Substrate maps from "Hydraulic and Substrate Maps of Reaches Used by Sturgeon (Genus Scaphirhynchus) in the Lower Missouri River, 2005-07"

Metadata:

• Identification_Information
• Data_Quality_Information
• Spatial_Data_Organization_Information
• Spatial_Reference_Information
• Entity_and_Attribute_Information
• Distribution_Information
• Metadata_Reference_Information

Identification_Information:

Citation:

Citation_Information:

Title:

Substrate maps from "Hydraulic and Substrate Maps of Reaches Used by Sturgeon (Genus Scaphirhynchus) in the Lower Missouri River, 2005-07"

Publication_Date: 2008

Originator: Joanna M. Reuter

Originator: Robert B. Jacobson

Originator: Caroline M. Elliott

Originator: Harold E. Johnson

Originator: Aaron J. DeLonay

Geospatial_Data_Presentation_Form: raster digital data

Series_Information:

Series_Name: U.S. Geological Survey Data Series

Issue_Identification: Data Series 386

Publication_Information:

Publication_Place: Reston, Virginia

Publisher: U.S. Geological Survey

Description:

Abstract:

A collection of reach-scale maps of hydraulic and substrate characteristics were generated for the habitat-use portion of an interdisciplinary sturgeon research project on the Lower Missouri River (from Gavins Point Dam to the junction with the Mississippi River). The maps were derived from hydroacoustic data sets that were collected for the purpose of assessing physical aquatic habitat in the vicinity of locations of adult shovelnose sturgeon (Scaphirhynchus platorynchus) and pallid sturgeon (S. albus). Hydroacoustic data sets were collected at the reach scale (mean reach length, 2.4 kilometers) in order to include the immediate vicinity of a targeted sturgeon location as well as the full range of habitat available at the bend and crossover scale. Reaches typically were surveyed on the day following the relocation of a telemetered sturgeon and at a discharge within 10 percent of the discharge on the sturgeon relocation date in order to characterize as closely as possible the channel morphology and flow-field conditions at the time that the sturgeon was present. One hundred fifty-three reaches were mapped during April-September in the years 2005 through 2007, with the majority of data collection occurring in the months of May and June (coinciding with the period of sturgeon migration and spawning in the Lower Missouri River). Interpolated maps (grid cell size, 5 meters) depict depth, generalized substrate, and depth-averaged velocity. Side-scan sonar imagery is also available for a subset of reaches.

Purpose:

The maps were derived from hydroacoustic data sets that were collected for the purpose of assessing physical aquatic habitat in the vicinity of locations of adult shovelnose sturgeon (Scaphirhynchus platorynchus) and pallid sturgeon (S. albus).

Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: 20050405

Ending_Date: 20070717

Currentness_Reference: ground condition

Status:

Progress: Complete

Maintenance_and_Update_Frequency: None planned

Spatial_Domain:

Bounding_Coordinates:

West_Bounding_Coordinate: -97.442

East_Bounding_Coordinate: -90.295

North_Bounding_Coordinate: 49.955

South_Bounding_Coordinate: 38.485

Keywords:

Theme:

Theme_Keyword_Thesaurus: ISO 19115 Topic Categories

Theme_Keyword: inlandWaters

Place:

Place_Keyword_Thesaurus: None

Place_Keyword: Missouri

Place_Keyword: Kansas

Place_Keyword: Iowa

Place_Keyword: Nebraska

Place_Keyword: South Dakota

Place_Keyword: USA

Access_Constraints: none

Use_Constraints: none

Point_of_Contact:

Contact_Information:

Contact_Organization_Primary:

Contact_Organization: U.S. Geological Survey, Columbia Environmental Research Center

Contact_Address:

Address_Type: mailing and physical address

Address: 4200 New Haven Road

City: Columbia

State_or_Province: MO

Postal_Code: 65201

Country: USA

Contact_Voice_Telephone: 573-875-5399

Data_Set_Credit:

Funding for this project was provided by the U.S. Army Corps of Engineers (USACE, Omaha District, Craig Fleming, Project Manager) and the U.S. Geological Survey (USGS). This work was part of the Comprehensive Sturgeon Research Project, a large, interdisciplinary, multiyear research project to which numerous individuals contributed. The following individuals, in particular, deserve mention: Matt Smith, Chad Vishy, Mark Laustrup, David Gaeuman, Kim Chojnacki, Emily Tracy-Smith, and Sandy Clark-Kolaks. Sturgeon tracking crews, under the supervision of Aaron DeLonay, were also essential to this work.

Native_Data_Set_Environment:

Microsoft Windows XP Version 5.1 (Build 2600) Service Pack 3; ESRI ArcCatalog 9.2.5.1450

Data_Quality_Information:

Logical_Consistency_Report:

Each individual reach map depicts physical conditions dependent on the discharge and channel morphology at the time of mapping; both of these factors are dynamic on the Lower Missouri River. For more information, see associated report: Reuter and others, 2008, USGS Data Series Report 386.

Completeness_Report:

Maps represent conditions in parts of the reach deep enough for the boat to navigate. In some cases, patches of data are missing due to poor quality GPS data or equipment malfunction. Some reaches are shorter than their planned length due to onset of inclement weather. For more information, see associated report: Reuter and others, 2008, USGS Data Series Report 386.

Lineage:

Process_Step:

Process_Description:

Hydroacoustic instrumentation included single-beam echo sounders, RoxAnn instruments (Marine Microsystems and Sonavision, Ltd., Aberdeen, United Kingdom), and acoustic Doppler current profilers (ADCP; Teledyne RD Instruments, Poway, California). Computers logged hydroacoustic data while the boat was driven along the planned transects from bank to bank or as depth allowed; transects ended where the water was too shallow for the boat to navigate (at depths less than approximately 0.6 meter). Boat speeds typically averaged around 2 meters per second for a survey, generally with lower speeds in shallow or slow water. In general, data collection followed standard procedures for hydroacoustic data as described in Elliott and others (2004).Two boats were used for the collection of depth, substrate, and velocity data: the R/V (research vessel) Lucien M. Brush and the R/V Slim Funk (fig. 4). Both boats had mounts that suspended the echo sounder and ADCP transducers in the water on the starboard side of the boat near the bow. The GPS antenna was mounted above the transducers. The R/V Funk worked primarily in the upstream segments of the river (Gavins Point, Ponca, Big Sioux, and Platte; fig. 1). The R/V Brush worked in the downstream segments (Kansas, Grand, and Osage; fig. 1). The instrument configuration varied slightly between the boats and from year to year (table 1). Substrate data sets were collected with RoxAnn instrumentation. RoxAnn instruments analyze the return signals from the echo sounder and generate two parameters, E1 and E2, based on the first and second returns, respectively (Hamilton, 2001). Two different RoxAnn instruments were used; an analog RoxAnn was used on the R/V Funk, and a digital model (RoxAnn GD) was used on the R/V Brush. Each RoxAnn instrument was kept on the same boat, and the units were not recalibrated through the study period. The computer operator on the boat monitored collection of RoxAnn data; however, few options exist to adjust quality characteristics during data collection. We developed an interpretational framework for mapping substrate classes using the RoxAnn substrate classification systems, validated through sediment sampling, side-scan sonar interpretation, and repeat substrate mapping. These methods generally follow those established by other seabed classification studies (Cholwek and others, 2000; Brown and others, 2005), although methods had to be optimized for the turbid and high-velocity conditions of the Lower Missouri River. In particular, high turbidity prevented us from using videography to establish correlations between acoustic signatures and substrate types. To generate substrate maps, RoxAnn data were first classified into three classes based on signatures of the E1 and E2 parameters, as described below. The RoxAnn-based classifications were supplemented with other geospatial data to produce the generalized substrate maps in this report. Three distinct signatures of E1 and E2 values are common in RoxAnn data on the Lower Missouri River (fig. 5). The first signature, defined by very high E1 or E2 values, corresponds to rock, gravel, and coarse, hard sand. The second signature is characterized by low and spatially uniform E1 values in combination with spatially fluctuating E2 values; this signature corresponds to sand dunes. Spatial variability in E2 was interpreted to be the result of differences in the hydroacoustic return across dune forms. The third signature, defined by low and spatially uniform E1 and E2, was interpreted to represent two distinct but hydroacoustically similar substrate types: fine sediment and transporting sand. This signature is associated with fine sediment (mud, silt) in areas of low velocity, such as behind wing dikes. Low, uniform E1 and E2 values were also recorded in the main channel, typically at relatively high discharges, and we interpret these patches to be transporting sand. The transporting sand is distinguished from sand dunes by consistently low values of E2, suggesting a more uniformly soft riverbed.For shallow and relatively slow moving water, we established “ground-truth” correlations between hydroacoustic signatures and sediment types through sampling with a 5-cm coring device or with a “mini ponar” sediment sampler. Retrieved sediments were classified qualitatively into dominant particle-size classes. In deep and swift parts of the Missouri River, direct sampling was not possible. For these areas, correlations between acoustic signatures and sediment type were established through comparisons with side-scan imagery from selected locations. Side-scan imagery provided reliable identification of gravel and cobble based on bright acoustic returns and variable texture. Mud was identified as uniform areas of low acoustic returns. Sand dunes were readily apparent based on morphology, and transported sand was apparent as blurry uniform areas within sand-dune fields. We developed an automated procedure to categorize data points into one of these three classes. To describe spatial variability, summary statistics were computed for E1 and E2 in the vicinity of each data point. For each data point, all other points within a 5-meter radius were identified, and quartile, mean, and standard deviation values were calculated. Following some exploration of data sets using multivariate statistics (discriminant analysis and K-means classification), as well as visual examination of the data sets, the third quartile for E1 and the third quartile for E2 emerged as reliable values for the basis of the classification. Distributions of the spatial third-quartile values for E1 and E2 were used to determine cutoff values between substrate classes. Populations of these values varied between the two RoxAnn instruments used, and values also varied by water temperature. To adjust for differences in environmental conditions and between instruments, we used relative cutoff values to define substrate classes based on the distribution of the spatial third-quartile E1 and E2 values in each reach (fig. 5B). RoxAnn data were brought into Hypack software with the RoxAnn selected as the echo sounder, and points with spurious depth values were deleted because E1 and E2 values associated with spurious depths were unreliable. Data were then exported from Hypack software to a text file and converted to a shapefile. For each data point, quartile values were calculated based on the data points falling within a 5-meter radius of the point. Cutoff values between classes were determined by computing the standard deviations of the spatial third-quartile values for E1 and E2, as described previously. Each point was then classified into one of three general substrate classes. After classifying each data point, grids of substrate were made based on a discrete-value gridding approach: First, each grid cell that contained substrate data points was assigned the substrate class with the majority representation in the cell. Next, cells without points were assigned the value based on the nearest neighbor grid cell with an assigned substrate class. The resulting grids were smoothed with a majority operation in a moving window of 3 by 3 cells; larger windows were used to break ties. The result was a substrate grid based on RoxAnn values only with three preliminary classes: fine sediment/transporting sand, sand dunes, and rock/gravel. Mud and transporting sand have similar RoxAnn signatures, but these substrate classes can be differentiated based on spatial context. We used the velocity maps to differentiate between these two classes, using a threshold value for transporting sand of 0.6 meter per second (m/s) based on Shield’s diagram for sediment transport (Knighton, 1998). Grid cells that were classified as fine sediment/transporting sand were thus reclassified to fine sediment if the velocity was less than 0.6 m/s or transporting sand if the velocity was greater than 0.6 m/s. The new substrate grids were blanked to the extent of the velocity grids. Bedrock and engineered rock structures at the margins of the channel were poorly represented in the initial substrate maps, largely because RoxAnn data were not viable for depths less than approximately 1.5 meters, the RoxAnn blanking depth. Therefore, we supplemented the substrate maps with two aerial-photograph-derived polygon data sets representing (1) distribution of navigation structures and bank revetments (U.S. Army Corps of Engineers, unpub. data, 2008) and (2) locations of bedrock (Laustrup and others, 2007). These supplemental data sets were superimposed onto the substrate grids, overriding existing classifications. Substrate data sets are not available for some mapped reaches for two main reasons. The R/V Brush was not instrumented with a RoxAnn instrument in 2005 (table 1), so no substrate grids are available for most of the reaches downstream from Rulo, Nebraska, for that year. Other reaches lack substrate grids due to instrument malfunction or poor data quality. The RoxAnn’s relatively large blanking distance, combined with generally poor performance in shallow water, resulted in rejection of data for the majority of the mapped reaches in the Gavins Point segment (fig. 1), which is characterized by relatively shallow depths.

Process_Date: 2005-2007

Spatial_Data_Organization_Information:

Direct_Spatial_Reference_Method: Raster

Spatial_Reference_Information:

Horizontal_Coordinate_System_Definition:

Planar:

Grid_Coordinate_System:

Grid_Coordinate_System_Name: Universal Transverse Mercator

Universal_Transverse_Mercator:

UTM_Zone_Number: 15

Transverse_Mercator:

Scale_Factor_at_Central_Meridian: 0.999600

Longitude_of_Central_Meridian: -93.000000

Latitude_of_Projection_Origin: 0.000000

False_Easting: 500000.000000

False_Northing: 0.000000

Planar_Coordinate_Information:

Planar_Coordinate_Encoding_Method: row and column

Coordinate_Representation:

Abscissa_Resolution: 5.000000

Ordinate_Resolution: 5.000000

Planar_Distance_Units: meters

Geodetic_Model:

Horizontal_Datum_Name: D_WGS_1984

Ellipsoid_Name: WGS_1984

Semi-major_Axis: 6378137.000000

Denominator_of_Flattening_Ratio: 298.257224

Entity_and_Attribute_Information:

Overview_Description:

Entity_and_Attribute_Overview:

2 = Sand (dunes); derived from RoxAnn. 3 = Revetment, gravel, hard sand; derived from RoxAnn. 4 = Fine sediment (mud, silt); derived from RoxAnn and velocity data. 5 = Transporting sand; derived from RoxAnn and velocity data. 6 = Bedrock; derived from aerial photography. 7 = Engineered structures (rock); derived from aerial photography.

Entity_and_Attribute_Detail_Citation: Reuter and others, 2008

Distribution_Information:

Distributor:

Contact_Information:

Contact_Organization_Primary:

Contact_Organization: U.S. Geological Survey, Columbia Environmental Research Center

Contact_Address:

Address_Type: mailing and physical address

Address: 4200 New Haven Rd

City: Columbia

State_or_Province: MO

Postal_Code: 65201

Country: USA

Contact_Voice_Telephone: 573-875-5399

Contact_Facsimile_Telephone: 573-876-1896

Resource_Description: U.S. Geological Survey Data Series 386

Distribution_Liability:

Although these data have been processed successfully on a computer system at the U.S. Geological Survey, no warranty expressed or implied is made regarding the accuracy or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty. This disclaimer applies both to individual use of the data and aggregate use with other data. It is strongly recommended that these data are directly acquired from a U.S. Geological Survey server, and not indirectly through other sources which may have changed the data in some way. It is also strongly recommended that careful attention be paid to the contents of the metadata file associated with these data. The U.S. Geological Survey shall not be held liable for improper or incorrect use of the data described and/or contained herein.

Custom_Order_Process: Please contact distributor.

Metadata_Reference_Information:

Metadata_Date: 20081104

Metadata_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Person: Joanna M. Reuter

Contact_Organization: U.S. Geological Survey

Contact_Address:

Address_Type: mailing and physical address

Address: 4200 New Haven Road

City: Columbia

State_or_Province: MO

Postal_Code: 65201

Country: USA

Contact_Voice_Telephone: 573-875-5399

Metadata_Standard_Name: FGDC Content Standards for Digital Geospatial Metadata

Metadata_Standard_Version: FGDC-STD-001-1998

Metadata_Time_Convention: local time

Metadata_Extensions:

Online_Linkage: <http://www.esri.com/metadata/esriprof80.html>

Profile_Name: ESRI Metadata Profile