slower rate than do common
alleles, so if it is suspected that important adaptations occur at low
frequency (for instance, because of recent environmental change), then
it is advisable to sample a larger number of sites. Further research is
ongoing in this area; in the meantime, G~ST~ or some comparable measure
of population differentiation is a suitable guide for the sampling
strategy.

One exception to this general null model is for populations that are
strongly differentiated along habitat lines (*e.g. ecotypes*). If the
reintroduction area is unusual habitat for a species, then it is worth
sampling any populations that occur in similar conditions, to increase
the likelihood of capturing alleles that offer adaptive benefit.

***Number of individuals to sample within populations.*** The underlying
theoretical basis for sampling multiple individuals within a population
is that populations are rarely truly *panmictic* (that is, with
completely randomized breeding). In plants, a large proportion of mating
occurs between neighboring individuals, even when pollination occurs via
an animal vector. In animal populations, a wide range of behavioral
adaptations exists that commonly concentrates breeding success in a few
individuals at any given time. The result is that populations are not
genetically homogeneous; to capture their genetic diversity adequately,
multiple individuals need to be sampled.

Again, a number of general guidelines have been released on this topic,
and again, there can be no hard and fast "magic numbers" that apply
across taxa (Brown et al. 1990; Brown and Briggs 1991). Plant studies
evaluated by the Center for Plant Conservation (Center for Plant
Conservation 1991) and its colleague institutions suggest that anywhere
from 10-50 individuals should be sampled per population, with the
understanding that there is bound to be considerable redundancy among
these samples. Sampling of propagules (seeds, vegetative shoots) has
less impact on the source population, although there is often lower
success associated with these life stages compared to outplanting
established plants (Guerrant 1992; Guerrant 1996).

***Number of years during which samples will be collected.*** For many
species, an adequate sample can be collected in a single year. However,
for many others, collecting may need to be distributed over a number of
years. Reasons for multiple-year collecting include:

-   Variable reproductive output (masting), where large numbers of
    individuals are reproductive or large numbers of offspring are
    produced only in certain years;

-   Small populations or species with low reproductive rates, where it
    is important to avoid depleting the pool of new individuals;

-   Annual organisms, for which gene pools may be significantly
    different from year to year, either by selection or by chance; and

-   Limited capacity to handle (store, propagate, release) collected
    material.

***Probability of a collected sample surviving to establishment***. In
the end, what counts in a reintroduction is the number of individuals in
the new population as well as their diversity (Menges 1991). However,
less than 100% of the samples (seeds, cutting, eggs, adults) collected
in the field will survive to establishment. Attrition occurs at every
step along the way: during the collecting process, transportation,
storage, propagation/curation, and outplanting/release. High initial
mortality rates are often observed in reintroduced populations, often
continuing for several years (Brown and Briggs 1991).

A simple calculation can help to account for attrition of collected
samples. Let *Ps* represent the survival probability of a collected
sample *s*, and *N* the number of individuals desired in the final
restored population. Then we account for attrition during the
reintroduction process by collecting
![](media/image4.wmf){width="0.3888888888888889in"
height="0.3333333333333333in"} samples in the field. For example,
suppose that trees dug for transplant have an ultimate survival rate of
40% from initial collecting to the third year of a reintroduction
project, and that we are trying to establish a population of 50 trees.
Correcting for attrition, an initial collection of (50/.40), or 125
individuals, will give us a good chance of ending up with the final
population size we wish (Brown and Briggs 1991).

## d. Genetic diversity within reintroduced populations.

As discussed above, breeding among closely related individuals can lead
to expression of unfavorable traits that compromise an organism's
ability to survive and reproduce. Individuals resulting from inbreeding
in populations where this did not occur naturally from highly inbred
lines can have stunted growth, altered behavior, deformed morphology,
poor physiological function; such individuals are also more likely to be
reproductively sterile. Hence, the genetic origin of individuals used in
a restoration project can influence whether a project succeeds or fails.
If source collections are made from diverse, naturally occurring
populations, the probability of breeding among close relatives is
reduced. A more diverse population may include individuals that can
tolerate a wider range of conditions. If, on the other hand, all
individuals in a restored population are genetically similar, and the
total population size is not large (fewer than 100 individuals), the
probability is great that their offspring will be homozygous at some
loci, and thus have reduced fitness. A genetically narrow population may
be able to survive only in a narrow range of conditions. While genetic
diversity is not always associated with *ecological amplitude*, in
general the correlation is positive (Huenneke 1991).

In addition to affecting how well a restored population succeeds in
current environmental conditions, genetic diversity may affect
performance over time. Important ecological traits, such as tolerance of
disturbance or climatic extremes often have a strong genetic basis. Such
traits need to be considered not only in terms of conditions at the time
of reintroduction, but in light of the natural range of variability over
many years or generations. If the goal of restoration is to establish
self-sustaining populations (Pavlik 1996), then the range of conditions
to which the population and its offspring will be exposed is a vital
consideration. Genetically uniform populations may do well one year when
conditions are favorable for their genotype, and then fail the next,
even though the range of environmental variation is within normal
limits. Such failures are even more likely in the case of less common
extreme events (Gaines and Denny 1993). Recalling from § 1.b and 1.d
that environmental conditions vary within an envelope of natural
variation, it is safe to assume that most reintroduced populations will
be exposed to a wide range of conditions over time. Hence, the genetic
diversity of reintroduced populations is a non-trivial consideration for
their long-term persistence (Montalvo et al. 1997).

It is not uncommon in restoration work for large numbers of individuals
to be released or outplanted, a large proportion of which fail to
survive beyond 2-3 years. This means that restoration releases are
subject both to the *founder effect* (the result of the initially
limited gene pool) and then further *genetic bottlenecks* as effective
population size diminishes due to mortality (Robichaux, Friar, and Mount
1997). If the initial outplanting or release is itself genetically
uniform (*e.g.*, hundreds or thousands of clonally-produced plants), the
resulting gene pool in the field can be quite narrow. Such apparently
large populations are, in genetic terms, very small (Brown and Briggs
1991).

Of course, genetically narrow populations occur in nature, often
resulting from similar forces (founder events and bottlenecks). For
example, aspen (*Populus tremuloides*) and many species in the Iridaceae
(*Iris*, *Lilium*) are often found in large clumps of many *ramets* of
very few *genets*, or even just one. Natural populations of species
where sexual (as opposed to vegetative or parthenogenic) reproduction
dominates are less likely to be genetically homogeneous (Meffe and
Carroll 1994).

The effects of genetic homogeneity in a reintroduced population may not
be immediately evident, but over a period of years the population may
have lower rates of growth, survival and reproduction, and may persist
less successfully through periods of natural environmental variability.

*What you can do:* Restorationists should be aware of the level of
genetic diversity that they are working with. Above all, restoration
planners and managers should understand how the plants and animals they
use were generated. Ask your nursery or whoever collected and propagated
your seed source (or your breeder, in the case of animals) what methods
were used, and what steps were taken to assure the presence of a
suitably wide range of genotypes. While clonally-produced flats of
thousands of identical plants may appear to offer short-term advantages
(as they do for agricultural crops) of predictable response to current
growing conditions, in the long run (again as with crops) such
populations may be less likely to persist and succeed in the face of
disease, competition, and climate variability. Of course, knowing the
methods by which individuals or material was produced provides genetic
information only by inference; it is unfortunately not common to have
good genetic data for reintroduction efforts.

## e. Genetic diversity among reintroduced populations.

The same principles apply to diversity among population diversity. Most
species have a degree of differentiation among populations (*i.e.*,
G~ST~ \> 0). Population geneticists debate whether these differences
have adaptive value in any given case -- that is, whether they are the
result of selection -- or whether they represent the effects of sampling
error (founder effects, drift, mutation). Nonetheless, a reasonable
precautionary position is to mimic the degree of genetic difference
found in natural populations of a species when (re)introducing
populations to the landscape.

Most species, however, have little or no published data on their
among-population genetic diversity. The few surveys that have been done
are invaluable sources of information, and restorationists should read
and cite them whenever possible. In some cases studies of *congeners*
can be used, although with the caveat that species that are closely
related phylogenetically are not always similar ecologically.

# 4. Resources.

A vast literature exists on genetic diversity, its distribution in space
and time, and its adaptive and ecological significance. A number of
excellent texts on population genetics provide greater depth on a number
of topics addressed briefly in this paper. Several of the growing
numbers of papers on the topic of restoration genetics are listed in the
literature cited section of this paper.

Conservation genetics is still is relatively small field, and
restoration genetics is in its infancy. Restoration practitioners and
scientists can contribute to the accumulation of knowledge in this area
by treating your restoration projects as experiments, and publishing
your results.

The Society for Ecological Restoration maintains an on-line *Directory
of Restoration Expertise* at www.ser.org. The IUCN also has published a
list of reintroduction practitioners (Soorae and Seddon 1998).
Individuals listed in each of these resources may be helpful with
restoration genetic issues.

## a. Web sites and organizations.

> **Society for Ecological Restoration**
>
> 1955 W. Grant Road, Suite 150
>
> Tucson, AZ 85745 USA
>
> Tel. (520) 622-5485
>
> Fax. (520) 622-5491
>
> Email: info@ser.org
>
> http://www.ser.org
>
> **Plant Conservation Alliance**
>
> Bureau of Land Management
>
> 1849 C Street NW, LSB-204
>
> Washington, DC 20240 USA
>
> Tel. (202) 452-0392
>
> http://www.nps.gov/plants/
>
> **Species Survival Commission Plants Programme**
>
> c/o International Union for Conservation of Nature (IUCN)
>
> Rue Mauverny 28
>
> CH-1196
>
> Gland, Switzerland
>
> Tel. 41/22/9990152
>
> Fax 41/22/999015
>
> http://www.iucn.org/themes/ssc/index.htm
>
> **Center for Plant Conservation**
>
> Missouri Botanical Garden
>
> P.O. Box 299
>
> St. Louis, MO 63166 USA
>
> Tel. (314) 577-9450
>
> http://www.mobot.org/CPC/
>
> **US Forest Service**
>
> Seed collecting guidelines:
>
> http://www.na.fs.fed.us/spfo/rngr/pubs/np97/consider.htm
>
> **National Forest Genetic Electrophoresis Laboratory (NFGEL)**
>
> 2480 Carson Road
>
> Placerville, CA 95667 USA
>
> Tel. (530) 622-1225
>
> Fax (530) 622-2633
>
> http://www.dendrome.ucdavis.edu/NFGEL/

## b. Literature cited.

Allen, G. A., J. A. Antos, and R. J. Hebda. 1996. Morphological and
genetic variation in disjunct populations of the avalanche lily,
*Erythronium montanum*. *Canadian Journal of Botany* 74 (3):403-.

BGCI. 1994. *A handbook for botanic gardens on the reintroduction of
plants to the wild*. Richmond, Surrey, UK. Botanic Gardens Conservation
International, in association with the IUCN Species Survival Commission,
Reintroduction Specialist Group. 42.

Britten, Roy J. 1986. Rates of DNA sequence evolution differ between
taxonomic groups. *Science* 231 (21 March):1393-1398.

Brown, A. H. D., and J. D. Briggs. 1991. Sampling strategies for genetic
variation in *ex situ* collections of endangered plant species. In
*Genetics and conservation of rare plants*, edited by D. A. Falk and K.
E. Holsinger. New York: Oxford University Press.

Brown, Anthony H. D., Michael T. Clegg, Alex L. Kahler, and Bruce S.
Weir, eds. 1990. *Plant population genetics, breeding, and genetic
resources*. Sunderland, MA: Sinauer Associates.

Center for Plant Conservation, CPC. 1991. Genetic sampling guidelines
for conservation collections of endangered plants. In *Genetics and
conservation of rare plants*, edited by D. A. Falk and K. E. Holsinger.
New York: Oxford University Press.

Chai, Chen Kang. 1976. *Genetic evolution*. Chicago: University of
Chicago Press.

Chesson, Peter L. 1985. Coexistence of competitors in spatially and
temporally varying environments: A look at the combined effects of
different sorts of variability. *Theoretical Population Biology*
28:263-287.

Clegg, Michael T. 1990. Molecular diversity in plant populations. In
*Plant population genetics, breeding, and genetic resources*, edited by
A. H. D. Brown, M. T. Clegg, A. L. Kahler and B. S. Weir. Sunderland,
MA: Sinauer Associates.

Clewell, Andre. F. 2000. Restoring for natural authenticity. *Ecological
Restoration* 18 (4): 216-217.

Cohen, D. 1966. Optimising reproduction in a randomly varying
environment. *Journal of Theoretical Biology* 12:119-129.

Crow, James F. 1986. *Basic concepts in population, quantitative, and
evolutionary genetics*. New York: W. H. Freeman & Co.

Delph, Lynda F., Cynthia Weinig, and Kelly Sullivan. 1998. Why
fast-growing pollen tubes give rise to vigorous progeny: the test of a
new mechanism. *Proceedings of the Royal Society of London (Botany)*
265:935-939.

Eckert, Christopher G., Domenica Manicacci, and Spencer C. H. Barrett.
1996. Genetic drift and founder effect in native *versus* introduced
populations of an invading plant, *Lythrum salicaria* (Lythraceae).
*Evolution* 50 (4):1512-1519.

Falk, Donald A. 1991. Joining biological and economic models for
conserving plant diversity. In *Genetics and conservation of rare
plants*, edited by D. A. Falk and K. E. Holsinger. New York: Oxford
University Press.

Falk, Donald A., and James Gibbs. *In prep.* Marginal and cumulative
diversity functions: collector\'s curves for alleles.

Falk, Donald A., and Kent E. Holsinger, eds. 1991. *Genetics and
conservation of rare plants*. New York: Oxford University Press.

Fowler, Norma. 1981. Competition and coexistence in a North Carolina
grassland. II. The effects of the experimental removal of species.
*Journal of Ecology* 69:843-854.

Freeman, Scott, and Jon C. Herron. 1998. *Evolutionary analysis*. Upper
Saddle River, New Jersey: Prentice-Hall.

Gaines, Steven D., and Mark W. Denny. 1993. The largest, smallest,
highest, lowest, longest, and shortest: Extremes in ecology. *Ecology*
74 (6):1677-1692.

Gilpin, Michael E., and Michael E. Soulé. 1986. Minimum viable
populations: the processes of species extinctions. In *Conservation
biology: The science of scarcity and diversity*, edited by M. E. Soulé.
Sunderland, MA: Sinauer Associates.

Glenne, G., and V. J. Tepedino. 2000. A Clark County dilemma: native
bees as agents of rare plant pollination and hybridization. Paper read
at Third Southwestern Rare and Endangered Plant Conference, at The
Arboretum at Flagstaff, Flagstaff, AZ.

Goldberg, Deborah E. 1987. Neighborhood competition in an old-field
plant community. *Ecology* 68 (5):1211-1223.

Grace, J. B., and D. Tilman, eds. 1990. *Perspectives on plant
competition*. San Diego, CA: Academic Press.

Guerrant, Edward O., Jr. 1992. Genetic and demographic considerations in
the sampling and reintroduction of rare plants. In *Conservation
biology: The theory and practice of nature conservation, preservation
and management*, edited by P. L. Fiedler and S. K. Jain. New York:
Chapman & Hall.

Guerrant, Edward O. 1996. Designing populations: Demographic, genetic,
and horticultural dimensions. In *Restoring diversity: strategies for
reintroduction of endangered plants*, edited by D. A. Falk, C. I. Millar
and M. Olwell. Washington, ED: Island Press.

Gurevitch, Jessica. 1986. Competition and the local distribution of the
grass *Stipa neomexicana*. *Ecology* 67 (1):46-57.

Hamrick, James L., and M. J. Godt. 1990. Allozyme diversity in plant
species. In *Plant population genetics, breeding, and genetic
resources*, edited by A. H. D. Brown, M. T. Clegg, A. L. Kahler and B.
S. Weir. Sunderland, MA: Sinauer Associates.

Hamrick, James L., M. J. W. Godt, D. A. Murawski, and M. D. Loveless.
1991. Correlations between species traits and allozyme diversity:
implications for conservation biology. In *Genetics and conservation of
rare plants*, edited by D. A. Falk and K. E. Holsinger. New York: Oxford
University Press.

Hamrick, James L., Y. B. Linhart, and J. B. Mitton. 1979. Relationships
between life history characteristics and electrophoretically detectable
variation in plants. *Annual Review of Ecology & Systematics*
10:173-200.

Hartl, Daniel L., and Andrew G. Clark. 1997. *Principles of population
genetics*. Third ed. Sunderland, MA: Sinauer Associates.

Hedrick, P. 1985. *Genetics of populations*. Portola Valley, CA: Jones &
Bartlett Publishers.

Huenneke, Laura F. 1991. Ecological implications of genetic variation in
plant populations. In *Genetics and conservation of rare plants*, edited
by D. A. Falk and K. E. Holsinger. New York: Oxford University Press.

Husband, Brian C., and Douglas W. Schemske. 1996. Evolution of the
magnitude and timing of inbreeding depression in plants. *Evolution* 50
(1):54-70.

IUCN/SSC. 1998. *IUCN guidelines for re-introductions*. Gland,
Switzerland and Cambridge, UK: IUCN/SSC Reintroduction Specialist Group.

Karp, Angela, Peter G. Isaac, and David S. Ingram, eds. 1998. *Molecular
tools for screening biodiversity*. Chapman & Hall.

Knapp, E. E., and A. R. Dyer. 1997. When do genetic considerations
require special approaches to ecological restoration? In *Conservation
Biology for the coming decade*, edited by P. L. Fiedler and P. Kareiva.
New York: Chapman and Hall.

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* 128:48-55.

Knapp, Eric E., and Kevin J. Rice. 1998. Comparison of isozymes and
quantitative traits for evaluating patterns of genetic variation in
purple needlegrass (*Nassella pulchra*). *Conservation Biology* 12
(5):1031-1041.

Koyama, H., and T. Kira. 1956. Intraspecific competition among higher
plants. VIII. Frequency distribution of individual plant weight as
affected by the interaction between plants. *J. Inst, Polytech. Osaka
City University* D7:73-94.

Landis, Thomas, and J.R. Thompson, eds. 1997. *National proceedings,
Forest and Conservation Nursery Associations*. Vol. Gen. Tech. Rep.
PNW-GTR-419. Portland, OR: Department of Agriculture, Forest Service,
Pacific Northwest Research Station.

Lesica, P., and F. W. Allendorf. 1999. Ecological genetics and the
restoration of plant communities: mix or match? *Restoration Ecology*
7:42-50.

Levin, Donald A. 1981. Dispersal *versus* gene flow in plants. *Annals
of the Missouri Botanical Garden* 68:232-253.

Manning, S. J., and M. G. Barbour. 1988. Root systems, spatial patterns,
and competition for soil moisture between two desert subshrubs.
*American Journal of Botany* 75:885-893.

McArdle, B. H. 1996. Levels of evidence in studies of competition,
predation, and disease. *New Zealand Journal of Ecology* 20:7-15.

Meffe, Gary K., and C. Ronald Carroll. 1994. *Principles of Conservation
Biology*. Sunderland, MA: Sinauer Associates.

Menges, Eric S. 1991. The application of minimum viable population
theory to plants. In *Genetics and conservation of rare plants*, edited
by D. A. Falk and K. E. Holsinger. New York: Oxford University Press.

Montalvo, A. M., S. L. Williams, K. J. Rice, S. L. Buchmann, C. Cory, S.
N. Handel, G. P. Nabhan, R. Primack, and R. H. Robichaux. 1997.
Restoration biology: a population biology perspective. *Restoration
Ecology* 5 (4):277-290.

Nei, Masatoshi. 1975. *Molecular population genetics and evolution*.
Edited by A. Neuberger and E. Tatum. Vol. 40, *Frontiers of Biology*.
Amsterdam: North-Holland.

Nekola, J. C., and P. S. White. 1999. The distance decay of similarity
in biogeography. *Journal of Biogeography* 26:867-878.

ONPS. 2001. *Guidelines on use of native plants for gardening*.
Portland, OR. Native Plant Society of Oregon. 3 pp.

Pantastico-Caldas, M., and D. L. Venable. 1993. Competition in two
species of desert annuals along a topographic gradient. *Ecology* 74
(8):2192-2203.

Pavlik, Bruce. 1996. Defining and measuring success. In *Restoring
diversity: strategies for reintroduction of endangered plants*, edited
by D. A. Falk, C. I. Millar and M. Olwell. Washington, ED: Island Press.

Primack, Richard B., and Hyesoon Kang. 1989. Measuring fitness and
natural selection in wild populations. *Annual Review of Ecology &
Systematics* 20:367-396.

Procaccini, G., and L. Piazzi. 2001. Genetic polymorphism and
transplanting success in the Mediterranean Seagrass, *Posidonia
oceanica* (L.) Delile. *Restoration Ecology* 9 (3):332-338.

Raven, Peter H., Ray F. Evert, and Susan E. Eichhorn. 1986. *Biology of
plants*. Fourth ed. New York: Worth Publishers.

Rehfeldt, G. E. 1990. Genetic differentiation among populations of
*Pinus ponderosa* from the upper Colorado River basin. *Botanical
Gazette* 151 (1):125-137.

Rieseberg, Loren H. 1991. Hybridization in rare plants: Insights from
case studies in *Cercocarpus* and *Helianthus*. In *Genetics and
conservation of rare plants*, edited by D. A. Falk and K. E. Holsinger.
New York: Oxford University Press.

Robichaux, Robert H., Elizabeth A. Friar, and David W. Mount. 1997.
Molecular genetic consequences of a population bottleneck associated
with reintroduction of the Mauna Kea Silversword (*Argyroxiphium
sandwicense* ssp. *sandwicense* \[Asteraceae\]). *Conservation Biology*
11 (5):1140-1146.

Schaal, Barbara A., Wesley J. Leverich, and Steven H. Rogstad. 1991.
Comparison of methods for assessing genetic variation in plant
conservation biology. In *Genetics and conservation of rare plants*,
edited by D. A. Falk and K. E. Holsinger. New York: Oxford University
Press.

Schoen, D. J., and A. H. D. Brown. 1993. Conservation of allelic
richness in wild crop relatives is aided by assessment of genetic
markers. *Proc. National Academy of Science (US)* 90:10623-10627.

Shaffer, Mark L., and Fred B. Samson. 1985. Population size and
extinction: A note on determining critical population sizes. *American
Naturalist* 125 (1).

Slatkin, M. 1987. Gene flow and population structure of natural
populations. *Science* 236:787-792.

Soorae, P. S., and P. J. Seddon, eds. 1998. *Re-introduction
practitioners directory*. Nairobi, Kenya and Riyahd, Saudi Arabia: IUCN
Species Survival Commission, Re-introduction Specialist Group.

Templeton, Alan R. 1991. Off-site breeding of animals and implications
for plant conservation strategies. In *Genetics and conservation of rare
plants*, edited by D. A. Falk and K. E. Holsinger. New York: Oxford
University Press.

Thompson, James D., and R. C. Plowright. 1980. Pollen carryover, nectar
rewards, and pollinator behavior with special reference to *Diervilla
lonicera*. *Oecologia* 46:68-74.

Tilman, David. 1999. The ecological consequences of changes in
biodiversity: a search for general principles. *Ecology* 80:1455-1474.

Tilman, David, and David Wedin. 1991. Plant traits and resource
reduction for five grasses growing on a nitrogen gradient. *Ecology* 72
(2):685-700.

Tuljapurkar, Shripad. 1989. An uncertain life: Demography in random
environments. *Theoretical Population Biology* 35:227-294.

Welden, C. W., W. L. Slauson, and R. T. Ward. 1988. Competition and
abiotic stress among trees and shrubs in northwest Colorado. *Ecology*
69:1566-1577.

White, Peter S., and Joan L. Walker. 1997. Approximating nature\'s
variation: selecting and using reference information in restoration
ecology. *Restoration Ecology* 5 (4):338-349.

Wilson, Scott D., and David Tilman. 1993. Plant competition and resource
availability in response to disturbance and fertilization. *Ecology* 74
(2):599-611.

Wright, Sewall. 1965. The interpretation of population structure by
F-statistics with special regard to systems of mating. *Evolution*
19:395-420.

Wright, Sewall. 1969. *The theory of gene frequencies*. Vol. 2. Chicago:
University of Chicago Press.

Wright, Sewall. 1978. *Variability within and among natural
populations*. Vol. 4. Chicago: University of Chicago Press.

Young, Andrew G., and Geoffrey M. Clarke, eds. 2000. *Genetics,
demography, and viability of fragmented populations*. Cambridge, UK:
Cambridge University Press.

***Some other relevant work in restoration genetics:***

Fenster, C. B. and M. R. Dudash. Genetic considerations for plant
population restoration and conservation, in Restoration of Endangered
Species, M. L. Bowles, and C. J. Whelan, Editors. 1994. Cambridge
University Press, p. 34-62.

Govindaraju, D. R. Gene flow, spatial patterns and seed collection
zones. Forest Ecology and Management, 1990. P. 291-302.

Handel, S. N., G. R. Robinson, and A. J. Beattie. Biodiversity resources
for restoration ecology. Restoration Ecology , 1994. 2:230-241.

Knapp, E. E., and K. J. Rice. Starting from seed: genetic issues in
using native grasses for restoration. Restoration and Management Notes,
1994. 12:p. 40-45.

Knapp, E. E., and K. J. Rice. Genetic structure and gene flow in *Elymus
glaucus* (blue wildrye): implications for native grassland restoration.
Restoration Ecology, 1996. 4: p. 1-10.

Knapp, E. E., and P. G. Connors. Genetic consequences of a
single-founder population bottleneck in *Trifolium amoenum* (Fabaceae).
American Journal of Botany, 1999. 86(1): p. 124-130.

Millar, C. I., and W. J. Libby. Disneyland or native ecosystem: genetics
and the restorationist. Restoration and Management Notes, 1989. 7: p.
18-24.

[^1]: Department of Ecology & Evolutionary Biology, and Society for
    Ecological Restoration, University of Arizona, Tucson, AZ

[^2]: US Geological Survey, Western Ecological Research Center, Three
    Rivers, CA

[^3]: Berry Botanic Garden, Portland, OR