Biology Manual

Oregon Department of Transportation

Prepared for


Prepared by

Mason, Bruce & Girard, Inc.

707 SW Washington Street, Suite 1300

Portland, Oregon97205

(503) 224-3445

June 30, 2009

MB&G Project Number: 010526

TABLE OF CONTENTS

I.Introduction

A.Purpose of Manual

B.Using the Manual

II.Project Delivery Lifecycle

A.Introduction

B.Planning

C.STIP Project Lifecycle

D.Maintenance

E.Miscellaneous

III.Aquatic Resources

A.Relevant Laws

B.Protected Species and Habitat

C.Process for Evaluating Aquatic Resources

D.Documents

E.Hot topics

IV.Wildlife Resources

A.Relevant Laws

B.Protected Species and Habitat

C.Process for Evaluating Wildlife Resources

D.Documents

E.Hot topics

V.Botanical Resources

A.Relevant Laws

B.Protected Species and Habitat

C.Process for Evaluating Botanical Resources

D.Documents

E.Hot topics

VI.Miscellaneous

A.Using Consultants

B.Links to other Disciplines’ Manuals

C.Safety Issues

D.Using the Project Spreadsheet

ODOT Biology Manual1

Tables

Table 1.Project Lifecycle Stages and Milestones...... 2

Table 2.Program Development Tasks and Descriptions...... 3

Table 3.Project Development Milestones and Tasks...... 5

Table 4.Project Delivery Team Members...... 7

Table 5.Project Team Member Responsibilities...... 8

Table 6.Construction Award Milestones and Tasks...... 8

Table 7.Construction Management Milestones and Descriptions...... 9

Table 8.Tasks to be Completed Before Onsite Work Begins...... 10

Table 9.NEPA Project Classifications and Descriptions...... 11

Table 10.List of CETAS Member Agencies...... 12

Table 11.List of Key STIP Participants...... 14

Table 12.Types of Modernization Projects...... 15

Table 13.Types of Preservation Projects...... 16

Table 14.Operations Sub-Programs and Types of Projects...... 16

Table15.Types of Bridge Projects...... 17

Table 16.List of Five STIP Safety Programs...... 17

Table 17.Types of Projects Included under the Safety Program...... 17

Table 18.Types of Special Programs...... 18

Table 19.List and Description of Maintenance Programs...... 19

Table 20.OTIA III Bridge Delivery Program Goals...... 21

Table 21.List of Elements Included in a Scoping Report...... 22

Table 22.ODOT Biologists Role during the Scoping Phase of a Project...... 23

Table 23.List of Elements in the Project Prospectus...... 23

Table 24.Role of the ODOT Biologistduring the Preliminary Plans Phase of a Project...... 25

Table 25.Role of the ODOT Biologists during the Advance Plans Phase of a Project...... 25

Table 26.Role of the ODOT Biologists during the Final Plans (PS&E) Phase of a Project...... 26

Table27.Role of the ODOT Biologists during the Pre-Construction Meeting for a Project...... 27

Table 28.Role of the ODOT Biologists during the Construction Phase of a Project...... 28

Table 29.List of Maintenance Activities addressed in the Blue Book...... 28

Table 30.Regulatory Liaison Agencies and positions...... 34

Table 31.Liaison Contact Examples...... 35

Table 32.No Effect Memorandum Scenarios...... 35

Table 33.Outline of NLAA Submittal Process...... 37

Table 34.Outline of NLAA Submittal Process...... 39

Table 35.Overview of ODFW Fish Passage...... 40

Table 36.Activities Requiring NOAA Fisheries Engineer Review and Approval...... 41

Table 37.Mitigation Banking Program Goals...... 43

Table 38.Biology-related Standard Specifications...... 46

Table 39.USFWS Candidate Wildlife Species...... 48

Table 40.List of Wildlife Survey Protocols...... 50

Table 41.Regulatory Liaison Agencies and positions...... 52

Table 42.Liaison Contact Examples...... 52

Table 43.No Effect Memorandum Scenarios...... 53

Table 44.Outline of NLAA Submittal Process...... 55

Table 45.Outline of LAA Submittal Process...... 55

Table 46.Biology-related Standard Specifications...... 59

Table 47.USFWS Candidate Botanical Species...... 62

Table 48.ODA Noxious Weed Control Program Goals...... 63

Table 49.ODA Noxious Weed Classification system...... 63

Table 50.Types of Botanical Survey Methodologies...... 65

Table 51.Regulatory Liaison Agencies and positions...... 66

Table 52.Liaison Contact Examples...... 67

Table 53.No Effect Memorandum Scenarios...... 67

Table 54.Outline of NLAA Submittal Process...... 69

Table 55.Outline of LAA Submittal Process...... 69

Table 56.Biology-related Standard Specifications...... 74

Table 57.Safety Training Opportunities...... 76

ODOT Biology Manual1

I.Introduction

A.Purpose of Manual

The ODOT Biology Manual (Manual) is a technical resource that presents biological information,policies,and procedures relevant to transportation projects. The Manual is designed to serve as a consolidated reference for the myriad of tasks undertaken by the ODOT Biology Program staff. The ODOT Biology Program is responsible for leading the compliance effort for federal, state, and local laws and ODOT policies that pertain to aquatic species, terrestrial species, and ecological systems during all phases of ODOT-managed transportation maintenance and construction activities. The Biology Program also fosters the conservation and enhancement of aquatic- and land-based biological resources during construction and maintenance of the state highway system.The Biologists that serve in each ODOT region play an integral rolein carrying out this mission, and this Manual was developed with their needs in mind. However, this compendium will also be useful to other ODOT staff with biology-related questions.

Information on state and federal environmental regulations and key ODOT policies is provided to aid staff in complying with the broad array of relevant mandates. The Manual can also be used as a starting point for research on a variety of biological issues, techniques, andspecies. For new staff, the Manual provides guidance on the Biologist’s role in the ODOT project development process and maintenance operation. Biology Program standards and procedures for fieldwork and the preparation of environmental compliance documents are also addressed. The Biology Manual is intended to be used in conjunction with other ODOT guidance documents, such as the ESA Guidance Manual and the Water Resources Manual. Links are provided throughout the Manual for the user to easily access relevant ODOT publications and other recommended sources of in-depth information.

B.Using the Manual

The following sections of this Manualprovide a discussion of the different subject areas that an ODOT Biologist needs to be familiar with in order to adequately perform their assigned duties. The Manual has four main sections: Project Delivery Lifecycle; Aquatic Resources; Wildlife Resources; and Botanical Resources. A fifth miscellaneous section addresses working with consultants, safety issues, other ODOT discipline resources, and the use of the Biology Program project spreadsheet.

The Manual also includes a Project Milestone Timeline that can be used as a quick reference for biologists. This Timeline presents when topics and deliverables discussed in the Manual need to be addressed during a project’s lifecycle.

Project Milestone Timeline

The ODOT Biology Manual is a living document that is revised on a regular basis to account for new information and policies. ODOT strives to keep the Manual up to date; however, it does not guarantee that the contents represent the most current information available. The user bears the responsibility for verifying that actions taken to comply with laws are based on the most recent version of the applicable regulationsand agency policies.

A list ofAcronyms and Abbreviations is provided for the user’s reference.

II.Project Delivery Lifecycle

A.Introduction

The ODOT project deliverylifecycle is a complete business process that begins with planning and analysis of potential projects and ends when a project is constructed and transferred to maintenance. The process has four stages:

  1. Program Development
  2. Project Development
  3. Award Construction Contract
  4. Construction Management

Each stage has componentproducts and activities. Table 1 summarizes the primary milestones associated with each stage of the ODOT project delivery lifecycle. The stages are discussed in the sections that follow. For detailed information regarding the project delivery lifecycle, refer to the 2009 ODOT Project Delivery Guide.

Table 1. ODOT Project Delivery Lifecycle Stages and Milestones

Stage / Stage Milestones
Program Development /
  • Transportation Planning
  • Management Systems Analysis
  • Identify Potential Projects
  • Draft Scope, Schedule, Cost Estimate – Draft Statewide Transportation Improvement Program(STIP) (multiple projects)
  • Project Selection – Final STIP

Project Development /
  • Start Project
  • Survey, Maps, Engineering & Environmental Reports
  • Approved Design
  • Right of Way & Permits
  • Preliminary Plans for Construction (Preliminary Plans)
  • Final Plans & Special Provisions (Advance Plans)
  • Plans, Specifications & Estimates for Construction (PS&E)

Award Construction Contract /
  • Advertise & Bid Opening for Design / Bid / Build
  • Award Contract

Construction Management /
  • Before On-Site Work Begins
  • On-Site Work Begins
  • On-Site Work Completed
  • Acceptance of Project
  • Transition to Maintenance

Source:ODOT Project Delivery Guide (2009)available at .

The descriptions of Program Development, Project Development, Award Construction Contract, and Construction Management in this section provide a general overview of these stages. Section C (STIP Project Lifecycle) will revisit these stages with a focus on the specific roles and responsibilities of the ODOT Biologist.

1.Program Development

Program development is whereODOT projects are created, beginning with transportation planning that identifies needs at the state and local levels. As these needs are revealed and explored, projects are born.

ODOT program development occurs on a two year budget cycle that culminates in the preparation of a list of prioritized major projects and programs known as the Statewide Transportation Improvement Program (STIP).The cycle ends (and begins anew) when the Oregon Transportation Commission and FHWA approve the biennial STIP. Identifying and planning for transportation needs is an ongoing process with periodic reviews.As shown in Table 1, program development has five major milestones, each with several processes and deliverables. Table 2presents a more detailed list and description of tasks associated with program development. Tasks that ODOT Biologists may be involved with are highlighted in red.

Table 2. Program Development Tasks and Descriptions

Program Development Tasks / Description
Assemble Scoping Team / The Project Leader (PL) will assemble the scoping team based on the resources assigned by the region. A broad-based, inter-disciplinary scoping team is needed so that the product of scoping truly considers all needs—from concept through maintenance, identifies critical issues and develops solutions.
Assemble Scoping Packets / The PL is responsible for assembling and distributing the scoping packets. A scoping packet provides basic information about the project. The packet will provide background information to the scoping team so the team can become familiar with the project and area.
Coordinate Scoping Trips / The scoping trip is a chance for the team to visit the project site and gather information that might not be available elsewhere.
Right-of-way and Utilities / Based on the preliminary project "footprint,” the assessment of the ROW impacts results in a cost estimate of land and damages.
Environmental1 / During the Draft STIP phase the Region Environmental Coordinator (REC) will participate in project scoping to provide a preliminary identification of possible environmental impacts:
  • ROW acquisition
  • Impacts on land use
  • Traffic patterns and flow
  • Wetlands
  • Streams
  • Water quality
  • Threatened and endangered species
  • Archeological and historical sites
  • Parks
  • Air
  • Noise
  • Energy
  • Hazmat sites
  • Visual resources
The REC will document this information in the draft Project Prospectus Part 3.
Access Management / Access management is a comprehensive approach to the management and regulation of driveways, medians, median openings, traffic signals, and freeway interchanges. During the Draft STIP phase a preliminary identification of possible access management impacts must be documented in order to complete the required deliverables.
Mobility / Mobility is best defined as the ease with which people and goods move throughout their community, state, and world. During project scoping the project team needs to consider the impacts on mobility and if a Transportation Management Plan needs to be developed for the project.
Develop Scoping Trip Notes and Environmental Reports / After completing the scoping trips and compiling the information, the Project Leader will need to complete the STIP Scoping Summary Report. The STIP Scoping Summary Report is broken down into six parts:
  • Project Scope of Work
  • Project Cost Estimate
  • Project Schedule
  • Project Approval
  • STIP Supporting Documentation
  • STIP Scoping Team

Develop the Project Prospectus1 / The Project Prospectus begins the process of prioritizing projects for the STIP.
Draft Public Involvement Plan / As stewards of the public trust, it is critical that ODOT meaningfully engages and involves the public regarding issues that impact them directly and follow the letter and intent of laws requiring public input on project plans. The PL is responsible for developing a draft communications plan.
Draft Resource Recommendations / Region Managers (RM) and the Major Projects Branch (MPB) manager begin the delivery method selection for proposed projects during the normal STIP update process every two years. Selection of the delivery method is incorporated into the preliminary scoping process.
Draft Project Schedule / Project schedules must be initiated, developed and published to the Regional Managers at the initial scoping of the project. The PL must develop a draft project schedule.
Prepare Preliminary Engineering and Construction Estimate / Each project will need cost estimates developed for:
  • Preliminary Engineering (PE): includes all work necessary to prepare a project for contract bidding.
  • Construction: includes all work necessary to construct or build the project to its designed specifications, using appropriate construction methods and practices, while providing a safe environment for both the traveling public and workers throughout the project.

Prepare Intergovernmental Agreements / ODOT enters into agreements with the party (or parties) to outline responsibilities for the various phases of project development to be performed. The type of agreement or agreements will depend upon the work to be covered and the identity of the other party.

1These tasks will be discussed in further detail in the following sections.

Source:ODOT Project Delivery Guide (2009)available at .

ODOT Biologists are not involved in all program development stages or milestones. During program development, ODOT Biologists may only be involved in project scoping and preparation of the project prospectus, and only in cases where it is requested by the Region Environmental Coordinator (REC). As such, a Biologist’s involvement in these activities will be discussed in further detail in following sections.

2.Project Development

The majority of an ODOT Biologist’s responsibility and work load are associated with the project development stage of the project delivery lifecycle. Table 3 includes a list of project development milestones and tasks associated with each milestone. Tasks that ODOT Biologists may be involved with are highlighted in red.

Table 3. Project Development Milestones and Tasks

Project Development Milestones / Tasks
Project Initiation /
  • Obtain expenditure account
  • Assemble Project Team
  • Review and confirm project scope
  • Prepare roadway conceptual design
  • Prepare contracts
  • Prepare IGA
  • Prepare stakeholder participation and communication plan
  • Create a project Sharepoint
/
  • Prepare project team work plan,preliminary survey, and base mapping
  • Prepare hazardous materials corridor study
  • Prepare environmental baseline report
  • Identify work zone traffic issues
  • Prepare pavement design
  • Prepare traffic counts and preliminary traffic analysis

Design Acceptance Phase (DAP) /
  • Update public involvement plan
  • Prepare mobility strategy and traffic management plan
  • Prepare DAP roadway design
  • Prepare DAP access management
  • Prepare DAP Environmental Studies1
  • Prepare DAP traffic design
  • Prepare DAP Geo/Hydro design and studies
  • Bridge type size and location
/
  • Prepare DAP survey
  • Prepare DAP utility conflict list
  • Prepare DAP draft railroad maps
  • Prepare DAP draft right-of-way map
  • Prepare DAP value engineering study
  • Prepare DAP construction estimate
  • Prepare DAP construction schedule
  • Prepare DAP review and completion

Preliminary Plans /
  • Update stakeholder participation and communication plan
  • Prepare noise mitigation final design
  • Prepare access modification and closure letters
  • Prepare utility test-hole excavation
/
  • Prepare preliminary plans
  • Revise construction cost estimate
  • Revise construction schedule
  • Combine preliminary special provisions
  • Prepare preliminary plan review and completion

Advance Plans /
  • Prepare ROW map and descriptions
  • Acquire ROW
  • Obtain ROW certification
  • Review and approve utility relocation plans
/
  • Prepare advanced plans
  • Compile advance special provisions
  • Draft PS&E submittal checklist
  • Prepare advance plans review and completion

Final Plans /
  • Update public involvement plan
  • Access management
  • Prepare final plans
  • Prepare final construction cost estimate
/
  • Prepare final construction schedule
  • Compile final special provisions
  • Revise PS&E submittal checklist
  • Prepare final plan review and completion

Plans Specifications & Estimates /
  • Manage the exception letter

Closeout /
  • Prepare project transition
  • Prepare project archives
  • Document lessons learned

i.PDT Membership, Roles & Responsibilities

The Project Delivery Team (PDT) is the core unit that is tasked with delivery of a project that meets the project needs, is delivered on time, and is within budget. Table 4 includes a list of the members of a PDT. These teams are established for each project in the STIP to ensure that the appropriate technical issues are addressed in decision processes in a timely manner. The composition of this team will vary depending on the project and will be consistent with its size and complexity. The PDT is the appropriate group to establish project strategies, resolve project issues, and ensure informed consent from project participants and stakeholders.

Table 4. Project Delivery Team Members

Members of Project Delivery Team
ODOT Project Leader
ODOT Construction Project Manager, Assistant PM, Project Coordinator or designee
ODOT District or Area Maintenance Manager or designee
ODOT Roadway Engineering Designer or Design Team Leader
ODOT Region Environmental Coordinator or Environmental Project Manager (if applicable)
ODOT Bridge Engineering Designer or Design Team Leader (if structural design is needed)
ODOT Traffic Services Team Member
ODOT Region Right-of-Way Agent (if right-of-way or easements are needed)
ODOT Transportation Planner / Analyst (if major transportation alternative analysis is needed)
Other ODOT staff, as needed (i.e. Aviation, Bicycle / Pedestrian, Transit, Traffic Safety, Freight, Rail Crossing, Planning, etc)1
LocalCity and/or CountyPublic Works, Planning or Community Development Department representatives1
Other Federal, State or Local public agency representatives1

1 These members may be added to the Team at the discretion of the initial Project Team.