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SOUTH DAKOTA DEPARTMENT OF TRANSPORTATION
AND
FEDERAL HIGHWAY ADMINISTRATION
SECTION 7 PROGRAMMATIC
BIOLOGICAL ASSESSMENT
January 5, 2004

Federal Highway Administration
116 East Dakota Avenue
Pierre, SD 57501
Telephone: (605) 224-8033
SD Department of Transportation
700 East Broadway
Pierre, SD 57501
Telephone (605) 773-3265
Contact Person: Ginger Massie Telephone: 224-7326 x3037

TABLE OF CONTENTS

  1. I. Service Activity and Basis for Biological Assessment
  2. II. Project Description and Replacement Process
    1. Local Government Assistance
    2. Major Drainage Structure Selection on State Highways
  3. III. Pertinent Species
    1. Topeka Shiner
    2. Least Tern
    3. Piping Plover
    4. Whooping Crane
    5. American Bald Eagle
    6. Eskimo Curlew
    7. Black-Footed Ferret
    8. Pallid Sturgeon
    9. American Burying Beetle
    10. Western Prairie Fringed Orchid
    11. Mountain Plover
    12. Scaleshell Mussel
  4. IV. Impacts of Transportation Projects on Threatened and Endangered Species
  5. V. Effects of the Proposed Action on Pertinent Species
  6. VI. Best Management Practices for Topeka Shiner Streams
  7. VII. Effects Detennination Matrix
  8. VIII. Cumulative Impacts
  9. IX. Administrative Summary of Effects Detennination
  10. X. Concluding Statements
  11. XI. Literature Cited
  12. XII. Attachments
    1. Special Provision for Construction [Attachnlent A]
    2. Box Culvert Typical Drawings [Attachment B]
    3. Steel Girder Bridge Typical Drawing [Attachment C]
    4. Topeka Shiner Streams [Attachment D]
    5. Stream Inlpact Tables and Charts [Attachment E]

1. SERVICE ACTIVITY AND BASIS FOR BIOLOGICAL ASSESSMENT

The primary goal ofthe South Dakota Department of Transportation (SDDOT) is to provide safe, efficient, dependable and environmentally responsible transportation facilities and services. The need to provide transportation for the state requires that SDDOT assume the role of developer. As a developer, the Department must obtain permits from federal, state, and local agencies when projects pass through sensitive areas, such as wetlands or stream corridors, or have the potential to impact threatened or endangered species. As a state agency, SDDOT is committed to preserving, protecting and enhancing the state's natural resources.

Funding for transportation projects is dependent upon the federal funding made available through the Federal Highway Administration (FHWA). Section 7(a) ofthe Endangered Species Act of 1973 as amended (Act) requires Federal agencies to evaluate the impact of their actions on threatened or endangered species, and ensure such actions are "not likely to jeopardize the continued existence ofany endangered or threatened species or result in the destruction or adverse modification of (its) habitat". To this end, SDDOT, the Federal Highway Administration (FHW A), and US Fish & Wildlife Service (FWS) have entered into a programmatic biological assessment. Because the transportation program is active throughout South Dakota (SD) and listed, proposed, and candidate species occur or have the potential to occur throughout SD, the action area for the biological assessment will be considered the entire state. However, this agreement is not valid for projects involving the main channel ofthe Missouri River. Construction projects affecting these areas will require a separate biological assessment.

This biological assessment will evaluate the effects of installing and maintaining bridges, box culverts including box culvert extensions, corrugated metal pipe (CMP), reinforced concrete pipe (RCP), and CMP or RCP pipe extensions on any and all listed or proposed species and their associated listed critical habitat. Under this agreement the term project construction or construction shall be used to denote bridge or culvert installation and/or maintenance work as described in the next section. This biological assessment is prepared in accordance with legal requirements set forth under Section 7 ofthe Endangered Species Act [16 U.S.C. IS36(c)].

II. PROJECT DESCRIPTION AND REPLACEMENT PROCESS

Typically, materials used for culverts are concrete or metal. Metal culverts are made from sheets of steel riveted together and coated with zinc to prevent rust. Metal culverts are normally corrugated and are referred to as corrugated metal pipe. Another type ofmetal pipe is a structural plate pipe that is made from many sheets of corrugated metal, which are normally bolted together at the job site. Culverts constructed from concrete are made with reinforcing steel inside the culvert. This is referred to as reinforced concrete pipe.

Culverts come in all sizes and shapes. For example, an arch pipe is used when the roadway is low and there is not enough room for a round pipe and a cattle pass pipe is used to move livestock or something other than water. The purpose of a culvert is to provide a means of passing a design storm discharge beneath a roadway or similar structure without causing excessive backwater or overtopping of the structure as well as preventing the creation of excessive downstream velocities. The design and use of culverts will depend on the available depth for installation, inlet and outlet conditions, general topography, upstream and downstream land use, development layout, flow rates and the level of protection that might be attainable. Please refer to Attachment A, the Special Provision for Construction Practices in Streams Inhabited by the Topeka Shiner developed by SDDOT and concurred by FWS for specific examples of stream diversion methods, water draw-down techniques, stream blocking devices, etc and the typical drawings oftwo box culverts and a bridge (Attachments B and C).

A. LOCAL GOVERNMENT ASSISTANCE

Local Government structure replacement projects are programmed in the Statewide Transportation Improvement Program (STIP) document based on a resolution/request from the local entity. The projects are programmed based on available funding, local priorities, and eligibility. Once in the STIP, the preliminary engineering (PE) begins approximately 3 years prior to desired construction to allow for environmental coordination, traffic counts, survey/hydraulics, foundations, plans & plans review, final plans, right ofway, utilities, letting, and construction.

Once the project is authorized for PE, a consultant selected by the county from the approved DOT retainer list, completes a project survey and hydraulic study to detennine what types of structures best fit the site based on Local Government Assistance (LGA) design standards. The consultant also tries to accommodate the county's needs for the site. Estimates of the options are sent to LGA along with the hydraulic information. County, Area Engineer, LGA, & Consultant representatives then meet on-site to select the structure based on the following items:

After consideration of all of the above, the type of structure is selected. A box culvert or pipe will be designed if hydraulically adequate due to reduced future maintenance. There will not be guardrail, bridge end markers, delineators, and other items to repair/replace. A pipe or box culvert also eliminates the need to evaluate roadway width or clear width conducive to agricultural traffic. Ifthe construction window is shortened due to harvest, traffic, or other issues, a pipe or culvert is usually the best option as it can be installed in a much shorter amount oftime than a bridge. A bridge is the structure choice if debris, ice, or hydraulic capacity ofa box is detennined to be a problem.

Local Government Culvert and Structure Footprint

The total structure footprint is generally contained within the current right-of-way (ROW) (33' to 50' either side of the centerline). County road widths are generally between 24' and 30'. Bridges are generally 30' total width with benns extending along the banks. Box culvert or pipe openings must be outside of the 10' clear zone. Culvert lengths average about 60', which includes the inlet and outlet riprap pads. High fill sections increase the length but are not needed on a regular basis.

Overall project grading to fit the structure into the road grade is kept to a minimum but must meet LGA design standards. This work generally occurs within the current ROW. Work easements are typically granted by landowners to accommodate the construction of proper slopes and ditches that may extend beyond the ROW.

B. MAJOR DRAINAGE STRUCTURE SELECTION ON STATE HIGHWAYS

The process for selecting structures for state highway proj ects is very similar to that of Local Government, with the exception of degree of consultant design. The department designs the majority ofthese structures. Highway projects involving existing and new crossings ofmajor drainages require special considerations for structure selection that may involve many different factors. Some ofthe factors considered in structure selection are as follows:

• Hydraulics - Structure type, size, locations and orientation must satisfy drainage/hydraulic design criteria

• Site Conditions & History - Topography, geology, record of flooding, evidence of debris and/or ice, need for livestock passage, etc.

• Cost - First cost of construction as well as life cycle costs including anticipated future maintenance needs (future structural repairs, maintenance along with operational type such as snow removal)

• Safety - Relative safety of structure alternatives. For example, clear zone length culverts are considered somewhat safer for the traveling public than bridge type structures due to the unobstructed clear roadway they provide (no obstacles within 30' ofthe edge of traffic lanes on new State highway construction). Bridge rail and associated approach guardrail by themselves are a hazard to the driver and also may result in additional safety problems due to causing snow drifting at bridge ends.

• Environmental- Type ofstream, impact on stream morphology, construction restrictions, endangered species, BMPs, etc.

• Right of Way and Landowner Issues - Impact to adjacent properties and accommodation ofrequests from landowners

• Traffic Handling, Construction Sequencing and Timing - Traffic control requirements, acceptable distance and duration oftraffic detouring, staged construction requirements, allowable windows of construction time, road closure limitations, etc.

• Location & Aesthetics - Design considering the setting and construction treatments that can be pleasing to the eye

Box Culvert and Bridge Structure Footprint

An example drawing of a typical average box culvert construction footprint in a fish passage stream is included for reference (Attachment B). Actual box culvert footprints can vary considerably depending on number and size ofbarrels, depth offill, number oftraffic lanes, skew angle, etc. An average length for a box culvert with wings and riprap on a two lane State highway would be 124 feet.

Bridges are typically 38' to 46' deck width on State Routes (2 lane facilities), with berms extending along the banks. The footprint is generally contained within the right-of -way (75' either side ofthe centerline). A typical drawing of a bridge is also included for reference (Attachment C).

III. PERTINENT SPECIES

T = Threatened

E = Endangered

P = Proposed

A. TOPEKA SHINER (E)

Effective January 14, 1999 the FWS listed the Topeka shiner (Notropis topeka) as an endangered species pursuant to the Endangered Species Act of 1973. The Topeka shiner is a small, stout minnow not exceeding 3 inches in length. Diagnostic features ofthe Topeka shiner are described as silvery sides with a well-defined dark stripe and a tail fin with a black wedgeshaped spot at the base. The species historic range encompassed portions of Iowa, Kansas, Minnesota, Missouri, Nebraska and SD. Currently, the Topeka shiner is found in highly disjunct population in headwater streams, occupying 10% of its historic range (USFWS(2) 1998). However, recent studies in South Dakota indicate the Topeka shiner still occupies a high percentage of its historic range (Cunningham 2002). Specific habitat features most commonly associated with Topeka shiners are small low order prairie streams with high water quality, cool temperaWres, perennial flows and clean gravel substrate. High water quality appears to be one of the most important components of suitable Topeka shiner habitat. USFWS (1993) noted, "The species appears dependent on high water quality as demonstrated by its characteristic occurrence in streams that drain areas ofupland prairie." Conversely, in Kansas streams where Topeka shiners have been extirpated USFWS (1993) also noted that, "conditions are generally eutrophic with a high degree of sedimentation present, presumably from intensive agricultural land-use practices." As expected with the species' dependence on high water quality, a clean gravel stream bottom appears to be the preferred spawning substrate. Specifically, USFWS (1993) noted, "a dependence on silt-free gravel for spawning may exist. This would explain usage of sunfish nests which are swept clean of silt prior to spawning."

Primary threats to the species survival have been generally described as habitat destruction, sedimentation, and changes in water quality. In a status report on Topeka shiners USFWS (1993) noted "the action most likely impacting the species to the greatest degree in the past is sedimentation and eutrophication from the intensive agricultural development ..."

Critical habitat was proposed for the Topeka shiner on August 22,2002. A final ruling is anticipated for publication in the Federal Register in August 2003. The proposal includes 186 stream segments in Iowa, Kansas, Minnesota, Nebraska, and South Dakota. Proposed areas of critical habitat include only those streams now occupied by the Topeka shiner that contain the physical and biological features essential to the conservation ofthe species (USFWS 2002). Proposed critical habitat in South Dakota includes portions ofthe Big Sioux, Vermillion, and James River watersheds [Federal Register: August 21, 2002 (Volume 67, Number 162)].

A list of known Topeka shiner locations in SD is found on Attachment D.

B. LEAST TERN (E)

The least tern (Sterna antillarum) was listed by the FWS on May 28, 1985 as an endangered species without critical habitat. The least tern is 8-9 inch long shorebird with a black crowned head, snowy white underside and forehead, grayish wings, orange legs and feet which are webbed, a yellow bill with black tip, and grayish wings that span 20 inches. Its' long black outermost wing feathers and short deeply forked tail make it conspicuous in flight. The species historically bred in isolated areas along the Missouri, Mississippi, Ohio, Red, and Rio Grande river systems. Their wintering habitat is not known, but most likely includes coastal areas of Central and South America. Least terns usually nest on open expanses of sand or small pebble beaches along shorelines, riverbanks, sandbars, and islands. Terns typically select nesting sites that are well drained and away from the water line, usually near a small ridge or piece of driftwood (Ducey 1981, Anderson 1983, Dryer and Dryer 1985). Sparsely vegetated sites or sites with other limited types of cover appear to be important as protection from weather extremes and predators ofyoung chicks (Thompson 1982). Their food source consists almost entirely of small fish and feeding requires shallow water areas with an abundant fish population near the nesting area (Hardy 1957, Bent 1922, Anderson 1983).

Major losses and alterations ofhabitat are the reasons for the decline ofthe least tern population. Shoreline, bank, and channel modifications from the construction of locks, dams, dikes, levees, and reservoirs have altered the natural forces necessary for maintaining tern habitat. Flooding can prevent or destroy nesting and can be a byproduct ofhabitat alteration (Hardy 1957, Ducey 1980, Wingfield 1980, Boyd 1984). Habitat losses can also be attributed to increased development, recreational uses, and natural erosion (Bent 1922, Crow 1974, Massey 1972, Ducey 1981). Predation, human and domestic pet disturbances or harassment, trampling by cattle, and flooding during the nesting season are other contributors to nesting failures (Bent 1922, Crow 1974, Grover 1979, Massey 1972, Ducey 1981). Pollution, including pesticides or herbicides, and its effect on water quality and aquatic habitat can adversely influence fish populations, thus impacting terns (Bent 1922, Hardy 1957, Wilbur 1974, Anderson 1983).

The least tern is a local summer resident of the Missouri and Cheyenne rivers in SD (SDOU 1991). It can be found migrating through virtually all ofSD with the exception ofthe Black Hills.

C. PIPING PLOVER (T)

The piping plover (Charadrius melodus) is currently listed as a threatened species in its SD range by the FWS. It was first listed on December 11, 1985 without critical habitat. On September 11,2002 FWS designated critical habitat for the Northern Great Plains population of piping plover. This designation includes 183,422 acres of habitat and 1,207.5 river miles in Minnesota, Montana, North Dakota, South Dakota, and Nebraska. The piping plover is described as a small (7 in. long, 15 in. wingspan) stocky shorebird having a sand-colored upper body, a white underside, and orange legs. During the breeding season, adults have a black forehead, a black breast band, and an orange bill. Three major nesting areas occur throughout North America; the shoreline of the Great Lakes, the shores ofrivers, lakes, and wetlands ofthe Great Plains, and along the Atlantic coast (USFWS 2000). Nest sites typically consist of sparsely vegetated sand bars associated within river systems or on prairie sloughs and saline wetlands with gradual non-vegetated shorelines.

The major cause of habitat loss in the Great Plains, a primary threat to this plover, has occurred through the construction ofreservoirs. Infrequent water releases from reservoirs for power production and other water demands often inundate nesting areas during the nesting season (USFWS 1987). Nesting habitat has also been severely degraded because high flows needed to eliminate vegetation from nesting sites rarely occur (Williams 1978, Ducey 1981, Faanes 1983, North 1986, Currier 1987 Ziewitz et al. 1992, Kirsch and Lingle, 1993). Human recreational disturbance also is a cause ofnest abandonment and failure (USFWS 1987). Piping plover threats associated with prairie sloughs and saline wetlands include wetland drainage, predation, and disturbance by livestock.

Approximately 287.5 miles ofMissouri River and Missouri River reservoir shoreline has been designated in South Dakota as critical habitat for the piping plover. The piping plover is described by the SD Ornithologists' Union (1991) as being a locally common summer resident of SD, primarily in the Missouri valley and its western tributaries.

D. WHOOPING CRANE (E)

On March 11, 1967, the whooping crane (Grus americana) was listed as an endangered species. The whooping crane is the tallest bird in North America standing 5 feet tall with a wingspan of 7.5 feet. Adult birds have an all white body with black legs and wing tips. The top and sides of the head are featherless and are bright red. They prefer freshwater marshes, shallow portions ofrivers, grain and stubble fields, shallow lakes and lagoons for feeding and loafing during migration. Roost sites usually are associated with shallow water in which they are able to stand (Ashton and Dowd 1991). Whooping cranes once ranged from the Arctic Sea to the high plateau of central Mexico and from Utah east to New Jersey, South Carolina, and Florida (Allen 1952, USFWS 1996). In the 19th century, the breeding range extended from central Illinois, northwest through northern Iowa, western Minnesota, northeastern North Dakota, southern Manitoba, and Saskatchewan to the area ofEdmonton, Alberta (USFWS 1996). Currently there are three wild and four captive localities where whooping cranes exist. The only self sustaining natural population is the AransaslW ood Buffalo population. Early 1999 counts numbered 177, 169 adults and eight juveniles (USFWS 2001). This population migrates from its nesting grounds in and around the Wood Buffalo National park through northeastern Alberta, southcentral Saskatchewan, northeastern Montana, western North and South Dakota, central Nebraska and Kansas, west-central Oklahoma and east-central Texas and winters along 'the central Texas Gulf ofMexico (USFWS 2001). Whooping cranes fonner breeding range in the midwestern United States has been altered by tillage agriculture and wetland drainage. The advent of habitat loss and other factors decreased the population to 16 individuals in 1941.

The whooping crane is described as being a rare spring and fall migrant of SD with accidental summer occurrences (SDOU 1991). During migration they often pause overnight to use wetlands for roosting and agricultural fields for feeding but seldom remain more than one night.

E. AMERICAN BALD EAGLE (T)

Listed as an endangered species on March 11, 1967, the American bald eagle (Haliaeetus leucocephalus) was down listed to a threatened species on July 12, 1995 without critical habitat. The U.S. Fish and Wildlife Service was proposing that the bald eagle be declared fully recovered by July 2000, but the decision is being delayed until they figure out how they will manage the species once it is taken offthe list. A white feathered head, neck, and tail are the distinguishing characteristics of the adult bald eagle. The distinguishing adult feathers typically appear at the age of four. The remainder ofthe eagle plumage is dark brown. The heavy yellow beak and distal one-half to two-thirds ofthe yellow tarsus are bare of feathers. The bald eagles can be found throughout North America. Eagles are usually associated with dominant or co-dominant trees in both the nesting and wintering periods. The vast majority ofbald eagle nests can be found within one-half mile ofwater and are rarely located greater than two miles from water (Gerrald et al.1975, McEwan and Hirth 1979, Todd 1979, Andrew and Mosher 1982, Haywood and Ohmart 1983, Green 1985). Nests, constructed primarily of sticks with other material added for lining, are almost exclusively found in live trees (Sherrod et al. 1976, Green 1985). Wintering sites consist of very large perch trees that are usually located near open water or in close proximity to other available prey items (Steenhof 1978, Keister and Anthony 1983, Green 1985).

The decline of the Bald Eagle coincided with the introduction of the pesticide DDT in 1947. Birds ofprey at the top ofthe food chain, such as eagles, ingested relatively high levels of the pesticide, which was concentrated in the fatty tissues oftheir prey. Eagles contaminated with DDT failed to lay eggs or produced thin eggshells that broke during incubation. In 1972 DDT was banned in the United States and a slow recovery for the Bald Eagle began. Although not directly resulting in the death of eagles, habitat destruction, disturbance, and encroachment by humans may have the biggest impact upon bald eagle populations. LeFranc and Millsap (1984) point out that most biologists agree that habitat loss is the greatest threat to the bald eagle. Winter roost abandonment has been documented when timber harvesting and home building has occurred close to the roost (Lish and Lewis 1975).

Bald Eagles have nested in Gregory, Brown, yankton, Bon Homme, Spink, Charles Mix, Union, Robert, Sanborn, Hutchinson, Bennett, Lyman, Marshall, Clay, Minnehaha, Hughes, and Meade Counties in SD (USFWS 2003). This bird winters regularly in large numbers along the Missouri River below the reservoirs from Pierre to Yankton and scattered locations across the state (SDOU 1991).

F. ESKIMO CURLEW (E)

Effective March 11, 1967 the FWS listed the Eskimo curlew (Numenius borealis) as an endangered species without critical habitat. It is described as a medium sized, approximately 12 inches long, shorebird that is dark rich cinnamon in color with a decurved bill (Ambrose 2000). It closely resembles the whimbrel except the Eskimo curlew has unbarred primaries whereas the whimbrel's primaries have barring on their underside (Gollop et alI986). The arctic tundra of Alaska and Canada are the nesting area ofthis curlew. Wintering areas are most probably the wet or dry pampas ofArgentina, Uruguay, southern Brazil and Chile (Gallop (2) 1986). Fall migrations occurred along the east coast ofNorth America while spring migrations took place in the central United States and provinces of Canada (Arrlbrose 2000). Diet includes insects, snails and berries throughout the year.

Overwhelming evidence indicates that unrestricted market hunting drastically and quickly reduced the population of curlews between the years of 1870 and 1890 (Banks 1977, Gollop (2) et al. 1986). During this same time period, the wintering grounds and nligrational habitat were being converted from native grasslands to tillage agriculture (Banks 1977). The fact that the population has not recovered since market hunting has stopped, indicates that other ecological factors most probably associated with habitat changes are affecting this species (Gollop et al. 1986).

Formerly a common to abundant spring SD migrant, the Eskimo curlew is now nearly extinct (SDOU 1991). The last confirmed sighting was in Nebraska in 1987 (Ashton, Diane E. and Eileen M. Dowd. 1991). The Eskimo curlew is listed as an extremely rare occurrence in Brown and yankton Counties in SD (USF & WS 2003).

G. BLACK-FOOTED FERRET (E)

The black-footed ferret (Mustela nigripes) was listed as an endangered species on March 11, 1967 without critical habitat. It is described as a member ofthe weasel family that is tan with black feet, black mask, and a black tipped tail. It is approximately 20 to 24 inches long including a tail that is 5 to 6 inches long. Male ferrets typically weigh more than females with their weights being between 24 and 40 ounces. A SD population that disappeared in the wild in 1974 was thought to be the last remaining population until ferrets were discovered in 1981 near Meeteetse, Wyoming. The Meeteetse population declined to 18 individuals in 1986-1987 due to canine distemper. These 18 ferrets were taken into captivity to prevent the species from extinction and to create a source for a captive propagation program (USFWS (2) 1995). Blackfooted ferrets feed primarily on prairie dogs and use their burrows for denning and shelter (Henderson et a11969, Forrest et aI1985). Historically black-footed ferrets occurred in the plains from Texas to southern Saskatchewan. Now black-footed ferrets are limited to seven captive populations and a few wild populations. As of October 2000 about 200 black-footed ferrets existed in the wild. The population in South Dakota accounted for 164 of the 200 individuals (USF&WS (2) 2003).

Primary threats to the black-footed ferret include predation, disease, and loss ofhabitat (USFWS (2) 1995, Andelt 1996). Multiple predators including coyotes, golden eagles, greathomed owls, prairie falcons, badgers, bobcats, and foxes can have a direct effect on ferrets and ferret populations. Poisoning ofprairie dogs and conversion ofnative old growth prairie to tillage agriculture are the two main threats to ferret habitat. Lockhart et al. (1998) stated that the most formidable challenge now facing ferret recovery is whether suitable prairie dog habitat can be secured to establish multiple, self-sustaining wild ferret populations.

Black-footed ferrets have been reintroduced in South Dakota in the Conata BasinlBadlands National Park, Buffalo Gap National Grasslands and on the Cheyenne River Sioux Tribal land located in Dewey and Ziebach counties (USFWS 2003). Populations may have become self-sustaining at only one site in South Dakota (Lockhart, Black-footed Ferret Coordinator, Federal Register, May 16,2003, p. 26499).

A May 16,2003 Final Rule published in the Federal Register approved the reintroduction of endangered black-footed ferrets into south-central South Dakota on the Rosebud Sioux Reservation. If this reintroduction program is successful, a wild population could be established in five years or less. A recent evaluation by the USFWS indicated that only ten sites exist in all ofNorth America that have prairie dog complexes of sufficient size and density to potentially support viable ferret populations (which include all current reintroduction sites).

H. PALLID STURGEON (E)

The pallid sturgeon (Scaphirhynchus albus) is currently listed as an endangered species by the FWS. It was first listed on September 6, 1990 without critical habitat. The pallid sturgeon is described as a dinosaur-like appearing fish with a flattened snout, long slender tail and armored with lengthwise rows ofbony plates instead of scales (USFWS 1998). This species of sturgeon can reach a weight of 100 pounds and a length of6 feet (Burton 2000). Historically, pallid sturgeon ranged approximately 3550 nli1es ofthe Missouri and Mississippi Rivers and their major tributaries (USFWS 1998). They have adapted to living near the bottom of large silty rivers in swift current. Preferred habitats include sand bars, sand flats, and gravel bars in a variety of depths. Although pallid sturgeon do not reach sexual maturity until the age ofthree or four and may go three to 10 years between spawnings (USGS 1995), a recent find ofnaturally reproduced pallid sturgeon, the first known in at least 50 years in the lower Missouri, is a reason for optimism for this species (Burton 2000).

All of the 3550 river miles that the pallid sturgeon inhabits have been affected by humans. Approximately 28 percent oftheir habitat has been impounded, 51 percent has been channelized, and the remaining 21 percent has altered flow due to impoundments (USGS 1995). Because the sturgeon's mobility, food habits, and life history adaptions are highly specific, the alteration of their habitat is seen as the major cause ofthe species decline (Beamesderfer and Farr 1997, Boreman 1997). Over harvest and pollution are also causes for declined sturgeon populations (Hurley et al 1987). The alteration oftheir habitat, over fishing, and pollution has left sturgeon populations depleted, threatened, or extinct almost everywhere they occur (Beamesderfer and Farr 1997).

The pallid sturgeon can be found in the Missouri River and some of its larger tributaries inSD.

1. AMERICAN BURYING BEETLE (E)

Listed as an endangered species on July 13, 1989, the American burying beetle (Nicrophorus americanus) is the largest carrion feeding insect in North America. The approximately 1-1.4 inches long shiny black body has four orange-red markings. The most identifiable mark is the orange-red marking on the beetle's pronotum, a large shield-like area behind the head. It also has orange facial markings and orange tips on the antennae (USFWS 1997). Once widely distributed throughout eastern North America, this species has disappeared from most ofits historic range. Historical records include 32 states, the District of Columbia, and 3 Canadian provinces encompassing the area from Nova Scotia and Quebec, South to Florida and west to Minnesota, South Dakota, Nebraska, Oklahoma, and Texas (Wells et al. 1983, Schweitzer and Master 1987). These beetles are now restricted to Rhode Island, Oklahoma, Kansas, Arkansas, South Dakota, and Nebraska (Backlund and Marone 1997, Bedick et al. 1999). Infonnation suggests that they can occupy a wide range ofhabitats with a slight preference for grasslands or oak understory hickory forests (USFWS 1997). Carrion selected by this beetle tends to be larger than that utilized by other burying beetles with an optimum weight between 3.5 and 7 ounces (Raithel and Amara11991).

There are many 'theories as to the demise ofthe American burying beetle including insecticide spraying, 'the presence ofa non-native and species-specific pathogen, and loss of habitat. The prevailing theory regarding the species decline is that ofhabitat fragmentation. Fragmentation oflarge expanses ofhabitat that supported high numbers of species may have been a factor in changing the species composition and lowering the reproductive success ofprey species of'the American burying beetle. This habitat fragmentation would also increase the edge effect ofhabitat beneficial to competing predators and scavengers. This is demonstrated in the fact that since the middle ofthe 19th century, two species ofbirds in the preferred weight range of the American burying beetle, the passenger pigeon and the greater prairie chicken, have been eliminated from eastern North America (USFWS 1997).

The current American burying beetle range presently known in South Dakota includes Gregory, Tripp, and Todd counties. However, a comprehensive status survey has never been completed in South Dakota so the beetle could and may occur in any county with suitable habitat. Suitable habitat is considered to be any site with significant humus or topsoil suitable for burying carrion. (USFWS 2003)

J. WESTERN PRAIRIE FRINGED ORCHID (T)

The western. prairie fringed orchid (Platanthera praeclara) was listed as a threatened species on September 28, 1989 without critical habitat. It is described as a herbaceous perennial plant that normally ranges from 12 to 34 inches tall. It typically has numerous coarse fleshy roots arising from a fleshy tuber. Each plant usually has a single unbranched stem bearing two to five oblong-elliptic leaves. Leaves are usually 3 to 6 in long and 0.4 to 1.6 in wide. The inflorescence consists of five to 25 flowers that are creamy white to white or rarely greenish white (USFWS (2) 1996). Flowers are characterized by a long narrow nectar spur and fragrance which are activated in the evening, indicating adaptation for pollination by nocturnal pollinators (Sheviak and Bowles 1986), specifically only by hawkmoths (USFWS (2) 1996). Historically, this orchid was distributed throughout much ofthe tallgrass prairie in the central United States and southern. Canada (Sheviak and Bowles 1986). This orchid is generally found in fire and grazing adapted grassland communities, most often on undisturbed, calcareous prairies and sedge meadows but occasionally can be found in disturbed sites in successional communities (USFWS (2) 1996). Three metapopulations, a population with several populations that total more than 3000 individuals, exist today; the Pembina Trail prairie complex of Minnesota (Sather 1991), the Sheyenne Delta ofNorth Dakota, and the Vita Prairies of Manitoba (USFWS (2) 1996). Other smaller populations can be found in Iowa, Kansas, Missouri and Nebraska.

Destruction ofhabitat, primarily for agricultural purposes, has been the principal cause for the decline ofthis species (USFWS (2) 1996). The remaining populations of orchids are threatened by competition by invasive species, habitat conversion and mismanagement of existing habitat by overgrazing, haying and fire suppression.

Currently, there are no known populations ofthis species in South Dakota although because ofthe ecology ofthis species, there is a possibility that plants may be overlooked. The orchid has the possibility ofoccurring in Bennett, Brookings, Brown, Clay, Codington, Day, Deuel, Grant, Lincoln, Minnehaha, Moody, Roberts, Todd, Turner, Union, and yankton counties (USFWS 2003).

K. MOUNTAIN PLOVER (P)

The proposal to list the mountain plover (Charadrius montanus) as a threatened species by the FWS occurred on February 16, 1999. This plover is described as a killdeer sized plover approximately 7 inches tall with a black cap, black loral stripe extending from the black bill to the eye, white supercilium and whitish forehead, foreneck, breast and belly but lacks the breast belt common to the killdeer and other plovers (USFWS 1999). States in which plovers breed include Colorado, Montana, Wyoming, Oklahoma, New Mexico, Kansas, Utah, Nebraska, and Texas (USFWS 1999) with the primary states being Colorado, Wyoming, and Montana (Graul and Webster 1976). The primary wintering area of this plover includes Sacramento, San Joaquin, and Imperial valleys of California (Knopf and Rupert 1995). The population is estimated at 8,000 to 10,000 individuals (Knopf 1996). Recent trends indicate the population has been declining at an annual rate of3.7% for more than 30 years which cumulatively accounts for a 63% dive in the last 25 years (Knopf and Rupert 1995). It is well documented that their preferred nesting habitat consists of slightly sloping, less than three percent, heavily grazed grasslands (Graul 1975, Wallis and Wershler 1981, Knowles et al. 1982, Olson 1985, Olson and Edge 1985, Parrish et al. 1993) or in association with prairie dog towns (Knowles et al. 1982, Olson 1985, Olson and Edge 1985) with vegetation heights of less than 4 inches. Preferred wintering habitat consists of sinlilar habitat (Knopf and Rupert 1995). Mountain plovers prey upon a variety of insects including beetles, grasshoppers, crickets, and ants (Bent 1929, Storer 1941, Goodrich 1945, Laun 1957, Baldwin 1971, Graul 1976, Olson 1985).

As is the case with most species with declining nurrlbers, habitat loss is the major reason for the decline ofthe mountain plover. Habitat loss has occurred by both agricultural practices and by human intrusion into its range (Cooke 1915, Schulenberg 1983, Leachman and Osmundson 1990). California alone, in the early 1900's, supported approximately 22 million acres of grassland with about 20 percent occurring in the central valley where plovers wintered. Presently only about 150,000 acres remain in the San Joaquin valley (Hunting 2000). Knopf and Rupert (1995) estimated less than four percent of native mountain plover habitat currently remams.

Historical records indicate the mountain plover was a rare breeder in Bennett and Fall Counties and a rare migrant through Beadle County, SD (USFWS (2) 2002).

L. SCALESHELL MUSSEL (E)

On October 9,2001, the FWS listed the scaleshell mussel (Leptodea leptodon) as endangered under the Endangered Species Act of 1973. The shell ofthis mussel grows to approximately 1 to 4 inches in length. The shells are elongated, very thin and compressed. The anterior end ofthe shell is rounded in both sexes while the posterior end varies between the sexes (USFWS (2) 1999). The outside ofthe shell has faint green rays and the inside is pinkish white or light purple and highly iridescent. This mussel historically occurred in 13 eastern states and 53 rivers. Currently it is found in only Mississippi, Oklahoma, and Arkansas in 13 river drainages (USFWS (2) 2001). They inhabit medium to large rivers with stable channels and good water quality. In Missouri, they specifically are found in clear unpolluted riffles with moderate current and firm gravel, cobble and sand substrates (Missouri 2000). The scaleshell mussel historically has been broadly distributed but locally rare. Within the last half century, it has become even more rare and range restricted (Szymanski 1998). Comparisons of past and current population numbers and threats indicate that 10 ofthe current popUlations are declining (USFWS (2) 2001).

Habitat alteration and pollution are the major threats to the scaleshell mussel. Impoundments, in-stream mining, and sedimentation are all examples of anthropogenic induced habitat alterations affecting scaleshells (Szymanski 1998). Pollution from both point and nonpoint sources is known to negatively impact this mussel. Szymanski (1998) pointed out that it is widely accepted that contaminants are at least partially responsible for decreases in population densities, ranges, and diversity ofunionids and that the scaleshell mussel appears to be especially susceptible to contamination and sedimentation. The fact that scaleshell populations are becoming smaller and more isolated is additional concerns for this species. Their life cycle, sedentary nature, and the lack of suitable habitat results in very slow population growth and dispersal. These factors, in combination with low recruitment generally associated with mussel populations, translate to decades needed to re-establish self-sustaining populations. Furthermore, fertilization success may be related to a certain population density with a certain threshold density required for any reproduction to occur. Many ofthe remaining scaleshell mussel populations may be at or below this threshold density (Szymanski 1998).

Scaleshell mussel habitat in SD includes the Missouri River in Clay, Union, and yankton counties (USFWS 2003). The scaleshell was last found on the Missouri River in South Dakota below Gavins Point Dam in 1983 (USFWS (2) 1999).

N. IMPACTS OF TRANSPORTATION PROJECTS ON THREATENED AND ENDANGERED SPECIES

There are four broad categories ofimpacts that may occur to wildlife/fish/plants as a result oftransportation projects including 1) habitat fragmentation, 2) habitat loss, 3) direct mortality, and 4) disturbance. Depending on individual project design and the surrounding landscape, these four impact types take different forms and may be direct or indirect.

Habitat Fragmentation: Transportation projects may fragment habitats when they create a physical or behavioral barrier to animal or fish movement. This barrier effect occurs when animals avoid habitat near roads, are physically unable to cross a road or culvert, or are killed while attempting to cross. All impact types discussed in this section potentially contribute to fragmentation.

Habitat fragmentation may occur if the swimming distance through a culvert is excessive; or ifthe crossing structure would otherwise impede migration of important fish or other important aquatic taxa, movement of fish within the stream can be adversely affected. In addition, construction methods used by contractors during construction or installation ofa culvert may create a barrier preventing fish migrating up or down stream.

Habitat Loss: Direct habitat loss occurs when the project footprint removes natural cover types. For example, loss ofriparian vegetation and wetland losses tied to highway construction, culverts, and bank channelization may occur. Riparian vegetation along stream and lake banks are known to be extremely important in reducing erosion and enhancing habitats for aquatic and other life forms.

In addition to effects that result from a simple loss of cover, the impact ofhabitat loss depends on the overall availability ofa habitat type in the project area and its role in an animal's life cycle. Loss of abundant habitat types may be relatively inconsequential; loss ofrare habitat types will have a greater impact, especially if it provides an essential resource for a species (e.g., nesting sites, important food sources). Other impacts discussed in this section may cause habitat loss indirectly by restricting access to habitat areas. Mechanisms of indirect habitat loss are often subtle, and it is important to consider all possibilities when screening a project for potential effects. For example, project-related disturbance effects may elicit an avoidance response, reducing or eliminating habitat use by a species in an area.

Direct Mortality: Wildlife/vehicle collisions nearly always result in death for the animal in question, and pose a safety hazard to the human occupants ofthe vehicle. Little quantitative data exist pertaining to which factors regulate rates of animaVvehicle collisions. Road improvements, such as greater roadway width and guardrails increase the difficulty of crossing highways for wildlife, require crossing animals to spend more time on the roadway, and may trap animals on the roadway. Bridge and culvert installations may actually reduce these occurrences because they can provide a safe passage for some animals trying to cross a highway.

Mortality of adult, larvae, or eggs of aquatic species may result from siltation during the construction phase or anyone ofthe other impacts noted. Exposure to high turbidity levels during the spawning period results in sedimentation ofspawning areas, suffocation of incubating eggs and blockage of larvae gills by fine sediments.

Disturbance: Disturbance results from many sources, including construction, day-to-day road operations, and increased human access to the area as a result ofroad improvements. Possible impacts of disturbance include direct mortality, temporary avoidance of an area, and permanent abandonment ofthe surrounding habitat. All these impacts may potentially interrupt activities (e.g., feeding, breeding, travel) essential to survival at both an individual and a species level. Disturbance may contribute to both habitat loss and fragmentation.

The impacts of construction-related disturbance are a function of the species susceptibility to disturbance, duration ofthe disturbance, area affected, type of disturbance (e.g., heavy equipment noise versus blasting noise), season, and time of day. Disturbances which last a long time, are loud, unpredictable, and/or affect large areas will be the most detrimental.

Day-to-day road operations have been shown to cause permanent disturbance effects. Many species are known to avoid areas of disturbance, reducing or eliminating the habitat value of these areas. Disturbance effects fronl highway operations include noise, visual stimuli, human activity, and pollution. Research (van der Zande 1980, Reijnen et al. 1995, Reijnen et al. 1996) indicates that breeding bird densities are reduced near roads, with the effect being greater for heavy traffic (50,000 cars/day) and reaching farther in open habitats (up to 6500 feet) as compared with forested habitats (up to 5000 feet). Permanent disturbance effects will contribute to both habitat loss and fragmentation.

V. EFFECTS OF THE PROPOSED ACTION ON PERTINENT SPECIES

Least tern: The least tern is a local summer resident of the Missouri and Cheyenne rivers in SD. It can be found nligrating through virtually all ofSD with the exception of the Black Hills. The occurrence of breeding least terns is localized and is highly dependent on the presence of dry, exposed sandbars and favorable river flows that support a forage fish supply and isolate the sandbars from the riverbanks. The majority nest on the lower Missouri River, particularly below the Gavins Point and Fort Randall Dams. The proposed action would have no effect on least terns because there would be no loss of nesting or foraging habitat due to the small area of construction activity in areas that have been previously disturbed. In addition, construction on the Missouri river is excluded under this agreement.

Piping plover: Approximately, 287.5 miles of Missouri River and Missouri River reservoir shoreline has been designated in South Dakota as critical habitat for the piping plover. The piping plover is described as being a locally common summer resident of SD, primarily in the Missouri valley and its western tributaries. In South Dakota, piping plovers nest mainly along the unrestricted stretches of the Missouri River below the Gavins Point and Fort Randall dams. Some birds also nest along Oahe Reservoir and on shorelines of alkaline wetlands in northeastern South Dakota. The proposed action would have no effect on piping plovers or their critical habitat because there would be no loss of nesting or foraging habitat due to the small area of construction activity in areas that have been previously disturbed, and because construction on the Missouri River or its reservoirs is excluded under this agreement.

Pallid sturgeon: Pallid sturgeon are slow growing fish that feed primarily on small fish and immature aquatic insects. This species of sturgeon is seldom seen and is one of the least understood fish in the Missouri and Mississippi River drainages. They prefer sand-covered portions of rivers with strong currents and high turbidity. Today's sturgeon populations are severely restricted due to dam construction along the length of the Missouri River. The proposed action will have no effect on the pallid sturgeon because construction on the Missouri River is excluded under this agreement.

Scaleshell mussel: The only occurrence documented in South Dakota was one scaleshell mussel found on the Missouri River below Gavin's Point Dam (Hoke 1983). A subsequent effort to locate the mussel or remnant shells (Clarke 1996) was unsuccessful. "With the best scientific infonnation we have available to us today, we consider the South DakotalNebraska population of the scaleshell mussel to be extinct, but as research continues, the possibility of finding some individuals always exists" said Ralph Morgenweck, Director of the Fish and Wildlife Service's Mountain-Prairie Region. The proposed action will have no effect on the scaleshell mussel because construction on the Missouri River is excluded under this agreement.

Bald eagles: Bald eagles usually inhabit forested areas near rivers and lakes and build nests in tall trees near water. Two hundred to three hundred bald eagles winter in South Dakota. Most of them concentrate near downstream areas of Missouri River dams, where they roost in remnant cottonwood forests. Bald eagles also winter in the Black Hills. Migrating bald eagles might be seen anywhere in the state. Proposed improvements would not likely adversely affect bald eagles because there would be no loss of nesting, roosting, or foraging habitat due to the small area of construction activity relative to regional habitat for bald eagles. No construction shall take place within ~ mile of a known active bald eagle nest without further consultation with FWS. FWS will update the location of known active bald eagle nests each year and provide SDDOT with information regarding the proximity of any eagle nests to a proposed construction project.

>Eskimo curlew and whooping crane: The proposed action would have no effect on the Eskimo curlew which is nearly extinct (SDOU 1991) or the whooping crane because it is unlikely that there are or will be individuals in the study area as both species are extremely rare spring/fall migrants of South Dakota. During migration the whooping crane rarely remains in one location more than one· night.

Black-footed ferrets: Black-footed ferrets currently exist in three reintroduction sites in SD, in the Conata BasinIBadlands National Park, Buffalo Gap National Grasslands, and on the Cheyenne River Sioux Tribal land located in Dewey and Ziebach counties. The proposed action would have no effect on black-footed ferrets outside the three-reintroduction sites in SD and the future reintroduction site on the Rosebud Sioux Reservation. Construction within the four reintroduction sites or future proposed areas would require further consultation with FWS.

American burying beetle: The current American burying beetle range in South Dakota includes Gregory, Tripp, and Todd counties although the beetle could and may occur in any county with suitable habitat. Suitable habitat is considered to be any site with significant humus or topsoil suitable for burying carrion. Consequently, the American burying beetle seems to be largely restricted to areas most undisturbed by human influence. Given this factor and the small area of construction activity covered by this document, the proposed action would have no effect on the American burying beetle.

Western prairie fringed orchid: The western prairie fringed orchid has the possibility of occurring in Bennett, Brookings, Brown, Clay, Codington, Day, Deuel, Grant, Lincoln, Minnehaha, Moody, Robert, Todd, Turner, Union, and yankton counties. Currently, there are no known populations of this species in South Dakota although there is a possibility that plants may be overlooked. The orchid is found in grassland communities, most often on undisturbed, calcareous prairies and sedge meadows but occasionally can be found in disturbed sites. Based on these factors and the small area of construction activity covered by this agreement, the proposed action would have no effect on the western prairie fringed orchid.

Mountain plover: Historical records indicate the mountain plover was a rare breeder of southwestern South Dakota. It is well documented that their preferred nesting habitat consists of slightly sloping, less than three percent, heavily grazed grasslands or in association with prairie dog towns with vegetation heights less than four inches. Because no suitable nesting habitat would be disturbed during construction and the small area of construction activity relative to regional habitat available, the proposed action would have no effect on the mountain plover.

Topeka shiner: Specific habitat features most commonly associated with Topeka shiners are small low order prairie streams with high water quality, cool temperatures, perennial flows and clean gravel substrate. High water quality appears to be one of the most important components of suitable Topeka shiner habitat. Primary threats to the species survival have been generally described as grassland loss in contributing watersheds, riparian loss, stream channelization, stream de-watering, and reductions in stream water quality. Critical habitat for the Topeka shiner has also been proposed but has not been finalized. Proposed areas of critical habitat include only those streams now occupied by the Topeka shiner that contain the physical and biological features essential to the conservation of the species (USFWS 2002). Proposed critical habitat in South Dakota includes portions of the Big Sioux, Vennillion, and James River watersheds [Federal Register: August 21,2002 (Volume 67, Number 162)]. Because direct "take" may occur as a result of in-stream construction activities, the proposed action may have an adverse affect on the Topeka shiner.

VI. BEST MANAGEMENT PRACTICES FOR TOPEKA SHINER STREAMS

Part of the management strategy needed for ensuring healthy Topeka shiner populations in South Dakota involve controlling the input of sediments into stream systems, especially from eroding stream banks. Infrastructure development, particularly road construction activities, can lead to significant stream bank erosion, most often at bridge or culvert crossings. The challenge is to balance the need for infrastructure development, since transportation is an essential element of modem commerce and economic viability, and its associated environmental consequences (e.g. soil erosion, modification of habitat). Fortunately, engineering mechanisms do exist that can prevent, halt, and/or control stream bank erosion during the repair, maintenance, and building of transportation infrastructure (Gray and Sotir 1996).

To this end, a list of possible best management practices have been developed that SDDOT will apply during the course of highway construction. These BMPs are needed since the evidence concerning the effects of erosion and sedimentation on aquatic ecosystem dynamics indicates substantial alterations occur at multiple trophic levels. These trophic level disturbances can create an aquatic condition intolerable to resident biota, thus leading to shifts in whole community structure. Abating those forces that precipitate erosion and sedimentation will reduce further stream bank erosion. This practice, in combination with stream restoration techniques, will help stabilize stream systems and allow resident species to thrive (Cunningham, 2000).

Both DOT agencies and FWS agree that the Road and Bridge Construction Best Management Practices for Stream Sites Inhabited by Notropis Topeka (Topeka shiner) (Cunningham 2000), local site-specific infonnation, and proposed construction project infonnation will continue to be used as the foundation to detennine BMPs. Additionally, Topeka shiner habitat has been delineated for SD using the best infonnation available. However, both mapping criteria and the best available scientific infonnation regarding the Topeka shiner are likely to evolve as we gain a better understanding of Topeka shiner habitat use through ongoing studies. The most up-to-date infonnation must always be considered and incorporated into the assessment process. Additionally, deficiencies relating to the most up-to-date infonnation must be acknowledged. The following factors regulate erosion and sedimentation and were taken into consideration when developing the SDDOT "Special Provision for Construction Practices in Streams Inhabited by the Topeka Shiner" (Attachment A):

Timing: Construction will be prohibited during the critical life history phases of spawning, egg incubation, as well as larval emergence and development. In South Dakota work shall initially be prohibited below the high bank (two year event) of the stream between May 15 and July 31. This will protect the Topeka shiner during spawning and larval emergence and development. FWS may approve work during the Topeka shiner spawning season if channel diversions are in place and functioning during the spawning season.

Minimize work area disturbance: The contractor shall minimize disturbance of the work area by limiting the working pad surface area and limiting removal of riparian vegetation. Existing vegetation left in place will keep stream banks stable and reduce erosion and sedimentation into the stream. Water from wet materials excavated and removed from within a cofferdam or Temporary Water Barrier shall have sediment removed prior to the effluent reentering the stream.

In those areas that must be disturbed, exposed surfaces shall not be left exposed for greater than one day if work is not occurring daily at that location. Exposed work areas within 100 feet of a FWS designated Topeka shiner stream shall be protected at the end of each workday with erosion control mats, plastic sheeting or. other approved methods. Disturbed idle construction areas within 100 feet of a FWS designated Topeka shiner stream, left for more than a day without continuous work, that are not pennanently seeded and mulched shall be covered with temporary mulch. All areas disturbed by construction activities shall be stabilized and restored with native vegetation when work in those areas is complete. SDDOT will contract separately with South Dakota Game, Fish & Parks or the Natural Resource Conservation Service for restoration of riparian habitat. Restoration of riparian habitat will not be site specific except for those individual construction sites recommended by the SDDOT biologist.

Designing, implementing, and monitoring erosion control measures are the most important aspect of preventing fine sediments from entering into stream systems. Construction activity zones above the stream particularly in areas that drain directly into the stream shall have silt fence or other appropriate erosion control measures properly installed. Appropriate temporary erosion control measures will be properly installed prior to earth disturbing activity and maintained throughout the construction activity. The Contractor will perfonn monitoring of erosion and sediment controls on a continuous basis, with thorough inspections during rainfall events and immediately make needed repairs or adjustments. These measures will mitigate habitat loss and prevent mortality of adult, larvae, or eggs of aquatic species resulting from siltation during the construction phase.

Stream Diversions: Temporary stream diversions shall be constructed to allow unobstructed flows and passage of fish. Unrestricted fish passage will be provided at all times. Earthen dams shall not be allowed. A flexible water barrier tube is recommended for use. Any excavated and unwashed granular material from the streambed shall not be released into the stream. Every effort will be made to limit strearrlbed disturbance and to isolate and capture sediment released during construction.

Box Culvert Design Considerations: The bottom of all box culverts are countersunk to the depth required in the final project plans and covered with natural substrate. Submerged culvert bottom depths range from 6 inches to 12 inches to allow for passage offish and to provide necessary habitat. Example - The box culvert bottom slab is lowered and covered with one foot of granular material between the flow line and the top of the bottom slab. In addition a six-inch deep low water channel in the granular material is provided. The box is designed to be one foot taller than what is hydraulically required. The one-foot of granular material is provided anytime fish habitat is an issue - not just on Topeka shiner streams (SDDOT 2003). Two researchers "recommended that all culverts be countersunk at least 15 em (6 inches) ..... " (Fitch 1997). Where possible, the base of the pipe or box culvert should be set into, rather than on the streambed (NSW Fisheries Policy 1999). Spanning the active channel and simulating a channel bottom through the culvert will satisfy most biological and hydrologic concerns (USFS 2002). A closed bottom structure should be designed and installed at the same slope as the stream, and should retain the same stream substrate characteristics within the culvert. For migrating fish, this would impose no changes or stress, nor induce any delays at the crossing structure in upstream migration (Be Ministry of Forests 2002). A six inch lip to divert flows in a double or triple box culvert into a single barrel (maximizing the water depth) may be utilized where necessary to allow fish passage. Or one barrel of the box culvert may be constructed lower than the other barrels to facilitate fish passage during low flow.

It is not considered necessary or practical to design culverts to pass fish at flood stage or continually. Fish generally move after flood peaks pass (ODFW 1999). The Oregon Department ofFish and Wildlife (ODFW) guidelines advise that the culvert should be designed to pass fish for at least 90% of the stream flows for a given season when fish are likely to pass. In other words the culvert should pose a fish passage problem only 10% of the time (ODFW 1999). Water velocity occurs when the potential energy due to differences in elevation is converted into velocity and other fonns of energy as water moves down hill. The greater the elevation change between the culvert inlet and the outlet the more challenging managing water velocity becomes. However, because glaciers repeatedly advanced into South Dakota during the Ice Age and covered most of the state east of the Missouri River, the land surface has been fonned and molded into a level and slightly rolling terrain. Therefore, there is usually little elevation change to contend with. On relatively flat streams (streams from 0-3%), several strategies can work to manage the small amount of potential energy (ODFW 1999). Roughness can be created to cause energy dissipation so that most of energy does not go into velocity production (ODFW 1999). Placing fill material in the bottom of culverts is a common method of increasing their roughness (FHWA 1991). A culvert placed flat (for streams up to 2-5% channel gradient) will also in general allow for fish passage especially ifback watered from the outlet side or embedded with natural streambed sediment. Culvert designs that retain natural morphological features of stream width, streambed composition, slope and cross-sectional area are preferred. A series of large culvert cells built to mimic the cross-sectional area of the stream is more beneficial to fish than a single cell culvert, as they will allow water velocity to remain similar to natural conditions (NSW Fisheries Policy 1999). The invert level of culverts should mimic the natural invert level of the stream bed so that water flow velocities both through, and downstream of, the culvert are the same as the natural flow rates upstream of the crossing (i.e. no detectable difference in flow rates). This will ensure that a discontinuity in the flow of the stream is avoided (Cotterell 1998).

A complete theoretical analysis of the hydraulics of a particular culvert installation is time-consuming and difficult. Flow conditions vary from culvert to culvert and they also vary over time for any given culvert. The barrel of the culvert may flow full or partly full depending upon upstream and downstream conditions, barrel characteristics, and inlet geometry (FHW A 1985). The hydraulic capacity of a culvert may be improved by appropriate inlet selection. Since the natural channel is usually wider than the culvert barrel, the culvert inlet represents a flow contraction and may be the primary flow control. "The inlet contraction zone, which results from a need to increase water velocity on entrance to the culvert and from horizontal cross-sectional area contraction, is usually quite short. It is the writers' experience that this zone usually occurs V over a distance of only a few feet, depending on culvert size" (FHW A 1991).

Natural streams are subject to the forces of moving water. Placing a culvert into this dynamic environment requires special attention to the effects of these natural forces on the culvert and the effect of the culvert on the stream channel. Past experience has shown problems, including erosion at the inlet and outlet and sediment buildup in the barrel. As the flow contracts and expands, vortices and scour holes may fonn upstream and downstream of the culvert floor. Protection against scour varies from riprap, wing-walls, cutoff walls, and the use of rougher materials in the culvert. Concrete aprons protect the channel and redistribute or spread the flow b( FHW A 1985). Riprap also has been used in many locations as a protective device to allow high velocity flow to return to an equilibrium stream flow without damaging or eroding threatened features (FHW A 1998). A stable channel is expected to balance erosion and sedimentation over l::- time; a culvert resting on such a channel bed behaves in a similar manner (FHWA 1985). .

Direct Mortality: All temporary storage facilities for hazardous materials must be located and protected to prevent accidental spills from entering streams within the construction area. No mechanized equipment will be allowed in the stream. Oversight for final water enclosures, de-watering, fish seining and any fish transfer or movement shall be conducted by a Biologist under contract to SDDOT. De-watering and construction activities within water enclosures shall not be done until the Biologist has confinned that all the fish have been moved from within the enclosure. In addition, the Special Provision states dewatering shall be done with pumping methods that will not transport fish through pumps or trap fish against intakes. Possibility for take could occur during seining of Topeka shiners or if the Biologist has not removed all of the fish from within the enclosure. The contractor is required to submit a detailed Construction Plan for approval two weeks prior to the preconstruction meeting. A copy of the plan will be forwarded to FWS. A preconstruction meeting shall be held with the Contractor, all Sub-Contractors, Project Engineers and personnel from the Environmental Office to ensure all permit conditions and plans are clearly understood.

developed, Steve Wall, Research Biologist, Wildlife and Fisheries Sciences, South Dakota State University, Brookings, South Dakota. will handle Topeka shiners in accordance with a special research permit issued by the FWS. No Topeka shiner fatalities have occurred in the six construction projects Steve Wall has monitored and seined fish. At four of the projects no Topeka shiners were found. At a bridge project in Hanson County, twenty-two Topeka shiners were moved and none were lost. Seven Topeka shiners were seined for a box culvert project in Duel County and none were lost (Steve Wall, per comm. 2003). The Research Biologist will continue to refine the current methods of fish transfer, stream diversion, and BMPs while at the project site. A report summarizing his findings and recommendations for any changes or additional BMPS for work in Topeka shiner streams will be prepared. SDDOT will contract with a biologist to continue the work Steve Wall is currently doing for construction projects on Topeka shiner streams. Photo documentation of the Topeka shiner stream before, during, and after construction will be taken by SDDOT personnel.

Attachment A is the Special Provision for Construction Practices in Streams Inhabited by the Topeka Shiner developed by SDDOT and concurred by FWS. Attachment A also includes the standard plates for construction projects that have been developed by SDDOT and concurred by FWS.

VII. EFFECTS DETERMINATION MATRIX

Based upon SDDOT project description, species habitat requirements and other data, the SDDOT construction program as defined in Section I. is having the following impacts upon listed and proposed species and their associated critical habitat.

Topeka Shiner ILTAA Least Tern NE Piping Plover NE Whooping Crane NE 22 American Bald Eagle Eskimo Curlew Black-Footed Ferret Pallid Sturgeon American Burying Beetle Western Prairie Fringed Orchid Mountain Plover Scaleshell Mussel ILTAA = Is Likely to Adversely Affect INLTAA = Is Not Likely to Adversely Affect INL T AA -D (Discountable Effects) INLT AA-I (Insignificant Effects) INLT AA-B (Beneficial Effects)

INLTAA-I NE NE NE NE NE NE NE NE = No Effect

VIII. CUMULATIVE IMPACTS

Cumulative effects include the effects of past, present, and future state, local or federal actions that are reasonably certain to occur in the action area considered in this document. One of the concerns of FWS is the amount of natural streambed that is being covered when bridges are replaced by box culverts. SDDOT analyzed the impact of box and pipe culvert construction over the James River Basin, Upper and Lower Big Sioux River Basin, and the Vermillion River Basin in South Dakota. Also included for additional information is historical data from three streams randoITlly selected in Lake and Miner counties.

The total stream length for Topeka shiner streams was obtained from Steve Wall, Research Biologist, Wildlife and Fisheries Sciences, South Dakota State University, Brookings, South Dakota. The SDDOT Environmental Office queried Pontis ® (a database that stores structure inventory and condition) for the different structure categories. The stream length impacted by structures within the listed stream segment was divided by the overall stream segment length resulting in the percentage of total stream length impacted by structures. This information is included in tables by river basin and used to determine the overall percentage of stream length impacted by structures. Pie charts have been developed using this information to provide a graphical representation of the amount of stream that is impacted by structures (Attachment E). The impacted stream length is minimal less than six tenths of one percent.

Stream impact lengths listed below for the different structure categories were averaged by program activity and by structure type. The average stream impact length includes the length of the structure, the structure aprons, and inlet/outlet stabilization. For example, state box culverts averaged 84 feet. An additional 40 feet was added to account for the average footprint of the aprons and streambed protection/stabilization.

County Bridge = 30'
County Box = 60'
State Bridge = 42'
State Box = 124'
Structures <20' = 50' (Includes smaller box and pipe culverts located on county roads)

Data used in the following analyses is attached. (See Attachment E).

James River Basin:

There are a total of 545 structures located on/over streams in the James River Basin. Three hundred and twelve structures are bridges with the remainder box or pipe culverts. Currently, approximately 0.51% of the streambeds in this basin are affected by culverts and bridges.

Big Sioux River Basin

The Big Sioux River Basin has a total of 369 structures. A total of 182 of the structures are bridges with the remainder box or pipe culverts. Only 0.63% of the streanlbed in the Big Sioux River basin is affected by culverts and bridges.

Vermillion River Basin

A total of338 structures are located in the Vermillion River Basin. State and county bridges account for 228 of these structures. Currently about 0.54% of the streambeds are affected by culverts and bridges.

Battle Creek - Lake County

Eighteen box culverts (1930 - 1940s vintage) and 4 bridges cross 15 miles of the Battle Creek stream channel. Assuming a 40-foot length per box culvert would mean approximately 0.9% of the strearrlbed is impacted by the box culverts. Since 1985 two new bridges have been constructed and three box culverts. All three box culverts (use 60-foot average length) have replaced existing box culverts so the % of the streambed impacted is 0.98%, an increase of 0.08%.

East Fork Vermillion River - Lake County:

Three box culverts (1930 - 1940s vintage) and 7 bridges cross approximately 25 miles of the East Fork of the Vermillion River. Again making the same assumptions as above, the box culverts impact 0.09% of the streambed. Since 1987 three new bridges have been constructed replacing existing structures so the percentage of the streambed impacted by box culverts has not changed.

West Fork Vermillion River - Miner County:

Two box culverts and 11 bridges cross 30 miles of mainstream channel. Since 1997 two new box culverts have been constructed replacing two bridges. Prior to 1997,0.05% of the streambed was impacted by box culvert structures. Impact to the channel length with the two new box culverts is about 60 feet each for a total of 120 feet including riprap erosion protection. Total length of channel replaced with concrete accounts for about 0.08% of the total stream length.

Future Construction Projects

The five-year construction program was developed through the coordinated efforts of the SDDOT, Transportation Commission, state and federal agencies, local and tribal governments, metropolitan planning organizations, public agencies, and public citizens. However, the five-year program is a planning guide only. The program is subject to revisions and changes which may be required by unforeseen situations such as funding reductions, increases in oil prices, right-of-way acquisition delays, or complex design and environmental issues which must be resolved.

Over the next five years, seven bridges on the State Highway system over Topeka shiner streams are estimated to be replaced with seven bridges. Therefore, there will be no change in the percentage of streambeds affected.

Within the next five years Local Government Assistance plans to replace approximately 214 structures. Based on past history (since 1992), about 52% or approximately 111 of those will end up being bridges and 103 will end up being reinforced box culverts. This means that about 1235 feet of streambed (assuming an average length of60 feet) may be impacted each year. Within the James River Basin, Upper & Lower Big Sioux Basin, and the Vermillion River Basin are about 1853 miles of streambed. Therefore, replacing 103 bridges over the next five years with box culverts would impact only about 0.063% of the streambed in these basins.

Summary:

The focus of transportation has shifted from construction on new alignment to maintenance/replacement of existing transportation facilities. New roads on new alignment are rarely constructed. Typically, box culverts replace existing box culverts although in some cases a box culvert may replace an existing bridge. Therefore, the cumulative impacts of new box culvert construction is negligible not only for the reasons cited above but also because of the research that has been done as noted below.

Box culverts are usually compatible because they are countersunk and can even be constructed to enhance resident stream fish abundance and diversity (Slawski and Ehlinger 1998). Box culverts, countersunk to maintain natural stream bottom, appear to provide suitable structure for fish passage (Wall and Berry 2002). Water velocity occurs when the potential energy due to differences in elevation is converted into velocity and other fonns of energy as water moves down hill. The greater the elevation change between the culvert inlet and the outlet the more challenging managing water velocity becomes. On relatively flat streams (streams from 0-3%) there is little elevation change to contend with and several strategies can work to manage the small amount of potential energy (ODFW 1999). Following are two of the strategies mentioned by the Oregon Department of Fish & Wildlife: Eliminate potential energy - make the culvert flat or create roughness to cause energy dissipation so that most of energy does not go into velocity production. Properly designed culverts do not produce water velocities that exceed fish swimming abilities (Behlke, et al. 1991). Recent research states "Topeka shiners are capable of swimming speeds faster than water velocities which they typically inhabit. Fishways and culverts, therefore, may be employed to facilitate dispersal and recolonization" (Adams et al. 2000). Although Topeka shiners typically occupy pool and slack water habitats and avoid water velocities> 10 cm/s, field and laboratory observations indicate substantial physical tolerance for faster flows (Adams et al. 2000).

IX. ADMINISTRATIVE SUMMARY OF EFFECTS DETERMINATION

The SDDOT is responsible for planning, developing and implementing improvement projects on transportation systems throughout the State. The responsibility includes construction, operation and maintenance of the 7,839 mile state highway system as well as providing assistance to local units of government for transportation improvements. Construction projects may have minor impacts on the environment such as resurfacing, pavement marking, and lighting projects or substantially more impact if the major project involves the reconstruction of a highway, bridge replacement or new highway construction. This document evaluates the effects of installing and maintaining bridges, box culverts including box culvert extensions, corrugated metal pipe, and reinforced concrete pipe as well as extensions on proposed, threatened, and endangered species.

The SDDOT projects, if implemented with self-imposed criteria, may affect but will not adversely affect or will have no effect on the listed, proposed, or candidate species in SD with the exception of the Topeka shiner.

x. CONCLUDING STATEMENTS

It is the position of the Federal Highway Administration that the SDDOT construction projects conducted throughout SD may affect but ARE NOT LlKEL Y TO ADVERSELY AFFECT or will have NO EFFECT on the following current listed species (least tern, piping plover, whooping crane, American bald eagle, Eskimo curlew, black-footed ferret, pallid sturgeon, American burying beetle, scaleshell mussel, western prairie fringed orchid, and mountain plover). SDDOT construction projects MAY ADVERSELY AFFECT the Topeka shiner.

As required by 50 CFR 402, reinitiation of fonnal consultation must be requested by FHW A or by FWS if: a) the amount or extent of taking specified in the incidental take statement is exceeded; b) new infonnation reveals effects of the action that may affect listed species or critical habitat in a manner or to an extent not previously considered; c) the identified action is subsequently modified in a manner or to an extent that causes an effect to the listed species or critical habitat not previously considered in the biological opinion; or, d) a new species is listed or critical habitat designated that may be affected by the identified action.

FHW AlSDDOT will provide FWS with an annual report on September 1 of each year that describes the number and location of projects authorized under this Programmatic Agreement. The report will document Topeka shiners moved and any take that may have occurred.

A. Concurrence --- Nonconcurrence ---

B. Fonnal consultation required __ _

C. Conference required ---

D. Infonnal conference required __ _

E. Remarks (attach additional pages as needed):

Project Leader
U. S. Fish and Wildlife Service
SD Ecological Service Office
Pierre, South Dakota

XI. LITERATURE CITED

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GRAUL, W. D. 1975. Breeding biology of the Mountain Plover. Wilson Bulletin. 87:6-31.

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GRAUL, W. D., and L. E. WEBSTER. 1976. Breeding status of the Mountain Plover. Condor. 78:265-267.

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HENDERSON, F. R., P. F. SPRINGER, and R. ADRIAN. 1969. The black-footed ferret in South Dakota. South Dakota Dept. of Game, Fish, and Parks. Tech. Bull. 4: 1-36.

HOKE, ELLET. 1983. Unionid mollusks of the Missouri River on the Nebraska border. Am. Mal.Bulletin., Vol. 1(1983):71-74

HUNTING, K. 2000. Mountain Plover (Charadrius montanus). California Dept. ofFish and Game. California Partners in Flight. Grassland Bird Conservation Plan.

HURLEY, S. T., W. A. HUBERT, and J. G. NICKUM. 1987. Habitats and movements of shovelnose sturgeons in the upper Mississippi river. Trans. of the American Fisheries Society. 116:655-662.

KEISTER, G. P. and R. G. ANTHONY. 1983. Characteristics of winter roosts and populations of bald eagles in the Klamath Basin of Oregon and California. pp. 95-100 In: Biology and management of bald eagles and ospreys. D. M. Bird, ed. Harpell Press, Ste. Anne de Bellevue, Quebec.

KIRSCH, E. M. and G. R. LINGLE.' 1993. Habitat use and nesting success of least terns along the lower Platte River, Nebraska. USGS. Northern Prairie Wildlife Research Center.

KNOPF, F. L., and J. R. RUPERT. 1995. Habits and habitats of Mountain Plovers in California. Condor. 97:743-751.

KNOPF, F. L. 1996. Mountain Plover (Charadrius montanus). The birds of North America, No. 211. The birds of North America, Inc., Philadelphia, PA.

KNOWLES, C. J., C. J. STONER and S. P. GIEB. 1982. Selective use of black-tailed prairie dog towns by mountain plovers. Condor. 84(1):71-74. Feb.

LAUN, C. H. 1957. A life history study of the mountain plover (Eupoda montana Townsend), on the Laramie Plains, Albany County, Wyoming. M. S. Thesis. University of Wyoming, Laramie.

LEACHMAN, B. and B. OSMUNDSON. 1990. Status of the mountain plover. A literature review. U. S. Fish and Wildlife Service, Office ofFish and Wildlife Enhancement, Golden, CO.

LeFRANC, M. N., JR., and B. A. MILLSAP. 1984. A summary of state and federal agency raptor management programs. Wildl. Soc. Bull. 12:274-282.

LISH, J. W. and J. C. LEWIS. 1975. Status and ecology of bald eagles wintering in Oklahoma. Proc. Ann. Conf. Southeastern Assoc. Game and Fish Commisso 29:415-423.

LOCKHART, M., V. ASTRID, P. MARINARI, P. GOBER. 1998. Black-footed ferret recovery update. 2 pp.

MASSEY, B. 1972. Report on the use of tract no. 8040, Huntington Harbor, by birds, with special reference to the California least tern. Env. Impacts Rept., Inc. 13 pp.

McEWAN, L. C. and D. H. HIRTH. 1979. Southern bald eagle productivity and nest site selection. 1. Wildl. Manage. 43 :585-594.

MISSOURI. 2000. Missouri Department of Conservation. Scaleshell mussel (Leptodea leptodon). Best Management Practices.

NORTH, M. R. 1986. Piping plover nesting success on Mallard Island, central North Dakota and implications for water level management. Prairie Naturalist 18(2):117-122.

NSW FISHERIES POLICY 1999. Policy and Guidelines for Bridges, Roads, Causeways, Culverts and Similar Structures. NSW Fisheries, Sydney, 19pp.

ODFW 1999. Oregon Department ofFish and Wildlife. Oregon Road/Stream Crossing Restoration Guide: Spring 1999. Appendix A: Guidelines and Criteria for Stream-Road Crossings.

OLSON, S. L. 1985. Mountain plover food items on and adjacent to a prairie dog town. Prairie Nat. 17(2):83-90.

OLSON, S. L., and D. EDGE. 1985. Nest site selection by mountain plovers in northcentral Montana. J. Range Mgmt. 38(3):280-282.

PARRISH, T. L., S. H. ANDERSON and W. F. OELKLAUS. 1993. Mountain plover habitat selection in the Powder River basin, Wyoming. Prairie Nat. 25(3):23-26.

RAITHEL, C. and M. J. AMARAL. 1991. American burying beetle (Nicrophorus americanus) Recovery plan. U. S. Fish and Wildlife Service.

REIJINEN, R., R. FOPPEN, C. TER BRAAK, and J. THISSEN. 1995. "The Effects of Car Traffic on Breeding Bird Populations in Woodland: III. Reduction of Density in Relation to Proximity of Main Roads," Journal of Applied Ecology, Vol. 32, pp.187-202.

REIJINEN, R., R. FOPPEN, and H. MEEUWSEN. 1996. ''The Effects of Traffic on the Density of Breeding Birds in Dutch Agricultural Grasslands," Biological Conservation, Vol. 75, pp 255-260.

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XII. ATTACHMENTS

ATTACHMENT A
STATE OF SOUTH DAKOTA
DEPARTMENT OF TRANSPORTATION
SPECIAL PROVISION
FOR
CONSTRUCTION PRACTICES IN STREAMS
INHABITED BY THE TOPEKA SIDNER

DECEMBER 9, 2003

Approved: 12-11-03
/s/ Brett E. Hestdalen
Pavement & Materials Engineer
Federal Highway Administration

I. DESCRIPTION

This project crosses a stream ~bited by the Topeka Shiner, a federally endangered species. In order to maintain the habitat necessary to support the Topeka Shiner, several conditions shall be met by the Contractor, during construction. These conditions are outlined in the following paragraphs.

II. MATERIALS (None Required)

III. CONSTRUCTION REQUIREMENTS

A. GENERAL CONSTRUCTION

Construction activities within the stream are prohibited from May 15 to July 31, unless the stream is completely separated from construction a!eas by a Tempqrary Water Barrier or cofferdam. Ifwork is to be done behind a Temporary Water Barrier or cofferdam between May 15 and July 31, the barrier must be in-place and initially de-watered prior to May 15. Temporary Water Barriers and cofferdams shall also be m-place and initially de;'watered prior to -ice up if winter work is planned.' Construction activities at all times within the' stream, along the stream banks, and in areas that drain into the stream will not be allowed unless comprehensive and effective erosion and sediment controls, that will prevent sediments from entering into the stream, are in-place and functioning properly. Erosion and sediment controls shall be left in place and maintained in good working condition until these areas are stabilized and re-vegetated.

The Contractor shall minimize disturbance of the work area by limiting the working pad surface area, and limiting removal of riparian vegetation to the greatest extent possible. Disturbed surfaces shall not be left exposed for greater than one day if work is not occurring daily at that location. Exposed work areas within 100 feet of a USFWS designated Topeka Shiner stream shall be protected at the end of each workday with erosion control mats, plastic sheeting or other approved methods. All areas disturbed by construction activities shall be stabilized and restored with native vegetation when work in those areas is complete. Disturbed idle construction areas within 100 feet of a USFWS designated Topeka Shiner stream, left for more than a day without continuous work, that are not permanently seeded and mulched or protected shall be covered with temporary mulch.

All temporary storage facilities for petroleum products, other fuels, and chemicals must be located and protected to prevent accidental spills from entering streams within the project area. Cement sweepings, washings, treatment chemicals, or grouting and bonding materials are prohibited from entering into the stream directly or from any locations where they can be washed into the stream by storm water runoff. No mechanized equipment will be allowed in the stream. If equipment cannot access the work area from shore, work platforms supported by piling driven into the channel bottom shall be constructed. Work berms shall not be constructed in the stream. Erosion control measures shall be placed at work berms adjacent to the stream.

Unrestricted fish passage must be provided at all times. Construction of temporary dams or diversions using earthen material is not allowed within the stream. Excavated material from the streambed shall not be released back into the stream. Every effort must be made to limit the extent of streambed disturbance and to isolate and capture sediment released during all phases of construction. In-stream dredging and disturbance of the streambed. not provided for in the plans, will not be allowed. This includes no removal of stream bottom substrate for construction materials. If modifications to the streambed cannot be avoided, the physical habitat features (pool-rille-run sequences) must be restored to pre-construction conditions. Water from wet materials excavated and removed from within a Temporary Water Barrier or cofferdam shall have sediment removed prior to the effluent reentering the stream. Sediment removal methods may include a detention pond, complete filtration at an upland site, or trickling through vegetation.

Temporary Water Barriers, cofferdams, and temporary works shall be removed with minimal disturbance to the streambed. Proper construction practices shall be used to minimize increases in suspended solids and turbidity in the waterway.

The Contractor shall submit a detailed Construction Plan, a nnmmum of 14 days prior to the preconstruction meeting, to the Engineer for approval. The plan shall include an Erosion and Sediment Control Plan with a complete description of products, materials and methods of installation and removal. The plan shall also include products, materials and methods of construction for Temporary Water Barriers and cofferdams including de-watering, handling, storage, and disposal of excavated material and pumped effluent. The Construction Plan shall include all necessary information to provide assurance that the special environmental conditions are adequately addressed. The plan will be forwarded to the Environmental and Bridge Offices for review and approval with a copy forwarded to the US Fish & Wildlife Service. Work shall not proceed without approval of the Construction Plan by the Environmental and Bridge Offices.

Oversight for final water enclosures, de-watering, fish seining and any fish transfer or movement shall be conducted by a Biologist under contract to SDDOT.

A pre-construction meeting shall be held with the Contractor, all Sub-Contractors, Project Engineer and personnel from the Environmental Office to ensure all permit conditions and plans are clearly understood.

The Contractor shall be familiar with provisions of the 404 . Permit. The' Contractor shall notify the Engineer if in-stream construction methods or material will be uSed' that are not covered in the 404 Pennit, .so an amendment to the 404 Permit can be processed'ifnecessary. The Contractor shall provide an estimated date at the pre-construction meeting when the Biologistwill be needed on site to monitor fmal water enclosures, de-watering, fish seining or any fish transfer. The contractor shall notify the Biologist two days before needed on site. The telephone number and name of the Biologist will be supplied to the Contractor at the pre-construction meeting.

The project will be inspected and evaluated daily by the Engineer to ensure that all construction requirements and environmental conditions are being met and that the stream and habitat are being protected. The Engineer has the authority to order different or have additional controls implemented to more effectively protect the stream. Construction methods that result in fish mortality shall cease and may resume only after the Engineer, in consultation with the Biologist, approves an acceptable plan. The Engineer shall be notified immediately if field conditions change, or if the project must be modified, so that coordination of pennits and approvals can be expedited.

B. TEMPORARYWATERBARRIERS

Temporary water barriers can consist of sheet piling, water fIlled bladders, portable cofferdams, sand bag dikes, or similar acceptable methods that completely and effectively isolate the stream from the work area. Temporary Water Barriers shall be clean and free of contaminants and sediments that can effect water quality. They shall also be installed by methods that minimize the introduction of sediments and contaminants into the water. Barriers that are constructed in the water shall be enclosed at the upstream side first and every effort shall be made to move any trapped fish out the downstream side before the downstream side is enclosed. If Temporary Water Barriers are overtopped after initial de-watering, every effort shall be made to move or remove trapped fish from within the enclosure before completely de-watering again. Movement of fish must be supervised by the Biologist.

Any excavation or removal of muck and debris from behind a Temporary Water Barrier enclosure shall be done by such methods that sediment and debris do not enter into the stream.

C. COFFERDAMS

Where cofferdams are required for deep foundations, the same provisions given for Temporary Water Barriers shall apply for cofferdams with the following exceptions: .

The Contractor shall provide a walkway along the inside perimeter of cofferdams, within one foot of the water surface, to provide access for seining operations. The last sheet piling to be installed shall be at the downstream end. A net or seine shall be used, vertically, inside the sheet pile cofferdam beginning at the upstream end to gradually force fish out the open downstream end. The cofferdam may then be completely enclosed by driving the last sheet pile.

Design of cofferdams shall be as specified in Section 423 of the Standard Specifications.

D. DE-WATERING

De-watering and construction activities within water enclosures shall not be done until the Biologist has confirmed that all the fish have been moved from within the enclosure. The intent is to ensure that no fish remain trapped within the enclosure after it is closed and de-watered.

Initial de-watering or de-watering after overtopping has occurred shall be done by an approved pumping method and shall not occur unless the Biologist is present or has cleared the enclosure for de-watering. Initial de-watering or de-watering after overtopping has occurred shall be done with pumping methods that will not transport fish through pumps or trap fish against intakes.

Effluent from the de-watering operation shall be pumped to an' upland site and the sediment removed prior to the effluent reentering the stream. Sediment removal methods may include a detention pond, complete filtration at in upland site or trickling through vegetation.

E. TEMPORARY WORKS (FALSEWORK AND WORK PLATFORMS)

Falsework or work platforms shall conform to Section 423 of the Standard Specifications and.any applicable requirements of this provision.

Temporary piling shall be cutoff at or driven flush with the streambed, or extracted when no longer needed.

The Contractor shall consider how falsework or work platforms will be installed and removed when preparing the Construction Plan and include any special construction methods or sequencing that may be required to protect the Topeka Shiner.

Design of temporary works shall be as specified in Section 423 of the Standard Specifications.

Removal of structures and obstructions shall conform to Section 110 of the Standard Specifications and any applicable requirements of this provision.

Construction, demolition and/or removal operations conducted over or in the vicinity of the stream, shall be controlled to prevent materials from falling in the waterway. Any materials that do fall into the waterway or into areas below the ordinary high water elevation (2-year flow) must be removed promptly by hand or with equipment located above the stream bank at the discretion of the Engineer. A platform suspended below the bridge shall be constructed to prevent material from entering the stream during demolition of the superstructure. A platform or similar device shall be constructed around the piers located in the stream to prevent material from entering the water during demolition of those piers. A Temporary Water Barrier shall be constructed around areas of removal that are below the waterline.

G. BOX CULVERTS AND PIPE

Construction of box culverts shall comply with all applicable requirements of this provision. Construction of pipe identified in the plans shall comply with all applicable requirements of this provision.

Temporary diversion channels for box culverts and pipe shall be constructed according to Standard Plate number 734.10. Temporary diversion channels shall be complete and in place prior to May 15 for work between May 15 and July 31 and shall also be in-place prior to ice up if winter work is planned. The Contractor s hall construct the temporary diversion channel to allow unrestricted fish passage even if the channel is dry at the start of construction.

The Contractor shall include details of products, materials and methods of construction for temporary diversion channels with his Construction Plan.

H. BOX AND PIPE CULVERT EXTENSIONS

Construction of box and pipe culvert extensions identified in the plans shall comply with a 11 applicable requirements of this provision.

The Contractor shall divert the stream and use phased construction to maintain unrestricted fish passage during construction activities. The contractor shall use phased construction to construct the temporary stream flow diversion even if the c~el is dry at the start of construction.

The Contractor's plan for the temporary stream diversion for box and pipe culvert extensions shall be included in his detailed Construction Plan that is submitted to the Engineer for approval. The temporary stream diversion for box and pipe culvert extensions shall be constructed according to the Contractor's approved plan details. Temporary stream diversions shall b e complete and in place prior to May 15 for work between May 15 and July 31· and shall also be in-place prior to ice up if winter work is planned.

The Contractor's detailed Construction Plan shall include temporary stream diversion layout for each phase, box extension construction joints, bar splicing details, diversion sequence, and any other special construction methods or sequencing that may be required to protect the Topeka Shiner.

IV. METHOD OF MEASUREMENT

A. Temporary Water ,Barriers: Temporary water barriers will be measured to the nearest foot.

B. Cofferdams: Measurement for cofferdams will be as per Section 423.4 of the Standard Specifications.

C. Dewatering: Measurement for dewatering will not be made

D. Temporary Works: Measurement for temporary works will be as per Section 423.4 of the Standard Specifications.

E. Removal of Structures and Obstructions: Measurement for removal of structures and obstructions shall be as per Section 110.4 of the Standard Specifications.

F. Temporary Diversion Channel for Box Culverts: Measurement for temporary diversion channel for box culverts shall be in accordance with Standard Plate number 734.10.

G. Temporary Stream Diversion for Box Culvert Extensions: Measurement for temporary stream diversions for box culvert extensions will be on a per each basis.

H. Temporary Stream Diversion for Pipe Culvert Extensions: Measurement for temporary stream diversions for pipe culvert extensions will be on a per each basis.

I. Erosion Control for Box Culvert Extension: Measurement for erosion and sediment control for box culvert extensions will not be made.

J. Erosion Control for Pipe Culvert Extension: Measurement for erosion and sediment control for pipe culvert extensions will not be made.

K. Erosion Control for Bridge: Meas~ement for erosion and sediment control for bridge will not be made.

V. BASIS OF PAYMENT

A. Temporary Water Barriers: Temporary water barriers will be paid for at the contract unit price per foot. Payment for this bid item shall be made only once at each plan shown location, regardless of the number of times the barrier is changed or moved. Payment will be full compensation for labor, equipment, materials, and all incidentals necessary for constructing the temporary water barrier.

B. Cofferdams: Payment for cofferdams shall be as specified in Section 423.5 of the Standard Specifications.

C. Dewatering: Payment for Dewatering will not be made. All costs associated with dewatering shall be incidental to the other bid items.

D. Temporary Works: Payment for temporary works shall be as specified in Section 423.5 of the Standard Specifications.

E. Removal of Structures and Obstructions: Payment for removal of structures and obstructions shall be as specified in Section 110.5 of the Standard Specifications.

F. Temporary Diversion Channel for Box Culverts and Pipe: Payment for temporary diversion channels for box culverts shall be in accordance with Standard Plate number 734.10.

G. Temporary Stream Diversion for Box Culvert Extensions: Temporary stream diversion for box culvert extensions will be paid for at the contract unit price per each. Payment for this bid item will be made only once, regardless of the number of times the diversion is changed or moved at this site. Payment will be full compensation for labor, equipment, materials, and all incidentals necessary for constructing the temporary diversion.

H. Temporary Stream Diversion for Pipe Culvert Extensions: Temporary stream diversion for pipe culvert extensions will be paid for at the contract unit price per each. Payment for this bid item will be made only once, regardless of the number of times the diversion is changed or moved at this site. Payment will be full compensation for labor, equipment, materials, and all incidentals necessary for constructing the temporary diversion.

I. Erosion Control for Box Culvert Extension: Erosion cpntrol for box culvert extension will be paid for at the contract lump sum price. The contract lump sum price shall be full compensation for all labor, equipment, materials, and incidentals necessary to install and maintain erosion and sediment control measures for box culvert extensions. Payment for erosion control measures not shown on the approved Construction P Ian will be measured and paid for under their respective bid items (i.e. silt fence, erosion bale, etc.).

J. Erosion Control for Pipe Culvert Extension: Erosion control for pipe culvert extension will be paid for at the contract lump sum price. The contract lump sum price shall be full compensation for all labor, equipment, materials, and incidentals necessary to install and maintain erosion and sediment control measures for pipe culvert extensions. Payment for erosion controt'measures not shown on the approved Construction Plan will b'e measured and paid for under their respective bid items (i.e. silt fence, erosion bale, etc.).

K. Erosion Control for Bridge: Erosion control for bridge will be paid at the contract lump sum price. The contract lump sum price will be full compensation for all labor, equipment, materials, and incidentals necessary to install and maintain erosion and sediment control measure! necessary for bridge construction. Payment for erosion control measures not shown on the appro d Construction Plan will be measured and paid for under their respective bid items (i.e. silt fence, eros on bale, etc.).

*****

ATTACHMENT B

ATTACHMENT C

ATTACHMENT D

Topeka Shiner Locations in South Dakota Waters,
Most Recent Collection Dates
Updated locations using information from GF&P, SDSU (Topeka Shiner location map - Steve Wall/Chuck
Berry), Ecocentrics, and East Dakota Water Development District (Craig Milewski) data
(Revised September 15,2003)

James River Watershed   Big Sioux River Watershed  
1 Dry Creek -'00  1 Beaver Creek -'01 
2 ElmRiver-'03  2 Big Sioux River -'71 
3 Enemy Creek -'00 3   Brookfield Creek -'99
4 Firesteel Creek -'00 4 Deer Creek1 -presumed occupied
5 Middle Pearl Creek -'00 5 Flandreau Creek2-'70
6 North Branch Dry Creek -'00 6 Four-mile Creek -'99
7 Pearl Creek -'00 7 Hidewood Creek -'99
8 Redstone Creek -'89 8 Medary Creek -'00
9 Rock Creek -'00 9 North Deer Creek -'00
10 Shue Creek -'00 10 Peg Munky Run -'01
11 South Branch Lonetree Creek -'00 11 Pipestone Creek -'00
12 Twelve-mile Creek -'00 12 Six-mile Creek -'00
13 Unnamed trib. Twelve-mile Creek -'02 13 Skunk Creek3 -'99
14 West Branch Firesteel Creek -'98 14 Slipup Creek -'99
15 WolfCreek -'97  15 South Fork North Deer Creek -'98
    16 Split Rock Creek -'00
    17 Spring Creek -'00
    18 Springwater Creek -'99
Vermillion River Watershed   19 Stray Horse Creek -'02
Blind Creek -'00 20 Tetonka Lake Drainage -'49
2 Camp Creek -'00  21 Unnamed trib.Beaver Creek -'99
3 East Fork Vermillion River -'92 22 Unnamed trib. Deer Creek -'00
4 Haram Creek -'03 23 Unnamed trib. Sixmi16 Creek4-'00
5 Long Creek -'00 24 Unnamed trib. Split Rock Creeks - presumed occupied
6 Saddle Creek -'00 24 Unnamed trib. Pipestone-exact date? 'OO?
7 Silver Lake Outlet -'00 25 West Pipestone Creek -'00
8 Turkey Ridge Creek -'00 26 Willow Creek -'39
9 Vermillion River -'99    
10 West Fork Vermillion River -'00 Missouri River Watershed (validity in doubt)  
    1 Cheyenne River embayment -'68-'69
    2 Moreau River embayment-'68-'69
    3 Grand River embayment -'68-'69

IDeer Creek - This waterway connects known occupied streams ofMedary and an unnamed tributary to Deer Creek, so it was presumed occupied and included in 2002 proposed critical habitat. Although no shiners have been collected from the waterway as of Sept. 2003, it is likely an occupied stream.

2F1andreau Creek - Known to be occupied on the MN side, presume SD is occupied as well. Last known SD record was in 1970.

3Skunk Creek - George Omninbam, Ecocentrics, reported Topeka shiner/sand shiner hybrids, not full Topekas.

4Unnamed Trib to Sixmile Creek - The Topeka shiner collection site on this tributary is very close to the mainstem of Sixmi1e Creek - Steve Wall didn't distinguish it from Sixmi1e, but FWS did in the proposed critical habitat rule of 2002. It is considered an occupied waterway.

SUnnamed Trib to Split Rock Creek - This waterway is not named on USGS maps, but is called Devils Gulch Creek in the SD Gazateer. It is located approximately ~ mile north of Garretson, and presumed occupied in SD because of recent records on Minnesota side and its connection to Split Rock.

ATTACHMENT E

Average stream Length Impacted by a Structure < 20' = 50'

Average Stream Length Impacted by a State Bridge = 42'

Average Stream Length Impacted by a State Box Culvert = 124'

Feature Interested Total Structures Total # Drainage Structures <20ft. Total # Structures >20ft.   # State/Other Boxes >20ft. # State/Other Bridges >20ft. Total Stream Length (miles) Total Structure Length (miles) Total Stream Occupied By Structure (%)
Elm River 27 5 22 0 20 0 2 91.3 0.18 0.194
Dry Creek 22 7 15 1 12 1 1 30.0 0.18 0.591
Enemy Creek 31 5 26 2 23 1 0 51.9 0.22 0.432
Firesteel Creek 46 21 25 1 21 0 3 87.5 0.35 0.404
Middle Pearl Creek 28 18 10 0 9 0 0 34.4 0.23 0.667
North BR Dry Creek 13 0 13 1 9 1 2 29.4 0.10 0.347
Pearl Creek 52 13 39 3 32 3 1 65.6 0.42 0.636
Redstone Creek 59 30 29 1 27 1 0 105.0 0.47 0.450
Rock Creek 53 23 30 4 24 1 1 84.4 0.43 0.511
Shue Creek 39 23 16 0 13 2 1 54.4 0.35 0.637
South BR Lonetree Creek 33 13 20 1 16 2 1 27.5 0.28 1.019
West BR Firesteel Creek 23 11 12 1 9 1 1 56.3 0.20 0.352
Wolf Creek 50 11 39 2 29 2 6 67.5 0.39 0.572
Twelve Mile Creek 69 12 57 7 47 2 1 57.5 0.52 0.896
Total 545 192 353 24 291 17 21 847.7    
                Total    
Total Impacted Stream lengths (ft.)   9600 n/a 1400 8730 2108 882 22760.00    
Total Impacted Stream lengths (miles)   1.82 n/a 0.27 1.65 0.40 0.17 4.31    
Percentage (%)   0.216 n/a 0.032 0.196 0.047 0.020 0.512    

James River Basin Structure on Topeka Shiner Streams: Impacted Stream Length 0.512%, Non-Impacted Stream Length 99.488%.

Vermillion River Basin

Average Stream Length Impacted by Structures <20' = 50'


Average Stream Length Impacted by a County Bridge >20' = 30'

Average Stream Length Impacted by a County Box Culvert >20' = 60'


Average Stream Length Impacted by a State Bridge >20' = 42'

Average Stream Length Impacted by a State Box Culvert >20' = 124'

Feature Interested Total Structures Total # Structures <20ft. Total # Structures >20ft. # County Boxes >20ft. # County Bridges >20ft. # State/Other Boxes >20ft. # State/Other Bridges >20ft. Total Stream Length (miles) Total Structure Length (miles) Total Stream Occupied By Structure (%)
Blind Creek 20 16 4 2 3 0 0 91.3 0.18 0.194
Camp Creek 11 9 2 0 1 1 0 15.6 0.11 0.733
East Fork Vermillion River 48 12 36 3 27 1 5 100.0 0.36 0.364
Long Creek 31 1 30 0 27 1 2 51.3 0.20 0.394
Saddle Creek 22 6 16 1 12 1 2 21.9 0.18 0.803
Turkey Ridge Creek 39 9 30 0 27 0 3 50.6 0.26 0.519
Vermillion River 69 1 68 4 51 1 12 97.5 0.46 0.476
West Fork Vermillion River 90 29 61 3 47 2 9 103.8 0.69 0.669
Silver Lake Creek LK Outlet 8 8 0 0 0 0 0 6.9 0.08 1.098
Total 338 91 247 12 195 7 33 468.9    
                TOTALS    
Total Structure Stream Length (ft.) n/a 4550 n/a 720 5850 868 1386 13374    
Total Structure Stream Length (miles) n/a 0.86 n/a 0.14 1.11 0.16 0.26 2.53    
Percentage (%) n/a 0.184 n/a 0.029 0.236 0.035 0.056 0.540    

Vermillion River Basin Structure on Topeka Shiner Streams: Impacted Stream Length 0.540%, Non-Impacted Stream Length 99.460%

Upper Big Sioux River Basin

Ave. Stream Length Impacted by Structures < 20' = 50'


Ave. Stream Length Impacted by State Bridge <20' = 42'

Ave. Stream Length Impacted by State Box Culvert <20' = 124'

Feature Interested Total Structures Total # Drainage Structures <20ft. Total # Structures >20ft.   # State/Other Boxes >20ft. # State/Other Bridges >20ft. Total Stream Length (miles) Total Structure Length (miles) Total Stream Occupied By Structure (%)
Tributary To Deer Creek 5 2 3 0 2 0 1 10.1 0.04 0.379
Deer Creek 25 13 12 1 6 3 2 32.0 0.25 0.797
Hidewood Creek 15 5 10 0 6 0 4 34.1 0.11 0.332
Medary Creek 26 9 17 2 10 0 5 33.5 0.20 0.611
North Deer Creek 38 22 16 2 8 0 6 42.8 0.32 0.758
Peg Munky Run Creek 13 7 6 1 2 0 3 17.1 0.11 0.660
Sixmile Creek 30 3 27 1 16 1 9 50.0 0.23 0.452
Stray Horse Creek 21 10 11 0 8 0 3 28.0 0.16 0.586
BR North Deer Creek - SF 6 0 6 1 1 1 3 21.6 0.06 0.298
Lake Tetonkoho Outlet 8 8 0 0 0 0 0 6.0 0.08 1.263
Total 187 79 108 8 59 5 36 275.2    
                Total    
Total Impacted Stream lengths (ft.) n/a 3950 n/a 480 1770 620 1512 8332.00    
Total Impacted Stream lengths (miles) n/a 0.75 n/a 0.09 0.34 0.12 0.29 1.58    
Percentage (%) n/a 0.272   0.033 0.122 0.043 0.104 0.573    

Upper Big Sioux River Basin Structure on Topeka Shiner Streams: Impacted Stream Length 0.573%, Non-Impacted Stream Length 99.427%

Lower Big Sioux River Basin

Ave. Stream Length Imapcted by a Structures < 20' = 50'


Ave. Stream Length Impacted by a County Bridge >20' = 30'

Ave. Stream Length Impacted by a County Box Culvert >20' = 60'


Ave. Stream Length Impacted by a State Bridge >20' = 42'

Ave. Stream Length Impacted by a State Box Culvert >20' = 124'

Feature Interested Total Structures Total # Structures <20ft. Total # Structures >20ft. # County Boxes >20ft. # County Bridges >20ft. # State/Other Boxes >20ft. # State/Other Bridges >20ft. Total Stream Length (miles) Total Structure Length (miles) Total Stream Occupied By Structure (%)
Beaver Creek 13 12 1 0 0 1 0 8.5 0.14 1.613
Tributary To Beaver Creek 6 6 0 0 0 0 0 5.6 0.06 1.015
Brookfield Creek 16 8 8 4 3 1 0 19.3 0.16 0.838
Flanddreau Creek 5 3 2 0 2 0 0 10.0 0.04 0.398
Pipestone Creek 16 0 16 0 15 0 1 28.9 0.09 0.322
Split Rock Creek 20 0 20 1 11 0 8 27.5 0.14 0.500
Spring Creek 18 1 17 1 13 0 3 20.4 0.12 0.581
West Pipestone Creek 35 21 14 0 11 0 3 40.8 0.29 0.699
Slip-Up Creek 23 20 3 0 2 1 0 22.9 0.22 0.979
Fourmile Creek 6 0 6 1 5 0 0 7.3 0.04 0.545
Willow Creek 21 8 13 2 8 1 2 27.4 0.18 0.669
Springwater Creek 3 3 0 0 0 0 0 0.6 0.03 4.735
Total 182 82 100 9 70 4 17 219.2    
                TOTALS    
Total Structure Stream Length (ft.) n/a 4100 n/a 540 2100 496 714 7950    
Total Structure Stream Length (miles) n/a 0.777 n/a 1.102 0.398 0.094 0.135 1.506    
Percentage (%) n/a 0.354 n/a 0.047 0.181 0.043 0.062 0.687    

Lower Big Sioux River Basin Structure on Topeka Shiner Streams: Impacted Stream Length 0.687%, Non-Impacted Stream Length 99.313%


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