CaliPopGen: A genetic and life history database for the fauna and flora of California

Nature Portfolio (Springer Nature) | July 5th, 2022

CaliPopGen is a database of population genetic data for native and naturalized eukaryotic species in California, USA. It summarizes the published literature (1985–2020)

CaliPopGen is a database of population genetic data for native and naturalized eukaryotic species in California, USA. It summarizes the published literature (1985–2020) for 5,453 unique populations with genetic data from more than 187,394 individuals and 448 species (513 species plus subspecies) across molecular markers including allozymes, RFLPs, mtDNA, microsatellites, nDNA, and SNPs. Terrestrial habitats accounted for the majority (46.4%) of the genetic data. Taxonomic groups with the greatest representation were Magnoliophyta (20.31%), Insecta (13.4%), and Actinopterygii (12.85%). CaliPopGen also reports life-history data for most included species to enable analyses of the drivers of genetic diversity across the state. The large number of populations and wide taxonomic breadth will facilitate explorations of ecological patterns and processes across the varied geography of California. CaliPopGen covers all terrestrial and marine ecoregions of California and has a greater density of species and georeferenced populations than any previously published population genetic database. It is thus uniquely suited to inform conservation management at the regional and state levels across taxonomic groups.

Central Valley Flood Protection Plan Appendix K. Synthesis of Fish Migration Improvement Opportunities in the Central Valley Flood System

California Department of Water Resources (DWR) | July 14th, 2016

Many instream structures in the Central Valley adversely affect native anadromous fish migration. These structures, often referred to as fish passage barriers, reduce or

Many instream structures in the Central Valley adversely affect native anadromous fish migration. These structures, often referred to as fish passage barriers, reduce or eliminate longitudinal habitat connectivity; prevent or limit access to critical spawning, rearing, and refuge habitat; create migration delays; and create lethal or sublethal conditions for native anadromous species (California Department of Water Resources [DWR] 2012a, 2014; National Marine Fisheries Service [NMFS] 2014). Fish passage barriers associated with the Central Valley flood system trigger compliance requirements under the federal and California Endangered Species Acts; necessitate recurring fish rescues; and impel additional permitting requirements, such as long-term mitigation (NMFS 2009; Vogel 2011; DWR 2012b; Johnson and Vincik 2012; Cannon 2013; Heise 2013; Hendrick and Swart 2013).  Identification of migration impediments and associated improvement opportunities in the flood system is needed for integrated flood management planning. Fish migration improvements can be integrated into flood risk reduction projects1 to yield cost efficiencies in the project planning and implementation phases, and they may result in long-term economic and environmental benefits (DWR 2014). Two documents, the Fish Passage Assessment (Attachment 9C of the Central Valley Flood Protection Plan [CVFPP]) and the Draft Central Valley Flood System Fish Migration Improvement Opportunities (FMIO) report have been prepared to assist in identifying and prioritizing fish migration improvement opportunities in the flood system. 

Central Valley Flood Protection Plan Conservation Strategy 2022 Update

California Department of Water Resources (DWR) | November 4th, 2022

The Central Valley Flood Protection Plan (CVFPP) Conservation Strategy (Conservation Strategy or Strategy) is a primary component of the CVFPP in accordance with the Cent

The Central Valley Flood Protection Plan (CVFPP) Conservation Strategy (Conservation Strategy or Strategy) is a primary component of the CVFPP in accordance with the Central Valley Flood Protection Act of 2008. It aligns with and contributes to the attainment of all CVFPP goals, while focusing on improving ecosystem quality, quantity, function, and sustainability within the Systemwide Planning Area (SPA). Its purpose is to provide actionable and measurable targets to improve riverine, aquatic, wetland, and riparian habitat in the flood system through the integration of ecological principles with flood risk reduction projects, operation and maintenance activities, institutional support, and other means (e.g., the remediation of fish passage barriers). The Conservation Strategy also provides data, information, and guidance to floodplain managers to assist in the development of multi-benefit flood infrastructure improvement projects by integrating project components and management strategies that benefit native species and their habitats.

Central Valley Flood Protection Plan: Conservation Strategy

California Department of Water Resources (DWR) | August 8th, 2017

In the Central Valley of California, flood risks, water supplies, and the functioning of ecosystems are linked, with actions in one area affecting the other areas. The ma

In the Central Valley of California, flood risks, water supplies, and the functioning of ecosystems are linked, with actions in one area affecting the other areas. The majority of flows that pass through the State Plan of Flood Control (SPFC) are regulated by reservoirs operated for flood management, water supply, water quality, power generation, wildlife and fisheries habitat, and recreation. Similarly, the system of river and bypass channels, levees, and water control structures in the Central Valley does more than just contain floodwaters that previously flooded the valley floor for months at a time. It supports agricultural uses in the bypasses, serves as valued recreational areas and open space, helps in the management of surface water supplies and management of groundwater and water quality, and provides critical remnant riparian and floodplain habitats for numerous fish and wildlife species. The Central Valley Flood Protection Plan (CVFPP) recognizes these interconnections in its approach to flood management. The CVFPP is a long-term planning document that provides a framework for prioritization of investments in the SPFC. It seeks to improve flood risk management (the primary goal), as well as improve operations and maintenance (O&M), promote ecosystem functions, improve institutional support, and promote multi-benefit projects where feasible (supporting goals) (California Department of Water Resources [DWR] 2012a). This Conservation Strategy (or Strategy) is an integral part of the CVFPP. It supports the attainment of all CVFPP goals, but focuses on the improvement of ecosystem functions through the integration of ecological restoration with flood risk reduction projects where feasible. This Conservation Strategy, including Appendices A-L, describes the basis for recommending various conservation actions and setting long-term objectives for the Central Valley flood management system as a whole. The integration of specific environmental restoration features with DWR’s proposed flood management system improvements is summarized in Chapters 2 and 3 of the CVFPP and will also be described further in the 2017 CVFPP update and supporting documents, such as the Sacramento River Basin-Wide Feasibility Study (BWFS) and the San Joaquin River BWFS. The Conservation Strategy and CVFPP as a whole would contribute to achieving the California Water Action Plan’s overarching goals of  reliability, restoration, and resilience (California Natural Resources Agency, California Department of Food and Agriculture, and California Environmental Protection Agency 2015, 2016). In particular, this Strategy and the CVFPP as a whole are integral to three of the 10 “key actions” identified in the California Water Action Plan: Increase flood protection. Protect and restore important ecosystems. Increase operational and regulatory efficiency. Note: This document has extensive appendices and errata. Appendix A: Regulatory Setting, Appendix B: Advance Mitigation; Appendix C: Description of Construction Activities for Structural Modifications; Appendix D: Vegetation Management Strategy; Appendix E: Invasive Plant Management Plan; Appendix F: Existing Conditions; Appendix G: Identification of Target Species and Focussed Conservation Plans; Appendix H: Central Valley Chinook Salmon Rearing Habitat Needed to Satisfy the Anadromous Fish Restoration Program (AFRP) Doubling Goal; Appendix I: Floodplain Restoration Opportunities Analysis; Appendix J: Existing Conservation Objectives from other Plans; Appendix K: Synthesis of Fish Migration Improvement Opportunities in the Central Valley Flood System; Appendix L: Measurable Objectives Development - Summary of Conservation Needs and Scale of Restoration Opportunities; 2016 CVFPP Conservation Strategy: Errata; Conservation Strategy Development Process Overview

Central Valley Project Improvement Act Implementation Plan For Fish Programs

U.S. Bureau of Reclamation (USBR) | July 20th, 2015

The purpose of this Plan is to describe the approach for prioritizing and implementing the anadromous fish-related provisions under the CVPIA over the next 5-10 years. Th

The purpose of this Plan is to describe the approach for prioritizing and implementing the anadromous fish-related provisions under the CVPIA over the next 5-10 years. This Plan will build upon the Final Restoration Plan (FRP, USFWS 2001) to integrate a decision-making framework across all programs with the goal of making all reasonable efforts to at least double natural production of anadromous fish in California’s Central Valley on a long-term, sustainable basis. The Plan develops an annual process for setting priorities and funding projects across CVPIA fish-related provisions and watersheds in the Central Valley. The new process uses an Adaptive Resource Management (ARM) approach with support from Decision-Support Models (DSMs) to prioritize implementation of management actions that have the highest probability of achieving biological objectives for wild populations of native anadromous fish. The ARM approach will also guide plans for monitoring and research by synthesizing existing monitoring data, annually updating DSMs using new information, and estimating the value of new information to the decision making process.

Central Valley Project: Issues and Legislation

Congressional Research Service (CRS) | November 25th, 2019

Challenges Facing the Sacramento-San Joaquin Delta: Complex, Chaotic, or Simply Cantankerous?

Delta Stewardship Council (Delta Council) | April 9th, 2015

In 2014, the California Natural Resources Agency and the U.S. Department of the Interior asked the authors of this paper, as four former leaders of The Delta Science Prog

In 2014, the California Natural Resources Agency and the U.S. Department of the Interior asked the authors of this paper, as four former leaders of The Delta Science Program, to summarize the challenges faced by water supply and ecological resource managers in this critically important region of Northern California. They concluded that the challenges are so complex as to meet the definition of a “wicked” problem. Such problems can’t be ignored, defy straightforward characterization, and have no simple solutions. Yet they must be actively managed to maximize beneficial and minimize adverse outcomes. In this context, the following paper calls for Delta management to become more nimble and better coordinated.

Changes in Riparian Vegetation in the Southwestern United States: Historical Changes along the Mojave River, California

U.S. Geological Survey (USGS) | January 31st, 2001

Changing ecosystems: a brief ecological history of the Delta

University of California, Davis (UC Davis) | February 15th, 2010

The San Francisco Estuary is a young estuary, about 6-10,000 years old in its present location. It became established during periods of high climatic variability (reflect

The San Francisco Estuary is a young estuary, about 6-10,000 years old in its present location. It became established during periods of high climatic variability (reflected in extreme floods and long droughts) compared to the relatively stable past 150 years. The Delta was formed as a huge freshwater marsh through the interaction of river inflow and the slow rise of sea level with the growth and decay of tules and other plants. This interaction resulted in the deposition of large amounts of organic matter, creating layers of peat that kept pace with sea level rise. These peat layers formed the soils of most of the present Delta ‘islands’, which were actually complex patches of floodable marsh. The channels among the islands were historically shifting, winding distributaries of the entering rivers that moved inflowing water through the Delta, providing access to upstream areas for large runs of migratory fish. The movement and quality of water in these channels was strongly affected by tidal action.  These attributes also created a complex of diverse and shifting habitats that supported a wide variety of functions for an ecological system in which there was no clear separation between aquatic and terrestrial components.

Characterization of brominated, chlorinated, and phosphate flame retardants in San Francisco Bay, an urban estuary

Science of the Total Environment (Elsevier) | February 20th, 2019

Flame retardant chemical additives are incorporated into consumer goods to meet flammability standards, and many have been detected in environmental matrices. A uniquely

Flame retardant chemical additives are incorporated into consumer goods to meet flammability standards, and many have been detected in environmental matrices. A uniquely wide-ranging characterization of flame retardants was conducted, including polybrominated diphenyl ethers (PBDEs) and 52 additional brominated, chlorinated, or phosphate analytes, in water, sediment, bivalves, and harbor seal blubber of San Francisco Bay, a highly urbanized estuary once considered a hot spot for PBDE contamination. Among brominated flame retardants, PBDEs remained the dominant contaminants in all matrices, though declines have been observed over the last decade following their phase-out. Hexabromocyclododecane (HBCD) and other hydrophobic, brominated flame retardants were commonly detected at lower levels than PBDEs in sediment and tissue matrices. Dechlorane Plus (DP) and related chlorinated compounds were also detected at lower levels or not at all across all matrices. In contrast, phosphate flame retardants were widely detected in Bay water samples, with highest median concentrations in the order TCPP > TPhP > TBEP > TDCPP > TCEP. Concentrations in Bay water were often higher than in other estuarine and marine environments. Phosphate flame retardants were also widely detected in sediment, in the order TEHP > TCrP > TPhP > TDCPP > TBEP. Several were present in bivalves, with levels of TDCPP comparable to PBDEs. Only four phosphate flame retardants were detected in harbor seal blubber: TCPP, TDCPP, TCEP, and TPhP. Periodic, multi-matrix screening is recommended to track contaminant trends impacted by changes to flammability standards and manufacturing practices, with a particular focus on contaminants like TDCPP and TPhP that were found at levels comparable to thresholds for aquatic toxicity.