Examining the causes and consequences of hybridization during Chinook salmon reintroductions: using the San Joaquin River as a restoration case study of management options

University of California, Davis (UC Davis) | June 15th, 2014

Successful salmonid restoration efforts depend upon an understanding of the evolutionary processes that historically shaped population diversity, as well as the realities

Successful salmonid restoration efforts depend upon an understanding of the evolutionary processes that historically shaped population diversity, as well as the realities of currently available, altered river systems. Habitat alterations over the past century have dramatically changed the ecological forces that shaped salmonid speciation and evolution, bringing formerly separate and distinct populations into contact and in some cases leading to hybridization. Hybridization can threaten the genetic diversity within salmonid species and may affect the outcomes of restoration efforts. Here we use the San Joaquin River Restoration as a case study to discuss some of the genetic challenges of Chinook salmon restoration in a newly reopened habitat. We discuss a range of genetic management strategies—from passive reintroduction to tightly managed, active reintroduction—and the strengths and weaknesses of each approach.

Feather River Salmonid Habitat Improvement Project Proposed Mitigated Negative Declaration

California Department of Water Resources (DWR) | October 6th, 2022

An initial study/proposed mitigated negative declaration (IS/MND) has been prepared to assess the proposed project’s potential effects on the physical environment and t

An initial study/proposed mitigated negative declaration (IS/MND) has been prepared to assess the proposed project’s potential effects on the physical environment and the significance of those effects. Based on the analysis conducted in the IS, DWR has determined that the proposed project would not have any significant adverse effects on the environment because environmental commitments and mitigation measures would be implemented to reduce impacts to a less-than-significant level.

Final Environmental Assessment Sacramento River Winter-Run Chinook Salmon Management Measures for Fisheries Managed under the Pacific Coast Salmon Fishery Management Plan

National Marine Fisheries Service (NMFS) | March 1st, 2018

Fish Bulletin 133. Ecological Studies of The Sacramento-San Joaquin Estuary Part 1: Zooplankton, Zoobenthos, and Fishes of San Pablo and Suisun Bays, Zooplankton and Zoobenthos of the Delta

California Department of Fish and Wildlife (CDFW) | September 9th, 1965

The Sacramento and San Joaquin Rivers have a common estuary. These two streams meet in the center of California's central valley to form the Delta (Figure 1). A hundred y

The Sacramento and San Joaquin Rivers have a common estuary. These two streams meet in the center of California's central valley to form the Delta (Figure 1). A hundred years ago the Delta was an extensive tidal marsh, but it has been almost entirely reclaimed for agriculture. The Delta now includes about 738,000 acres of land and water, 700 miles of navigable channels, and 30 large, below sea level islands. About 39,000 acres are covered by water. Some Delta channels are edged with narrow stretches of intertidal marsh but most of them have steep banks of mud or are covered with large cobbles to prevent erosion. They vary in width from a few hundred feet to a mile and are seldom more than 30 to 40 feet deep. In some areas there are small "waste" islands that flood during high tides. These waste islands and levees that surround all Delta channels are covered with an assortment of emergent aquatic plants, grasses, forbs, shrubs, and trees. Water heading toward the sea from the Delta passes through Suisun Bay, which is merely the wide combination of the Sacramento and San Joaquin Rivers below the Delta. Thirty-six percent of Suisun Bay is flooded by less than 3 feet of water at mean lower-low tide, and at this stage about 3,000 acres of intertidal zone is exposed. Richard Painter (see p. 40) has included a map of the 6-foot contour. From Suisun Bay the water flows through the 6-mile long and up to 100 feet deep Carquinez Strait into San Pablo Bay. Almost 60 percent of San Pablo Bay's 73,000 acres is less than 6 feet deep at mean lower-low tide. San Pablo Bay has a much more extensive intertidal area than Suisun Bay. San Pablo Bay water flows into San Francisco Bay and then through the narrow Golden Gate into the Pacific Ocean. The investigations reported on in this bulletin were geographically limited to the upper and middle portions of the estuary—from the Delta through San Pablo Bay. We have not investigated below San Pablo Bay. McCarty et al (1962) described south San Francisco Bay, and Storrs, Selleck, and Pearson (1964) described north San Francisco Bay. Gillian (1957) wrote an interesting and useful popular account of the entire bay.

Fish Collections and Secondary Louver Efficiency at the Tracy Fish Collection Facility: October 1993 to September 1995

U.S. Bureau of Reclamation (USBR) | May 29th, 1998

Fish Restoration Program Agreement Implementation Strategy for Habitat Restoration and Other Actions for Listed Delta Fish

California Department of Water Resources (DWR) | March 6th, 2012

The Fish Restoration Program Agreement (FRPA) (Appendix A), between the Department of Fish and Game (DFG) and the Department of Water Resources (DWR), was signed on Octob

The Fish Restoration Program Agreement (FRPA) (Appendix A), between the Department of Fish and Game (DFG) and the Department of Water Resources (DWR), was signed on October 18, 2010. FRPA addresses specific habitat restoration requirements of the US Fish and Wildlife Service (USFWS) and National Marine Fisheries Service (NMFS) biological opinions (Biological Opinions) for State Water Project (SWP) and Central Valley Project (CVP) operations. FRPA is also intended to address the habitat requirements of the DFG Longfin Smelt Incidental Take Permit (ITP) for SWP Delta operations. The primary objective of the FRPA program is to implement the fish habitat restoration requirements and related actions of the Biological Opinions and the ITP in the Delta, Suisun Marsh, and Yolo Bypass and is focused on 8,000 acres of intertidal and associated subtidal habitat to benefit delta smelt, including 800 acres of mesohaline habitat to benefit longfin smelt, and a number of related actions for salmonids. DFG and DWR intend that habitat restoration actions implemented in compliance with the USFWS biological opinion that also meet the habitat restoration requirements of the ITP will operate to satisfy the acreage requirements of the ITP. The purpose of this Implementation Strategy is to describe the process by which DWR and DFG will implement the FRPA program, and to satisfy Section B of FRPA. Section B of FRPA requires DWR, with assistance from DFG, to develop an Implementation Schedule that will identify restoration actions, estimated costs, targeted acreage, and a timeline for DWR’s implementation of restoration actions to satisfy DWR’s obligations under the Biological Opinions and ITP. Appendix B lists the specific habitat restoration requirements of FRPA, the Biological Opinions, and the ITP that pertain to this program. This document lays out the strategy to address these requirements. In addition, DWR and DFG will complete the necessary environmental compliance documents to implement site specific habitat restoration projects; this may include tiering from existing programmatic documents where appropriate. Pursuant to FRPA, DFG will work cooperatively with and assist DWR in establishing the management and financial framework necessary to implement the FRPA program. DWR, with assistance from DFG, will begin a process to fund, plan, and implement actions, including aquatic habitat restoration to benefit delta smelt, longfin smelt, and winter-run and spring-run Chinook salmon (hereafter referred to as Covered Fish Species) to mitigate impacts to these species caused by the SWP Delta operations. Specifically, these actions include: • Delta Smelt Biological Opinion Reasonable and Prudent Alternative (RPA) Component 4; • NMFS Biological Opinion RPA Actions 1.2.6 and 1.6.2 in partnership with the US Bureau of Reclamation (Reclamation); • NMFS Biological Opinion RPA Action Suite 1.6 and 1.7. FRPA will not be lead, but will provide funding and technical support assistance only; • ITP Condition 7. DWR’s obligations focus on delta smelt, longfin smelt, and winter-run and spring-run salmon, and may also benefit steelhead, sturgeon, and other native fish species.

Fishes, Hydrology, and Ecology of the Klamath River Basin

National Academy of Sciences (NAS) | February 11th, 2008

The Klamath River basin in southern Oregon and northern California is the focus of a prominent conflict over competing uses for water in the American West. Management mea

The Klamath River basin in southern Oregon and northern California is the focus of a prominent conflict over competing uses for water in the American West. Management measures for the protection of threatened and endangered fish species in the basin that have left less water available for irrigation have increased tensions among farmers and other stakeholders and brought into question the scientific justification of these measures. Two National Research Council studies evaluate a series of federal scientific assessments and recommend scientifically justified approaches to the problem.

Floodplain farm fields provide novel rearing habitat for Chinook salmon

PLOS | June 7th, 2016

When inundated by floodwaters, river floodplains provide critical habitat for many species of fish and wildlife, but many river valleys have been extensively leveed and f

When inundated by floodwaters, river floodplains provide critical habitat for many species of fish and wildlife, but many river valleys have been extensively leveed and floodplain wetlands drained for flood control and agriculture. In the Central Valley of California, USA, where less than 5% of floodplain wetland habitats remain, a critical conservation question is how can farmland occupying the historical floodplains be better managed to improve benefits for native fish and wildlife. In this study fields on the Sacramento River floodplain were intentionally flooded after the autumn rice harvest to determine if they could provide shallow-water rearing habitat for Sacramento River fall-run Chinook salmon (Oncorhynchus tshawytscha). Approximately 10,000 juvenile fish (ca. 48 mm, 1.1 g) were reared on two hectares for six weeks (Feb-March) between the fall harvest and spring planting. A subsample of the fish were uniquely tagged to allow tracking of individual growth rates (average 0.76 mm/day) which were among the highest recorded in fresh water in California. Zooplankton sampled from the water column of the fields were compared to fish stomach contents. The primary prey was zooplankton in the order Cladocera, commonly called water fleas. The compatibility, on the same farm fields, of summer crop production and native fish habitat during winter demonstrates that land management combining agriculture with conservation ecology may benefit recovery of native fish species, such as endangered Chinook salmon.

Flow Augmentations Modify an Estuarine Prey Field

University of California, Davis (UC Davis) | June 15th, 2023

Franks Tract Futures

Delta Stewardship Council (Delta Council) | April 26th, 2022