Monitoring in the San Francisco Estuary has fluctuated in sampling effort over time with changes to resources, objectives, and unforeseen events. I designed an approach to evaluate how reduced sampling would alter our ability to describe the status and trends of key species. This approach can evaluate the sensitivity of the estuary monitoring program to disruptions in sampling and whether sampling effort could be reduced without compromising the information provided by these surveys. I simulated reduced sampling on top of the historical data record (1985 – 2018) by selectively removing data and evaluating the impact on model inference. The same model structure is fit to the full dataset and several reduced datasets representing simulations of reduced sampling effort. Model predictions from reduced models are then compared to those from the full model to evaluate how reduced sampling may have affected our ability to detect key patterns in the data. In a case study, I applied this approach to Sacramento Splittail abundance trends from the Bay Study and the Suisun Marsh Fish Study otter trawls. Sampling reductions of 10 and 20% had fairly low impacts on the overlap of reduced model predictions with those from the full model. These results demonstrate the utility of my approach, but they are not generalizable beyond our ability to detect trends in Splittail abundance from Bay Study and Suisun Marsh Fish Study otter trawl data. A thorough analysis should run these simulations on multiple species and multiple parameters (e.g., abundance, distribution, length). By simulating sampling reductions on top of historical conditions, this approach could evaluate differential impacts in varying environmental or historical conditions (e.g., droughts, species declines, invasions). In addition, it can easily be extended to other functional groups (e.g., zooplankton, phytoplankton) as well as physical parameters (e.g., temperature, salinity, Secchi depth).

Evolutionary responses to opposing directions of natural selection include trade-offs, where the phenotype balances selective forces, and compensation, where other traits reduce the impact of one selective force. Zooplankton pigmentation protects from ultraviolet radiation (UVR) but attracts visual predators. This trade-off is understudied in the ocean where planktonic larvae in surface waters face ubiquitous UVR and visual predation threats. We tested whether crab larvae can behaviorally reduce UVR risk through downward swimming or expansion of photoprotective chromatophores. Then we examined whether more pigmented larvae are more heavily predated by silverside fish under natural sunlight in the tropics in three UVR treatments (visible light, visible + UVA, visible + UVA + UVB). Lastly, we tested the behavioral chromatophore response of larvae to predation threats in two light treatments. Armases ricordi avoided surface waters after exposure to sunlight with UVR. Armases ricordi, Armases americanum, and Eurypanopeus sp. consistently expanded chromatophores in UVR or visible light, while Mithraculus sculptus and Mithraculus coryphe showed no response. Fish preferred pigmented larvae on sunnier days in visible light lacking UVR. Lastly, both M. coryphe and M. sculptus unexpectedly expanded chromatophores in fish cues, but responses were inconsistent over trials and across light treatments. The more consistent larval responses to UVR than to predator cues and the lack of predator preferences in natural light conditions suggest that UVR may have a stronger influence on pigmentation than predation. This study improves our understanding of planktonic adaptation to countervailing selection caused by visual predation and exposure to UVR.

The San Francisco Estuary (estuary) and the Sacramento–San Joaquin Delta (the Delta) in California face significant challenges in managing water resources during extended droughts. Zooplankton are a vital trophic link between phytoplankton producers and higher-level consumers such as predatory zooplankton and fish. However, there is still much to be learned about what drives zooplankton abundance and how they respond to drastic changes in environmental conditions, such as droughts. We found that during drought years zooplankton abundance and distribution changes varied for examined taxa. Significant declines in the abundance of Daphnia spp. and the copepod Pseudodiaptomus forbesi occurred in the Suisun Marsh and Suisun Bay regions. In contrast, abundance of the non-native copepod Limnoithona tetraspina increased in Suisun Marsh and the South-Central Delta during those same drought conditions. Salinity is a strong determinant of the presence and abundance of the studied taxa, and we showed that changes in the distribution of salinity as a result of low outflow conditions were an important factor in the regional abundance of zooplankton. Because of the expected increase in the frequency and severity of regional droughts, understanding how these conditions affect zooplankton in the estuary will benefit scientists and resource managers who aim to improve conditions for native fishes.

Plankton live under the countervailing selective pressures of predation and ultraviolet radiation (UVR). In lakes, zooplankton are transparent reducing visibility to predatory fishes but are pigmented in the absence of fishes, hypothetically reducing UVR damage. In the sea, planktivorous fishes are widespread, so plankton typically are transparent and ascend to productive surface waters at night to forage and descend during the day to reduce visibility to predators. However, larvae of some species face the unique constraint of traveling in surface currents in the daytime during migrations between adult and larval habitats. We would expect these larvae to be transparent since companion studies demonstrated increased predation risk of pigmented larvae under strong sunlight. Paradoxically, larvae range from being darkly to lightly pigmented. We hypothesize that some larvae are more heavily pigmented to reduce UVR damage, while other species travelling in subsurface currents with low UVR might be more transparent. Linking larval morphology to depth-dependent selective pressures would add a key element to help improve predictions of larval vertical distributions, which are important for simulating larval transport trajectories. We quantitatively tested the hypothesis that selection may have favored photoprotective pigmentation for larvae in the predominantly transparent plankton community while testing the differential effects of UVA and UVB radiation. We measured larval pigmentation of 12 species of crabs and exposed them to visible light only, visible + UVA, or visible + UVA + UVB in the tropics. Controlling for phylogeny, more pigmented species survived UVR better than less pigmented species, especially on sunnier days, though intraspecific comparisons for four species were equivocal. Most species died even from UVA exposure, which has long been regarded as relatively harmless despite penetrating deeper underwater than UVB. Thus, we demonstrate with a phylogenetically controlled analysis that crab larvae are pigmented in the predominantly transparent planktonic community to protect from UVR, improving our understanding of the selective forces acting on animal coloration and the factors determining planktonic distributions, survival, and dispersal. This linkage of morphology with susceptibility will be important for developing mechanistic models of environmental stress responses to better predict larval dispersal in current and future climates.

Zooplankton provide critical food for threatened and endangered fish species in the San Francisco Estuary (estuary). Reduced food supply has been implicated in the Pelagic Organism Decline of the early 2000s, and further changes in zooplankton abundance, seasonality, and distribution may continue to threaten declining fishes. While we have a wealth of monitoring data, we know little about the abundance trends of many estuary zooplankton species. To fill these gaps, we reviewed past research and then examined trends in seasonality and abundance from 1972 to the present of three key but understudied zooplankton species (Bosmina longirostris, Acanthocyclops spp., and Acartiella sinensis) that play important roles in the estuary food web. We fit Bayesian generalized additive mixed models of each taxon’s relationship with salinity, seasonality, year, and geography on an integrated database of zooplankton monitoring in the upper estuary. We found marked changes in the seasonality and overall abundance of each study species. Bosmina longirostris no longer peaks in abundance in the fall months, Acanthocyclops spp. precipitously declined in all months and lost its strong relationship with salinity, and A. sinensis adult abundance has become more strongly related to salinity while juveniles have developed wider seasonal abundance peaks. Through these analyses, we have documented the relationship of each species with salinity and seasonality since the beginning of monitoring or their introduction, thus increasing our understanding of their ecology and importance in the estuary. These results can inform food-web models, be paired with fish data to model the contributions of these species toward fish abundance trends and be mirrored to elucidate other species’ trends in future studies.

Multi-year droughts are ever-present and transformational features of California’s Mediterranean climate and can fundamentally affect the water quality and the ecosystem responses of the San Francisco Estuary and the Sacramento–San Joaquin Delta. This study assessed data collected by long-term monitoring programs over the past 46 water years (1975–2021) to evaluate how water quality in the estuary changes during multi-year droughts. Data were aggregated by region (South-Central Delta, North Delta, confluence, Suisun Bay, and Suisun Marsh) and season, then differences between multi-year drought periods, multi-year wet periods, and neutral periods were compared using generalized linear models. We found that multi-year drought periods altered multiple physical and chemical parameters in the estuary, increasing water temperature, salinity, water clarity, and nutrient levels. This trend was consistent across regions and seasons, with few exceptions. Increases in these parameters during drought periods were likely caused by reduced Delta inflows that intensified in each successive dry year because of reduced precipitation and managed estuarine inflows and outflows. Drought periods did not substantially affect tidal velocities within the estuary, which remained mostly consistent across wet and drought periods. Trends in chlorophyll concentrations during drought periods were more nuanced with higher concentrations occurring in the South-Central Delta region and during the winter and spring. Together, these results characterized drought in the estuary as warm, clear, high in nutrients, with patchy phytoplankton blooms (as indexed by chlorophyll), all of which have implications for higher trophic levels. Considering that droughts are expected to increase in frequency and intensity in California with climate change, understanding the effects of multi-year droughts on the water quality conditions of the estuary can help inform water management decisions.

The Sacramento–San Joaquin Delta (Delta) is a case-study of the Anthropocene “great accelerations,” with exponentially increasing temperatures and sea level over time, leading to rapid change in other ecosystem components. In nearly all these interconnected changes and across scales, primary producers play a major role, with diverse effects that mitigate or exacerbate the rapid change induced by climate or other human-driven perturbations. Through this anthropocentric lens, primary producers can be viewed as performing numerous ecosystem services—which ultimately benefit humans—as well as ecosystem disservices, which negatively affect human communities. For example, through carbon sequestration, wetlands can perform ecosystem services of mitigating warming at a global scale and combating relative sea-level rise at a local scale, while generating food that supports regional food webs and fisheries. On the other hand, invasive aquatic vegetation (IAV) can trap sediment before it reaches wetlands, exacerbating local subsidence and relative sea-level rise while incurring great costs to recreation, fishing, and agencies tasked with its control. Effectively managing these ecosystem services and disservices requires understanding how they are connected. For example, wetland restoration often creates opportunities for IAV, which may inhibit sediment deposition on the wetland and out-compete native species. As the Delta science community works toward a more integrative understanding of how different components of the Delta interact as a whole and across scales, the pervasive effects of the ecosystem services and disservices of primary producers serve as foundational knowledge. In this topically themed edition of State of Bay–Delta Science, we review these effects. Individual contributions focus on the historical ecology of the primary productivity of aquatic vegetation, the ecology and control of invasive aquatic vegetation, harmful algal blooms, carbon sequestration and subsidence reversal by wetlands, and remote sensing methods for quantifying the ecosystem services and disservices of Delta primary producers.

Morphological defences of plankton can include armour, spines and coloration. Spines defend from gape-limited fish predators, while pigmentation increases visibility to fishes but defends from ultraviolet radiation (UVR). Planktonic crab larvae (zoeae) exhibit inter- and intraspecific variability in the lengths of defensive spines, extent of pigmentation and body size. The determinants of this variability and the relationships among these traits are largely unknown. Larvae may employ generalized defences against the dual threats of UVR and predation or specialized defences against their primary threat, with an unknown role of allometric or phylogenetic constraints. Generalization would result in longer spines compensating for the increased predation risk imposed by darker pigments, while specialization would lead to more investment in either defence from predation (long spines) or UVR (dark pigments), at the expense of the other trait. We examined (a) the relationship between spine lengths and pigmentation, (b) the scaling of spine lengths with body size, and (c) phylogenetic constraint in spine lengths, pigmentation, and body size, among and within 21 species of laboratory-hatched and 23 species of field-collected crab larvae from Panama and California. We found a negative relationship between spine length and pigmentation among species from laboratory and field. Within species, we found a marginally significant negative relationship among field-collected larvae. Spine lengths showed positive allometric scaling with carapace length, while spine and carapace lengths, but not pigmentation, had significant phylogenetic signals. The negative relationship we observed between pigmentation and spine length supports our defence specialization hypothesis. Positive allometric scaling of spine lengths means larger larvae are better defended from predators, which may indicate that larvae face greater predation risk as they grow larger. Phylogenetic constraint may have arisen because related species encounter similar predation threats. Conversely, phylogenetic constraint in the evolution of spine lengths may induce convergent behaviours resulting in related species facing similar predation threats. Our results improve understanding of the evolution of the larval morphology of crabs, morphological defences in the plankton and evolutionary responses of morphology to multiple spatially segregated selective forces. A free Plain Language Summary can be found within the Supporting Information of this article.