U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2006–1305

Genetic Considerations for the Restoration of Smooth 

Cordgrass (Spartina alterniflora) Within Its Native Range
Genetic Considerations for the Restoration 

of Smooth Cordgrass (Spartina alterniflora) 

Within Its Native Range

By Steven E. Travis, C. Edward Proffitt, and Keith R. Edwards

Open-File Report 2006–1305

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

DIRK KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia 2006

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Suggested citation:

Travis, S. E., Proffitt, C. E., and Edwards, K. R., 2006, Genetic considerations for the restoration of smooth cordgrass 

(Spartina alterniflora) within its native range: U.S. Geological Survey Open-File Report 2006-1305, 11 pages.

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ii
iii

Contents

General Overview ..........................................................................................................................................1

Applying genetic principles to the restoration of salt marsh communities .........................................5

Summary and Recommendations .............................................................................................................10

References Cited..........................................................................................................................................11

Figures

1. Salt marsh developing on dredged sediments in the Sabine National Wildlife Refuge, La..... 2

2. An example of the role of genetic variation in the adaptation of a population to a change in 

its environment ..................................................................................... 3

3. The range of elevations at which smooth cordgrass is capable of colinizing will be 

determined by variation in traits related to wateruptake/conservation.................... 3

4. The change in inbreeding over time at varying population size.................................... 4

5. An example of outbreeding depression brought about by translocating individuals across 

populations adapted to different environmental conditions................................... 4

6. Smooth cordgrass patches growing along the margin of a borrow ditch in a created 

wetland.......................................................................................................................................... 5

7. A satellite photo of the western Calcasieu Lake estuary where it overlaps with the Sabine 

National Wildlife Refuge......................................................................... 5

8. The passive colonization by smooth cordgrass at a created site................................... 6

9. Outcrossing rates track clonal diversity in smooth cordgrass...................................... 7

10. The predicted change in clonal diversity over time for an initial seedling recruiter............ 7

11. Increasing clone size associated with increasing genetic diversity in older marshes......... 7

12. Stem density and average stem height differences between smooth cordgrass clones...... 8

13. Smooth cordgrass clones classified as functional types according to the light and crowding 

conditions they provide for other colonizing plant species................................... 9

14. Genetic isolation-by-distance in smooth cordgrass................................................... 9

15. The effects of smooth cordgrass transplantation on survival and growth ...................... 10
Tables

1. A comparison of genetic diversity among four smooth cordgrass populations............................6

iv
Abstract 

In order to remain viable over many generations, plant 

populations require the ability to respond adaptively to a 

changing environment. Such adaptive potential is directly 

controlled by underlying genetic variation, which can be 

measured in terms of both heterozygosity at the individual 

level and clonal, or genotypic diversity, at the population 

level. This report summarizes research relating to the 

importance of genetic diversity in the restoration of salt 

marsh smooth cordgrass, Spartina alterniflora, a dominant 

member of low elevation intertidal marshes throughout 

the northern Gulf of Mexico and Atlantic Coasts of North 

America. Recent research has indicated that S. alterniflora

is a partially clonal species characterized by the recruitment 

of seedlings exclusively during the initial colonization phase 

of population establishment. A major consequence of this 

finding is that clonal diversity generally peaks rather early 

in the development of a restored marsh, depending on the 

rate of natural immigration and/or the clonal diversity of 

planting units, and then undergoes a steady decline over 

geological time spans because of stochastic mortality and 

intraspecific competition. Low levels of clonal diversity 

resulting from restricted immigration or clonally depauperate 

planting materials in turn places strict limits on opportunities 

for outcrossing in a species known to suffer from severe 

inbreeding depression. Low clonal diversity may further lead 

to declining levels of heterozyosity of individual clones, which 

directly affects competitive ability. In addition, the planting 

of genetically diverse plant materials should take into account 

the genetic and adaptive differentiation that takes place 

when plant populations are widely separated in space and/or 

dwell under varying sets of environmental conditions. Thus, 

steps should be taken to ensure that S. alterniflora clones 

developed for restorative plantings are both genetically diverse 

and sufficiently pre-adapted to environmental conditions 

at the proposed restoration site. This can be achieved by 

growing plant materials collected from local sources and by 

either taking care to maintain relatively high levels of clonal 

diversity or by planting clones at sufficiently low densities that 

they will not quickly grow to monopolize a restoration site 

without first producing several generations of sexual recruits 

through crosses with nearby native populations.

General Overview

The ultimate goal of ecosystem restoration is the 

establishment of structural and functional equivalency 

between restored and natural communities. In other words, 

the restorationist generally desires that the restored community 

will develop towards a similar suite of species, in similar 

proportions and exhibiting similar levels of productivity, 

nutrient cycling, etc., to some predetermined target or 

reference community (fig. 1). For many restoration projects, 

a logical first step in this process is the reintroduction of 

the dominant primary producers characterizing the target 

community, which then act as ecosystem engineers by rapidly 

improving the conditions for colonization by other, more 

sensitive species (e.g., Bruno, 2000). Because restoration 

biology is so often concerned with the factors affecting the 

successful establishment of plant populations, many of the 

guiding principles of methodology have been borrowed 

from population biology. Population biology, in turn, 

relies on the principles of population ecology (or the study 

of how populations interact with the various elements of 

their environment) and population genetics (or the study 

of how gene pools are altered over time in response to 

these interactions). Thus, it is instructional to begin any 

consideration of the role of genetics in restoration biology 

with some basic principles of population genetics. 

Plants, like all organisms, are able to persist unaided 

in nature only if they are properly adapted to their surrounding 

environment. Furthermore, if their environment should change 

in a way that directly impacts their ability to survive and 

reproduce, their persistence will depend on their ability to alter 

their adaptations accordingly. At the heart of each adaptation, 

be it morphological or physiological, is a single gene or suite 

of genes controlling its expression. Even adaptations that are 

“adjustable,” that is adaptations that plants can alter in real 

time as their environment undergoes rapid changes, are only 

adjustable within limits that are dictated by underlying genes.

Genetic Considerations for the Restoration of Smooth 

Cordgrass (Spartina alterniflora) Within Its Native Range

By Steven E. Travis, C. Edward Proffitt, and Keith R. Edwards
 Genetic Considerations for the Restoration of Smooth Cordgrass (Spartina alterniflora) Within Its Native Range

In reality, the fate of individual plants is rarely a 

matter of direct concern, but rather the fate of populations. 

Populations, like individuals, are controlled by genes, although 

in this case it is the entire collection of genes dispersed 

across all of the member individuals, otherwise known as the 

“gene pool,” that comprises the operational unit upon which 

the environment acts. Through sexual reproduction and the 

cellular processes of random assortment and recombination, 

this gene pool is reshuffled with each passing generation, 

giving rise to a nearly limitless supply of individuals upon 

whose suites of adaptations the local environment can act. 

Thus, a population is provided with an effective mechanism 

for altering its adaptations over time in response to a 

fluctuating environment.

In order for two individuals to express variation 

in an adaptive trait they must also vary at the level of their 

genes. This variation is constantly being generated through a 

natural process of random mutation, which simply involves an 

alteration of the sequence of nucleotide building blocks within 

a gene. Each time a gene takes on a slightly altered form, 

a new “allele” is said to have arisen. In theory, the number 

of alleles representing any given gene is limited only by the 

number of individuals comprising a population. At the level 

of genes then, it is changes in the frequencies of these alleles, 

each of which affects some outward adaptation in a slightly 

different way, that drives the overall level of adaptation 

exhibited by a population (fig. 2 is a classic example of the 

role of genetic variation in the adaptation of a population to a 

change in its environment). 

If one assumes that populations exist along a 

continuum of genetic variation from one extreme, in which all 

individuals possess exactly the same alleles for every gene, 

to another, in which every individual possesses a completely 

unique set of alleles, it is easy to visualize how populations 

may differ in their responsiveness to environmental change. 

A population composed of a genetically identical set of 

individuals will have very little ability to respond, even 

if it is capable of sexual reproduction, because no new 

allelic combinations will be possible. On the other hand, 

a population in which no two individuals possess the same 

alleles for any given gene is not likely to be particularly well 

adapted to any particular set of environmental variables, and in 

order to avoid local extinction may be forced to adjust its allele 

frequencies more rapidly than would be possible through a 

limited number of breeding cycles. Thus, the ideal population 

exists somewhere in the middle of this genetic diversity 

continuum and exhibits a preponderance of individuals with 

matching alleles that render them generally well adapted to 

current environmental conditions, while harboring a sufficient 

quantity of alternative alleles to enable the population to adjust 

as conditions change.

For the purpose of restoring populations, there are 

several critical elements to consider. First, because every 

environment, no matter how stable, is constantly fluctuating 

on some level, every viable population will require genetic 

variation in order to make adjustments. A straightforward 

Figure 1. Salt marsh developing on dredged sediments in the

Sabine National Wildlife Refuge, La.: (A) an aerial perspective of a

1- to 2-year-old site showing circular smooth cordgrass (Spartina 

alterniflora) clones, (B) a 4- to 6-year-old site, with subjects

positioned to mark the edges of two consecutive years’ growth of

a single smooth cordgrass clone, (C) a 14- to 16-year-old marsh

dominated by typical salt marsh grasses: smooth cordgrass,

saltmeadow cordgrass (Spartina patens), and saltgrass (Distichlis 

spicata).

!	

"	

#	
example involves the introduction of a disease organism 

into a restored population. If a gene that controls disease 

resistance exists in only one form, and that form happens to 

be ineffective against the introduced pathogen, then the entire 

population may be lost. If, on the other hand, that gene exists 

in multiple forms, there is an improved chance that some 

individuals will harbor resistance and will thus enable the 

population to persist. In addition, it is important to consider 

that every environment is heterogeneous on some level, and 

without genetic variation a population may lack the ability 

to fully exploit that environment. For example, consider the 

situation in which elevation, and thus the availability of water, 

varies across an otherwise homogeneous environment (fig. 3). 

If every individual in the population is genetically predisposed 

to growing where water is readily available, then all but the 

lowest elevations within a site may remain uncolonized.

The level of genetic variation exhibited by a 

population will also impact its ability to propagate itself 

through sexual reproduction, because every gene in higher 

organisms exists in duplicate, with one copy coming from 

the maternal parent and the other from the paternal parent. 

Many new alleles arising through mutation will, by chance, be 

maladapted to prevailing environmental conditions; however, 

the environment will only be capable of eliminating these 

alleles if they are not masked by the normal, or wild type 

allele, represented in their homologous gene. If the alleles are 

masked, they are free to build up in a population as recessive 

alleles and to establish a mutational load. This mutational 

load will remain largely hidden from the environment unless 

genetic variation falls below the level at which individuals 

begin to reproduce with their close genetic relatives, or in 

the case of plants, with themselves, through the process 

of self-fertilization (fig. 4). Such inbreeding will greatly 

increase the probability that duplicate maladapted alleles 

will be brought together within a single individual and be 

expressed as a maladapted trait. To illustrate this process, 

consider the situation in which a maladapted recessive allele 

exists, along with a wild type allele, in only one individual 

of a large population. As long as this individual crosses with 

other, genetically distinct individuals, there is no chance 

its offspring will inherit two copies of the recessive allele; 

whereas, if the population becomes so small that it is forced 

to cross with itself, one in every four of its offspring will, 

by chance, express this maladapted trait. When many genes 

become involved in this process, virtually all of an individual’s 

offspring are likely to decline in their level of adaptation to 

the local environment in a process known as “inbreeding 

depression.”

MM or Mm mm

1848

1 % 99 %

1848

1 % 99 %

s = 30 %

1868

8% 92%

1868

8% 92%

Figure 2. A classic example of the role of genetic variation in the adaptation of a population to a change in its environment. Prior

to the industrial revolution, peppered moth populations in England were dominated by the nonmelanistic color morph (an adaptation

for avoiding predators while resting on the lichen-covered bark of trees). During the industrial revolution, the burning of coal

released soot into the environment, darkening the bark of trees and thus favoring the melanistic color morph. This color difference

is controlled by a single gene, represented with “m” in its nonmelanistic, recessive form, and with “M” in its melanistic, dominant

form. The rate of increase in the frequency of the melanistic color morph can be predicted from population genetics theory if its

relative advantage over the nonmelanistic form, s (30% in this case), is known.

Topographic Elevation

Low High

C

olonization by

S

m

o

oth C

ordgrass

Lo

w

High

Increasing Genetic Variation

Figure 3. For a dominant intertidal plant such as smooth

cordgrass, the range of elevations at which it is capable of

colonizing will be determined, at least in part, by the amount of

genetic variation in traits related to water uptake/conservation. 

In this figure, the solid line represents a clonally homogeneous

population, while the dashed and dotted lines represent

increasing levels of clonal diversity.

General Overview   
 Genetic Considerations for the Restoration of Smooth Cordgrass (Spartina alterniflora) Within Its Native Range

1.0

0.5

0.0

0 10 20 30 40 50

N = 5

N = 25

N = 50

N = 100

C

N = 500 oefficient of Inbreeding, f

Time in Generations, t

Figure 4. The change in inbreeding over time at varying

population size = N. The inbreeding coefficient is a measure of

the average probability that any given gene will be represented by

identical alleles inherited from a common ancestor.

combinations of alleles, because most adaptations are affected 

by several different genes, and it is the interactions among the 

alleles for these genes as much as the alleles themselves that 

control the expression of outward character states. If these 

combinations are broken, the level of adaptation may decline 

precipitously in a process known as outbreeding depression 

(fig. 5). Thus, if there is a good chance that a restored 

population will be interbreeding with natural populations in 

the area, it is critically important that the restored population 

should harbor similar alleles. In order to ensure that this is the 

case, populations should never be restored from individuals 

collected long distances from the restoration site. Gauging 

this distance can be difficult, but a good rule-of-thumb is to 

consider that if two populations had no conceivable chance 

of genetic exchange under natural conditions, they should 

probably not be allowed to exchange alleles in the context of 

restoration either.

In summary, the ideal restored population should 

harbor an amount of genetic diversity and a suite of alleles 

that is consistent with other natural populations in the local 

region. Since the local environment is constantly reworking 

this variation, it is safe to assume that what we can observe 

from natural populations is almost certainly what works best 

under prevailing conditions. To seriously alter this variation 

is to create a population that is maladapted and which will be 

extremely unlikely to meet long-term restoration goals.

A second genetic consideration for restoration is 

whether and at what frequencies the alleles present in the 

restored population match those that are adaptive under local 

environmental conditions. For example, if the plant species 

in question is characterized by a broad geographical range 

encompassing a wide range in temperature, then a population 

drawn from the colder end of the range would likely possess a 

set of alleles for cold tolerance that would be poorly adapted 

to a site existing at the warmer end of the range. Furthermore, 

even if two environments appear to be identical, if the 

populations occupying them are widely separated in space and 

have had little opportunity for allelic exchange, they will likely 

have evolved alternative sets of alleles for coping with their 

respective environments. Bringing these populations together 

and allowing them to interbreed may create maladapted 

Transfer

50 99 % 1 %

N = 1,000

1 % 99 %

N = 50

Random

Mating

75 %

25 %

Figure 5. An example of outbreeding depression brought about by translocating individuals across populations adapted to different

environmental conditions. A large (size N = 1,000), predominantly melanistic population of peppered moths living in a sooty environment

is used to augment a small (N = 50), nonmelanistic population living in a clean environment, resulting — after a single generation of

random mating — in a population of mostly melanistic individuals lacking in the cryptic coloration necessary for predator avoidance.
Applying Genetic Principles to the 

Restoration of Salt Marsh Communities

Smooth cordgrass (Spartina alterniflora) is a 

dominant member of low elevation, intertidal salt marshes 

throughout much of the northern Gulf of Mexico and Atlantic 

coasts of the United States and has been used extensively 

as an aid to offsetting coastal land loss. This is a robust 

species, capable of tolerating relatively extreme environmental 

conditions such as salinities approaching 70 ppt, at least in part 

caused by its clonal growth habit (fig. 6). Clonality enables 

the plant, or genet, to spread its risk of mortality over many 

hundreds or thousands of individual stems, or ramets, some 

of which may fortuitously find themselves growing under 

relatively benign conditions, even when the majority are under 

extreme stress. Thus, smooth cordgrass is able to provide a 

certain buffering capacity for the community as a whole, while 

providing critical habitat for both invertebrates (shellfish, 

crustaceans, etc.) and vertebrates (larval fish, waterfowl, semiaquatic rodents and their associated predators) (Travis and 

others, 2002a).

vicinity of the restoration and may offer the advantage of 

a more diverse gene pool that is preadapted to the suite of 

environmental conditions existing at the site.

In order to shed light on how passive colonization 

compares to active planting in maintaining genetically 

viable populations over the long-term, considerable effort 

by researchers at the USGS National Wetlands Research 

Center (Lafayette, La.), in cooperation with McNeese State 

University (Lake Charles, La.) and the University of Louisiana 

at Lafayette, has gone into studying the dynamics of passive 

colonization by smooth cordgrass at both natural and created 

sites in the gulf coast region. This work began in 1998 at 

the Sabine National Wildlife Refuge (Sabine NWR) in 

southwestern Louisiana, where four separate marsh creation 

projects have restored over 1,000 hectares of emergent 

salt marsh since 1983 (fig. 7). These sites are interspersed 

with small areas of undisturbed, native marsh, providing 

an opportunity for comparison with an appropriate target 

ecosystem. Based on aerial photographs of the area, which 

allow us to track the history of saltwater intrusion into the 

surrounding Calcasieu Lake estuary, we have dated the oldest 

salt marshes at approximately 50 years old.

Passive colonization of created sites is dependent 

on the rafting of both floating vegetation mats, which 

transport fragments of clones, and seeds (fig. 8). Thus, 

initial colonization is entirely dependent on at least partial 

inundation. Nevertheless, even at sites where episodes of tidal 

inundation are rare, clonal spread and sexual reproduction, 

combined with occasional inundation resulting from sustained 

winds blowing water into the estuary from the Gulf of Mexico 

to the south, have been sufficient to bring about > 50% 

colonization of sites as large as 300 hectares within a period 

of just 3 years (Proffitt and Young, 1999). Although smooth 

cordgrass has generally been noted for its low seed viability, 

widespread seedling recruitment was found to occur on bare 

sediments during peak years at the Sabine NWR.

Figure 6. Smooth cordgrass patches growing along the margin

of a borrow ditch resulting from the construction of a containment

levee around a created wetland. Because of the rarity of flooding

on many created sites, standing water salinites can reach very

high levels, giving an advantage to clones that are spread out over

a relatively broad elevational gradient.

The various methods used to restore smooth 

cordgrass to intertidal salt marsh generally fall into two 

categories, passive colonization and active planting. Whether 

the restoration site has been intentionally created from open 

water, such at through the deposition of sediments dredged 

from nearby navigation channels, or whether it is undergoing 

mitigation following some high impact disturbance such 

as a chemical spill, active planting would seem to provide 

the advantage of more rapid coverage of the site. Passive 

colonization, however, can be a relatively rapid process if a 

ready supply of potential immigrants exists in the immediate 

1999

1996

Calcasieu Ship

Channel

1983

1993

1993

1 km

Figure 7. A satellite photograph of the western Calcasieu

Lake estuary where it overlaps with the Sabine National Wildlife

Refuge. Four salt marsh sites were created from dredged

sediments by the U.S. Army Corps of Engineers in 1983, 1993, 1996,

and 1999 (outlined in black).

Applying Genetic Principles to the Restoration of Salt Marsh Communities   
   Genetic Considerations for the Restoration of Smooth Cordgrass (Spartina alterniflora) Within Its Native Range

(A)

Ramet

(B)

Established Clones

Figure 8. The passive colonization by smooth cordgrass at a

created site: (A) a vegetation mat with a live ramet sprouting in

the upper right portion of the photograph, (B) a seedling fringe

growing on either side of a dry tidal creek (established clones can

be seen growing in the background).

Polulation Age (Yrs) <H> <P>

Reference 40-50 0.21 0.77

1983 Site 14 0.24 0.82

1993 Site 4 0.19 0.55

1996 Site 1 0.26 0.68

Table 1. A comparison of genetic diversity among four

smooth cordgrass populations — three created and one natural

(reference), varying in age from 1 to 50 years at the Sabine

National Wildlife Refuge: <H> = average heterozygosity, or the

average proportion of genetic loci at which a randomly chosen

individual would be expected to possess two alternate alleles;

<P> = proportion of polymorphic loci, where a polymorphic locus

is defined as having two alleles, each at a frequency of < 0.95.

From a population genetics perspective, a logical 

first question in evaluating the adaptive potential of restored 

smooth cordgrass populations is how quickly are natural 

levels of genetic diversity attained? To answer this question, 

populations growing on three created sites ranging in age from 

2 to 15 years were compared to an adjacent reference marsh 

using neutral molecular markers in the form of amplified 

fragment length polymorphisms (AFLPs) run on a random 

sample of 20-35 individuals per site (Travis and others, 

2002b). Overall, the findings indicated that the gene pool 

available for colonization was sufficiently diverse to establish 

equivalent levels of diversity across all populations within just 

2 years (table 1), buoyed by an estimated migration rate of 3.6 

migrants (either pollen or seeds) per generation. Population 

genetics theory predicts that an average of just 1 migrant per 

generation is sufficient to create panmixis, or the complete 

homogenization of diverse gene pools over time, and thus 

the adaptive potential of the smooth cordgrass populations 

growing on created sites at the Sabine NWR appears to be 

high.

In clonal species such as smooth cordgrass, genetic 

diversity, which is calculated as an overall population average 

using a variety of statistics such as average heterozygosity, 

may paint only half of the picture. This is because clonal 

species have the capacity to colonize entire sites starting 

from just one or several clones. Even if these clones were 

highly heterozygous (i.e., genetically diverse) the adaptive 

potential of the population would still be limited, as would the 

potential for avoiding the deleterious effects of inbreeding. 

Thus, another important question is how quickly are natural 

levels of clonal diversity attained on passively colonized 

sites? In this case, a clear relationship was observed between 

clonal diversity and marsh age when 12 ramets were sampled 

from each of 20 patches at 4 sites, with the lowest diversity 

occurring on the youngest sites, then increasing to a predicted 

maximum of > 0.90 (on a scale of 0 to 1) at approximately 30 

years, followed by a gradual decline (Travis and others, 2004). 

Of equal importance, outcrossing rates were found to track 

clonal diversity very closely (fig. 9), and the consequences of 

self-fertilization were severe, with the evidence suggesting that 

selfed seedlings were rarely surviving to reach sexual maturity.

One of the more illuminating findings to come 

from studies of clonal diversity in smooth cordgrass is that 

seedling recruitment occurs almost exclusively on bare 

substrate. This helps to explain not only the aforementioned 
in clonal diversity noted in the previous study was found to 

hold true over geologic time, with a decrease in diversity 

of approximately 1 percent per 100 years. A concomitant 

increase in the maximum diameter of individual clones 

was noted, indicating that older marshes are increasingly 

dominated by a decreasing number of competitively superior 

clones over time. Evidence that these clones were drawing 

their advantage from comparatively high levels of genetic 

diversity came in the form of an increasingly positive 

relationship between average heterozygosity and clone 

size with increasing age of marsh (fig. 11). This is the first 

real indication of a direct link between genetic diversity 

at the individual level and fitness in smooth cordgrass. In 

0.0

0.2

0.4

0.6

0.8

1.0

2 yr 5 yr 16 yr 50 yr

Outcrossing Rate/Clonal Diversity

Age of Marsh

Clonal Diversity

(No Data)

Figure 9. Outcrossing rates track clonal diversity very closely

among four smooth cordgrass populations varying in age from 2

to 50 years. Here, outcrossing is defined as any sexual cross that

does not involve self-fertilization, and clonal diversity is measured

as the complement of the Simpson diversity index.

decline in clonal diversity beyond a marsh age of 30 years, 

but also the lack of seedling recruitment in established smooth 

cordgrass populations that has been noted by other researchers 

(e.g., Hartman, 1988). Clonal plants are considered to fall 

into two distinct categories based on their seed dispersal 

capabilities: (1) those with large seeds adapted for germinating 

in established populations, known as repeated seedling 

recruiters, and (2) those with small seeds adapted for longrange dispersal and colonization of novel environments, 

known as initial seedling recruiters. The latter category, 

which we now know to include smooth cordgrass, exhibits 

declining clonal diversity over time in established populations, 

because in the absence of new clones a gradual attrition 

of the founding population will occur through stochastic 

mortality and possibly through competition if some clones are 

competitively superior. This is an extremely important finding 

for restoration, because it suggests that smooth cordgrass 

populations founded from a small number of clones, whether 

through passive colonization or active planting, will peak at 

very low levels of clonal diversity and only need to experience 

small additional losses to achieve a genetic monoculture (fig. 

10), which would represent a dead-end from both an adaptive 

and a reproductive perspective.

In order to evaluate whether such monocultures are 

ever actually achieved under natural conditions, as well as 

how the negative consequences of low clonal diversity may 

be avoided in very old populations, a broader comparison of 

natural populations was conducted, encompassing the entire 

Louisiana coastline (Travis and Hester, 2005). Population 

ages were estimated from published sediment core data 

that utilized radiocarbon dating throughout the Mississippi 

deltaic plain. In total, 8 natural populations ranging in age 

from approximately 6 to 1,500 years were compared for both 

clonal diversity and maximum clone diameter, and the decline 

Passive colonization with a

ready supply of immigrants or

active planting with a large

number of clones

Passive colonization of an

isolated site, or active

planting with a small number

of clones

Clo

n

al Div

ersity

Age of Marsh

Figure 10. The predicted change in clonal diversity over time

for an initial seedling recruiter such as smooth cordgrass. The

initially slow increase in clonal diversity is caused by the spatial

isolation of early colonizers, such that sexual reproduction is

only possible through self-fertilization, and the majority of the

seed progeny suffer mortality from inbreeding depression. The

steady state achieved in the upper plot might be expected with

a relatively high frequency of low-level disturbances, which

occasionally create bare substrate for colonization by seedlings. 

Note that the lower plot quickly declines to a monoculture caused

by the gradual loss of most of the founding clones.

R2 = 0.6765

-0.02

0.02

0.06

0.10

0.14

0.18

0 500 1,000 1,500

Age of Marsh (yr)

Regression Slope of Clone

Size on Heterozygosity

Figure 11. Increasing clone size associated with increasing

genetic diversity (heterozygosity) in older marshes, indicating the

competitive advantage enjoyed by highly heterozygous clones.

Applying Genetic Principles to the Restoration of Salt Marsh Communities   
   Genetic Considerations for the Restoration of Smooth Cordgrass (Spartina alterniflora) Within Its Native Range

As a means of directly assessing the importance 

of clonal diversity to the development of species-rich salt 

marsh plant communities, two independent experiments were 

conducted. First, the growth experiment just described was 

revisited after 3.5 years, at which time all 5 experimental 

clones were measured for colonization by other plant species, 

both along their peripheries and in their interiors, which tend 

to undergo a natural process of senescence over time (Proffitt 

and others, 2005). Whether a particular smooth cordgrass 

clone tended to facilitate or suppress colonization tended to 

depend not only on the light and water requirements of the 

colonizing species, but also on the average per-unit biomass 

exhibited by the clone, which was a general indicator of light 

and heat penetration to the soil surface (fig. 13). Using two of 

the more common colonists, the annuals Salicornia bigelovii

and Aster subulatus var. subulatus, as examples, the abundance 

of each species varied by location, with S. bigelovii preferring 

the edges of smooth cordgrass clones and A. subulatus

preferring to colonize clone centers. Location also affected S. 

bigelovii’s performance relative to each experimental clone, 

while A. subulatus consistently performed poorly relative 

to the tallest clone in the experiment because of an apparent 

intolerance for shade. A second experiment explored the 

potential facilitative effects of smooth cordgrass on a perennial 

shrub, Baccharis halimifolia, by comparing the rate of seed 

settling and seedling growth inside and outside of clones. 

The experiment showed that while significantly fewer seeds 

settled inside clones, seedlings nevertheless gained a clear 

advantage in terms of both survival and growth (Egerova and 

others, 2003). Such preferences make it very conceivable that 

a smooth cordgrass community characterized by low clonal 

addition, this work revealed a mechanism by which long-lived 

populations maintain relatively high levels of outcrossing, via 

the fragmentation of clones and intermingling of ramets from 

distinct genets.

Because each of the aforementioned studies draws 

inferences about the adaptive potential of populations 

from neutral DNA markers, i.e., nongene sequences that 

are invisible to natural selection, it is important to address 

whether the genetic differences noted among clones actually 

translate into adaptive differences linked to survival, growth, 

and reproduction. For this purpose, a large common-garden 

experiment was conducted at a newly created site in the 

Sabine NWR (Proffitt and others, 2003). A total of 5 large 

clones that had naturally colonized a separate area of restored 

marsh were transplanted for this experiment, with 35 separate 

plantings consisting of 10 ramets each, established in a 

randomized block configuration. Each planting was measured 

for survival and growth over a period of 18 months, and 

higher levels of variation among than within clonal replicates 

was taken as evidence of heritable differences. Mortality as 

a result of transplantation shock varied significantly among 

clones and was directly related to differences in elevation 

across the experimental site for 2 of the 5 clones. One clone 

was superior to all others at achieving rapid lateral growth at 

all elevations. Notably, the clones exhibiting the highest stem 

densities also tended to display the shortest mean stem heights, 

while the sparsest clones tended to be the tallest, showing a 

clear tradeoff in resource allocation (fig. 12). Overall, these 

differences highlight the structural heterogeneity imparted 

to smooth cordgrass communities by interclonal variation in 

morphologies and ecological tolerances. 

0

50

100

150

200

250

A B C D E

Genotype

N

u

m

b

e

r

o

f

Ste

m

s

/

m

2

(A)

0

20

40

60

80

100

A B C D E

Genotype

H

eig

ht (c

m) (B)

Figure 12. Stem density (A) and average stem height (B) differences between experimental smooth cordgrass clones. Significant

differences between clones C (blue) and D (red) illustrate a tradeoff in resource allocation between growth forms.
diversity might directly exclude some potential colonists, if 

none of the clones present were of the preferred functional 

type, or indirectly exclude them if their facilitative effect on a 

competing colonist was particularly strong.

A critical element promoting the establishment of 

clonal diversity in restored smooth cordgrass populations is 

gene flow, whether by clone fragmentation, by seed dispersal, 

or by pollen dispersal. While there are no published studies of 

pollen dispersal in smooth cordgrass, estimates for a closely 

related congener, saltmeadow cordgrass (Spartina patens), 

suggest average dispersal distances of just 3 m (Silander and 

Antonovics, 1979), so the potential for pollen dispersal to 

contribute significantly to interpopulation gene flow in smooth 

cordgrass is likely to be limited. On the other hand, direct 

evidence of the limits to seed dispersal in smooth cordgrass 

exists in the form of local genetic structure developing 

within young populations, as exemplified by elevated levels 

of genetic relatedness among neighboring clones(Travis 

and others, 2004). Locally structured populations likely 

develop as a result of seeds germinating in close proximity 

to their parents and siblings, which creates the potential for 

inbreeding among genetic relatives (beyond that which may 

occur through self-fertilization). Nevertheless, seed dispersal 

may be enhanced by the presence of open water margins at 

the edges of populations, as suggested by a study that tracked 

smooth cordgrass recovery following a dieback from a severe 

drought (Edwards and others, 2005). In this instance, many 

seedlings could be clearly observed within the recovering 

marsh, which was both slightly more genetically diverse than 

and slightly differentiated from an adjacent population that 

had remained relatively unaffected by the drought. These 

results suggest that these seedlings had germinated from seeds 

rafting in from other areas. The rafting of clone fragments has 

also been observed (Proffitt and Young, 1999), but may be an 

effective form of dispersal only during high level disturbances. 

Overall, the combined mechanisms of clone fragmentation 

and seed dispersal have resulted in a general pattern of genetic 

isolation-by-distance in smooth cordgrass, with a relatively 

high degree of population mixing at distances of up to 

approximately 350 km (Travis and Hester, 2005) (fig. 14). 

Biomass (g/m2)

0 200 400 600 800 1000

Percent Light Penetration

0

20

40

60

80

100

Edge Functional Type

Clones C, D, E

Center Functional Type

Clones A, B, C, D

Center Functional Type

Clone E

Edge Functional Type

Clones A, B

Biomass (g/m2)

0 200 400 600 800 1000

Percent Light Penetration

0

20

40

60

80

100

Edge Functional Type

Clones C, D, E

Center Functional Type

Clones A, B, C, D

Center Functional Type

Clone E

Edge Functional Type

Clones A, B

Figure 13. Smooth cordgrass clones classified as functional

types according to the light and crowding conditions they

provide for other colonizing plant species. Because clones

characteristically undergo a process of center senescence, the

function they provide at the center to potential colonists does not

necessarily match the function they provide at the edge.

0.00

0.05

0.10

0.15

0.20

0.25

0 100 200 300 400 500

Geographic Distance (km)

G

enetic

Distanc

e (θ) 0.00

0.05

0.10

0.15

0.20

0.25

0 100 200 300 400 500

Geographic Distance (km)

G

enetic

Distanc

e (θ)

Figure 14. Genetic isolation-by-distance in smooth cordgrass,

where θ represents the proportion of overall genetic variation

attributable to differentiation among populations. Values of θ do

not generally begin to exceed 0.15, considered a moderate degree

of genetic differentiation, until geographic distances exceed 300-

400 km.

Ongoing research at the USGS National Wetlands 

Research Center (Lafayette, La.) is directly addressing 

issues of smooth cordgrass transplantation conducted for 

the purpose of salt marsh restoration, as well as the potential 

for outbreeding depression associated with transplantation 

activities. The success of restoring habitats through the 

transplantation of plant materials depends critically on 

the degree to which the donor populations happen to 

be preadapted to the restoration site, which may be a 

simple matter of physical proximity. Assessing levels of 

preadaptation may be greatly simplified through the use of 

neutral genetic markers in species such as smooth cordgrass, 

which exhibit a pattern of isolation-by-distance. Using a 

common-garden approach, a comparison of growth and 

reproductive performance among representatives from 23 

smooth cordgrass populations collected at sites ranging from 

Texas to Maine is being conducted in order to determine 

the strength of the relationship between preadapation and 

geographical and latitudinal distance from the donor site (fig. 

15). In addition, genetic differentiation between each donor 

site and a natural population growing immediately adjacent 

to the common-garden site is being evaluated to determine 

the comparative value of DNA fingerprinting as a predictor of 

preadaptation. Eight clones have been transplanted from each 

donor site and grown in a randomized block configuration 

Applying Genetic Principles to the Restoration of Salt Marsh Communities   
10 Genetic Considerations for the Restoration of Smooth Cordgrass (Spartina alterniflora) Within Its Native Range

0.00

0.20

0.40

0.60

0.80

1.00

25 30 35 40 45

Latitude (Degrees)

R2 = 0.6597

(A)

0.0

0.5

1.0

1.5

2.0

2.5

0.00 0.20 0.40 0.60

Genetic Distance (θ)

Bio

m

a

s

s (total ste

m

h

eig

ht X

width

X 10-5)

R2 = 0.5207

(B)

Figure 15. The effects of smooth cordgrass transplantation

on survival and growth: (A) Survivorship correlates most

strongly with the latitude of the donor site, with the high latitude

populations suffering the highest mortality in Louisiana at a

latitude of 25 degrees; (B) Growth (measured using a surrogate

for biomass) correlates most strongly with the level of genetic

differentiation between the donor populations and a reference

population growing adjacent to the common-garden site.

over a slight elevational gradient at the Sabine NWR. Nine 

independent variables are being used to compare survival, 

growth, photosynthetic rate, and reproduction. A multivariate 

stepwise discriminant function analysis has identified a 

group of 5 variables that are useful in discriminating among 

the donor materials, while a structural equation modeling 

approach is being used to determine the relative contributions 

of geographic versus genetic distance in predicting variations 

in performance.

Summary and Recommendations

The overall implications of this research for smooth 

cordgrass restoration can be summarized as follows. First, 

smooth cordgrass plants selected for restoration that are 

low in genetic diversity, as measured by statistics such as 

average heterozygosity, will be at a competitive disadvantage 

relative to those representing natural populations. As shown, 

natural levels of genetic diversity develop quickly through 

passive colonization as long as a ready source of immigrants 

is available, and most actively planted clones will have been 

selected for growth characteristics that are reflective of 

high levels of genetic diversity. Thus, genetic diversity is 

unlikely to affect the immediate success of smooth cordgrass 

restorations, but rather will only become an issue if conditions 

leading to inbreeding act over time to lower it significantly. 

Second, the primary circumstance promoting inbreeding is 

low clonal diversity, which can develop through the passive 

colonization of physically isolated sites or the active planting 

of sites with a highly limited number of smooth cordgrass 

clones. This is largely a consequence of the ability of smooth 

cordgrass to rapidly overgrow sites via clonal spread, coupled 

with the inability of seedlings to become established once 

colonization is complete. Clonal diversity also ensures 

maximal coverage of sites varying in key environmental 

parameters such as elevation and facilitates the development 

of structural heterogeneity, ultimately leading to colonization 

by a diverse assemblage of plant species characteristic of gulf 

coast salt marshes. The continual decline in clonal diversity 

that occurs over thousands of years in smooth cordgrass 

populations renders it particularly important that high 

levels of clonal diversity be established at the outset of any 

restoration project in order to assure its long-term viability. 

Finally, attention should be paid, at the outset of any smooth 

cordgrass restoration project involving active transplantation, 

to the genetic and geographic distances between the donor 

and recipient sites. Materials taken or developed from distant 

sources may be maladapted to the restoration site and/or may 

contain genes that do not mix well with those of adjacent 

populations. 

The overall recommendations for habitat restoration 

using smooth cordgrass stemming from this research are 

straightforward. Passive colonization is generally a highly 

effective method of restoring natural levels of genetic 

and clonal diversity on created sites; however, if a site is 

particularly isolated, such as would be expected for a barrier 

island, or if the potential for erosion of the site is particularly 

high, transplantation may still be desirable. In the latter 

situation, planting the donor materials at relatively low 

densities would be optimal for promoting natural levels of 

diversity. This practice will provide ample opportunity for 

crossbreeding with clones from neighboring populations and 

recruitment of the resultant seedlings prior to the complete 

coverage of the site. In the case of isolated sites, there is 

simply no substitute for developing plant materials that are 
highly diverse genetically and clonally prior to initiating 

the restoration program; otherwise, the low clonal diversity 

thus established may doom the resulting population to 

extinction, which may only require a single catastrophic 

event such as a disease outbreak to occur. In all situations, 

care should be taken not to transplant materials across donor 

and transplantation sites that are separated by more than 

approximately 300-400 km unless the proper steps have 

been taken to assure adequate levels of preadaptation. While 

these simple guidelines cannot anticipate every possible 

contingency, such as the effects of major storm events or 

human errors committed during preparation of the restoration 

site, if properly followed they should help to optimize the 

viability of restored smooth cordgrass populations and greatly 

enhance their probability of persisting well into the future.

References Cited

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communities through habitat modification by Spartina 

alterniflora: Ecology, v. 81, p. 1,179-1,192.

Edwards, K. R., Travis, S. E., and Proffitt, C. E., 2005, 

Genetic effects of a large-scale Spartina alterniflora 

(smooth cordgrass) dieback and recovery in the northern 

Gulf of Mexico: Estuaries, v. 28, p. 204-214.

Egerova, J., Proffitt, C. E., and Travis, S. E., 2003, Facilitation 

of survival and growth of Baccharis halimifolia L. by 

Spartina alterniflora Loisel in a created Louisiana salt 

marsh: Wetlands, v. 23, p. 250-256.

Hartman, J. M., 1988, Recolonization of small disturbance 

patches in a New England salt marsh: American Journal of 

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R., and Travis, S. E., 2005, Spartina alterniflora genotype 

influences facilitation and suppression of high marsh 

species colonizing an early successional salt marsh, Journal 

of Ecology: v. 93, p. 404-416.

Proffitt, C.E., Travis, S. E., and Edwards, K. R., 2003, 

Genotype and elevation influence Spartina alterniflora

colonization and growth in a created salt marsh: Ecological 

Applications, v. 13, p. 180-192.

Proffitt, C. E., and Young, J., 1999, Salt marsh plant colonization, growth, and dominance on large mudflats created 

using dredged sediments, in Rozas, L. P., Nyman, J. A., 

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E., eds., Proceedings -- Recent research in coastal Louisiana 

-- natural system function and response to human influence: Louisiana Sea Grant College Program, Baton Rouge, 

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Silander, J. A., and Antonovics, J., 1979, The genetic basis of 

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Travis, S., Proffitt, E., Edwards, K., Hartman, G., and Haigh, 

G., 2002a, Text box 7.2 -- Ongoing dredged material marsh 

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G., and Streever, W., Approaches to coastal wetlands 

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Travis, S. E., and Hester, M. W., 2005, A space-for-time substitution reveals the long-term decline in genotypic diversity 

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a span of 1,500 years: Journal of Ecology, v. 93, p. 417-430.

Travis, S. E., Proffitt, C. E., Lowenfeld, R. C., and Mitchell, T. 

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among differently aged populations of Spartina alterniflora

on restored versus natural wetlands: Restoration Ecology, v. 

10, p. 37-42.

Travis, S. E., Proffitt, C. E., and Ritland, K., 2004, Population 

structure and inbreeding vary with successional stage in created Spartina alterniflora marshes: Ecological Applications, 

v. 14, p. 1,189-1,202. 

References Cited 11