Upper Mississippi River Restoration Program

Upper Mississippi River Restoration Program

Long Term Resource Monitoring


Vegetation Update Title Page


Sampling procedures are described in detail in Yin et al. (2000). The following is a brief description of the overall design.


The objective of the sampling program was to accumulate data on the distribution, frequency of occurrence, and relative abundance of aquatic vegetation within pools over a long period (>50 years) using a standardized protocol across the system. 


A stratified random approach was initiated in 1998. Sampling sites were distributed in shallow water areas where water depth was less than or equal to 3 m at flat-pool condition. After 1998, sampling sites were distributed in less than or equal to 2.5 m depth. Deeper water areas generally do not support aquatic vegetation. Shallow water areas were divided into several habitat types (strata), including main channel borders, secondary channels, contiguous backwaters, isolated backwaters, and impounded areas (Figure 1). Sampling efforts were proportional to acreage and perceived habitat heterogeneity of each stratum, except for the isolated backwater areas where sample sites are limited because they are time consuming to conduct. Some areas were excluded from the sampling because of safety concerns and difficulties with access.

Site Selection

A 50- X 50-m grid was generated and overlaid onto the stratified aquatic areas. Nodes of the grid were geospatially registered (Universal Transverse Mercator coordinates), and nodes that fell in the sampling strata were eligible for selection. Sites are reselected annually using a random number generator except for Pool 8 where the sample sites were held constant between 2002 and 2004. We navigated to the general area of a site using an enlarged hard-copy map and then switched to global positioning system (GPS) equipment with differentially corrected signals as the boat approached the targeted location. The boat was anchored at bow and stern when both the easting and northing coordinates displayed on the GPS unit were within 10 m (- or +) of their selected node. The actual GPS coordinates were read and recorded twice at each site, once immediately after the boat had been anchored and again before the boat was released for departure.

Equipment and Definitions

Photo of the sampling rake.Submersed aquatic vegetation was collected using a long-handled, double-headed rake modified from Jessen and Lound (1962) and Deppe and Lathrop (1992). The rake is 36 cm (14 inches) wide, has 14, 5-cm (2 inches) long teeth on each side, and was made by welding two square-headed garden rakes together. The teeth are divided and marked into five equal parts (or 20% increments). The handle is about 3 m long, with a rope extension, and is scaled at 10-cm increments. Aquatic vegetation or aquatic species refer to the following plant types or life forms: submersed (S), rooted floating–leaf (F), and emergent (E).

Site and Subsampling Areas

Subsampling area arrangement around the boat

Each site had six subsampling areas, each of which was a rectangular area approximately 1.5 m long and 0.36 m wide (the width of the rake head). One subsampling area was located off each corner of the boat and the other two were located, one each, off the left and right sides. Number of sample sites can be found in Table 1.



Sampling and Data Recording

Individual species and different life forms of aquatic vegetation (e.g., submersed and rooted floating–leaf) were recorded as either present or absent at each subsampling area based on visual examination and a rake sample. When present, submersed species were given a density rating (see data at lower left) based on their thickness on the rake teeth. When present, rooted floating–leaf and emergent species were given a percent cover rating based on visual examination (see data at lower right). Species that had not been recorded in the six subsampling areas but were observed at the site were recorded and marked as "additional species." Fassett (1957), Voss (1972, 1985), and Gleason and Cronquist (1991) were the primary references used for plant identification. Scientific nomenclature and common names are based on those found in the U.S. Department of Agriculture's PLANTS Database (USDA, NRCS 2004; http://plants.usda.gov/).

Submersed vegetation
density ratings

Emergent and rooted floating-leaf vegetation cover ratings

Percent of rake teeth filled
Density rating
Percent of area covered
Cover rating

no plants retrieved


Computation of Summary Indexes

Summary indices were computed for individual strata as well as entire pools.  In addition, Pool 4 was split into upper and lower sections divided by Lake Pepin because the two sections displayed distinctly different vegetation dynamics.  In Pool 26, data from the lower 12 miles of the Illinois River were computed separately from the Mississippi River portion because the data represent two different rivers.


Percent frequency of occurence values in this report was computed by dividing the number of sites where a species was recorded by the number of sites investigated in the stratum and then multiplied by 100 to convert it into a percentage.

Abundance index formula

The frequency value in a pool was computed by averaging the frequency values of the shallow water strata, weighted by acreage:

Abundance index formula for a stratum

where Fj is the frequency in stratum j and Sj is the acreage of stratum j.


Abundance Index

An index was created to measure the quantity of a submersed species using both presence or absence and plant density rating data recorded in the six subsampling areas. We called it the abundance index to differentiate it from the frequency index. The abundance index was computed according to the following formula:

Abundance index formula for a pool

where Vi is the presence or absence (1,0) and Ri is the plant density ranking (0,1,2,3,4,5) data for the ith subsampling areas at the site (i = 1,2,3,4,5,6). Data are treated before computation so that Vi = 1 if Ri >= 1 and, vice versa, Ri >= 1 if Vi = 1.

The abundance index for a stratum was computed as the simple average of all its sites.

Percent cover formula for rooted floating leaf and emergent lifeforms

The abundance index for a pool was computed as the average of all shallow water strata, weighted by acreage:

Percent cover formula for a pool

where Aj is the abundance index of the species in stratum j and Sj is the acreage of stratum j.


Percent Cover (rooted floating–leaf and emergent life form)

The percent cover of rooted floating–leaf and emergent life forms in a stratum was computed using the following formula:

Image of the stratified random sampling rake

where Lj is the cover rating at individual sites and A is the midpoint of the corresponding percent cover, and M is the total number of sites in the stratum.

Percent cover in a pool was computed as the average of all shallow water strata, weighted by acreage:

Image of the subsampling areas around the boat

where Cj is percent cover in stratum j and Sj is the acreage of stratum j.


Chronological Summary of Method Changes

Prior to the beginning of stratified random sampling in 1998, vegetation transect data have been collected every year starting in 1991 to 2000 and were collected in the months of May through August (except for La Grange Pool that has some September data as well). There was a 3-year overlap of sampling methods during this transition so temporal patterns between the two methods could be evaluated. Data can be downloaded from the Vegetation Transect Database Browser with reports found at Vegetation Annual Status Reports.
Year 1998: Sampling sites were distributed among locations within strata less than or equal to 3-m water

Year 1999: In 1999, sample sites were restricted to areas less than or equal to 2.5 m water depth.


In 1998, the target number of sites was 550 for all pools.  The target number of sites changed to 600 in Pool 8 and 650 in Pool 26 in 1999.  Changes in the target number of sites were based on the variance from the previous year.


Year 2000: The target number of sites was changed to 635 in Pool 4, 650 in Pool 8, 580 in Pool 13, 400 in Pool


26, and 430 in La Grange Pool based on the variance from the previous year.


Year 2001: The target number of sites was changed to 650 in Pool 4, 670 in Pool 8, 610 in Pool 13, and 420 in


Pool 26 based on the variance from the previous year.  In Pool 11, 568 sites were sampled to provide data on other pools in the system.


Year 2002: The target number of sites was changed to 635 in Pool 4, 650 in Pool 8, and 580 in Pool 13 based


on the variance from the previous year. Sites were sampled in Pools 5 (404), 7 (406), and 12 (405) and Alton Pool (513) to help determine how representative the standard pools (4, 8, 13, and 26 and La Grange Pool) were of the Upper Mississippi River System. 

A drawdown was conducted in Pool 8 in 2001 and 2002.  In 2002, we revisited the 2001 sites in Pool 8 (except for 20 isolated backwater sites) to allow for the calculation of change estimates for not only the pool and strata but also for individual sites, thereby increasing the statistical power to identify drawdown related vegetation responses.


Year 2003: In 2003, 650 sites were sampled in Pool 8 and 580 sites in Pool 13 based on the variance from the


previous year.  Because of budget reductions, no LTRMP-funded aquatic vegetation sampling was conducted in Pools 4 and 26 and La Grange Pool.  However, aquatic vegetation was sampled from the three pools by other agencies using LTRMP protocols, and the data were graciously provided to the LTRMP.  

Pool 26 was sampled by the Illinois Natural History Survey under a grant provided by the National Great Rivers Research and Education Center.  La Grange Pool was sampled by the Illinois Natural History Survey under a grant provided by the Illinois Department of Natural Resources.  Aquatic vegetation data from Pool 4 were provided by the U.S. Fish and Wildlife Service and the Division of Fisheries, Minnesota Department of Natural Resources. Two strata, isolated backwater, and Lake Pepin were not sampled. 

In 2003, we again revisited the sites selected in Pool 8 (except for the 20 isolated backwater sites) in 2001 to continue to monitor vegetation response to the drawdown.


Year 2004: Sampling was conducted in LTRMP key Pools 4, 8, 13, and 26 of the Mississippi River and La Grange


Pool of the Illinois River. Sample size was adjusted based on the variance from the previous year (Table 1).

In 2004, we again revisited the sites selected in Pool 8 (except for the 20 isolated backwater sites) in 2001 to continue to monitor vegetation response to the drawdown.


Year 2005–Present: Sampling was conducted in LTRMP key Pools 4, 8, and 13.


In 2005, a 5-year plan was developed for the LTRMP. Within this plan, the data collection portion of the Program was reduced to a level that could be accomplished annually over the 5-year period given budget constraints. Under this plan based on guidance from the LTRMP Analysis Team and Environmental Management Program Coordinating Committee, the vegetation component will only conduct long-term sampling in Pools 4, 8, and 13 (450 sites per pool) under the minimum sustainable program.

In 2011, the sampling frame (i.e., map used to randomly draw sample sites) of Pool 13 was reduced permanently to eliminate a potential safety hazard to the field crew. The excluded area is part of the former Savanna Army Depot (now part of the Lost Mound Refuge). The reduced area eliminates 132 out of 13396 elements (i.e., potential sample sites) in the BWC and BWI strata in the frame. The summary statistics were recalculated for all previous years to reflect the sampling frame change by removing previous-year sites that fall in the removed portion of the frame.

Also, in previous years, standard deviations of the means were estimated using the Proc Surveymeans procedure of SAS in which standard deviations were adjusted down assuming our samples are from a finite population (For more details, see http://www.umesc.usgs.gov/ltrmp/stats/means.html#t7). We now abandon this correction because the "finite population" is an artifact of the grid system we used to select random sites. Hereafter standard deviations are estimated with the assumption that the samples are drawn from an infinite population.

In 2012, the summary statistics for Pool 4 were adjusted from representing the pool as an upper and lower half, divided in the middle of Lake Pepin (Figure A), to reflecting the data and the pool by its three geomorphic reaches (Thieling et al. 2000); upper Pool 4, Lake Pepin and lower Pool 4 (Figure B).

Pool4Strata_pre2012 Pool4_Strata_2012
Figure A. Figure B.

Content manager: Dr Yao Yin

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