scholarly journals Ancient DNA analysis of archaeological specimens extends Chinook salmon’s known historic range to San Francisco Bay’s tributaries and southernmost watershed

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0244470
Author(s):  
Richard B. Lanman ◽  
Linda Hylkema ◽  
Cristie M. Boone ◽  
Brian Allée ◽  
Roger O. Castillo ◽  
...  
Keyword(s):  
Native American ◽  
San Francisco ◽  
Ancient Dna ◽  
Chinook Salmon ◽  
Habitat Restoration ◽  
Dna Analysis ◽  
Oncorhynchus Tshawytscha ◽  
Anthropogenic Impacts ◽  
Bay Area ◽  
Guadalupe River

Understanding a species’ historic range guides contemporary management and habitat restoration. Chinook salmon (Oncorhynchus tshawytscha) are an important commercial and recreational gamefish, but nine Chinook subspecies are federally threatened or endangered due to anthropogenic impacts. Several San Francisco Bay Area streams and rivers currently host spawning Chinook populations, but government agencies consider these non-native hatchery strays. Through the morphology-based analysis of 17,288 fish specimens excavated from Native American middens at Mission Santa Clara (CA-SCL-30H), Santa Clara County, circa 1781–1834 CE, 88 salmonid vertebrae were identified. Ancient DNA sequencing identified three separate individuals as Chinook salmon and the remainder as steelhead/rainbow trout (Oncorhynchus mykiss). These findings comprise the first physical evidence of the nativity of salmon to the Guadalupe River in San Jose, California, extending their documented historic range to include San Francisco Bay’s southernmost tributary watershed.

scholarly journals Ancient DNA Analysis of Archaeological Specimens Extends Chinook Salmon’s Known Historic Range to San Francisco Bay and Its Southernmost Watershed

2020 ◽  
Author(s):  
Richard B. Lanman ◽  
Linda Hylkema ◽  
Cristie M. Boone ◽  
Brian Alleé ◽  
Roger O. Castillo ◽  
...  
Keyword(s):  
Native American ◽  
San Francisco ◽  
Ancient Dna ◽  
Chinook Salmon ◽  
Habitat Restoration ◽  
Dna Analysis ◽  
Oncorhynchus Tshawytscha ◽  
San Francisco Bay ◽  
Bay Area ◽  
Guadalupe River

Understanding a species’ historic range guides contemporary management and habitat restoration. Chinook salmon ( Oncorhynchus tshawytscha ) are an important commercial and recreational gamefish, but nine Chinook subspecies are federally threatened or endangered due to anthropomorphic impacts. Several San Francisco Bay Area streams and rivers currently host spawning Chinook populations, but government agencies consider these non-native hatchery strays. Using ichthyofaunal analysis of 17,288 fish specimens excavated from Native American middens at Mission Santa Clara circa 1781-1834 CE, 86 salmonid vertebrae were identified. Ancient DNA sequencing identified three of these as from Chinook salmon and the remainder from steelhead trout. These findings comprise the first physical evidence of the nativity of salmon to the Guadalupe River in San Jose, California, extending their historic range to include San Francisco Bay’s southernmost watershed.

scholarly journals Managed Wetlands Can Benefit Juvenile Chinook Salmon in a Tidal Marsh

2021 ◽  
Author(s):  
Nicole M. Aha ◽  
Peter B. Moyle ◽  
Nann A. Fangue ◽  
Andrew L. Rypel ◽  
John R. Durand
Keyword(s):  
San Francisco ◽  
Growth Rates ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Nursery Habitat ◽  
San Francisco Estuary ◽  
Rice Fields ◽  
Fish Growth ◽  
Juvenile Chinook Salmon ◽  
Juvenile Chinook

AbstractLoss of estuarine and coastal habitats worldwide has reduced nursery habitat and function for diverse fishes, including juvenile Chinook salmon (Oncorhynchus tshawytscha). Underutilized off-channel habitats such as flooded rice fields and managed ponds present opportunities for improving rearing conditions and increasing habitat diversity along migratory corridors. While experiments in rice fields have shown enhanced growth rates of juvenile fishes, managed ponds are less studied. To evaluate the potential of these ponds as a nursery habitat, juvenile Chinook salmon (~ 2.8 g, 63 mm FL) were reared in cages in four contrasting locations within Suisun Marsh, a large wetland in the San Francisco Estuary. The locations included a natural tidal slough, a leveed tidal slough, and the inlet and outlet of a tidally muted managed pond established for waterfowl hunting. Fish growth rates differed significantly among locations, with the fastest growth occurring near the outlet in the managed pond. High zooplankton biomass at the managed pond outlet was the best correlate of salmon growth. Water temperatures in the managed pond were also cooler and less variable compared to sloughs, reducing thermal stress. The stress of low dissolved oxygen concentrations within the managed pond was likely mediated by high concentrations of zooplankton and favorable temperatures. Our findings suggest that muted tidal habitats in the San Francisco Estuary and elsewhere could be managed to promote growth and survival of juvenile salmon and other native fishes.

Energy dynamics and growth of Chinook salmon (Oncorhynchus tshawytscha) from the Central Valley of California during the estuarine phase and first ocean year

2010 ◽  
Vol 67 (10) ◽  
pp. 1549-1565 ◽  
Author(s):  
R. Bruce MacFarlane
Keyword(s):  
San Francisco ◽  
Chinook Salmon ◽  
Climate Models ◽  
Oncorhynchus Tshawytscha ◽  
Energy Content ◽  
Central Valley ◽  
Energy Dynamics ◽  
Period Data ◽  
Energy Gains ◽  
Engraulis Mordax

The greatest rates of energy accumulation and growth in subyearling Chinook salmon ( Oncorhynchus tshawytscha ) occurred during the first month following ocean entry, supporting the importance of this critical period. Data from an 11-year study in the coastal ocean off California and the San Francisco Estuary revealed that juvenile salmon gained 3.2 kJ·day–1 and 0.8 g·day–1, representing 4.3%·day–1 and 5.2% day–1, respectively, relative to estuary exit values. Little gain in energy (0.28 kJ·day–1) or size (0.07 g·day–1) occurred in the estuary, indicating that the nursery function typically ascribed to estuaries can be deferred to initial ocean residence. Calculated northern anchovies ( Engraulis mordax ) equivalents to meet energy gains were one anchovy per day in the estuary (8% body weight·day–1) and about three per day immediately following ocean entry (15% body weight·day–1). Energy content in the estuary was positively related to higher salinity and lower freshwater outflow, whereas in the ocean, cooler temperatures, lower sea level, and greater upwelling resulted in greater gains. These results suggest that greater freshwater flows, warmer sea temperatures, and reduced or delayed upwelling, all of which are indicated by some (but not all) climate models, will likely decrease growth of juvenile Chinook salmon, leading to reduced survival.

Consequences of potential density-dependent mechanisms on recovery of ocean-type chinook salmon (Oncorhynchus tshawytscha)

2004 ◽  
Vol 61 (4) ◽  
pp. 590-602 ◽  
Author(s):  
Correigh M Greene ◽  
Timothy J Beechie
Keyword(s):  
Density Dependence ◽  
Chinook Salmon ◽  
Habitat Restoration ◽  
Oncorhynchus Tshawytscha ◽  
High Sensitivity ◽  
Leslie Matrix ◽  
Relative Importance ◽  
Density Dependent ◽  
Habitat Area ◽  
Leslie Matrix Model

Restoring salmon populations depends on our ability to predict the consequences of improving aquatic habitats used by salmon. Using a Leslie matrix model for chinook salmon (Oncorhynchus tshawytscha) that specifies transitions among spawning nests (redds), streams, tidal deltas, nearshore habitats, and the ocean, we compared the relative importance of different habitats under three density-dependent scenarios: juvenile density independence, density-dependent mortality within streams, delta, and nearshore, and density-dependent migration among streams, delta, and nearshore. Each scenario assumed density dependence during spawning. We examined how these scenarios influenced priorities for habitat restoration using a set of hypothetical watersheds whose habitat areas could be systematically varied, as well as the Duwamish and Skagit rivers. In all watersheds, the three scenarios shared high sensitivity to changes in in nearshore and ocean mortality and produced similar responses to changes in other parameters controlling mortality (i.e., habitat quality). However, the three scenarios exhibited striking variation in population response to changes in habitat area (i.e., capacity). These findings indicate that nearshore habitat relationships may play significant roles for salmon populations and that the relative importance of restoring habitat area will depend on the mechanism of density dependence influencing salmon stocks.

scholarly journals Survival of a threatened salmon is linked to spatial variability in river conditions

2021 ◽  
Author(s):  
Colby L. Hause ◽  
Gabriel P. Singer ◽  
Rebecca A. Buchanan ◽  
Dennis E. Cocherell ◽  
Nann A. Fangue ◽  
...  
Keyword(s):  
Pacific Northwest ◽  
Chinook Salmon ◽  
Habitat Restoration ◽  
Oncorhynchus Tshawytscha ◽  
Central Valley ◽  
Data Generation ◽  
Habitat Variability ◽  
River Habitat ◽  
San Joaquin River ◽  
The Pacific

AbstractExtirpation of the Central Valley spring-run Chinook Salmon ESU (Oncorhynchus tshawytscha) from the San Joaquin River is emblematic of salmonid declines across the Pacific Northwest. Habitat restoration and fish reintroduction efforts are ongoing, but recent telemetry studies have revealed low outmigration survival of juveniles to the ocean. Previous investigations have focused on modeling survival relative to river discharge and geographic regions, but have largely overlooked the effects of habitat variability. To evaluate the link between environmental conditions and survival of juvenile spring-run Chinook Salmon, we combined high spatial resolution habitat mapping approaches with acoustic telemetry along a 150 km section of the San Joaquin River during the spring of 2019. While overall outmigration survival was low (5%), our habitat-based classification scheme described variation in survival of acoustic-tagged smolts better than other candidate models based on geography or distance. There were two regional mortality sinks evident along the longitudinal profile of the river, revealing poor survival in areas that shared warmer temperatures but that diverged in chlorophyll-α, fDOM, turbidity and dissolved oxygen levels. These findings demonstrate the value of integrating river habitat classification frameworks to improve our understanding of survival dynamics of imperiled fish populations. Importantly, our data generation and modeling methods can be applied to a wide variety of fish species that transit heterogeneous and diverse habitat types.

“Hardhats May Be Misunderstood”

2020 ◽  
Vol 89 (2) ◽  
pp. 264-296
Author(s):  
Allyson P. Brantley
Keyword(s):  
Native American ◽  
Civil Rights ◽  
Oral History ◽  
San Francisco ◽  
San Francisco Bay Area ◽  
New Right ◽  
Labor Dispute ◽  
Bay Area ◽  
Civil Rights Movements ◽  
Consumer Movements

Drawing on organizational records, the progressive press, and oral history archives, this article explores the development of a multiracial, coalition-backed boycott of Coors beer in the 1970s and 1980s. It focuses on the boycott’s expansion from a localized labor dispute in the San Francisco Bay Area to a national, politicized campaign. It argues that the Coors boycott and its array of backers, representing labor, Chicana/o, queer, black, Native American, and leftist circles, demonstrate the vibrancy, creativity, and evolution of activism in the decades following the civil rights movements. Instead of seeing the move to coalition and consumer movements as conservative, this article identifies the Coors boycott as an example of ongoing grassroots efforts to forge solidarity and oppose business conservatives and the New Right.

scholarly journals Optimizing an eDNA protocol for monitoring endangered Chinook Salmon in the San Francisco Estuary: balancing sensitivity, cost and time

2019 ◽  
Author(s):  
Thiago M. Sanches ◽  
Andrea M. Schreier
Keyword(s):  
Dna Extraction ◽  
San Francisco ◽  
Chinook Salmon ◽  
Magnetic Beads ◽  
Oncorhynchus Tshawytscha ◽  
Environmental Dna ◽  
San Francisco Estuary ◽  
Time Cost ◽  
Dna Yield ◽  
Pcr Inhibitor

AbstractEnvironmental DNA (eDNA) analysis has gained traction as a precise and cost effective method for species and waterways management. To date, publications on eDNA protocol optimization have focused primarily on DNA yield. Therefore, it has not been possible to evaluate the cost and speed of specific components of the eDNA protocol, such as water filtration and DNA extraction method when designing or choosing an eDNA pipeline. At the same time, these two parameters are essential for the experimental design of a project. Here we evaluate and rank different eDNA protocols in the context of Chinook salmon (Oncorhynchus tshawytscha) eDNA detection in an aquatic environment, the San Francisco Estuary. We present a comprehensive evaluation of multiple eDNA protocol parameters, balancing time, cost and DNA yield. For estuarine waters, which are challenging for eDNA studies due to high turbidity, variable salinity, and the presence of PCR inhibitors, we find that a protocol combining glass filters and magnetic beads, along with an extra step for PCR inhibitor removal, is the method that best balances time, cost, and yield. In addition, we provide a generalized decision tree for determining the optimal eDNA protocol for other studies on aquatic systems. Our findings should be applicable to most aquatic environments and provide a clear guide for determining which eDNA pipeline should be used for a given environmental condition.Author SummaryThe use of environmental DNA (eDNA) analysis for monitoring wildlife has steadily grown in recent years. Though, due to differences in the ecology of the environment studied and the novelty of the technique, eDNA currently shows a lack of standards compared to other fields. Here we take a deep look into each step of an eDNA assay, looking at common protocols and comparing their efficiencies in terms of time to process the samples, cost and how much DNA is recovered. We then analyze the data to provide a concise interpretation of best practices given different project constraints. For the conditions of the San Francisco Estuary we suggest the use of glass fiber filtration, the use of paramagnetic beads for DNA extraction and the use of a secondary inhibitor removal. We expect our findings to provide better support for managers to decide their standards ahead of project submission not only for estuarine conditions but for other waterine conditions alike.

Thermal heterogeneity, stream channel morphology, and salmonid abundance in northeastern Oregon streams

2003 ◽  
Vol 60 (10) ◽  
pp. 1266-1280 ◽  
Author(s):  
Joseph L Ebersole ◽  
William J Liss ◽  
Christopher A Frissell
Keyword(s):  
Rainbow Trout ◽  
Chinook Salmon ◽  
Habitat Restoration ◽  
Oncorhynchus Tshawytscha ◽  
Cold Water ◽  
Stream Water ◽  
Stream Channels ◽  
Explanatory Variables ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Thermal Heterogeneity

Heterogeneity in stream water temperatures created by local influx of cooler subsurface waters into geomorphically complex stream channels was associated with increased abundance of rainbow trout (Oncorhynchus mykiss) and chinook salmon (Oncorhynchus tshawytscha) in northeastern Oregon. The addition of cold water patch frequency and area as explanatory variables in salmonid habitat models indicated that doubling of cold water patch frequency was associated with increases in rainbow trout and chinook salmon abundances of 31% and 59%, respectively. Doubling of cold water patch area was associated with changes of 10% in rainbow trout abundance but was not associated with chinook abundance after accounting for other habitat factors. The physiognomy, distribution, and connectivity of cold water patches, important attributes determining the effectiveness of these habitats as thermal refuges for stream fishes, were associated with channel bedform and riparian features. Monitoring of thermal heterogeneity and salmonid populations in response to ongoing habitat restoration efforts will provide additional insights into causal relationships among these factors.

scholarly journals Placing Refuge and the Archaeology of Indigenous Hinterlands in Colonial California

2015 ◽  
Vol 80 (4) ◽  
pp. 695-713 ◽  
Author(s):  
Tsim D. Schneider
Keyword(s):  
Native American ◽  
San Francisco ◽  
San Francisco Bay Area ◽  
Ways Of Knowing ◽  
Native People ◽  
Bay Area ◽  
Spanish Missions ◽  
European Colonialism ◽  
Colonial California ◽  
Economic Choices

Indigenous negotiations of European colonialism in North America are more complex than models of domination and resistance reveal. Indigenous people—acting according to their own historically and culturally specific ways of knowing and being in the world—developed strategies for remaking their identities, material choices, and social configurations to survive one or multiple phases of colonization. Archaeologists are making strides in documenting the contingencies and consequences of these strategies, yet their focus is often skewed toward sites of contact and colonialism (e.g., missions and forts). This article examines places of refuge for native people navigating colonial programs in the San Francisco Bay area of California. I use a resistance-memory-refuge framework to reevaluate resistance to Spanish missions, including the possible reoccupation of landscapes by fugitive orfurloughed Indians. Commemorative trips to shellmounds and other refuges support the concept of an indigenous hinterland, or landscapes that, in time, provided contexts for continuity and adjustment among Indian communities making social, material, and economic choices in the wake ofmissionization. By viewing colonialism from the outside in, this reoriented approach can potentially enhance connections between archaeological and Native American communities.

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