SFEWS: Volume 19, Issue 3
In our September issue new research and commentary provide insights on several topics: how to integrate zooplankton science to inform estuary management; how simulated fishing can avoid missed fish and detect gear bias in the water; why juvenile Chinook Salmon length-at-date criteria don't match genetic run assignments; whether declines in breeding waterfowl population relate to wetland habitat and salinity; and what kinds of food web support can be achieved by use of a managed flow pulse.
Photo: Forster’s Terns at Crown Beach, public domain. Attribution: © Ingrid Taylar, Creative Commons 2.0 Generic license.
Catch as Catch Can
"Catchability" refers to the relationship between catch rate and the true population. Ecological monitoring programs use catch per unit of effort (CPUE) to standardize catch and monitor changes in fish populations; however, CPUE is proportional to the portion of the population that is vulnerable to the type of gear used in sampling, which is not necessarily the entire population. Tobais' simulation combines a module for sampling conditions with a module for individual fish behavior to estimate the proportion of available fish that would escape from the sample. The method is applied to the case study of the well monitored fish species Delta Smelt (Hypomesus transpacificus) in the San Francisco Estuary, where it has been hypothesized that changing water clarity may affect catchability for long-term monitoring studies.
Waterfowl Reproductive Success Depends on High Water, Low Salt
Availability of wetlands with low salinities during the breeding season can influence waterfowl reproductive success and population recruitment. Salinities as low as 2 ppt (3.6 mS/cm) can impair duckling growth and influence behavior, with mortality occurring above 9 ppt (14.8 mS/cm). Schacter et al. used satellite imagery to quantify the amount of available water, and sampled surface water salinity at Grizzly Island, in the brackish Suisun Marsh, at three time-periods during waterfowl breeding (April, May, July) over 4 years (2016–2019). Among their findings was during peak duckling production in May, 81%–95% of available water had salinity above 2 ppt, and 5%–21% was above 9 ppt. Local waterfowl populations would benefit from management practices that provide fresher water during peak duckling production in May and retain more water through July.
Deep Dives Among Waterbird Populations in South SF Bay
In south San Francisco Bay, former salt ponds now managed as wildlife habitat support large populations of breeding waterbirds. In 2006, the South Bay Salt Pond Restoration Project began the process of converting 50% to 90% of these managed pond habitats into tidal marsh. Hartman et al. compared waterbird populations in south San Francisco Bay before (2001) and after (2019) approximately 1,300 ha of managed ponds were breached to tidal action to begin tidal marsh restoration. Study results showed average annual nest abundance declined during 2017–2019 by 53%, 71%, and 36%, for American Avocets, Back-necked Stilts, and Forster’s Terns, respectively. All three species established nesting colonies on newly constructed islands within remaining managed ponds; however, these new colonies did not make up for the steep declines observed at other historical nesting sites. For future wetland restoration, retaining more managed ponds that contain islands suitable for nesting may help to limit further declines in breeding waterbird populations.
Managed Pulse Flows as Food Web Support
While freshwater inflow has been a major focus of resource management in estuaries, including the upper San Francisco Estuary, there is a growing interest in using focused flow actions to maximize benefits for specific regions, habitats, and species. To test this concept, in summer 2016, Frantzich et al. used a managed flow pulse to target an ecologically important region: a freshwater tidal slough called the Cache Slough Complex. Their goal was to improve estuarine habitat by increasing net flows through CSC to enhance downstream transport of lower trophic-level resources, an important driver for fishes such as the endangered Delta Smelt. Simulations using a 3-D hydrodynamic model (UnTRIM) indicated that the managed flow pulse had a large effect on the net flow of water through Yolo Bypass, and between the CSC and further downstream. The managed flow pulse resulted in increased densities of zooplankton (copepods, cladocerans) demonstrating potential advection from upper floodplain channels into the target CSC and Sacramento River regions. Though conducted during a single year, this study may provide an instructive example of how a relatively modest change in net flows can generate measurable changes in ecologically relevant metrics, and how an adaptive management action can help inform resource management.
Length-at-Date Criteria and Genetic Run Assignments
Four distinct runs of Central Valley Chinook Salmon are named after their primary adult return times: fall, late-fall, winter, and spring run. Estimating the run-specific composition of juveniles entering and leaving the Sacramento–San Joaquin Delta is crucial for assessing population status and processes that affect juvenile survival through the Delta. Historically, the run of juvenile Chinook Salmon captured in the field has been determined using a length-at-date criteria (LDC); however, LDC run assignments may be inaccurate if there is high overlap in the run-specific timing and size of juveniles entering and leaving the Delta. In this study, Brandes et al. use genetic run assignments to assess the accuracy of LDC at two trawl locations in the Sacramento River (Delta entry) and at Chipps Island (Delta exit).Across years, there was extensive overlap among the distributions of run-specific fork lengths of genetically identified juveniles, indicating that run compositions based on LDC assignments would tend to underestimate fall-run and especially late-fall-run compositions at both trawl locations, and greatly overestimate spring-run compositions (both locations) and winter-run compositions (Chipps Island). We therefore strongly support ongoing efforts to include tissue sampling and genetic run identification of juvenile Chinook Salmon at key monitoring locations in the Sacramento–San Joaquin River system.
Pelagic fish in the San Francisco Estuary are harder to catch in recent decades. Over the past thirty years, Delta Smelt catch in the Fall Midwater Trawl Survey has declined by 99%, Longfin Smelt catch has declined by over 95%, and even the notoriously hardy Striped Bass have declined by over 75%. To manage the system and reverse these declines, we need a better understanding of the “bottom-up” processes that exert control on these populations—we need to study fish food. In other words, in addition to studying fish directly, we need to increase our understanding of what pelagic fish eat: zooplankton. In this essay, Hartman et al. break down not only what fish eat (zooplankton) and why they are important drivers of species abundance in higher trophic areas of the food web, but also how scientists and natural resources managers can communicate better to understand which zooplankton data can inform and develop management-relevant questions.
Volume 15, Issue 1, 2017
Central Valley Joint Venture Special Issue
Despite massive losses of habitat, the Central Valley’s wetlands, riparian forests, and grassland–oak savannah woodlands still provide some of the most important bird habitat in North America. Nearly three million ducks, two million geese, and 350,000 shorebirds continue to overwinter in this region (Shuford et al. 1998; Olson 2014), making the Central Valley an internationally important area for migratory waterbirds in the Pacific Flyway. Prioritization of conservation actions in the Central Valley for these waterbirds and landbirds is a critical step toward increasing their populations.
Papers in this special issue address the challenges of setting conservation objectives for birds in California’s Central Valley. These papers use the best available science and local data to set objectives in a manner that is transparent, well-documented, and repeatable.
A Bioenergetics Approach to Setting Conservation Objectives for Non-Breeding Shorebirds in California’s Central Valley
An extensive network of managed wetlands and flooded agriculture provides habitat for migrating and wintering shorebirds in California’s Central Valley. Yet with over 90% of historical wetlands in the region lost, Central Valley shorebird populations are likely diminished and limited by available habitat. To identify the timing and magnitude of any habitat limitations during the non-breeding season, we developed a bioenergetics model that examined whether currently available shorebird foraging habitat is sufficient to meet the daily energy requirements of the shorebird community, at either the baseline population size surveyed from 1992 to 1995 or double this size, which we defined as our long-term (100-year) population objectives. Using recent estimates of the extent of managed wetlands and flooded agriculture, satellite imagery of surface water, energy content of benthic invertebrates, and shorebird metabolic rates, we estimated that shorebird foraging habitat in the Central Valley is currently limited during the fall. If the population sizes were doubled, we estimated substantial energy shortfalls in the fall (late July–September) and spring (mid-March–April) totaling 4.02 billion kJ (95% CI: 2.23–5.83) and 7.79 billion kJ (2.00–14.14), respectively. We then estimated long-term habitat objectives as the minimum additional shorebird foraging habitat required to eliminate these energy shortfalls; the corresponding short-term (10-year) habitat objectives are to maintain an additional 2,160 ha (5,337 ac) of shallow (<10 cm) open water area in the fall and 4,692 ha (11,594 ac) in the spring. Because the Central Valley is one of the most important regions in the Pacific Flyway for migrating and wintering shorebirds, we expect that achieving these habitat objectives will benefit shorebirds well beyond the Central Valley. Our bioenergetics approach provides a transparent, repeatable process for identifying the timing and magnitude of habitat limitations as well as the most efficient strategies for achieving conservation objectives.
- 2 supplemental PDFs
The Central Valley of California provides important breeding habitat to numerous species of wetland-dependent birds, despite the loss of over 90% of naturally occurring wetlands. A majority of shorebirds breeding in this region rely on shallow-flooded habitat adjacent to sparsely vegetated uplands as provided by rice (Oryza sativa), managed wetlands, and other habitats. We estimated the current extent of potential breeding shorebird habitat provided by rice and managed permanent and semi-permanent wetlands in each of four major planning regions of the Central Valley, and estimated the average breeding densities and current population sizes of two species of shorebirds: the Black-Necked Stilt (Himantopus mexicanus) and American Avocet (Recurvirostra americana). Using a population status framework based on principles of conservation biology, we estimated that stilt populations are small (<10,000 individuals) or very small (<1,000 individuals) in three of the four planning regions, and avocet populations are small or very small in all four planning regions. We then used the framework to define long-term (100-year) population objectives for stilts, avocets, and a third species, Killdeer (Charadrius vociferous), designed to meet our long-term conservation goal of supporting self-sustaining, genetically robust, and resilient populations of breeding shorebirds in the Central Valley. We also estimated the long-term species’ density and wetland habitat objectives necessary to achieve the population objectives for all three species. The corresponding short-term (10-year) conservation objectives are to restore semi-permanent wetlands to provide an additional 11,537 ha (28,508 ac) of habitat for breeding shorebirds (by planning region: 2,842 ha in Sacramento, 2,897 ha in Yolo–Delta, 2,943 ha in San Joaquin, and 2,855 ha in Tulare), and to enhance existing habitat to support density objectives. Our approach provides a transparent, repeatable process for defining science-based conservation objectives for breeding shorebirds and their habitats in the Central Valley, which can help unite stakeholders around common goals and motivate conservation actions.
Birds associated with wetlands have declined historically across North America from extensive habitat loss and degradation. Among the regions most affected is California’s Central Valley, where over 90% of the wetland base has been lost. Still, this region remains of continental importance to waterbirds. On-the-ground conservation efforts for all bird groups are the focus of the Central Valley Joint Venture, guided by a periodically updated implementation plan. To track progress toward goal attainment, that plan sets time-bound, quantitative conservation goals. Lacking robust data on the size and trends of populations of most species of waterbirds in the Central Valley, we set conservation goals for this group by selecting 10 focal species. These species are of heightened conservation concern or are otherwise representative of the habitat needs of Central Valley waterbirds. Given the great loss of historical habitat, we assumed focal species populations have declined by ≥ 50%. Hence, we defined population objectives for most focal species as increasing their current populations by 10% over 10 years and doubling them in 100 years. The corresponding habitat objectives are to increase wetlands or enhance suitable crops for waterbirds in proportion to the population objectives. These include an increase over 10 years of 7,948 ha (19,641 acres) of winter seasonal wetlands, 921 ha (2,276 acres) each of semi-permanent and summer seasonal wetlands, and 573 ha (1,416 acres) of strategically placed riparian forest. Agricultural needs include additional winter flooding of 15,160 ha (37,461 acres) of rice and 2,137 ha (5,281 acres) of corn. We distributed the habitat objectives across five planning regions, in some cases favoring proportionally larger increases in those regions with the greatest need. To maximize success, however, conservationists must take into account the specific needs of individual waterbird species, as a one-size-fits-all approach will not support the highest diversity of waterbirds.
Population and Habitat Objectives for Avian Conservation in California's Central Valley Riparian Ecosystems
Riparian ecosystems provide important ecosystem services and recreational opportunities for people, and habitat for wildlife. In California’s Central Valley, government agencies and private organizations are working together to protect and restore riparian ecosystems, and the Central Valley Joint Venture provides leadership in the formulation of goals and objectives for avian conservation in riparian ecosystems. We defined a long-term conservation goal as the establishment of riparian ecosystems that provide sufficient habitat to support genetically robust, self-sustaining, and resilient bird populations. To achieve this goal, we selected a suite of 12 breeding riparian landbird focal species as indicators of the state of riparian ecosystems in each of four major Central Valley planning regions. Using recent bird survey data, we estimated that over half of the regional focal species populations are currently small (< 10,000) and may be vulnerable to extirpation, and two species have steeply declining population trends. For each focal species in each region, we defined long-term (100-year) population objectives that are intended to be conservation endpoints that we expect to meet the goal of genetically robust, self-sustaining, and resilient populations. We then estimated the long-term species density and riparian restoration objectives required to achieve the long-term population objectives. To track progress toward the long-term objectives, we propose short-term (10- year) objectives, including the addition of 12,919 ha (31,923 ac) of riparian vegetation in the Central Valley (by planning region: 3,390 ha in Sacramento, 2,390 ha in Yolo–Delta, 3,386 ha in San Joaquin, and 3,753 ha in Tulare). We expect that reaching these population, density, and habitat objectives through threat abatement, habitat restoration, and habitat enhancement will result in improvements to riparian ecosystem function and resilience that will benefit other wildlife populations and the people of the Central Valley and beyond.
- 2 supplemental PDFs
Population and Habitat Objectives for Avian Conservation in California’s Central Valley Grassland–Oak Savannah Ecosystems
In California’s Central Valley, grassland and oak savannah ecosystems provide multiple economic and social benefits, ecosystem services, and vital bird habitat. There is a growing interest in protecting, restoring, and managing these ecosystems, and the Central Valley Joint Venture (CVJV) provides leadership in the formulation of conservation goals and objectives. We defined a long-term goal of protecting, restoring, and managing Central Valley grassland and oak savannah ecosystems so that they are capable of supporting genetically robust, self-sustaining, and resilient wildlife populations. To measure progress toward this goal, we selected a suite of 12 landbird focal species that primarily breed in grasslands and oak savannahs as indicators of the state of these ecosystems on the Central Valley floor (primary focus area) and in the Central Valley’s surrounding foothills (secondary focus area). Using data on current densities and habitat extent, we estimated that at least three of the focal species populations in the primary focus area and at least two of the focal species populations in the secondary focus area are currently small (<10,000 individuals) and may be vulnerable to extirpation. Furthermore, at least two species appear to have steeply declining population trends. We defined long-term (100-year) population objectives for each focal species that we expect to meet the goal of genetically robust, self-sustaining, and resilient populations. We then estimated corresponding short-term (10-year) habitat objectives of 4,183 ha of additional grassland and 3,433 ha of additional oak savannah that will be required to make progress toward the long-term objectives. We expect that habitat restoration and enhancement efforts aimed at reaching these long-term conservation objectives will result in improvements to the function of Central Valley grassland and oak savannah ecosystems.
- 1 supplemental PDF
Bird Species at Risk in California’s Central Valley: A Framework for Setting Conservation Objectives
Populations of many species of birds are declining worldwide from habitat loss and degradation and the effects of contamination, disease, and alien species. Effects have been great in California’s Central Valley from the loss of over 90% of its historical wetland and riparian habitats. Conservation initiatives at various geographic scales have ranged from protecting and restoring habitats or ecosystems for broad suites of species to ones identifying individual declining and vulnerable taxa and spurring actions to halt or reverse their population declines. In taking the first approach, the Central Valley Joint Venture initially focused on restoring habitats and populations of wintering and breeding waterfowl but currently promotes the conservation of all birds. This joint venture is setting population and habitat objectives for seven taxonomic or habitat bird groups, but to date little attention has been paid to at-risk species of particular conservation concern. We identified 38 at-risk species, subspecies, or distinct populations of birds that warrant heightened conservation efforts in the Central Valley. At-risk birds are unevenly distributed among subregions and habitat types in this valley, but most face the primary threat of habitat loss and degradation. The treatment of at-risk species varies greatly among the seven bird groups considered by the joint venture, and, overall, conservation objectives are not addressed specifically for 50% of the region’s at-risk taxa, though some surely benefit from objectives set for other groups. To adequately treat at-risk species, we recommend a framework for setting conservation objectives that evaluates assumptions about limiting factors, considers objectives already set for threatened and endangered species, assesses whether objectives set for other groups or focal species meet the needs of at-risk species lacking such objectives, establishes objectives for at-risk species for habitats or seasons not currently considered, and highlights information gaps to be filled to effectively set new or refined objectives.
Quantitative population objectives are necessary to successfully achieve conservation goals of secure or robust wildlife populations. However, existing methods for setting quantitative population objectives commonly require extensive species-specific population viability data, which are often unavailable or are based on estimates of historical population sizes, which may no longer represent feasible objectives. Conservation practitioners require an alternative, science-based method for setting long-term quantitative population objectives. We reviewed conservation biology literature to develop a general conceptual framework that represents conservation biology principles and identifies key milestones a population would be expected to pass in the process of becoming a recovered or robust population. We then synthesized recent research to propose general hypotheses for the orders of magnitude at which most populations would be expected to reach each milestone. The framework is structured as a hierarchy of four population sizes, ranging from very small populations at increased risk of inbreeding depression and extirpation (< 1,000 adults) to large populations with minimized risk of extirpation (> 50,000 adults), along with additional modifiers describing steeply declining and resilient populations. We also discuss the temporal and geographic scales at which this framework should be applied. To illustrate the application of this framework to conservation planning, we outline our use of the framework to set long-term population objectives for a multi-species regional conservation plan, and discuss additional considerations in applying this framework to other systems. This general framework provides a transparent, science-based method by which conservation practitioners and stakeholders can agree on long-term population objectives of an appropriate magnitude, particularly when the alternative approaches are not feasible. With initial population objectives determined, long-term conservation planning and implementation can get underway, while further refinement of the objectives still remains possible as the population’s response to conservation effort is monitored and new data become available.