U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2011–1038

Vegetation Communities at Big Muddy National Fish and 

Wildlife Refuge, Missouri
Cover: Wetland area classified as the National Vegetation Classification System Midwest Ephemeral Pond (CEGL002430), and the 

same area as mapped from 2007 U.S. Department of Agriculture National Agricultural Imagery Program aerial photographs (inset).
Vegetation Communities at Big Muddy 

National Fish and Wildlife Refuge, Missouri

By Matthew A. Struckhoff, Keith W. Grabner, and Esther D. Stroh

Open-File Report 2011–1038

U.S. Department of the Interior

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

KEN SALAZAR, Secretary

U.S. Geological Survey

Marcia K. McNutt, Director

U.S. Geological Survey, Reston, Virginia: 2011

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Although this report is in the public domain, permission must be secured from the individual copyright owners to 

reproduce any copyrighted materials contained within this report.

Suggested citation:

Struckhoff, M.A., Grabner, K.W., and Stroh E.D, 2011, Vegetation communities at Big Muddy National Fish and Wildlife Refuge, Missouri: U.S. Geological Survey Open-File Report 2011–1038, 29 p. with Appendix.
iii

Contents

Abstract...........................................................................................................................................................1

Introduction.....................................................................................................................................................1

Study Area.......................................................................................................................................................2

Methods...........................................................................................................................................................4

Identification of Potential Vegetation Communities........................................................................4

Data Collection......................................................................................................................................5

2002–04 Previously Collected Vegetation Data.......................................................................5

2007 New Data..............................................................................................................................5

Data Analysis.........................................................................................................................................7

Map Production.....................................................................................................................................8

Community Delineation...............................................................................................................8

Final Community Polygon Classification and Boundary Adjustment ..................................8

Results .............................................................................................................................................................8

Vegetation Communities of Big Muddy National Fish and Wildlife Refuge................................8

Analyses of Plot Vegetation Data.....................................................................................................10

Wooded Communities ...............................................................................................................10

Herbaceous Communities ........................................................................................................14

Map Production...................................................................................................................................19

Management Implications..........................................................................................................................23

References Cited..........................................................................................................................................26

Figures

1. Map showing Big Muddy National Fish and Wildlife Refuge management units, 

Missouri, USA, 2006......................................................................................................................3

2. Diagram showing monumentation used to permanently mark plots ...................................6

3. Diagram showing Beyond North American Weed Management Association 

(NAWMA) plot design used during 2007 sampling..................................................................6

4. Graph showing non-metric Multidimensional Scaling output for woody 

communities based on woody stem basal area ....................................................................15

5. Graph showing non-metric Multidimensional Scaling output for woody 

communities based onwoody stem density. .........................................................................16

6. Graph showing non-metric Multidimensional Scaling output for herbaceous 

communities with vectors indicating direction of increase for those species 

most correlated with the data structure.................................................................................20

7. Map showing vegetation for portion of floodplain at Overton Bottoms 

unit at Big Muddy National Fish and Wildlife Refuge, Missouri .........................................21

8. Map showing vegetation for upland section of Saint Aubert Island unit 

at Big Muddy National Fish and Wildlife Refuge, Missouri.................................................24
iv

Tables

1. Existing and potential National Vegetation Classification System (NVCS)

Associations at Big Muddy National Fish and Wildlife Refuge ............................................9

2. Existing ruderal vegetation associations and other mapped features at Big Muddy

National Fish and Wildlife Refuge............................................................................................10

3. Woody species measures for woody dominated vegetation associations as

classified based on field data and observations...................................................................12

4. Multiple-Response Permutation Procedure results for woody communities based

on woody stem basal area ........................................................................................................17

5. Multiple-Response Permutation Procedure results for woody communities based

on woody stem density ..............................................................................................................18

6. Results of Multiple Response Permutation Procedure analysis of herbaceous

communities ................................................................................................................................20

7. Polygon count and area for mapped communities at Big Muddy National Fish and

Wildlife Refuge............................................................................................................................22
v

Multiply By To obtain

Length

inch (in) 2.54 centimeter (cm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Area

acre 4,047 square meter (m2

)

acre 0.4047 hectare (ha)

acre 0.004047 square kilometer (km2

)

square foot (ft2

) 0.09290 square meter (m2)

square mile (mi2

) 259.0 hectare (ha)

square mile (mi2

) 2.590 square kilometer (km2) 

Inch/Pound to SI

Multiply By To obtain

Length

cemtimeter (cm) 0.39 inch (in)

meter (m) 3.281 foot (ft) 

kilometer (km) 0.6214 mile (mi)

meter (m) 1.094 yard (yd) 

Area

square meter (m2

) 0.0002471 acre 

hectare (ha) 2.471 acre

square kilometer (km2

) 247.1 acre

hectare (ha) 0.003861 square mile (mi2

) 

SI to Inch/Pound

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83).

Conversion Factors

Introduction 1

Abstract 

New and existing data were used to describe and map 

vegetation communities at Big Muddy National Fish and 

Wildlife Refuge. Existing data had been gathered during the 

growing seasons of 2002, 2003, and 2004. New data were 

collected in 2007 to describe previously unsampled communities and communities within which insufficient data had 

been collected. Plot data and field observations were used to 

describe 17 natural and semi-natural communities at the Association level of the National Vegetation Classification System 

(NVCS). Four ruderal communities not included in the NVCS 

are also described. Data were used to inform delineation of 

communities using aerial photos from 2000, 2002, 2003, 2005, 

2006, and 2007. During this process, eleven additional land 

cover classes including cultural features, managed vegetation communities, and water features were identified. These 

features were mapped, some were described, but no vegetation 

data were collected. In 2009, nearly all community polygons 

were field visited and classified to the Association level. When 

necessary, polygon boundaries were adjusted based on field 

observations. The final map includes 482 polygons of 27 land 

cover classes encompassing 3,174 hectares on 5 units of the 

refuge. Data and information will inform the development of 

the refuge Comprehensive Conservation Plan.

Introduction

Historically, the lower portion of the Missouri River, 

from Sioux City, Iowa to Saint Louis, Missouri, consisted of 

braided and shifting channels, numerous snags, islands, sandbars, oxbow lakes, and ephemeral wetlands (Galat and others, 

1998; Funk and Robinson, 1974; Weaver, 1960). Before channel management and engineering, the Missouri River flood 

plain supported a diverse suite of forested communities, shrublands, prairies, swamps, and marshes (Nigh and Schroeder, 

2002). Flooding cycles included an early spring flood (because 

of upstream snowmelt), followed by an early summer flood 

(because of continued upstream snowmelt and rainfall), and 

by a gradually diminished river flow during the summer and 

into the fall and winter (Galat and others, 1998). This flooding 

cycle, as in most riparian systems, helped to produce a mosaic 

of vegetation and wetland communities (Gurnell, 1997).

The Missouri River historically has been used as a 

transportation corridor, but the constantly shifting channel, 

dynamic sandbars, and the presence of partially buried and 

floating logs made river navigation treacherous. From 1832 

to 1900 the first attempt at managing the river for transportation was attempted; large woody debris was removed from the 

channel to improve navigation (Funk and Robinson, 1974). 

From 1884 to 1902, management of the Missouri River was 

the responsibility of the Missouri River Commission, with 

the objective of improving the navigation of the river through 

uniformly contracting the width of the river, fixing its location and protecting all banks from erosion (Suter, 1887, in

Funk and Robinson, 1974). In 1912, the U.S. Army Corps of 

Engineers (USACE) began construction of a levee system, and 

by 1933 the river channel was being improved for navigation (Funk and Robinson, 1974). Recent river management 

includes the construction of wing dikes and revetments to 

stabilize the river bank and to create a narrowed, self-dredging 

navigation channel (Jacobson, 2006). The results of river 

management have been a loss of wetlands and riparian forest 

habitat but an increase in agriculture along the Missouri River 

corridor (Galat and others, 1998).

In 1993, 1995 and 1996, the Lower Missouri River 

flooded, inundating nearly the entire flood plain from Kansas 

City to Saint Louis, Missouri (Galat and others, 1998). These 

multiple, record-setting floods stimulated a reevaluation of 

river management (Galat and others, 1998). State and federal 

programs were established to purchase or protect lands within 

the Missouri River flood plain. In 1993 and 1994, Congress 

authorized and provided funding for the U.S. Fish and Wildlife Service (USFWS) to establish the Big Muddy National 

Fish and Wildlife Refuge (BMNFWR) on more than 6,400 

hectares (ha; 16,000 acres [ac]) between Kansas City and 

Saint Louis, Missouri (U.S. Fish and Wildlife Service, 1999). 

The BMNFWR began acquiring land in 1995 and currently 

manages approximately 4,500 ha (11,000 ac); most are lands 

made unsuitable for agriculture by scouring and sand deposition during the floods of 1993 and 1995. More recently, the 

refuge has been authorized to expand to 24,280 ha (60,000 ac) 

and has begun negotiations to acquire lands to meet that target. 

The goals for the BMNFWR, as outlined in the environmental 

Vegetation Communities at Big Muddy National Fish and 

Wildlife Refuge, Missouri

By Matthew A. Struckhoff, Keith W. Grabner, Esther D. Stroh
2 Vegetation Communities at Big Muddy National Fish and Wildlife Refuge, Missouri

impact statement prepared for this proposed expansion (U.S. 

Fish and Wildlife Service, 1999), are:

• Restore natural flood-plain conditions and associated 

native habitats including bottomland forest, wetlands, 

wet prairie, and other grasslands.

• Restore natural riverine functions on public lands by 

connecting the river with the flood plain, allowing 

some natural meandering, widening the channel, and 

creating sandbars, chutes, sloughs, and other aquatic 

features.

• Restore habitat sufficient to protect federally-listed 

threatened and endangered species and candidate species within the project area.

• Conserve, manage, and restore biodiversity and abundance of native endemic fish and wildlife populations.

• Provide additional public areas for compatible fish and 

wildlife-oriented recreation, and increase public understanding of Missouri River resources.

To meet the goals outlined in the Interim Comprehensive 

Management Plan, BMNFWR staff must know the current 

condition of vegetation, plant communities, and wildlife 

habitat within the refuge. Vegetation data had been collected 

in 2002, 2003 and 2004 in association with 400 bird survey 

points in 3 coarse vegetation types (early successional forest, 

mature forests, and wet prairies). These data had not been 

subsequently analyzed. In 2006, as part of the USGS Science 

Support Partnership (SSP) Program, a study was initiated to 

describe and map vegetation on the five units of Big Muddy 

National Fish and Wildlife Refuge for which these data had 

been collected. In 2007, additional funds provided for the 

establishment and sampling of permanent monitoring plots at 

locations that had been classified as wet prairies before 2002, 

and in herbaceous communities at the Boone’s Crossing unit. 

The purpose was to use existing and new data to identify, 

describe and map existing BMNFWR vegetation communities 

to the Association level of the United States National Vegetation Classification System (NVCS). This level of vegetation 

classification is suitable to describe vegetation communities at 

scales relevant to management prescriptions (The Nature Conservancy, 1994), and could be useful for planning objectives in 

the refuge’s Comprehensive Management Plan.

Study Area

At the initiation of this project, Big Muddy National 

Fish and Wildlife Refuge included eight units along the Missouri River between Kansas City, Missouri and Saint Louis, 

Missouri (fig. 1). Most of the property in these units is in the 

flood plain of the Missouri River, though the units at Overton 

Bottoms and Saint Aubert Island also include small upland 

parcels.

Big Muddy units are distributed between two ecoregions 

(Bailey and others, 1994; Keys and others, 1995); three units 

in the Central Dissected Till Plains Section of the Prairie Parkland Province, and five units in the Ozark Highlands Section 

of the Eastern Broadleaf Forest Province (fig. 1). Ecological 

sections are regions ranging from hundreds to thousands of 

square miles in area and containing similarities in climate, 

geomorphology, primary soil groups, and potential vegetation 

formations (Cleland and others, 1997). Nigh and Schroeder 

(2002), identified ecoregional variation in current vegetation communities along the Missouri River at the ecological 

section scale. All of the sampled and mapped units are in the 

Ozark Highlands Section.

What follows is a summary of the acquisition history and 

status of tracts at the various units when they were acquired 

(unless otherwise indicated, agricultural production ceased 

when tracts were acquired):

• Lisbon Bottom (2,014 ac; 815 ha): 1,783 acres (89 

percent) managed in the U.S. Department of Agriculture Natural Resource Conservation Service (USDANRCS) Wetland Reserve Program (WRP) when 

acquired (1995–97) 

• Jameson Island (1,871 ac; 757 ha): 1,760 acres (94 

percent) in the WRP when acquired (1995–98)

• Overton Bottoms (2,548 ac; 1031 ha):

• 1995–2000: 747 acres acquired, of which 483 acres 

(65 percent) were in the WRP

• 1998: the refuge began managing a 1,300 acre tract 

owned by the U.S. Army Corp of Engineers

• 2006: 501 acre tract added, of which 492 acres (98 

percent) were in the WRP

• Saint Aubert Island (1,124 ac; 455 ha): land acquired 

between 1993 and 1997, none in the WRP

• Boone’s Crossing (572 ac; 231 ha): land acquired in 

2002 and 2004, none in the WRP

• Jackass Bend (844 ac; 342 ha):

• 444 acres acquired in 1997, of which 400 acres (90 

percent) were in the WRP

• Approximately 400 acres have been added since, 

none in the WRP

• Agricultural production continued on approximately 

40 acres until 2007

• Baltimore Bottom (1,626 ac; 658 ha):

• 1,490 acres acquired in 2002, of which 620 acres 

(42 percent) were in the WRP. Remaining 136 acres 

acquired after 2002.
Study Area 3

! ! !

!!

!

! !

Jackass Bend

Jameson

Island

Lisbon

Bottom Cranberry

Bend

Overton

Bottoms

Boone's

Crossing

Saint

Aubert

Island

Baltimore

Bottom

Ozark Highlands

Central Dissected Till Plains

Osage

Plains

Mississippi River

Alluvial Basin

Missouri River

94° 92° 90°

40°

38°

36°

Kansas City

Saint Louis

0

0 25 50 75 100 MILES

Base from Bailey, R.G., Aver, P., King, T., and McNab, W.H., 1994 25 50 75 100 KILOMETERS

Ecoregions and subregions of the United States:

Washington D.C., U.S. Forest Service, 1:7,500,000

Universal Transverse Mercator projection, NAD83

Zone 15N

Refuge units

! Not mapped during project

! Mapped during project

EXPLANATION

Figure 1. Big Muddy National Fish and Wildlife Refuge management units, Missouri, USA, 2006.
4 Vegetation Communities at Big Muddy National Fish and Wildlife Refuge, Missouri

• Agricultural production on about 50 percent until 

2007, with decreasing amounts until agricultural production ceased in 2009

• Cranberry Bend (599 ac; 242 ha):

• 85 acres in 1995, 460 acres in 2000, and 54 acres in 

2008; none in WRP when acquired

• Row crops on approximately 30 percent of the unit 

until 2009

Habitat management has varied by unit on the refuge. 

All units have received herbicide applications to control 

exotic species, notably Japanese hops (Humulus japonicus) 

and garlic mustard (Alliaria petiolata) in wooded communities, and Johnson grass (Sorghum halepense) in herbaceous 

communities. As part of efforts to create side channels and 

shallow-water habitat, chutes have been constructed at Overton Bottoms and Jameson Island. These projects converted 

wide swaths of flood plain to riparian habitat, and dumped 

large quantities of dredge material onto the adjacent flood 

plains. Habitat management on about 10 percent of Overton 

Bottoms has included planting of hard mast tree species, seedings of Eastern gamagrass (Tripsacum dactyloides), plantings 

of prairie cordgrass (Spartina pectinata), and seeding of native 

forbs and grasses. Larger percentages of Baltimore Bottom 

and Cranberry Bend (about 18 and 40 percent, respectively) 

have received a similar mix of management treatments. About 

40 acres at Jackass Bend have been planted in hard mast trees, 

of which about 15 acres also were planted with mixed native 

seeds and about 25 were planted with Virginia wildrye (Elymus virginicus).

Methods

Identification of Potential Vegetation 

Communities

Potential vegetation communities were identified that 

could occur within the refuge by conducting a literature 

review and interviewing ecologists familiar with the vegetation along the Missouri River. Potential vegetation refers to 

vegetation communities that are likely to naturally develop on 

a given site when ecological processes such as fire and flooding are present. In North America, presettlement vegetation is 

commonly considered to be representative of potential vegetation; however, management of the river and flood plain has 

altered much of the hydrologic regime that drove the historic 

distribution of plant communities. In this context, pre-settlement vegetation patterns may not accurately predict current 

potential vegetation.

Information concerning historic vegetation came primarily from Harlan (2002) who used General Land Office 

(GLO) land survey notes collected in the early 1800s to create 

a coarse historic map for the Missouri River valley before 

large-scale settlement by non-indigenous Americans. Based 

on witness trees and general descriptions provided during the 

survey effort, Harlan classified vegetation as either forest, 

woodland, open woodland, prairie, or barren. Maps generated 

from Harlan’s (2002) work showed that during the GLO survey, the areas that encompass the refuge units were dominated 

by woodlands. The Overton Bottoms unit was the only unit 

that contained more forested areas than woodlands during the 

GLO survey.

A more complete description of Missouri River riparian vegetation in western Missouri was conducted by Weaver 

(1960). Weaver’s work discusses of the origin and development of streams, vegetation, soils, forests, swamps, marshes, 

and prairies on flood plains along the Missouri River. Weaver 

(1960) divided flood plains into two broad types; 1) low 

bottoms that occur near the river channel and are subject to 

occasional or frequent flooding, and 2) high bottoms that 

occur on wider and flatter parts of the flood plain, usually near 

bluffs. Low bottom forests contained cottonwood (Populus 

deltoides) and willows (Salix spp.). Better drained low bottom forest sites included trees such as white ash (Fraxinus 

americana), green ash (Fraxinus pennsylvanica), slippery elm 

(Ulmus rubra), American elm (Ulmus americana), boxelder 

(Acer negundo), hackberry (Celtis occidentalis), black walnut 

(Juglans nigra), sycamore (Platanus occidentalis), silver 

maple (Acer saccharinum), honey locust (Gleditsia triacanthos), and Kentucky coffeetree (Gymnocladus dioicus). High 

bottom forests occupied a minor part of the Missouri River 

bottoms, but species composition tended to resemble that 

found in forests on well-drained low flood plains. As defined 

by Weaver, swamps in the low bottoms contained a mix of 

bulrushes (Scirpus spp.), cattail (Typha spp.), reed (Phragmites australis), broadfruit bur-reed (Sparganium eurycarpum), arrowhead (Sagittaria latifolia), and water plantain 

(Alisma spp.). Marshes contained sedges (Carex spp.), rushes 

(Juncus spp.), spike rushes (Eleocharis spp.), rice cutgrass 

(Leersia oryzoides), reed canary grass (Phalaris arundinacea), 

and smartweeds (Polygonum spp.). Prairie occurred on the low 

and high bottoms. Low bottoms contained wet, coarse-grass 

prairies comprised of switchgrass (Panicum virgatum), Canada 

wildrye (Elymus canadensis), and prairie cordgrass (Spartina 

pectinata). Prairies containing big bluestem (Andropogon 

gerardii), little bluestem (Schizachyrium scoparium), Indiangrass (Sorghastrum nutans) and Eastern gamagrass (Tripsacum 

dactyloides) occurred on better drained soils on high bottoms. 

Low bottoms also contained abandoned river channels, lakes, 

ponds, marshes, sandbars, grasslands, and shrublands. 

Historic vegetation appears to have varied by ecological section. Presettlement vegetation along the river within 

the Central Dissected Till Plains Section was predominantly 

wet prairie and marshes, with narrow bands of bottomland 

forests (Harlan, 2002; Nigh and Schroeder, 2002). In this section, the Missouri River flood plain is broad, a few miles to 

10 miles wide, and is bordered by conspicuous bluff lines of 

adjacent loess hills. Within the Ozark Highlands Section, the 

Missouri River is bordered by limestone bluffs and the flood 
Methods 5

plain constricts to a few miles wide or less. Presettlement 

flood-plain vegetation in this section was mostly bottomland 

forests dominated by willow (Salix spp.), cottonwood (Populus deltoides), sycamore (Platanus occidentalis), elm (Ulmus

spp.), silver maple (Acer saccharinum), and hackberry (Celtis

spp.; Harlan, 2002; Nigh and Schroeder, 2002). Mixed-hardwood forests that included oak (Quercus spp.), sugar maple 

(Acer saccharum), black walnut (Juglans nigra), and hickories 

(Carya spp.) occurred on high terraces (Nigh and Schroeder, 

2002). Though masked by anthropogenic disturbance (particularly agriculture), differences in flood-plain vegetation along 

the Missouri river at the ecological sections scale persist to 

this day (Nigh and Schroeder, 2002). 

 The primary source for information on existing and 

potential vegetation was the National Vegetation Classification System (NVCS; The Nature Conservancy, 1994). This 

system was developed with seven levels. The physiognomic 

levels (System, Class, Subclass, Group, and Formation) are a 

modification of the United Nations Educational, Scientific, and 

Cultural Organization (UNESCO) world classification of vegetation (Maybury, 1999). They are based on the physiognomic 

characteristics of the dominant vegetation, including whether 

communities are forested or herbaceous, and whether trees are 

broad-leaved or needle-leaved, deciduous or evergreen. The 

two lowest levels, Alliance and Association, are determined 

by floristic composition and are described using procedures 

outlined in Grossman and others (1998). Classes in the Alliance and Association levels are defined by the dominant and 

characteristic species found within them. The NVCS has been 

adopted through the Formation level by the Federal Geographic Data Committee for use by all U.S. federal agencies.

NatureServe, in cooperation with numerous conservation agencies and organizations, maintains and updates all 

vegetation descriptions in the NVCS (NatureServe, 2009). A 

relevant published reference stemming from this effort is The 

Plant Communities of the Midwest (Faber-Langendoen, 2001). 

Other published works that informed the analysis include The 

Terrestrial Natural Communities of Missouri (Nelson, 2005), 

and the Edward “Ted” and Pat Jones—Confluence Point Station Park Revegetation and Restoration Plan (McCarty and 

others, 2004). These documents provided comprehensive 

descriptions of potential vegetation communities and NVCS 

associations that may occur along the Missouri River. These 

sources were augmented with information gathered from 

Timothy Nigh (oral and written communs., 2006). Mr. Nigh is 

a Resource Scientist with the Missouri Department of Conservation, a local expert on Missouri vegetation, and a contributor 

to the Plant Communities of the Midwest (Faber-Langendoen, 

2001). At about the approximate time of the creation of 

BMNFWR, Mr. Nigh and then refuge biologist Maureen Gallagher had identified the potential vegetation types that could 

occur on the refuge. This list was used in conjunction with 

presettlement references cited above to compile a complete list 

of potential NVCS vegetation communities for the refuge.

Data Collection

2002–04 Previously Collected Vegetation Data

Between 2002 and 2004 a survey of bottomland vegetation communities was conducted for a resident and migratory 

songbird study and a study of the ecology and rehabilitation 

of flood-plain forests (Bezzerides and others, 2003; Young, 

2004). Vegetation data were collected at points stratified by 

broad vegetation types: early successional forests, mature forests, or wet prairies (broadly defined to include all nonwooded 

areas on the flood plain). Within a 0.10 ha (17.85 meter (m) 

radius) circular plot, individual species and total vegetative cover were estimated in each of five strata (upper-upper 

canopy, upper canopy, mid-canopy, shrub canopy, and 

groundflora canopy). A variable-radius subplot was used to 

collect data necessary to estimate stem density and basal area 

within each stratum (excluding ground flora). Variable-radius 

plots were used to facilitate data collection within habitats 

with high variation in stem density. Plot area for each stratum 

was determined by the smallest plot size—0.10 ha (radius: 

17.85 m), 0.0625 ha (14.1m), 0.025 ha (8.92 m), 0.006 ha 

(4.46 m), or 0.0016 ha (2.23 m)—within which 50 stems were 

recorded. Each stem was recorded as live or dead, identified 

to species and its diameter at breast height (DBH, 1.4 m above 

the ground) was measured to the nearest 0.5 centimeter (cm). 

Additional environmental data collected at each sample point 

included soil texture, if water was present, habitat type (forest 

or open), and global positioning system (GPS) coordinates. 

2007 New Data

The sampling area for new data included only those 

areas that had been delineated as wet prairie before sampling 

in 2002, as well as herbaceous communities at the Boone’s 

Crossing unit (acquired in 2007). At Boone’s Crossing, 

herbaceous communities were delineated using 2006 USDA 

National Agricultural Imagery Program (NAIP) data obtained 

from the Missouri Spatial Data Information Service (MSDIS, 

2006). Data collection began in July, 2007, with the bulk of 

the sampling occurring between August 22 and October 12. 

Sampling was delayed because of late spring (May and June) 

flooding, which prevented access to many of the sites and 

delayed plant development, hindering identification in the field 

until approximately August 1. 

GIS data and handheld GPS receivers were used to find 

the approximate (within 10 m) locations of plots sampled 

in 2002 and 2003. At Boone’s Crossing, points were randomly located within each herbaceous polygon delineated on 

NAIP photos. Magellan (Thales) ProMark 3 GPS receivers 

were used with an external NAP100 antenna (Magellan, San 

Dimas, Calif.). This system achieves submeter, post-processed 

accuracy, well within the needs of current management goals 

and the goals of this research. The location of the new plot 

center was recorded by noting the height of the antenna above 

the ground and taking GPS reading for the duration of plot 
6 Vegetation Communities at Big Muddy National Fish and Wildlife Refuge, Missouri

vegetation sampling, usually between 20 minutes and one 

hour.

Plot center was permanently marked (fig. 2). A 10-foot 

(ft) section of ultraviolet (UV) radiation-resistant, polyvinyl 

chloride (PVC) electrical conduit was cut approximately 0.6 m 

(2 ft) from the flared end. A fifteen (15) cm piece of 3/8-inch 

rebar was placed through a hole drilled just below the flared 

end. A piece of corrosion resistant wire was used to secure the 

rebar and to attach a corrosion resistant tag engraved with the 

plot name. This item was then driven into the ground until the 

rebar was flush with the ground, with the flared end of conduit 

sticking up. The remaining segment of conduit (approximately 

2.4 m in length) was then nested in the exposed, flared end of 

the buried conduit to enable rapid relocation of plot center. 

The rebar is included to allow for relocation of the plot center 

using a metal detector, should the more visible portions of the 

monument become lost or obscured (for example, as a result 

of flooding).

To sample vegetation, the Beyond North American Weed 

Management Association (NAWMA) plot (Stohlgren and others, 2008) was used, a modified version of multiscale circular 

plots used in the U.S. Forest Service Inventory and Analysis 

program (Frayer and Furnival, 1999). The Beyond NAWMA 

plot is one of many recommended by the National Institute 

of Invasive Species Science (NIISS, 2007) for monitoring 

invasive nonnative plant species, a secondary objective of the 

2007 sampling. The Beyond NAWMA Plot (fig. 3) is a 7.32 m 

fixed-radius plot, with a total sample area of 168 square meters 

(m2

). Three transect lines are located at azimuths of 30 degrees 

(°), 150°, and 270° from plot center, radiating out to the plot 

edge. Transects are temporarily flagged at the outer terminus 

to delineate the perimeter of the plot. Vegetation quadrats 

(1 m2) are located on the clockwise side of each transect with 

two of their corners at 4.57 m and 5.57 m (15 ft and 18.3 ft) 

along the transects. These corners were marked using survey 

flags with metal pins.

Within each quadrat, all herbaceous species and woody 

species providing foliar cover below one meter were identified 

and the foliar cover of each was estimated to the nearest 1 percent. Cover was estimated to the nearest 1 percent for each 

of the following microhabitat variables: dead wood, dung, 

fungus, lichen, litter/duff, live tree bole and visible roots, mineral soil/sediment, moss, road, rock, standing/flooded water, 

stream, and trash/junk . Within the 7.32 m radius plot, all identified species that were not previously recorded in the quadrats 

were recorded as present. All woody stems were identified to 

species and the DBH was measured. Total canopy cover for 

the plot was estimated, and the following environmental data 

were recorded for the plot: slope, aspect, elevation, distance 

to water, distance to road, and distance to crops. Notation was 

also made of any human or other animal disturbance. Photographs were collected from the plot center oriented along 

each of the three transects; included within each photograph 

was an indication of the plot and transect. The primary references for plant identification were Flora of Missouri (Steyermark, 1963), and Steyermark’s Flora of Missouri Volume 1 

(Yatskievych, 1999) and Volume 2 (Yatskievych, 2006). Plant 

nomenclature followed the USDA-PLANTS database (USDA, 

NRCS, 2009). 

Data were collected using the EcoNab data collection tool 

(available free from the NIISS website) on handheld PDAs 

with the PalmTM operating system. This program includes 

features designed to ensure data quality, including requiredentry data fields, a subprogram to aid in the management and 

identification of unknown species, and regionally customizable look-up tables for species. Data were downloaded to and 

managed within the VegSurvey Database (.mdb format), also 

available free from the NIISS website (www.niiss.org).

2.4 meter (8 foot), non-flared end of 3/4 inch ultraviolet (UV) 

radiation-resistant polyvinyl chloride (PVC) electrical conduit

15 centimeter (6 inch) piece of 3/8-inch rebar

(enables relocation of plot using metal detector

should monument become buried or upright pole 

break off). Rebar and identification tag secured 

with corrosion resistant wire

0.6 meter (2 foot), flared end of 3/4 inch 

UV radiation-resistant PVC electrical 

conduit driven into the ground

Ground

Figure 2. Monumentation used to permanently mark plots.

Figure 3. Beyond North American Weed Management 

Association (NAWMA) plot design used during 2007 sampling.

(T2)

150 ̊

(T1)

30 ̊

(T3)

270 ̊

1-meter

squared

quadrat

24 feet (7.32m)

(inside corner 

4.57 meters 

from plot 

center)
Methods 7

Data Analysis

Three primary metrics derived from field data were 

used for data analysis: percent cover data for all species, and 

density (stems/ha) and basal area (m2/ha) for woody species 

summarized by canopy position. Before multivariate analyses, 

plots were subjectively assigned to a NVCS association by 

comparing field observations and plot data to NVCS association descriptions and information gleaned from local experts 

on flood-plain communities. Plots were assigned to the association that best matched current conditions, with a secondary 

designation for those plots that were difficult to classify.

Discrepancies were noticed in how field crews assigned 

stems to strata between 2002 and 2004; therefore, information concerning specific strata and woody stems were not 

retained for multivariate analyses. For example, occasionally 

a plot with most of its stems assigned to the upper-canopy in 

2002 would have virtually no stems assigned to this stratum 

in subsequent sampling years, but would instead have nearly 

all of its stems assigned to the mid-canopy. These types 

of discrepancies point to the potential for sampling biases 

between sample events and suggest sampling inconsistency 

between years; therefore, for multivariate analyses, all woody 

stems measurements from all strata were combined to generate 

plot-level (rather than strata-specific) basal area and density 

estimates for each species. This was not a concern for ground 

flora data.

Multivariate analysis was conducted in three stages using 

PC-ORD V. 5.0 (McCune and Mefford, 1999; McCune and 

Mefford, 2006). First, outlier analysis was used to identify 

samples with potentially anomalous values for one or more 

species. Second, Non-metric Multidimensional Scaling (NMS) 

was used to examine similarities between plots and to identify 

species’ abundances that were driving the relations between 

communities. NMS was also used to identify and potentially 

reclassify plots that did not match other plots assigned the 

same NVCS association. Finally, Multi-Response Permutation 

Procedure (MRPP) was used as a statistical test for differences 

between groups of plots based on the NVCS type assigned.

A standard initial procedure during multivariate analysis is to identify outliers, sample units with extreme values 

for one or more variables or with unusual combinations of 

values for multiple variables. For example, extreme values 

for particular variables can skew data, masking the effects of 

other variables and thereby limiting the interpretive value of 

multivariate analyses (McCune and Grace, 2002). As another 

example, the extreme values for certain variables may also 

identify a particular group of sample units as a unique class 

within the data set. Possible solutions to outliers can include, 

but are not limited to 1) adjustment of the complete data set 

using standard data transformation, such as conversion to 

logarithmic scale; 2) removal of anomalous sample units from 

further analysis because they hinder interpretation of data for 

other sample units; or 3) retaining them in further analyses 

because they represent a unique type and there is little reason 

to suspect that inclusion hinders interpretation of multivariate 

analyses. Outlier analysis was based on the Sorensen (BrayCurtis) distance of each plot from mean distance between 

sample units, and sample units were flagged that were more 

than two standard deviations away from the mean. Once outliers were identified, plots were reviewed to determine how 

outliers or the larger data set should be treated.

Once outlier analyses were performed, NMS was used 

to explore the relation between plots and assigned NVCS 

associations. NMS is an iterative ordination process to find 

the best fit of data in a reduced number of dimensions and has 

been described as the most effective ordination method for 

ecological community data (McCune and Grace, 2002). The 

advantages for NMS are: 1) avoiding the assumption of linear 

relations among variables, 2) ranking distances are used to linearize distances measured in species and environmental space, 

and 3) it allows the use of any distance measure or relativization (McCune and Grace, 2002). Analysis using NMS yields 

a measure of final stress (lack of fit; scale of 1 to 100) and a 

graphical output of plots, species, or both according to ordination scores. When considering the NMS graphical output, the 

proximity of plots to one another reflects their similarity in 

terms of species composition and abundance. As with other 

ordination techniques, one also can measure and represent 

the relation of individual species to the data structure using 

correlation coefficients (r) for each species relative to each 

axis. The sum of the squared r values (multiple r2

) represents 

the amount of variation in the data explained by that species’ 

abundance values. NMS was used to 1) assess the similarity of 

plots within the various types to their assigned classification, 

2) identify plots that may have been poorly classified, and 3) 

identify the species’ abundance measures most correlated with 

the data structure, as indicated by the multiple r2. NMS analyses were conducted on overstory density and basal area for 

forested plots and on groundflora cover data for herbaceous 

plots.

Subsequent to outlier and NMS analyses and adjustments 

made to community classification based on them, MultiResponse Permutation Procedure (MRPP) was used to test for 

differences between vegetation communities based on their 

final classification (McCune and Grace, 2002). Because MRPP 

is a nonparametric analysis method, it can handle nonlinear 

relations or data with skewed frequency distributions—the 

types of data commonly encountered in vegetation community analysis (McCune and Grace, 2002). MRPP analysis 

yields the output variable A (the chance-corrected withingroup agreement), which describes the measure of similarity 

between sample units within a group; the test statistic T, which 

describes the separation between groups; and a p-value for T. 

The variable A ranges from 0 (heterogeneity within groups 

equals expectations by chance) to 1 (all items within a group 

are identical). For ecological data, values for A are usually 

below 0.1, while A values of greater than 0.30 can safely 

be interpreted as indicating high similarity within analyzed 

groups (McCune and Grace, 2002). For the test statistic T, 

the more negative value for T indicates a stronger separation 
8 Vegetation Communities at Big Muddy National Fish and Wildlife Refuge, Missouri

between groups. The p-value indicates how likely differences 

between groups (the T statistic) could be because of chance.

Map Production

Community Delineation

Vegetation communities were delineated in ArcMap 

9.3.1 using NAIP photos obtained from the MSDIS. These 

photos were true-color for 2002, 2005, 2006, and 2007 and 

were color-infrared for 2003. U.S. Army Corps of Engineers 

true color aerial photos from 2000 were also used. Differences 

and similarities in color and texture were used to delineate 

polygons of different vegetation types on the photos. Existing 

vegetation data points were overlaid on the NAIP images to 

classify polygons and identify image signatures for vegetation 

communities. The refuge provided additional spatial data layers that documented past management on specific refuge units. 

These data assisted in identifying patterns that were caused 

by management actions, such as, hard mast tree plantations or 

warm season grass plantings. A draft vegetation community 

map was completed in the spring of 2008.

Final Community Polygon Classification and 

Boundary Adjustment

Because of an exceptionally wet growing season in 2008, 

refuge units were inundated most of the growing season and 

vegetation was unable to develop enough for plant community 

identification; therefore, work was delayed for one year, and 

final map classification data were collected during the 2009 

growing season. Further, the 2008 flooding combined with 

extensive flooding in early 2009 created substantial changes in 

the vegetation between the last year of data collection (2007) 

and the production of the map. This was particularly true in 

low lying areas, where persistent ponding of water caused 

changes from communities dominated by weedy native species or non-native species to ephemeral wetlands that were 

dominated by native hydrophilic species.

Rather than adopt accuracy assessment procedures 

typically used in the production of remotely-sensed maps, 

sampling resources were used during the final stage of map 

production to visit and classify as many mapped polygons as 

possible and to adjust polygon boundaries where field observations supported doing so. Three factors contributed to this 

decision. First, the primary goal was a finished product that 

gave the most accurate representation of the current vegetation 

on the refuge, rather than a map with known and suspected 

errors as is produced by standard remote sensing efforts. 

Second, accuracy assessments are only meaningful if applied 

to areas where there is a reasonable expectation that the map 

incorporates data and information relevant to all, or nearly all, 

mapped classes. During this study, resource limitations prevented the collection of plot data for many community types 

(particularly those in the uplands), such that this criterion 

for accuracy assessment was not met. Finally, observations 

in 2007, 2008 and 2009 indicated that flooding during those 

years was causing rapid change in herbaceous and forested 

communities on the flood plains, such that even if the preliminary map accurately reflected conditions from when the data 

were collected it was unlikely to reflect conditions at the end 

of the project. 

Once a preliminary map had been created, each previously unsampled polygon was populated with a classification 

point at its approximate center. Sampling crews then visited 

each map classification point, and assigned the polygon to 

a given community type based on comparisons between: 1) 

field observations, and 2) local and global NVCS descriptions 

developed by NatureServe (2009). Routes were planned to 

enable the field crew to visit previously sampled polygons and 

assess the accuracy of classification based on plot data without 

actually revisiting all sample points from previous years. If the 

previous classification based on plot data seemed incorrect or 

no longer appropriate because of changes in vegetation, a new 

classification was assigned to the polygon. Additionally, 2009 

field observations and handheld GIS data loggers were used 

to identify adjustments that should be made to community 

boundaries. All field data were then used to adjust the final 

map within the ArcMap GIS platform.

Results

Vegetation Communities of Big Muddy National 

Fish and Wildlife Refuge

A review of literature concerning historic, current, and 

potential vegetation communities of the Missouri River flood 

plain identified 25 potential bottomland vegetation associations that had a high likelihood of occurring within the refuge 

(table 1). Many of these communities are now extremely rare 

within Missouri as a result of conversion to agriculture and 

river management. Primary among these are nonforested wetlands, wet-mesic prairies, and bottomland oak woodlands and 

forests, many of which were not encountered during this study, 

though they potentially exist within the Missouri River flood 

plain (table 1). During data collection for this project, communities were identified that tentatively matched the NVCS 

descriptions for 11 of these types; 6 forests, 1 woodland, 

1 shrubland, and 3 herbaceous communities. Existing or newly 

collected plot data were available for four of the above forests, 

the woodland, the shrubland, and two of the herbaceous communities. Plot data were also available for three ruderal communities not described by the NVCS; Herbaceous Old Fields, 

Woody Old Fields, and Johnson Grass communities.

During the project, 6 upland oak forest types, 2 bottomland hardwood types, and 1 herbaceous community type 

described by the NVCS were encountered (table 1), but no 

plot data were collected. Local descriptions (appendix 1) 

for these types are based on observations made during map 
Results 9

Table 1. Existing and potential National Vegetation Classification System (NVCS) Associations at Big Muddy National Fish and Wildlife 

Refuge.

[NC, not considered; Y, yes; ?, status in Missouri uncertain; N, no; bold text indicates communities encountered during project.]

NVCS common name NVCS code Nelson1 type On

refuge2

In

Missouri3

Forest

Upland

White Oak–Red Oak–Sugar Maple Mesic Forest CEGL002058 Dry-Mesic Loess/Glacial Till Forest NC Y

White Oak/Dogwood Dry–Mesic Forest CEGL002066 Dry-Mesic Loess/Glacial Till Forest NC Y

White Oak–Mixed Oak Dry–Mesic Alkaline Forest CEGL002070 Dry-Mesic Limestone/Dolomite Forest NC Y

Midwest Post Oak–Blackjack Oak Forest CEGL002075 Dry Limestone/Dolomite Woodland NC Y

Black Oak–White Oak–Hickory Forest CEGL002076 Dry-Mesic Loess/Glacial Till Forest NC Y

Ozark Red-cedar–Hardwood Forest CEGL004803 Dry Limestone/Dolomite Woodland NC ?

Temporarily Flooded

Midwestern Cottonwood–Black Willow Forest CEGL002018 Riverfront Forest Y Y

Black Willow Riparian Forest CEGL002103 Riverfront Forest Y N

Silver Maple–Elm Forest CEGL002586 Wet Bottomland Forest Y Y

Central Green Ash–Elm–Hackberry Forest CEGL002014 Wet-Mesic Bottomland Forest Y

Ash–Oak–Sycamore Mesic Bottomland Forest CEGL002410 Wet-Mesic Bottomland Forest Y Y

Pin Oak Mixed Hardwood Depression Forest CEGL002432 Wet-Mesic Bottomland Forest N Y

Bur Oak–Swamp White Oak Mixed Bottomland Forest CEGL002098 Wet-Mesic Bottomland Forest N Y

Box-elder Floodplain Forest CEGL005033 Wet-Mesic Bottomland Forest Y Y

Woodland

Cottonwood Floodplain Woodland CEGL002017 Wet-Mesic Bottomland Woodland Y Y

Burr Oak Bottomland Woodland CEGL002140 Wet-Mesic Bottomland Woodland N Y

Shrubland

Sandbar Willow Shrubland CEGL008562 Riverfront Shrubland Y Y

Northern Buttonbush Swamp CEGL002190 Shrub Swamp N Y

Herbaceous

Central Cordgrass Wet Prairie CEGL002224 Wet Bottomland Prairie N Y

Central Wet-Mesic Tallgrass Prairie CEGL002024 Wet-Mesic Bottomland Prairie N Y

Bulrush–Cattail–Burreed Shallow Marsh CEGL002026 Freshwater Marsh N Y

Midwest Cattail Deep Marsh CEGL002233 Freshwater Marsh N Y

Midwest Mixed Emergent Deep Marsh CEGL002229 Freshwater Marsh N Y

American Lotus Aquatic Wetland CEGL004323 Freshwater Marsh N ?

Water lily Aquatic Wetland CEGL002386 Freshwater Marsh N Y

River Bulrush Marsh CEGL002221 Freshwater Marsh N Y

Central Midwest Sedge Meadow CEGL005272 Freshwater Marsh N Y

Midwest Ephemeral Pond CEGL002430 Freshwater Marsh Y Y

Eastern Great Plains Saline Marsh CEGL002043 Saline Seep Y Y

Great Plains Acidic Seep CEGL002235 Acid Seep Y ?

Sparse Herbaceous

Riverine Sand Flats CEGL002049 Sandbar/Stream-bank/Riverbank Y Y

1

Nelson, P.W., 2005, The Terrestrial Natural Communities of Missouri: The Missouri Natural Areas Committee, The Missouri Department of Natural 

Resources, Jefferson City, Missouri, 550 p.

2

Unpublished document by Timothy Nigh (Resource Scientist, Missouri Department of Conservation) and Maureen Gallagher (Biologist, formerly with Big 

Muddy National Fish and Wildlife Refuge).

3

NatureServe, 2009, NatureServe Explorer: An online encyclopedia of life [web application], Version 7.1: NatureServe, Arlington, Virginia, accessed 28 

December, 2009, www.natureserve.org/explorer.
10 Vegetation Communities at Big Muddy National Fish and Wildlife Refuge, Missouri

production and familiarity with each type from previous work 

within the study area. Eleven additional water and cultural 

feature classes (such as ponds and roads) were identified and 

mapped, some of which are described in appendix 1.

The locations of identified and mapped communities are 

documented in spatial data collected during final map production, during which nearly every mapped polygon was visited 

and classified. Table 1 lists potential NVCS community types 

for the refuge and indicates their suspected status in Missouri 

(NatureServe, 2009) and on the refuge (T.A. Nigh, Resource 

Scientist, Missouri Department of Conservation, oral and 

written communs., 2006–07; M. Gallagher, Biologist, Big 

Muddy National Fish and Wildlife Refuge, 2006, unpub. data). 

Table 2 lists ruderal communities and other cultural features 

encountered during this study.

Analyses of Plot Vegetation Data

Communities were classified by comparing plot data and 

field observations made during 2007 and 2009 to NVCS association descriptions (Faber-Langendoen, 2001; NatureServe, 

2009), statewide community descriptions (Nelson, 2005) and 

incorporating the opinions of local experts on Missouri River 

flood-plain communities (T.A. Nigh, Resource Scientist, 

Missouri Department of Conservation, oral and written communs., 2006-07; M. Gallagher, Biologist, Big Muddy National 

Fish and Wildlife Refuge, unpub. data). Multivariate analyses 

were based on each plot’s most recent data (2002, 2003, 2004, 

or 2007). Analyses of woody communities were based on plotlevel basal area and density data for woody species; analyses 

of herbaceous communities were based on ground flora cover 

estimates. In subsequent sections, communities currently recognized by the NVCS are referred to by their NVCS common 

name, followed by their NVCS code, which is formatted as 

CEGL00#### for terrestrial communities (NatureServe, 2009).

Wooded Communities

Comparisons of data and field observations to NVCS 

description for potential communities within the study area 

(Faber-Langendoen, 2001; NatureServe, 2009) provided for 

an initial identification of eight woody community types in 

bottomlands for which there were plot data. These include 

two expressions (mature and immature) of the Midwestern 

Cottonwood–Black Willow Forest (CEGL002018). The 

identified communities share many species, with cottonwood 

(Populus deltoides), willow (Salix spp.), and snags (standing dead woody stems with a diameter at breast height) being 

Table 2. Existing ruderal vegetation associations and other mapped features at Big Muddy National Fish and Wildlife Refuge.

Community name Comment

Ruderal communities

Herbaceous old field Found in bottoms; Extremely variable; succeeding toward Polygonum wetland (CEGL002430) in low-lying 

areas

Fescue field Upland communities dominated by tall fescue (Festuca arundinacea) with mixed forbs common to old fields

Bottomland woody old field Appears to be succeeding toward either the Central Green Ash–Elm–Hackberry Forest (CEGL002014) or 

the Ash–Oak–Sycamore Mesic Bottomland Forest (CEGL00410) 

Upland woody old field Dominated by Honey locust (Gleditsia triacanthos) and eastern redcedar (Juniperus virginiana). Susceptible 

to invasion by the nonnative invasive sericea lespedeza (Lespedeza cuneata)

Johnson grass Dominates in many drier old fields in the flood plain

Other features

Levee Usually dominated by tall fescue (Festuca arundinacea) and managed (typically mowed) to maintain access. 

Does not include abandoned levees with high woody stem density

Plantation Planted trees (Quercus macrocarpa, Quercus palustris, Quercus lyrata, Quercus bicolor, Quercus rubra, 

Carya illinoinensis, Fraxinus pennsylvanica and Juglans nigra are common), often with a cover crop such 

as Elymus virginicus, Agrostis gigantea or Setaria viridis

Pond Human-constructed water feature; may include Polygonum wetland (CEGL002430) or Riverine Sand Flats 

(CEGL002049) at margins

Railroad

River Water adjacent to main channel

Road

Row crop Agriculturally managed, most likely for corn or soybeans

Scour Naturally occurring pond; likely includes Polygonum wetland (CEGL002430) or Riverine Sand Flats 

(CEGL002049) at margins

Utility right-of-way Shrubby or herbaceous depending on time since last vegetation control effort
Results 11

particularly abundant in all community types (table 3). Cottonwood was found in 89 percent of the 132 wooded plots, while 

willows and snags were found in 73 percent of the plots. Other 

frequently encountered species in forested plots included 

boxelder (Acer negundo), silver maple (Acer saccharinum), 

ash (Fraxinus spp.), and sycamore (Platanus occidentalis). 

The low species diversity across the study area facilitated classification, as shifts in dominance from one or two species to 

a few other species were easily identified. In many cases, the 

absence of a given species, such as cottonwood, was important 

in determining which association type a plot represented.

The high frequency (0.73) and densities of snags is consistent with common patterns of stand development. Forests 

progress through four stages during development: stand initiation, stem exclusion, understory reinitiation, and old growth 

(Oliver and Larson, 1990). During the stand initiation stage, 

trees, shrubs, and herbaceous vegetation invade disturbed land 

and begin to colonize the open ground. During the stand initiation stage plants grow to occupy all of the available growing 

space and stem densities can become extremely high. Once all 

of the growing space is occupied, stands enter the stem-exclusion stage, in which plants compete for light, water, nutrients, 

and physical space. The stem-exclusion stage is characterized 

by an increase in mortality (Oliver and Larson, 1990) and, 

therefore, a higher density of dead stems.

As the refuge acquired land from willing sellers after 

the 1993 and 1995 floods, many parcels of land on the refuge 

entered the stand initiation stage. The data suggest that during the 2002–04 sample period, many of the forested stands 

had entered the stem-exclusion stage, accounting for the high 

frequency and density of snags in the data from that period. 

Evidence gathered during 2007 and 2009 support that stem 

exclusion was continuing. This stand-wide mortality is being 

augmented by mortality caused by flooding, the effects of 

which tend to be patchily distributed within established stands 

because of variation in flood intensity (depth, water speed and 

duration) as determined by landscape characteristics. 

The most frequently encountered woody community was Midwestern Cottonwood–Black Willow Forest 

(CEGL002018), which accounted for 68 percent of all the 

forested plots (91 out of 134; table 3). This forest type is 

dominated by cottonwood (Populus deltoides) with varying amounts of willow (Salix spp.). This community had a 

wide range of expression (appendix 1), from newly established thickets, to young stands in the stem-exclusion stage 

of development, to stands of mature cottonwoods that had 

established on unprotected flood plains where there was no 

agricultural activity before acquisition by the refuge. It also 

included small areas dominated by black willow (Salix nigra) 

that were tentatively classified as the Black Willow Riparian Forest (CEGL002103). Newly established stands had the 

highest stem densities, the greatest abundance of Salix spp., 

and sparse ground flora resulting from shading because of 

the dense woody stem growth of stand initiation. In 10 to 

15 year-old stands entering the next stage of forest development, stem exclusion tends to eliminate Salix interior as it 

becomes shaded by the higher growing cottonwoods and black 

willow (though these species become less dense, too). Stem 

mortality increases the amount and the spatial heterogeneity 

of sunlight reaching the ground flora, increasing its diversity. 

Mature cottonwood forests have a more complex structure, 

with multiple canopy layers where cottonwood shares dominance with other species, a variable shrub layer, and diverse 

ground flora. Mature Midwestern Cottonwood–Black Willow 

Forests (CEGL002018) and Black Willow Riparian Forests 

(CEGL002103) were retained as unique types for multivariate 

analysis.

Cottonwood Floodplain Woodland (CEGL002017) 

accounted for 16 percent (21 out of 134) of the plots dominated by woody species (table 3). The NVCS description 

emphasizes a few characteristics about this type: 1) canopy 

of cottonwoods (Populus deltoides) and other species with a 

cover below 60 percent, or if higher, 2) a poorly developed 

understory and shrub layer, and 3) a diverse ground flora 

dominated by bottomland grasses, such as prairie cordgrass 

(Spartina pectinata) and sedges (Carex spp.). For classification purposes, it was recognized that ground flora had not had 

sufficient time to establish and diversify since acquisition by 

the refuge, and that the structure of the canopy was dynamic in 

relatively young stands of cottonwood. This is particularly true 

in areas where flooding and stem exclusion appear to be pushing succession toward a woodland type; therefore, when classifying communities as the Cottonwood Floodplain Woodland, 

more attention was given to structure and cover in the upper 

strata with less emphasis on the composition of the ground 

flora. Generally, the woodland classification was reserved for 

those communities with less than 60 percent cover and poorly 

developed understory and shrub layers.

Sandbar Willow Shrubland (CEGL008562) represented 

5 (4 percent) out of 132 wooded plots sampled (table 3). Salix 

interior was the dominant species in these communities, with 

lesser and more variable amounts of Salix nigra and Salix 

caroliniana. Cottonwood (Populus deltoides) was at most 

co-dominant with Salix, and even when fully developed, this 

community was characterized by a low canopy (about 5 m) 

comprised of small diameter stems. These characteristics differentiate the sandbar willow shrubland from the woodland 

and forest communities and are consistent with the NVCS 

Association description. Despite high densities of willow and 

cottonwood, the sandbar willow shrublands have low basal 

areas for these species (table 3). The ground flora layer is 

variable in structure and composition, ranging from little or no 

vegetation below dense thickets of willow to almost complete 

herbaceous cover in openings resulting from uneven establishment of woody species or flooding.

Box-elder Floodplain Forests (CEGL005033) and Silver 

Maple–Elm Forests (CEGL002586) were identified on 11 

(8 percent) and 2 (2 percent) of 132 wooded plots (table 3). 

Following the NVCS description for each type, these classifications were reserved for sites dominated (greater than 50 percent cover) by Acer negundo and Acer saccharinum, respectively. Other frequently abundant species in both types include 
12 Vegetation Communities at Big Muddy National Fish and Wildlife Refuge, Missouri

Table 3. Woody species measures for woody dominated vegetation associations as classified based on field data and observations.

[ha, hectare; m2, square meter; CEGL00xxxx, National Vegetation Classification System (NVCS) code; n, sample size; Species with basal area less than 0.001 

m2/ha are excluded.]

Scientific name Mean density (stems/ha) Mean basal area (m2/ha) Frequency

Cottonwood Floodplain Woodland–CEGL002017 (n = 21)

Populus deltoides Bartr. ex Marsh. 1,287.3 4.942 0.95

Salix interior Rowlee 1,699.0 1.874 .41

Unknown snag 941.5 .289 .18

Salix nigra Marsh. 80.0 .289 .09

Platanus occidentalis L. 10.8 .074 .09

Acer negundo L. 8.1 .016 .09

Acer saccharinum L. 21.6 .009 .05

Morus L. 2.7 .008 .05

Salix caroliniana Michx. 1.8 .001 .05

Juniperus virginiana L. 8.1 .001 .09

Prunus americana Marsh. 8.1 .001 .05

Black Willow Riparian Forest–CEGL002103 (n = 7)

Salix nigra Marsh. 588.6 5.066 1.00

Salix caroliniana Michx. 422.9 3.789 0.29

Unknown Snag 931.4 2.914 1.00

Populus deltoides Bartr. ex Marsh. 442.9 2.661 1.00

Salix interior Rowlee 457.1 1.373 .86

Salix L. 120.0 .511 .29

Acer negundo L. 51.4 .057 .29

Morus L. 14.3 .015 .29

Vitis L. 62.9 .004 .43

Celtis L. 5.7 .002 .14

Platanus occidentalis L. 5.7 .001 .14

Silver Maple Floodplain Forest–CEGL002586 (n = 2)

Acer saccharinum L. 195.0 31.337 1.00

Unknown snag 85.0 4.172 1.00

Morus L. 55.0 2.694 0.50

Populus deltoides Bartr. ex Marsh. 5.0 2.209 .50

Acer negundo L. 20.0 .515 .50

Vitis L. 105.0 .513 .50

Gleditsia triacanthos L. 5.0 .245 .50

Fraxinus L. 15.0 .014 .50

Campsis radicans (L.) Seem. ex Bureau 5.0 .004 .50

Mature Cottonwood–Willow Forest–CEGL002018 (n = 5)

Populus deltoides Bartr. ex Marsh. 50.8 12.730 0.60

Acer negundo L. 284.9 6.188 1.00

Acer saccharinum L. 78.9 4.588 .80

Platanus occidentalis L. 95.1 3.562 1.00

Carya Nutt. 9.6 2.576 .40

Morus L. 196.0 1.713 1.00

Unknown snag 96.7 1.620 1.00

Vitis L. 313.5 0.749 1.00

Salix L. 2.0 .304 .20

Ulmus L. 13.1 .126 .40

Toxicodendron radicans (L.) Kuntze 49.2 .072 .60

Celtis L. 6.0 .065 .20

Cornus L. 33.6 .020 .40

Campsis radicans (L.) Seem. ex Bureau 19.2 .012 .20
Results 13

Table 3. Woody species measures for woody dominated vegetation associations as classified based on field data and observations.

[ha, hectare; m2, square meter; CEGL00xxxx, National Vegetation Classification System (NVCS) code; n, sample size; Species with basal area less than 0.001 

m2/ha are excluded.]

Scientific name Mean density (stems/ha) Mean basal area (m2/ha) Frequency

Sandbar Willow Shrubland–CEGL008562 (n = 5)

Populus deltoides Bartr. ex Marsh. 3,641.1 6.850 0.80

Salix interior Rowlee 2,587.0 5.367 1.00

Salix L. 160.0 1.586 .20

Unknown snag 2,064.0 .758 .60

Salix nigra Marsh. 64.0 .478 .40

Salix caroliniana Michx. 24.0 .313 .20

Vitis L. 120.0 .012 .20

Platanus occidentalis L. 27.9 .006 .40

Box-elder Forest–CEGL005033 (n = 11)

Acer negundo L. 482.4 8.979 0.91

Morus L. 87.7 6.129 .73

Acer saccharinum L. 110.2 3.906 .73

Unknown snag 119.6 3.861 .91

Platanus occidentalis L. 80.2 1.671 .82

Vitis L. 307.4 1.080 .82

Ulmus L. 58.4 .855 .36

Robinia pseudoacacia L. 0.9 .787 .09

Populus deltoides Bartr. ex Marsh. 11.2 .453 .45

Fraxinus L. 1,067.3 .401 .64

Celtis L. 91.2 .285 .45

Carya Nutt. 1.8 .111 .09

Cornus L. 26.4 .028 .18

Toxicodendron radicans (L.) Kuntze 7.3 .024 .09

Salix interior Rowlee 75.6 .006 .09

Salix nigra Marsh. 3.6 .006 .18

Salix L. 1.8 .001 .09

Immature Cottonwood–Willow Forest–CEGL002018 (n = 79)

Populus deltoides Bartr. ex Marsh. 2,008.4 12.099 1.00

Salix interior Rowlee 1,083.9 2.674 0.86

Unknown snag 2,068.3 1.582 .87

Salix nigra Marsh. 80.3 .407 .36

Acer negundo L. 207.1 .342 .34

Salix caroliniana Michx. 38.0 .248 .29

Platanus occidentalis L. 49.3 .215 .20

Morus L. 6.0 .064 0.05

Acer saccharinum L. 33.0 .052 .07

Salix L. 4.7 .044 .03

Vitis L. 126.9 .016 .25

Celtis L. 0.1 .015 .01

Campsis radicans (L.) Seem. ex Bureau 115.5 .014 .28

Cornus L. 4.7 .006 .05

Toxicodendron radicans (L.) Kuntze 6.2 .002 .03

Fraxinus L. 5.2 .002 .07

Woody old field (n = 4)

Platanus occidentalis L. 29.7 0.071 0.25

Fraxinus L. 89.1 .061 .25

Celtis L. 609.0 .048 .50

Populus deltoides Bartr. ex Marsh. 14.9 .029 .25

Salix nigra Marsh. 14.9 .001 .25

Ulmus L. 14.9 .001 .25
14 Vegetation Communities at Big Muddy National Fish and Wildlife Refuge, Missouri

cottonwood (Populus deltoides), black willow (Salix nigra), 

mulberry (Morus spp.), and elm (Ulmus spp.). Most forests 

identified as the boxelder and silver maple types were mature, 

having established on fallow lands long before the floods of 

1993 and 1995. Both types tended to include cottonwoods as 

an emergent canopy component. 

Communities in which vegetative cover from woody 

stems in the shrub or tree layers exceeded approximately 20 

percent but did not match any recognized NVCS community 

type were classified as Woody Old Fields. These comprised 3 

percent (4 out of 132) of the forested plots. This community 

tended to have low woody stem density and low basal area and 

was dominated by ruderal species such as hackberry (Celtis

spp.), ash (Fraxinus spp.), and elm (Ulmus spp.; table 3). 

Cottonwood (Populus deltoides) and willow (Salix spp.) were 

present but not dominant in this type. Tree density ranged from 

20 to 410 stems/ha with a mean of 130.0 stems/ha; basal area 

ranged from 0.002 to 0.051 m2/ha with a mean of 0.035 m2/ha. 

Woody old fields appear to be succeeding toward the Central 

Green Ash–Elm–Hackberry Forest (CEGL002014), a type 

with which it shares many dominant species.

Multivariate analysis using Non-metric Multidimensional 

Scaling (NMS) reveals four primary groups of community 

types (fig. 4 and fig. 5); 1) mature forests, 2) woody old fields, 

3) cottonwood woodlands, and 4) immature cottonwood 

forests and willow thickets. The mature forest group includes 

Box-elder Floodplain Forests (CEGL005033), Silver Maple–

Elm Forests (CEGL002586), and mature Midwestern Cottonwood–Black Willow Forests (CEGL002018). Analyses using 

Multiple Response Permutation Procedure (MRPP) indicates 

that these communities cannot be identified as unique groups; 

results change between analysis based on basal area and analysis based on density (table 4 and table 5). This reflects the fact 

that within the study area, these community types were usually 

encountered as mature forests within which cottonwoods 

share dominance with other species. Not coincidentally, they 

also tend to occur in the same locations—outside of protected 

levees in locations lacking agricultural production before 

1993. The small sample size for the silver maple forest may 

have made it difficult to detect differences between it and the 

other types.

Cottonwood Floodplain Woodlands (CEGL002017) and 

Woody Old Fields are two community types found in close 

proximity to each other in the NMS outputs (fig. 4 and fig.

5), reflecting their shared characteristics of low overall basal 

area and density. Comparisons between these types using 

MRPP indicate significant differences based on density data 

(T = -3.012; table 5), but not based on basal area (T = -1.242; 

table 4). In the field, they are discernable from each other by 

differences in species assemblage and structure. Cottonwood 

woodlands are dominated by moderate to large diameter cottonwood (Populus deltoides) and willow (Salix spp.) stems. 

Woody Old Fields currently are dominated by uniformly 

short, small diameter stems of species that thrive in former 

agricultural flood plains, including ash (primarily Fraxinus 

pennsylvanica), hackberry (Celtis spp.), sycamore (Platanus 

occidentalis) and elm (Ulmus spp.). The structure of Woody 

Old Fields should change as woody stems mature.

The final group of communities includes immature Midwestern Cottonwood–Black Willow Forests (CEGL002018), 

Sandbar Willow Shrublands (CEGL008562), and Black 

Willow Riparian Forests (CEGL002103). Within the NMS 

analyses (fig. 4 and fig. 5), there is substantial overlap among 

the three types, though MRPP analysis based on density 

identifies significant differences between them (table 5). The 

sandbar willow shrubland has a distinct structure (high stem 

density and low canopy) and species composition (dominance 

by Salix interior) that justify retaining and mapping it as a distinct type. Similarly, MRPP analyses based on basal area and 

density indicate that the black willow forest type is statistically 

discernable from the cottonwood forest; however, the NVCS 

description for the black willow forest suggests that it is not 

extant in the study area and that small areas fitting the description for the type are a common component of the cottonwoodwillow forest. This is consistent with observations made in 

the field, where examples of the black willow forest tended 

to be small inclusions within a matrix cottonwood-willow 

forest. Given these facts, a decision was made to map locations initially classified as the Black Willow Riparian Forest 

(CEGL002103) as the Midwestern Cottonwood–Black Willow 

Forest (CEGL002018). Observations made during 2007 and 

2009 suggest that flooding in low-lying cottonwood forests 

appear to be driving succession toward the black willow type. 

Given time, the Black Willow Riparian Forest (CEGL002103) 

type may become a more abundant and distinct type worthy 

of recognition within the refuge and throughout the Missouri 

River flood plain. 

The species with the highest correlation to the data structure in the NMS outputs are cottonwood (Populus deltoides; 

basal area multiple r2

 = 0.45, density multiple r2 = 0.37), snags 

(basal area multiple r2 = 0.36, density multiple r2 = 0.40), and 

sandbar willow (Salix interior; basal area multiple r2 = 0.22, 

density multiple r2 = 0.33). Other species with high correlation coefficients included mulberry (Morus spp.), ash (Fraxinus spp.), silver maple (Acer saccharinum) and boxelder 

(Acer negundo), which tended to have inverse relations with 

the above species. These results reflect the observable species abundance gradients (table 3) and suggest that the NMS 

analyses grouped plots based upon the same criteria identified 

through subjective analysis of the data and field observations.

Herbaceous Communities

The combined plot data from all sampling events support 

the occurrence of four recognizable herbaceous community 

types on bottomlands of the refuge. Four plots being managed via seeding of warm season grasses match the NVCS 

description for the Central Wet-Mesic Tallgrass Prairie 

(CEGL002024). This type is characterized by grasses such as 

big bluestem (Andropogon gerardii), little bluestem (Schizachyrium scoparium), Indiangrass (Sorghastrum nutans), 

and Eastern gamagrass (Tripsacum dactyloides). Midwest 
Results 15

Figure 4. Non-metric Multidimensional Scaling output for woody communities based on woody stem basal area.

Vegetation Association 

 (National Vegetation Classification System code)

Woody Old Field

Cottonwood Floodplain Woodland (CEGL002017)

Silver Maple–Elm Forest (CEGL002586)

Black Willow Riparian Forest (CEGL002103)

Box-elder Floodplain Forest (CEGL005033)

Sandbar Willow Shrubland (CEGL008562)

Immature Midwestern Cottonwood–Black Willow Forest (CEGL002018) 

Midwestern Cottonwood–Black Willow Forest (CEGL002018) 

Axis 1

Immature Cottonwood Forests 

and Willow Thickets

Mature Forests

Cottonwood Woodlands

EXPLANATION

Woody Old Fields
16 Vegetation Communities at Big Muddy National Fish and Wildlife Refuge, Missouri

Figure 5. Non-metric Multidimensional Scaling output for woody communities based on 

woody stem density. 

Axis 1

Immature Cottonwood Forests 

and Willow Thickets

Mature Forests

Cottonwood Woodlands

Woody Old Fields

Vegetation Association 

 (National Vegetation Classification System code)

Woody Old Field

Cottonwood Floodplain Woodland (CEGL002017)

Silver Maple–Elm Forest (CEGL002586)

Black Willow Riparian Forest (CEGL002103)

Box-elder Floodplain Forest (CEGL005033)

Sandbar Willow Shrubland (CEGL008562)

Immature Midwestern Cottonwood–Black Willow Forest (CEGL002018) 

Midwestern Cottonwood–Black Willow Forest (CEGL002018) 

EXPLANATION
Results 17

Table 4. Multiple-Response Permutation Procedure results for woody communities based on woody stem basal area.[CEGL00####, National Vegetation Classification System code. The sample size is given in the shaded cells. The chance corrected within group agreement, A, is in the lower left. The test statistic, T, is in the upper right, with bold indicating a significant difference between associations (p < 0.05)]

Mature 

Midwestern 

Cottonwood– BlackWillow 

Forest 

(CEGL002018)

Immature

Midwestern

Cottonwood– 

Black Willow 

Forest 

(CEGL002018)

Cottonwood 

Floodplain 

Woodland 

(CEGL002017)

Box-elder 

Floodplain Forest 

(CEGL005033)

Silver Maple– 

Elm Forest

(CEGL002586)

Sandbar 

Willow 

Shrubland 

(CEGL008562)

Black Willow 

Riparian Forest 

(CEGL002103)

Woody old field

Mature 

Midwestern

Cottonwood– 

Black Willow

Forest

(CEGL002018)

5 -3.988 -3.433 -2.607 -1.631 -3.066 -4.280 -2.181

Immature 

Midwestern 

Cottonwood– 

Black Willow 

Forest

(CEGL002018)

0.020 79 -6.806 -11.727 -1.501 -1.198 -2.367 -4.289

Cottonwood 

Floodplain 

Woodland 

(CEGL002017)

.045 .025 21 -9.840 -1.962 -2.038 -4.247 -1.242

Box-elder

Floodplain Forest 

(CEGL005033)

.037 .046 .089 11 -1.288 -6.591 -6.130 -4.399

Silver Maple– 

Elm Forest 

(CEGL002586)

.107 .010 .040 .026 2 -2.115 -1.976 -2.975

Sandbar 

Willow 

Shrubland 

(CEGL008562)

.116 .006 .029 .106 .148 5 -1.754 -3.866

Black Willow 

Riparian Forest 

(CEGL002103)

.109 .011 .051 .082 .079 .051 7 -4.458

Woody old field .058 .021 .017 .055 .122 .095 .091 4
18 Vegetation Communities at Big Muddy National Fish and Wildlife Refuge, Missouri Table 5. Multiple-Response Permutation Procedure results for woody communities based on woody stem density. [CEGL00####, National Vegetation Classification System code. The sample size is given in the shaded cells. The chance corrected within group agreement, 

A, is in the lower left. The test statistic, 

T, is in the 

upper right, with bold indicating a significant difference between associations (p < 0.05)]

Mature 

Midwestern 

Cottonwood–

Black Willow

Forest 

(CEGL002018)

Immature 

Midwestern 

Cottonwood–

Black Willow

Forest 

(CEGL002018)

Cottonwood 

Floodplain 

Woodland 

(CEGL002017)

Box-elder 

Floodplain Forest 

(CEGL005033)

Silver Maple– 

Elm Forest

(CEGL002586)

Sandbar 

Willow 

Shrubland 

(CEGL008562)

Black Willow 

Riparian Forest 

(CEGL002103)

Woody old field

Mature

Midwestern

Cottonwood– 

Black Willow

Forest

(CEGL002018)

5 -14.323 -8.055 -1.0671 -2.277 -5.267 -6.356 -4.583

Immature 

Midwestern 

Cottonwood– 

Black Willow

Forest

(CEGL002018)

0.063 79 -20.761 -21.905 -5.205 -4.086 -5.800 -6.641

Cottonwood 

Floodplain 

Woodland 

(CEGL002017)

.138 .077 21 -12.071 -3.215 -3.946 -7.176 -3.012

Box-elder

Floodplain Forest 

(CEGL005033)

.024 .080 .141 11 -1.178 -7.441 -8.490 -3.032

Silver Maple– 

Elm Forest 

(CEGL002586)

.128 .030 .081 .027 2 -2.928 -3.617 -2.944

Sandbar 

Willow 

Shrubland 

(CEGL008562)

.296 .018 .136 .162 .261 5 -4.169 -3.755

Black Willow 

Riparian Forest 

(CEGL002103)

.244 .023 .112 .146 .192 .136 7 -4.827

Woody old field .141 .029 .052 .041 .128 .137 .122 4
Results 19

Ephemeral Pond (CEGL002430) communities are found at 

locations on the flood plain where water collects because of 

terrain and poorly-drained soils. They are dominated by smartweeds (Polygonum spp.) and sedges (Cyperus spp., and Carex

spp.). Communities dominated by Johnson grass (Sorghum 

halepense) and ticktrefoil (Desmodium spp.) were classified 

as Johnson Grass communities, a type not recognized by the 

NVCS (NatureServe, 2009). This community is of interest 

because Johnson grass is a noxious weed for which the refuge 

has implemented a control program. Herbaceous Old Fields 

(another type not recognized in the NVCS) are dominated by 

herbaceous vines (Ipomoea spp., Calystegia spp., Cynanchum 

laeve and the noxious weed, Convolvulus arvensis), ragweed 

(Ambrosia spp.), and exotic grasses such as foxtail (Setaria 

viridis) and barnyard grass (Echinochloa crus-galli). Trumpet creeper (Campsis radicans) is also abundant. Numerous 

other herbaceous communities, including Riverine Sand Flats 

(CEGL002049) and various cultural types were encountered 

during map production, though no plot data were collected.

NMS analysis based on ground flora cover data indicates 

distinct clusters for the Central Wet-Mesic Tallgrass Prairie 

(CEGL002024) and the Johnson Grass communities (fig. 6). 

Both of these communities are characterized by a few dominant species, making their classification in the field relatively 

consistent. The prairie community also reflects the effect of a 

single management effort applied across a contiguous area to 

encourage that type. The broader expression of the Midwestern Ephemeral Pond (CEGL002430) and the Herbaceous Old 

Field types (fig. 6) is probably because of numerous factors. 

First, because plots represent communities from a broad range 

of times since the cessation of agricultural practices, numerous 

successional stages are represented. Second, sampling covered 

a broad spectrum of time following various flood events 

within each sampling season; sampling shortly after flood 

waters recede will detect a distinct set of species compared 

to sampling conducted with greater temporal separation from 

flood events. Finally, the Herbaceous Old Field type served 

as a catch-all for types not matching the other communities 

identified (preliminary attempts to identify subtypes within the 

old field class proved unreliable). The overlap between the two 

communities can be explained by the fact that most Polygonum wetlands are converting from herbaceous old fields and 

retain many of the species associated with the latter type. 

MRPP analysis (T = -6.880, A = 0.085, p < 0.05) indicates 

that all of the herbaceous communities are distinct from one 

another, except when comparing Polygonum wetlands to Herbaceous Old Fields (table 6).

Moisture gradients appear to drive most of the differences 

between herbaceous community types. The output from the 

NMS analysis of herbaceous communities includes vectors 

representing the species most closely correlated (multiple r2

greater than 0.3) to the data structure (fig. 6). Vectors begin 

at the origin, with the direction of the vector indicating the 

direction of increase, and the length of the vector indicating the relative correlation of each species. The separation 

of the Central Wet-Mesic Tallgrass Prairie (CEGL002024) 

along the vertical axis is driven, in large part, by a suite of 

species that can tolerate seasonally drier conditions, such as 

Croton spp., Diodia teres, Paspalum laeve, and Sorghastrum 

nutans as shown on figure 6. The expected management 

gradient separating the Central Wet-Mesic Tallgrass Prairie 

(CEGL002024) from the other types was not identified, as 

Sorghastrum nutans is the only species with a high correlation 

that also was included in the seed mixture used to promote the 

prairie community. Johnson Grass and Herbaceous Old Field 

communities are separated along Axis 1 (fig. 6) by a shift from 

dominance by species that thrive in flood-prone areas, such as 

Lippia lanceolata and Xanthium spp., toward dominance by 

trumpet creeper (Campsis radicans), cover for which diminished substantially in response to flooding during the 2007 and 

2008 growing seasons. Axis 2 is correlated with a shift from 

species that were more abundant in higher, drier flood-plain 

land forms (Aster pilosus, Desmodium paniculatum and Solidago altissima) to species that were more commonly found in 

lower, wetter flood-plain landforms during this study, such as 

Cynanchum laeve and Ipomoea spp. (vectors for these species 

are excluded for simplicity).

Map Production

The final map includes 482 polygons of 27 vegetation community types (some described communities were 

not included in the final map) and covers 3,174 hectares on 

five units of the refuge (table 6). By far, the most abundant 

mapped community is the Midwestern Cottonwood–Black 

Willow Forest (CEGL002018), with 106 polygons covering more than one-half of the mapped area. This community 

was dominant at all management units of the refuge, with a 

mean stand size of 17 ha. Also abundant was the Cottonwood 

Floodplain Woodland (CEGL002017), which covered 214 ha 

in 26 polygons, primarily at Overton Bottoms, Lisbon Bottom, 

and Saint Aubert Island. Other abundant bottomland communities included the Sandbar Willow Shrubland (CEGL008562; 

147 ha), the Riverine Sand Flats (CEGL002049; 107 ha), the 

Midwest Ephemeral Pond (CEGL002430; 94 ha), and the 

Silver Maple–Elm Forest (CEGL002586; 78 ha).

Most of the ruderal communities were mapped at the 

Overton Bottoms unit (fig. 7). These were dominated by 

Herbaceous Old Fields (92 ha), a type with a wide expression 

that seems to be limited to higher, drier bottomland landforms. 

Also abundant are woody old fields, covering approximately 

84 ha in both upland and bottomland expressions. The least 

abundant ruderal community was the Johnson Grass type, 

which was mapped on 31 ha.

Less abundant were communities of particular interest to 

the refuge (table 7). The Central Wet-Mesic Tallgrass Prairie (CEGL002024) occurred on only four patches covering 

37 ha. These were located in areas that have been managed 

for the type using drill and broadcast seeding. Also uncommon was the Ash–Oak–Sycamore Mesic Bottomland Forest 
20 Vegetation Communities at Big Muddy National Fish and Wildlife Refuge, Missouri

Figure 6. Non-metric Multidimensional Scaling output for herbaceous communities with vectors indicating direction of increase 

for those species most correlated with the data structure.

Croton spp.

Diodia teres

Paspalum laeve

Sorghastrum nutans

Campsis radicans

Xanthium spp.

Lippia lanceolata

Axis 1 Axis 2

Axis 1

Herbaceous old field

Johnson grass

Central Wet-Mesic Tallgrass Prairie (CEGL002024)

Midwest Ephemeral Pond (CEGL002430)

EXPLANATION

Table 6. Results of Multiple Response Permutation Procedure analysis of herbaceous communities.

[CEGL00####, National Vegetation Classification System code. The sample size is given in the shaded cells. The chance corrected within group agreement, 

A, is in the lower left. The test statistic, T, is in the upper right, with bold indicating a significant difference between associations (p < 0.05).]

Herbaceous old field Johnson grass Midwest Ephemeral Pond 

(CEGL002430)

Central Wet-Mesic

Tallgrass Prairie 

(CEGL002024)

Herbaceous old field 11 -3.192 0.088 -5.767

Johnson grass .066 3 -4.541 -3.002

Midwest Ephemeral Pond 

(CEGL002430) -.001 .076 14 -5.934

Central Wet-Mesic 

Tallgrass Prairie 

(CEGL002024)

.095 .212 .080 4
Results 21

Figure 7. Vegetation for portion of floodplain at Overton Bottoms unit at Big Muddy National Fish and Wildlife Refuge, 

Missouri.

92°35' 92°34' 92°33'

38°58'

38°57'

Central Wet-Mesic Tallgrass Prairie (CEGL002024)

EXPLANATION

National Vegetation Classification System Communities (code)

Midwestern Cottonwood–Black Willow Forest (CEGL002018)

Cottonwood Floodplain Woodland (CEGL002017)

Silver Maple–Elm Forest (CEGL002586)

Box-elder Floodplain Forest (CEGL005033)

Sandbar Willow Shrubland (CEGL008562)

Midwest Ephemeral Pond (CEGL002430)

Other Features

Johnson grass

Herbaceous old field

Bottomland woody old field

Plantation

Levee

River

Scour

Road

Railroad

0 0.5 KILOMETERS

0 0.5 MILES

Base imagery from U.S. Department of Agriculture,

National Agricultural Imagery Program, 2007

Universal Transverse Mercator projection, NAD83

Zone 15N
22 Vegetation Communities at Big Muddy National Fish and Wildlife Refuge, Missouri

Table 7. Polygon count and area for mapped communities at Big Muddy National Fish and Wildlife Refuge.

[NA, not applicable] 

National Vegetation Classification System (NVCS) 

common name or project community name

NVCS

code

Number 

of plots

Number 

of map 

points

Number of 

mapped 

polygons 

(mapped as)

Total 

mapped 

area 

(hectares)

Forest

Upland

White Oak–Red Oak–Sugar Maple Mesic Forest CEGL002058 0 4 8 14.73

White Oak/Dogwood Dry-Mesic Forest CEGL002066 0 4 5 21.48

White Oak–Mixed Oak Dry-Mesic Alkaline Forest CEGL002070 0 1 0

(CEGL002066)

0

Midwest Post Oak–Blackjack Oak Forest CEGL002075 0 2 0

(CEGL004803)

0

Black Oak–White Oak–Hickory Forest CEGL002076 0 7 6 26.78

Ozark Red-cedar–Hardwood Forest CEGL004803 0 9 11 59.75

Bottomlands

Midwestern Cottonwood–Black Willow Forest CEGL002018 84 132 106 1892.02

Black Willow Riparian Forest CEGL002103 7 6 0

(CEGL002018)

0

Silver Maple–Elm Forest CEGL002586 2 17 15 77.81

Central Green Ash–Elm–Hackberry Forest CEGL002014 0 1 0

(CEGL002586)

0

Ash–Oak–Sycamore Mesic Bottomland Forest CEGL002410 0 2 2 5.27

Box-elder Floodplain Forest CEGL005033 11 18 22 14.55

Woodland

Cottonwood Floodplain Woodland CEGL002017 21 41 26 213.75

Shrubland

Sandbar Willow Shrubland CEGL008562 5 57 66 147.11

Herbaceous

Central Wet-Mesic Tallgrass Prairie CEGL002024 4 8 4 36.61

Midwest Ephemeral Pond CEGL002430 14 34 42 94.10

Riverine Sand Flats CEGL002049 0 16 17 107.09

Ruderal

Herbaceous old field NA 11 19 22 92.57

Fescue field NA 0 5 5 14.63

Bottomland woody old field NA 4 24 9 34.74

Upland woody old field NA 0 5 10 50.02

Johnson grass NA 3 12 18 31.09

Other features

Levee NA 0 8 13 12.71

Plantation NA 0 5 5 17.34

Pond NA 0 11 12 7.59

Railroad NA 0 5 3 7.68

River NA 0 17 33 84.48

Road NA 0 7 17 23.94

Row crop NA 0 2 2 20.97

Scour NA 0 2 3 13.41

Utility right-of-way NA 0 0 1 2.72
Management Implications 23

(CEGL002410; 5 ha), which was limited to a few narrow 

ravines in the upland parcel at Overton Bottoms. 

The uplands were dominated by white oak forests 

(table 7; fig. 8). The White Oak–Red Oak–Sugar Maple Mesic 

Forest (CEGL002058) was mapped on 15 ha, primarily low, 

mesic, north-facing slopes. Often, this community was associated with limestone bluffs, where sugar maple became more 

dominant and the canopy tended to be patchy. On dry-mesic 

slope positions, there is a transition to the White Oak/Dogwood Dry-Mesic Forest (CEGL002066; 21 ha). This can be 

replaced by an alkaline version (CEGL002070) where carbonate bedrock is at or near the surface, but the few examples 

observed were too small to warrant inclusion in the final map. 

However, species that thrive on base-saturated soils, especially Chinkapin oak (Quercus muehlenbergii) and white ash 

(Fraxinus americana), were abundant throughout the uplands, 

suggesting a strong potential for the alkaline type. Even drier 

landscape positions support the Black Oak–White Oak–

Hickory Forest (CEGL002076; 27 ha) and then the Ozark 

Red-cedar–Hardwood Forest (CEGL004803; 60 ha). The 

latter type tends to be limited to upper south-facing slopes. 

Ruderal community types in the uplands include Fescue Field 

and Upland Woody Old Fields, two types whose differences 

appear to arise from differences in the time since the cessation 

of agricultural activity, especially hay production

Management Implications

Record flooding in 1993 and 1995 across broad areas 

on the refuge allowed establishment of abundant Midwestern 

Cottonwood–Black Willow Forests (CEGL002018). Stands 

of this type appear to have entered a stem-exclusion stage 

consistent with wholesale stand regeneration. Suppressed 

stems are being shaded out, creating canopy gaps that will last 

until the crowns of surviving trees expand to fill the vacated 

space. At the same time, flood dynamics are creating a more 

heterogeneous structure by increasing mortality in low lying 

areas where flooding appears to be more intense (deeper and 

more prolonged with greater flow rates). This action appears to 

create greater mortality in cottonwoods than in willows, which 

might drive succession towards the Black Willow Riparian 

Forest (CEGL002103), a type that was tentatively identified 

but not mapped on the refuge. Study data suggest that the 

global description for the Black Willow Riparian Forest should 

indicate this type as extant in Missouri and the study area. 

The refuge will be an excellent location to test whether Black 

Willow Riparian Forest can sustain itself as successional and 

disturbance processes continue. 

The Silver Maple–Elm Forest (CEGL002586) is currently 

limited to riverfront locations outside of protected levees and 

adjacent to back channels, sloughs and scours. It is reasonable to expect this type to expand, but that expansion will be 

limited by the availability of suitable sites. From a habitat 

perspective, it does not appear to be particularly different from 

mature cottonwood forests, with which it shares many species. 

Management directed toward increasing the abundance of the 

silver maple forest may prove unreliable and inefficient given 

the risk of high-intensity floods.

Box-elder Floodplain Forest (CEGL005033) appears to 

be limited to stable protected landforms that had been removed 

from agricultural production before the floods in 1993 and 

1995: it is dominated by mature trees, primarily boxelder with 

an emergent canopy of cottonwoods. The NVCS description 

of this type suggests that it represents a ruderal community 

indicative of past agricultural activity (NatureServe, 2009). Its 

presence may be hindering the establishment of communities 

that would otherwise be found in the flood plains (for example, where it is found, there are few cottonwood seedlings or 

saplings). As these stands mature, they may yield to mixed 

bottomland forests with a greater abundance of hardwood species, particularly ash (Fraxinus spp.), oak (Quercus spp.) and 

pecan (Carya illinoinensis), seedlings of which are occasionally found beneath the canopy of the boxelder forests.

The refuge is particularly interested in increasing the 

abundance of mixed hardwood bottomland communities, but 

these are rarely encountered on the flood plains of the refuge. 

Only two examples of a mixed hardwood type were found 

which matched the description for the Ash–Oak–Sycamore 

Mesic Bottomland Forest (CEGL002410) and these were 

found in draws of the upland parcel at Overton Bottoms. These 

represent a forest type intermediate between oak-dominated 

bottomland forests and the Central Green Ash–Elm–Hackberry 

Forest (CEGL002014). Only one example of the latter type 

was identified during sampling, of a size too small to map; 

however, bottomland old fields with high woody stem densities appear to be succeeding toward the CEGL002014 type. 

Management practices encouraging oak production in woody 

old fields may be an efficient means of shifting the successional trajectory of old fields toward the Ash–Oak–Sycamore 

Mesic Bottomland Forest (CEGL002410) to meet the management objective of increasing the abundance of mixed-hardwood forests.

Cottonwood Floodplain Woodlands (CEGL002017) have 

become established on higher, somewhat drier flood-plain 

landforms. They are not subject to the same flood intensity 

that can be found in lower areas, and appear to be stable. As 

natural thinning progresses in Midwestern Cottonwood–Black 

Willow Floodplain Forests (CEGL002018), they may succeed 

toward the woodland type. The open canopy of the woodland 

type appears to make it susceptible to invasion by Johnson 

grass.

Sandbar Willow Shrublands (CEGL008562) are abundant adjacent to channels, chutes and sloughs, where dynamic 

flooding creates a mosaic of deposition and scour features. 

They can also be found on the flood plain in low lying areas 

with high flood intensity. Though the type is abundant and 

in little danger of extirpation from the refuge, changes in 

its abundance could be affected by alterations that increase 

the heterogeneity of the river channel morphology. Management for shallow water habitat and the creation of chutes and 
24 Vegetation Communities at Big Muddy National Fish and Wildlife Refuge, Missouri

Figure 8. Vegetation for upland section of Saint Aubert Island unit at Big Muddy National Fish and Wildlife Refuge, 

Missouri.

91°53'30" 91°53' 91°52'30"

38°38'30"

38°38'

EXPLANATION

National Vegetation Classification System Communities (code)

Midwestern Cottonwood–Black Willow Forest (CEGL002018)

Chinkapin Oak–Red-cedar Dry Alkaline Forest (CEGL004803)

Black Oak–White Oak–Hickory Forest (CEGL002076)

White Oak/Dogwood Forest (CEGL002066)

White Oak–Red Oak–Sugar Maple Mesic Forest (CEGL002058)

Other Features

Fescue field

Upland woody old field

Utility right-of-way

Pond

Railroad

0 300 METERS

0 1,000 FEET

Base imagery from U.S. Department of Agriculture,

National Agricultural Imagery Program, 2006

Universal Transverse Mercator projection, NAD83

Zone 15N
Management Implications 25

other novel avenues for stream flow are possible management 

actions that would change the abundance of this type.

Expressions of the Central Wet-Mesic Tallgrass Prairie (CEGL2024)) are determined predominantly by specific 

management actions to increase that type on the refuge, most 

notably, seeding warm-season grasses. If the refuge is able 

to control or reverse the spread of the nonnative invasive 

Johnson grass (Sorghum halepense), the prairie type should 

become more abundant. Prescribed fire is a common tool used 

to stimulate prairie restoration, but its use on the refuge may 

increase the abundance of Johnson grass, which is found at 

many locations throughout the refuge and increases in abundance in response to fire. Given the small area classified as the 

prairie community type, it is difficult to assess landform-based 

differences in the success or failure of management actions 

intended to increase the prairie community.

Flooding in 2007, 2008, and 2009 has dramatically 

increased the abundance of the Midwest Ephemeral Pond 

community (CEGL002430). Many locations that would have 

been classified as Herbaceous Old Field based on 2002–04 

data had converted to this wetland type by the final sampling 

for map production in 2009. This is even true for areas in 

which 2007 data suggested an old field type. Not surprisingly, this type can be found in low, water-retaining areas 

on the flood plain. The examples with the deepest and most 

prolonged flooding appear to be succeeding toward the 

Northern Buttonbush Swamp (CEGL002190) or the similar 

Southern Buttonbush Shrubland (CEGL002191). Buttonbush 

(Cephalanthus occidentalis) and Hibiscus spp., are becoming 

established, along with a variety of sedges. Efforts to increase 

the length of time water occupies these sites may further this 

succession.

Riverine Sand Flats (CEGL002049) were limited to point 

bars and high and low mud banks along the river channel 

and secondary chutes. They occasionally occur on high flats 

where flooding has removed woody vegetation and deposited sand or mud. In terms of species composition and flood 

dynamics, this type is little different than the Riverine Mud 

Flats (CEGL002314), a type excluded because “sand” better described the dominant substrate in the study area. Also, 

the sand flats description is consistent with Nelson’s (2005) 

sandbar community for Missouri. The abundance of this community will most likely be affected by changes to the fluvial 

dynamics of the river itself. The species composition of this 

type is extremely variable.

It is difficult to predict the successional trajectory of 

ruderal communities. Recent prolonged flooding has lead 

to dramatic changes in the most abundant ruderal community type, bottomland herbaceous old fields. An increase in 

abundance of hydrophilic species, especially Polygonum spp., 

has directed succession in low lying areas toward the Midwest 

Ephemeral Pond (CEGL002430). For example, some communities that were identified as Herbaceous Old Fields dominated 

by drought tolerant grasses during sampling in 2007 were 

reclassified as the wetland type based on evidence collected 

during 2009 sampling. This change can be attributed to the 

flooding that occurred in the intervening years. At the same 

time, flooding has induced mortality among many woody species, especially trumpet creeper (Campsis radicans), shifting 

communities from the woody old field to the herbaceous old 

field or, in some cases, directly to the wetland type. Periods 

of prolonged drought might reverse these trends. Meanwhile, 

woody stems such as Celtis laevigata, Platanus occidentalis

and Fraxinus pennsylvanica are colonizing drier old fields 

and pushing succession toward the Central Green Ash–Elm –

Hackberry Forest (CEGL002014). In some areas, Johnson 

grass is creating a static herbaceous community within which 

desirable native species struggle to establish.

Upland community distribution can most readily be 

understood within the context of moisture gradients. Progression from low, north-facing slopes to drier summits is accompanied by a progression from red oak (Quercus rubra) and 

white oak (Q. alba) forests with sugar maple (Acer saccharum) through white oak dominated forests to mixed oak-hickory (Carya spp.) forests. Dry, upper south-facing slopes support open forests; however, the NVCS description for Ozark 

Red-cedar–Hardwood Forest (CEGL004803) is likely correct in its assertion that the type represents a fire-suppressed 

expression of an oak-dominated woodland (NatureServe, 

2009). Fire suppression, along with the effects of past grazing, 

likely increased overall stem density and the abundance of 

eastern redcedar (Juniperus virginiana). Some sampling points 

within polygons classified as the CEGL004803 type originally 

had been identified as the Midwest Post Oak–Blackjack Oak 

Forest (CEGL002075), which is considered a fire-suppressed 

expression of an oak woodland without eastern redcedar. 

With management to remove eastern redcedar and decrease 

overall stem density (prescribed burning, for example), 

areas currently mapped as the Ozark Red-cedar–Hardwood 

Forest (CEGL004803) should start to resemble an Ozark–

Ouachita Post Oak–Blackjack Oak / Little Bluestem Woodland (CEGL002149), which may have been more abundant 

historically.

A woody old field type can be found in the uplands, 

usually on summits and shoulders suitable for grazing. In the 

uplands, the dominant species in old fields are honey locust 

(Gleditsia triacanthos) and eastern redcedar (Juniperus virginiana). The presence of these long-lived species may hinder 

succession toward more desirable, oak-dominated forests and 

woodlands by suppressing establishment and survival of species indicative of those types. Fescue fields in the uplands only 

recently have been removed from grazing or hay production 

management. These will likely succeed toward the woody old 

field type. Both communities are susceptible to invasion by the 

nonnative invasive, Lespedeza cuneata, which can be found in 

abundance in upland locations at Saint Aubert Island.
26 Vegetation Communities at Big Muddy National Fish and Wildlife Refuge, Missouri

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Appendix 1

The Microsoft Office Word document Appendix_1.docx compiles global descriptions of 

National Vegetation Classification System vegetation associations maintained by NatureServe 

(2009) with notes on local expressions of communities encountered during this study. 
Publishing support provided by: 

Rolla Publishing Service Center 

For more information concerning this publication, 

contact:

Director, USGS Columbia Environmental Research Center

4200 New Haven Road

Columbia, MO 65201

(573) 875–5399

Or visit the Columbia Environmental Research Center 

Web site at:

http://www.cerc.usgs.gov/

Struckhoff and others—Vegetation Communities at Big Muddy National Fish and Wildlife Refuge, Missouri—Open-File Report 2011–1038