Geology Reports⌕ Search

SEARCH · Geology Reports

Results for “Food Webs”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 901 records · Page 50Linked to original sources
USGS2013

Quagga and zebra mussels: biology, impacts, and control

Quagga and Zebra Mussels: Biology, Impacts, and Control , Second Edition provides a broad view of the zebra/quagga mussel issue, offering a historic perspective and up-to-date information on mussel research. Comprising 48 chapters, this second edition includes reviews of mussel morphology, physiology, and behavior. It details mussel distribution and spread in Europe and across North America, and examines policy and regulatory responses, management strategies, and mitigation efforts. In addition, this book provides extensive coverage of the impact of invasive mussel species on freshwater ecosystems, including effects on water clarity, phytoplankton, water quality, food web changes, and consequences to other aquatic fauna. It also reviews and offers new insights on how zebra and quagga mussels respond and adapt to varying environmental conditions. This new edition includes seven video clips that complement chapter text and, through visual documentation, provide a greater understanding of mussel behavior and distribution.

Book↗
USGS2002

Impacts of aquatic nonindigenous invasive species on the Lake Erie ecosystem

Lake Erie is particularly vulnerable to the introduction and establishment of aquatic nonindigenous invasive species (NIS) populations. A minimum of 144 aquatic NIS have been recorded in the Lake Erie basin including several species [e.g., Eurasian watermilfoil ( Myriophyllum spicatum ); zebra mussel ( Dreissena polymorpha ); quagga mussel (Dreissena bugensis); an amphipod (Echinogammarus ischnus); round goby (Neogobius melanostomus); and sea lamprey ( Petromyzon marinus )] that have had discernible impacts on the lake's ecology. NIS pose threats to the Lake Erie ecosystem for a variety of reasons including their ability to proliferate quickly, compete with native species, and transfer contaminants (e.g., PCBs) and disease through the food web. Six of the 14 beneficial use impairments listed in Annex 2 of the Great Lakes Water Quality Agreement are impaired in Lake Erie, in part as a result of the introduction of NIS. The Lake Erie Lakewide Management Plan (LaMP) has adopted an ecosystem approach to restore beneficial use impairments in the lake. Furthermore, a research consortium, known as the Lake Erie Millennium Network, is working alongside the LaMP, to address research problems regarding NIS, the loss of habitat, and the role of contaminants in the Lake Erie ecosystem.

Conference Paper↗
USGS2001

Time series of suspended-solids concentration, salinity, temperature, and total mercury concentration in San Francisco Bay during water year 1998

Many physical processes affect how constituents within San Francisco Bay vary. Processes and their associated time scales include turbulence (seconds), semidiurnal and diurnal tides (hours), the spring-neap tidal cycle (days), freshwater flow (weeks), seasonal winds (months), ecological and climatic changes (years), and geologic changes (thousands of years). Continuous time series of data on basic state variables of the bay, such as suspended-solids concentration (SSC), salinity, and water temperature, provide insight on the effect and relative importance of physical processes on the bay. SSC time series and Regional Monitoring Program (RMP) water-quality data can be used to calculate time series of some traceelement concentrations (Schoellhamer, 1997a, 1997b). The purpose of this chapter is to describe qualitatively time series of SSC, salinity, water temperature, and mercury during water year 1998 (October 1997 through September 1998). Salinity, temperature, and sediment are important components of the San Francisco Bay estuarine system. Salinity and temperature affect the hydrodynamics (Monismith et al., 1996; Schoellhamer and Burau, 1998), geochemistry (Kuwabara et al., 1989), and ecology (Cloern, 1984; Nichols et al., 1986; Jassby et al., 1995) of the bay. Suspended sediments limit light availability in the bay, which, in turn, limits primary production (Cloern, 1987; Cole and Cloern, 1987), and thus food for higher trophic levels. Sediments deposit in ports and shipping channels, which must be dredged to maintain navigation (U.S. Environmental Protection Agency, 1992). Potentially toxic substances, such as metals and pesticides, adsorb to sediment particles (Kuwabara et al., 1989; Domagalski and Kuivila, 1993; Flegal et al., 1996; Schoellhamer, 1997a, 1997b). The transport and fate of suspended sediments are important factors in determining the transport and fate of constituents adsorbed on the sediments. For example, the concentration of suspended particulate chromium in the bay appears to be controlled primarily by sediment resuspension (Abu-Saba and Flegal, 1995). Concentrations of dissolved trace elements are greater in South Bay than elsewhere in San Francisco Bay, and bottom sediments are believed to be a significant source (Flegal et al., 1991). The sediments on the bay bottom provide habitat for benthic communities that can ingest these substances and introduce them into the food web (Luoma et al., 1985; Brown and Luoma, 1995, Luoma 1996). Bottom sediments also are a reservoir of nutrients that contribute to the maintenance of estuarine productivity (Hammond et al., 1985).

California↗
USGS1994

Central San Francisco Bay suspended-sediment transport processes study and comparison of continuous and discrete measurements of suspended-solids concentrations

Sediments are an important component of the San Francisco Bay estuarine system. Potentially toxic substances, such as metals and pesticides, adsorb to sediment particles. The sediments on the bottom of the Bay provide the habitat for benthic communities which can ingest these substances and introduce them into the food web. The bottom sediments are also a reservoir of nutrients. The transport and fate of suspended sediment is an important factor in determining the transport and fate of the constituents adsorbed on the sediment. Suspended sediments also limit light availability in the bay, which limits photosynthesis and primary production, and deposit in ports and shipping channels, which require dredging. Dredged materials are disposed in Central San Francisco Bay.

California↗
USGS1996

Central San Francisco Bay suspended-sediment transport processes and comparison of continuous and discrete measurements of suspended-solids concentrations

Sediments are an important component of the San Francisco Bay estuarine system. Potentially toxic substances, such as metals and pesticides, adsorb to sediment particles (Kuwabara and others, 1989; Domagalski and Kuivila, 1993). Sediments on the bottom of the bay provide the habitat for benthic communities that can ingest these substances and introduce them into the food web (Luoma and others, 1985). Nutrients, metals, and other substances are stored in bottom sediments and pore water in which chemical reactions occur and which provide an important source and/or sink to the water column (Hammond and others, 1985; Flegal and others, 1991). The transport and fate of suspended sediment is an important factor in determining the transport and fate of the constituents adsorbed on the sediment. Seasonal changes in sediment erosion and deposition patterns contribute to seasonal changes in the abundance of benthic macroinvertebrates (Nichols and Thompson, 1985). Tidal marshes are an ecologically important habitat that were created and are maintained by sedimentation processes (Atwater and others, 1979). In Suisun Bay, the maximum suspended-sediment concentration marks the position of the turbidity maximum, which is a crucial ecological region in which suspended sediment, nutrients, phytoplankton, zooplankton, larvae, and juvenile fish accumulate (Peterson and others, 1975; Arthur and Ball, 1979; Kimmerer, 1992; Jassby and Powell, 1994). Suspended sediments confine the photic zone to the upper part of the water column, and this limitation on light availability is a major control on phytoplankton production in San Francisco Bay (Cloern, 1987; Cole and Cloern, 1987). Suspended sediments also deposit in ports and shipping channels, which must be dredged to maintain navigation (U.S. Environmental Protection Agency, 1992).

California↗
USGS2000

Nutrient pollution of coastal rivers, bays, and seas

Over the past 40 years, antipollution laws have greatly reduced discharges of toxic substances into our coastal waters. This effort, however, has focused largely on point-source pollution of industrial and municipal effluent. No comparable effort has been made to restrict the input of nitrogen (N) from municipal effluent, nor to control the flows of N and phosphorus (P) that enter waterways from dispersed or nonpoint sources such as agricultural and urban runoff or as airborne pollutants. As a result, inputs of nonpoint pollutants, particularly N, have increased dramatically. Nonpoint pollution from N and P now represents the largest pollution problem facing the vital coastal waters of the United States. Nutrient pollution is the common thread that links an array of problems along the nation’s coastline, including eutrophication, harmful algal blooms, ”dead zones,” fish kills, some shellfish poisonings, loss of seagrass and kelp beds, some coral reef destruction, and even some marine mammal and seabird deaths. More than 60 percent of our coastal rivers and bays in every coastal state of the continental United States are moderately to severely degraded by nutrient pollution. This degradation is particularly severe in the mid Atlantic states, in the southeast, and in the Gulf of Mexico. A recent report from the National Research Council entitled “Clean Coastal Waters: Understanding and Reduc- ing the Effects of Nutrient Pollution” concludes that: Nutrient over-enrichment of coastal ecosystems generally triggers ecological changes that decrease the biologi- cal diversity of bays and estuaries. While moderate N enrichment of some coastal waters may increase fish production, over-enrichment generally degrades the marine food web that supports commercially valuable fish. The marked increase in nutrient pollution of coastal waters has been accompanied by an increase in harmful algal blooms, and in at least some cases, pollution has triggered these blooms. High nutrient levels and the changes they cause in water quality and the makeup of the algal community are detrimental to the health of coral reefs and the diversity of animal life supported by seagrass and kelp communi- ties. Research during the past decade confirms that N is the chief culprit in eutrophication and other impacts of nutrient over-enrichment in temperate coastal waters, while P is most problematic in eutrophication of freshwa- ter lakes. Human conversion of atmospheric N into biologically useable forms, principally synthetic inorganic fertilizers, now matches the natural rate of biological N fixation from all the land surfaces of the earth. Both agriculture and the burning of fossil fuels contribute significantly to nonpoint flows of N to coastal waters, either as direct runoff or airborne pollutants. N from animal wastes that leaks directly to surface waters or is volatilized to the atmosphere as ammonia may be the largest single source of N that moves from agricultural operations into coastal waters. The National Research Council report recommended that, as a minimum goal, the nation should work to reverse nutrient should be taken to assure that the 40 percent of coastal areas now ranked as healthy do not develop symptoms of nutrient pollution in 10 percent of its degraded coastal systems by 2010 and 25 percent of them by 2020. Also, action should be taken to assure that the 40 percent of coastal areas now ranked as healthy do not develop symptoms of nutrient pollution. Meeting these goals will require an array of strategies and approaches tailored to specific regions and coastal ecosystems. There is an urgent need for development and testing of techniques that can reliably pinpoint the sources of N pollutants to an estuary. For some coastal systems, N removal during treatment of human sewage may be sufficient to reverse nutrient pollution. For most coastal systems, however, the solutions will be more complex and may involve controls on N compounds emitted during fossil fuel combustion as well as incentives to reduce over-fertilization of agricul- tural fields and nutrient pollution from animal wastes in livestock feedlot operations.

Alabama, California, Connecticut, Delaware, Florid↗
USGS2016

Lake Ontario benthic prey fish assessment, 2015

Benthic prey fishes are a critical component of the Lake Ontario food web, serving as energy vectors from benthic invertebrates to native and introduced piscivores. Since the late 1970’s, Lake Ontario benthic prey fish status was primarily assessed using bottom trawl observations confined to the lake’s south shore, in waters from 8 – 150 m (26 – 492 ft). In 2015, the Benthic Prey Fish Survey was cooperatively adjusted and expanded to address resource management information needs including lake-wide benthic prey fish population dynamics. Effort increased from 55 bottom trawl sites to 135 trawl sites collected in depths from 8 - 225m (26 – 738 ft). The spatial coverage of sampling was also expanded and occurred in all major lake basins. The resulting distribution of tow depths more closely matched the available lake depth distribution. The additional effort illustrated how previous surveys were underestimating lake-wide Deepwater Sculpin, Myoxocephalus thompsonii , abundance by not sampling in areas of highest density. We also found species richness was greater in the new sampling sites relative to the historic sites with 11 new fish species caught in the new sites including juvenile Round Whitefish, P rosopium cylindraceum , and Mottled sculpin, Cottus bairdii . Species-specific assessments found Slimy Sculpin, Cottus cognatus abundance increased slightly in 2015 relative to 2014, while Deepwater Sculpin and Round Goby, Neogobius melanostomus, dramatically increased in 2015, relative to 2014. The cooperative, lake-wide Benthic Prey Fish Survey expanded our understanding of benthic fish population dynamics and habitat use in Lake Ontario. This survey’s data and interpretations influence international resource management decision making, such as informing the Deepwater Sculpin conservation status and assessing the balance between sport fish consumption and prey fish populations. Additionally a significant Lake Ontario event occurred in May 2015 when a single juvenile Bloater Coregonus hoyi , was captured during the spring bottom trawl survey at 95m (312 ft) near Oswego, NY. This native, deep-water prey fish, last captured in Lake Ontario survey trawls in 1983, is part of an international, collaborative coregonid restoration effort in the Great Lakes.

Lake Ontario↗
USGS2016

The Mississippi River: A place for fish

The Mississippi River flows 3,734 km from its source at Lake Itasca, Minnesota to its outlet at the Gulf of Mexico. Along its course, it collects water from portions of two Canadian provinces and 41 % of the conterminous United States. Although greatly altered for navigation and flood control throughout much of its length, the Mississippi River remains an important fishery resource that provides habitat for 188 species of fishes and recreational and commercial fishing opportunities. The objectives of this chapter are to describe the contemporary fisheries habitat throughout the Mississippi River, identify how management to achieve human benefits influences the fishes and their habitats, and summarize efforts to conserve and enhance fish habitat. The 826-km headwater reach is entirely in Minnesota and remains largely unaltered. The reaches that extend 1,059 km from St. Anthony Falls, Minnesota to above the confluence with the Missouri River near St. Louis, Missouri have been altered by impoundment that has affected floodplain function, increased sedimentation of backwaters, and homogenized the formerly diverse aquatic habitats. After the confluence with the Missouri River, the Mississippi River flows freely for 1,849 km to the Gulf of Mexico. The alterations of the free-flowing reaches of greatest significance to the fisheries resource are reducing the duration and height of the flood pulse as a consequence of shortening the river channel, disconnection of the river from its historic and present floodplain, and loss of secondary channel-island complexes. Engineering features to improve commercial navigation have also added habitat and, when wisely manipulated, can be used to rehabilitate habitat. Some aspects of water quality have improved, but legacy chemicals and nutrient-laden inflows and sediments remain problems. Although true restoration in the sense of restoring all environmental conditions to an unaltered state is unlikely, the future value of the Mississippi River as a fisheries resource will depend on actively maintaining diverse and accessible aquatic habitats to support food webs and water quality suitable for fishes.

Book chapter↗
USGS2017

Lake Ontario benthic prey fish assessment, 2016

Benthic prey fishes are a critical component of the Lake Ontario food web, serving as energy vectors from benthic invertebrates to native and introduced piscivores. Beginning in 1978, Lake Ontario benthic prey fishes were assessed using bottom trawls collected from the lake’s south shore (depth range: 8 – 150 m). Historically, the survey targeted the then dominant species, Slimy Sculpin, however in 2015, the Benthic Prey Fish Survey was cooperatively expanded to a whole-lake survey, to address resource management information needs related to Round Goby, Deepwater Sculpin, and nearshore native fishes. In 2016, 142 trawls were collected at 18 transects, and spanned depths from 6 – 225 m. Trawl catches indicated the benthic and demersal prey fish community was dominated by Round Goby, however the proportional importance of native Deepwater Sculpin is increasing. Species-specific assessments found lake-wide Round Goby density (~600 fish per hectare) was slightly lower in 2016 relative to 2015. Deepwater Sculpin density has generally increased since 2004. In 2016 their estimated density was greater than 100 fish per hectare. Slimy Sculpin density (15 fish/ha) was similar to the past 3 years. Catches of juvenile Slimy Sculpin continue to be low relative to historic catches and the timing of their decline coincides with the proliferation of Round Goby. Additionally, we found a strong negative relationship between trawl catches of Round Goby and near-shore native benthic and demersal fishes such as Trout-perch, Johnny Darter and Spottail Shiner. The introduction of Round Goby and the reappearance of native Deepwater Sculpin have shaped the Lake Ontario benthic prey fish community.

Lake Ontario↗
USGS2001

Seabird tissue archival and monitoring project: Protocol for collecting and banking seabird eggs

Archiving biological and environmental samples for retrospective analysis is a major component of systematic environmental monitoring. The long-term storage of carefully selected, representative samples in an environmental specimen bank is an important complement to the real-time monitoring of the environment. These archived samples permit: The use of subsequently developed innovative analytical technology that was not available at the time the samples were archived, for clear state-of-art identification an~ quantification of analytes of interest, The identification and quantification of analytes that are of subsequent interest but that were not of interest at the time the samples were archived, and The comparison of present and past analytical techniques and values, providing continued credibility of past analytical values, and allowing flexibility in environmental monitoring programs. Seabirds, including albatrosses, pelicans, cormorants, terns, kittiwakes, murres, guillemots, and puffins spend most of their lives at sea and have special adaptations for feeding in the marine environment, including the ability to excrete the excess salt obtained from ingesting seawater. Many species nest in dense groups (colonies) on steep, precipitous sea-cliffs and headlands. Seabirds are long-lived and slow to mature. They occupy high positions in the marine food web and are considered sensitive indicators for the marine environment (prey includes krill, small fish, and squid). Breeding success, timing of nesting, diets, and survival rates may provide early indications of changing environmental conditions (e.g., see Hatch et aI., 1993). Chemical analysis of seabird tissues, including egg contents, can be particularly useful in determining whether contaminants (and potential biological effects) associated with human industrial activities, such as offshore petroleum and mineral exploration and development, are accumulating in marine environments. The collection and archival of seabird tissues over a period of several years will be a resource for future analyses, providing samples that can be used to determine historical baseline contaminant levels.

Report↗
USGS2017

Snake River Fall Chinook Salmon life history investigations

Predation by nonnative fishes is one factor that has been implicated in the decline of juvenile salmonids in the Pacific Northwest. Impoundment of much of the Snake and Columbia rivers has altered food webs and created habitat favorable for species such as Smallmouth Bass Micropterus dolomieu . Smallmouth Bass are common throughout the Columbia River basin and have become the most abundant predator in lower Snake River reservoirs (Zimmerman and Parker 1995). This is a concern for Snake River Fall Chinook Salmon Oncorhynchus tshawytscha (hereafter, subyearlings) that may be particularly vulnerable due to their relatively small size and because their main-stem rearing habitats often overlap or are in close proximity to habitats used by Smallmouth Bass (Curet 1993; Tabor et al. 1993). Concern over juvenile salmon predation spawned a number of large-scale studies to quantify its effect in the late 1980s, 1990s, and early 2000s (Poe et al. 1991; Rieman et al. 1991; Vigg et al. 1991; Fritts and Pearsons 2004; Naughton et al. 2004). Smallmouth Bass predation represented 9% of total salmon consumption by predatory fishes in John Day Reservoir, Columbia River, from 1983 through 1986 (Rieman et al. 1991). In transitional habitat between the Hanford Reach of the Columbia River and McNary Reservoir, juvenile salmon (presumably subyearlings) were found in 65% of Smallmouth Bass (>200 mm) stomachs and comprised 59% of the diet by weight (Tabor et al. 1993). Within Lower Granite Reservoir on the Snake River, Naughton et al. (2004) showed that monthly consumption (based on weight) ranged from 5% in the upper reaches of the reservoir to 11% in the forebay. However, studies in the Snake River were conducted soon after Endangered Species Act (ESA) listing of Snake River Fall Chinook Salmon (NMFS 1992). During this time, Fall Chinook Salmon abundance was at an historic low, which may explain why consumption rates were relatively low compared to those from studies conducted in the Columbia and Yakima rivers where abundance was higher (e.g., Tabor et al. 1993; Fritts and Pearsons 2004). We speculate that predation on subyearlings by Smallmouth Bass in the Snake River may have increased in recent years for several reasons. Since their ESA listing, recovery measures implemented for Snake River Fall Chinook salmon have resulted in a large increase in the juvenile population (Connor et al. 2013). Considering that subyearlings probably now make up a larger portion of the forage fish population, it is plausible they should make up a large portion of Smallmouth Bass diets. Second, migrating subyearlings delay downstream movement in the transition zones of the Clearwater River and Snake River for varying lengths of time (Tiffan et al. 2010), which increases their exposure and vulnerability to predators. Spatial overlap in locations of Smallmouth Bass and subyearlings that died during migration provides support for this (Tiffan et al. 2010). Finally, the later outmigration of subyearlings from the Clearwater River results in their presence in Lower Granite Reservoir during the warmest summer months when predation rates of Smallmouth Bass should be highest. In 2016, we focused our efforts on Smallmouth Bass predation in Lower Granite Reservoir downstream of the transition zones and the confluence area where we worked during 2012–2015. Similar to past years, our first objective was to quantify Smallmouth Bass consumption rates of subyearlings, determine relative bass abundance, and describe bass diets. In addition, Tiffan et al. (2016a) posited that predation risk to subyearlings may be higher in shoreline habitats that are more suitable for Smallmouth Bass and lower in shoreline habitats that are more suitable for subyearlings. To test this hypothesis, our second objective examines the relationship between Smallmouth Bass predation of subyearlings and habitat suitability.

Idaho, Washington↗
USGS2010

Assessing the response of the Pamlico Sound, North Carolina, USA to human and climatic disturbances: Management implications

The Pamlico Sound (PS) with its sub-estuaries is the largest lagoonal ecosystem in the United States. It exhibits periodically strong salinity stratification and an average freshwater residence time of 1 year for the sound proper. This relatively long residence time promotes effective use and cycling of nutrients, allowing the system to support high rates of primary and secondary production, and serve as a vitally important fisheries nursery. This hydrologic characteristic also makes the system highly sensitive to nutrient over-enrichment and eutrophication. The PS is experiencing ecological change in response to increasing human activity and climatic perturbations. Human impacts include a rise in nutrient, sediment, and other pollutant loads that accompany urbanization and agricultural and industrial growth in its watersheds and airsheds. Since the mid-1990s, the PS has witnessed a sudden rise in tropical storm and hurricane impacts, with eight hurricanes and four tropical storms having made landfall in the PS watershed during the 1996 to 2007 period. Each of these storms had unique hydrologic, nutrient, and other pollutant loading effects. In addition, since the early 2000s, the region has experienced record droughts, which are continuing. Variable freshwater discharges from storms and droughts have caused large oscillations in nutrient enrichment, reflected ultimately in differential phytoplankton production, biomass, and community compositional responses. Floodwaters from the two wettest hurricanes, Fran (1996) and Floyd (1999), and from Tropical Storm Ernesto (2006) exerted long-term (months) effects on hydrology, nutrient loads, and algal production. Windy but relatively dry hurricanes, like Irene (1999) and Isabel (2003), caused strong vertical mixing, storm surges, but relatively minor changes in river flow, flushing, and nutrient loads. These contrasting effects are accompanied by biogeochemical (hypoxia, nutrient cycling) and habitat alterations, and associated food web disturbances. Each storm type influenced algal growth and compositional dynamics; however, their respective ecological impacts differed substantially. Changes in hydrologic and wind forcing resulting from changes in frequency and intensity of storms and droughts strongly influence water and habitat quality. These changes must be integrated with nutrient loading/dilution effects when assessing and predicting ecological responses to nutrient and hydrologic variability on this and other large lagoonal ecosystems.

North Carolina↗
USGS2017

Genomics of Arctic cod

The Arctic cod (Boreogadus saida) is an abundant marine fish that plays a vital role in the marine food web. To better understand the population genetic structure and the role of natural selection acting on the maternally-inherited mitochondrial genome (mitogenome), a molecule often associated with adaptations to temperature, we analyzed genetic data collected from 11 biparentally-inherited nuclear microsatellite DNA loci and nucleotide sequence data from from the mitochondrial DNA (mtDNA) cytochrome b (cytb) gene and, for a subset of individuals, the entire mitogenome. In addition, due to potential of species misidentification with morphologically similar Polar cod (Arctogadus glacialis), we used ddRAD-Seq data to determine the level of divergence between species and identify species-specific markers. Based on the findings presented here, Arctic cod across the Pacific Arctic (Bering, Chukchi, and Beaufort Seas) comprise a single panmictic population with high genetic diversity compared to other gadids. High genetic diversity was indicated across all 13 protein-coding genes in the mitogenome. In addition, we found moderate levels of genetic diversity in the nuclear microsatellite loci, with highest diversity found in the Chukchi Sea. Our analyses of markers from both marker classes (nuclear microsatellite fragment data and mtDNA cytb sequence data) failed to uncover a signal of microgeographic genetic structure within Arctic cod across the three regions, within the Alaskan Beaufort Sea, or between near-shore or offshore habitats. Further, data from a subset of mitogenomes revealed no genetic differentiation between Bering, Chukchi, and Beaufort seas populations for Arctic cod, Saffron cod (Eleginus gracilis), or Walleye pollock (Gadus chalcogrammus). However, we uncovered significant differences in the distribution of microsatellite alleles between the southern Chukchi and central and eastern Beaufort Sea samples of Arctic cod. Finally, using ddRAD-Seq data, we identified species-specific markers and in conjunction with mitogenome data, identified an Arctic cod x Polar cod hybrid in western Canadian Beaufort Sea. Overall, the lack of genetic structure among Arctic cod within the Bering, Chukchi and Beaufort seas of Alaska is concordant with the absence of geographic barriers to dispersal and typical among marine fishes. Arctic cod may exhibit a genetic pattern of isolation-by-distance, whereby populations in closer geographic proximity are more genetically similar than more distant populations. As this signal is only found between our two fartherest localities, data from populations elsewhere in the species’ global range are needed to determine if this is a general characteristic. Further, tests for selection suggested a limited role for natural selection acting on the mitochondrial genome of Arctic cod, but do not exclude the possibility of selection on genes involved in nuclear-mitogenome interactions. Unlike previous genetic assessment of Arctic cod sampled from the Chukchi Sea, the high levels of genetic diversity found in Arctic cod assayed in this study, across regions, suggests that the species in the Beaufort and Chukchi seas does not suffer from low levels of genetic variation, at least at neutral genetic markers. The large census size of Arctic cod may allow this species to retain high levels of genetic diversity. In addition, we discovered the presence of hybridization between Arctic and Polar cod (although low in frequency). Hybridization is expected to occur when environmental changes modify species distributions that result in contact between species that were previously separated. In such cases, hybridization may be an evolutionary mechanism that promotes an increase in genetic diversity that may provide species occupying changing environments with locally-adapted genotypes and, therefore, phenotypes. Natural selection can only act on the standing genetic variation present within a population. Therefore, given its higher levels of genetic diversity in combination with a large population size, Arctic cod may be resilient to current and future environmental change, as high genetic diversity is expected to increase opportunities for positive selection to act on genetic variants beneficial in different environments, regardless of the source of that genetic variation.

OCS Study↗
USGS2014

Proper handling of animal tissues from the field to the laboratory supports reliable biomarker endpoints

In the endeavor to assess potential effects to the Gulf of Mexico ecosystem from the Mississippi Canyon 252 incident, referred to as the Deepwater Horizon oil spill, various environmental data have been collected. Whereas initial efforts have included satellite tracking and sediment and water sampling to estimate the geographical scope of oiling, research on biological samples can provide insights into potential physiological responses to oil if it was present in the food web, sediment, or water column. Fish species are ideal model organisms for studying responses to water- and sediment-borne contaminants due to their life history (Jenkins et al. 2014), and several Gulf of Mexico fish species were studied by scientists after this incident. Typical field data collected on fish reflect organism condition and include observations such as fish length, weight, gonad condition, condition factor (weight in relation to length), parasite load, and color of organs (Schmitt and Dethloff 2000). However, if physiological responses occurred due to oil exposure, effects would not be immediately visible using organism-level observations alone. Changes occur first at the organ, tissue, cell, or molecular levels, and these responses can be measured by using biomarker assays (van der Oost et al. 2003).

Book chapter↗
USGS2018

Smallmouth bass predation on subyearling fall Chinook salmon in Lower Granite Reservoir, 2016–2017

Predation by nonnative fishes is one factor that has been implicated in the decline of juvenile salmonids in the Pacific Northwest. Impoundment of much of the Snake and Columbia Rivers has altered food webs and created habitat favorable for species such as smallmouth bass Micropterus dolomieu. Smallmouth bass are common throughout the Columbia River basin and have become the most abundant predator in lower Snake River reservoirs (Zimmerman and Parker 1995). This is a concern for Snake River fall Chinook salmon Oncorhynchus tshawytscha (hereafter, subyearlings) that may be particularly vulnerable due to their relatively small size and because their main-stem rearing habitats often overlap or are in close proximity to habitats used by smallmouth bass (Curet 1993; Tabor et al. 1993). Concern over juvenile salmon predation spawned a number of large-scale studies to quantify its effect in the late 1980s, 1990s, and early 2000s (Poe et al. 1991; Rieman et al. 1991; Vigg et al. 1991; Fritts and Pearsons 2004; Naughton et al. 2004). Smallmouth bass predation represented 9% of total salmon consumption by predatory fishes in John Day Reservoir, Columbia River, from 1983 through 1986 (Rieman et al. 1991). In transitional habitat between the Hanford Reach of the Columbia River and McNary Reservoir, juvenile salmon (presumably subyearlings) were found in 65% of smallmouth bass (>200 mm) stomachs and comprised 59% of the diet by weight (Tabor et al. 1993). Within Lower Granite Reservoir on the Snake River, Naughton et al. (2004) showed that monthly consumption (based on weight) ranged from 5% in the upper reaches of the reservoir to 11% in the forebay. However, studies in the Snake River were conducted soon after Endangered Species Act (ESA) listing of Snake River fall Chinook salmon (NMFS 1992). During this time, fall Chinook salmon abundance was at an historic low, which may explain why consumption rates were relatively low compared to those from studies conducted in the Columbia and Yakima Rivers where abundance was higher (e.g., Tabor et al. 1993; Fritts and Pearsons 2004). We speculate that predation on subyearlings by smallmouth bass in the Snake River may have increased in recent years for several reasons. Since their ESA listing, recovery measures implemented for Snake River fall Chinook salmon have resulted in a large increase in the juvenile population (Connor et al. 2013). Considering that subyearlings probably now make up a larger portion of the forage fish population, it is plausible they should make up a larger portion of smallmouth bass diets. Second, migrating subyearlings delay downstream movement in the transition zones of the Clearwater River and Snake River for varying lengths of time (Tiffan et al. 2010), which increases their exposure and vulnerability to predators. Spatial overlap in locations of smallmouth bass and subyearlings that died during migration provides support for this (Tiffan et al. 2010). Finally, the later outmigration of subyearlings from the Clearwater River results in their presence in Lower Granite Reservoir during the warmest summer months when predation rates of smallmouth bass should be highest. In 2016 and 2017, we focused our smallmouth bass predation efforts in Lower Granite Reservoir downstream of the transition zones and the confluence area where we worked during 2012–2015. This report primarily covers results from 2017 but some results from 2016 are also included for comparison. Similar to past years, our first objective was to quantify smallmouth bass consumption rates of subyearlings, determine bass abundance, and describe bass diets. In addition, Tiffan et al. (2016a) posited that predation risk to subyearlings may be higher in shoreline habitats that are more suitable for smallmouth bass and lower in shoreline habitats that are more suitable for subyearlings. To test this hypothesis, our second objective was to examine the relationship between smallmouth bass predation and subyearling habitat suitability. Our final objective was to combine estimates of consumption with smallmouth bass abundance to derive estimates of total Chinook salmon losses to smallmouth bass for 2016 and 2017.

Idaho, Washington↗
USGS2019

Polychlorinated biphenyls (PCBs) in the Pacific sand lance, Puget Sound, Washington

Forage fish are small, abundant, schooling planktivores that form a critical link in marine food webs by transferring energy from plankton up to birds, fishes, and marine mammals. Forage fishes in Puget Sound include the iconic Pacific herring as well as lesser known species such as surf smelt and the Pacific sand lance. There are significant knowledge gaps regarding the basic life history and population status of Pacific sand lance and no information regarding potential stressors such as contaminants.

Washington↗
USGS2018

Describing the distribution and productivity of biota along a nearshore to offshore gradient

The Lake Michigan Lakewide Action and Management Plan (LAMP) proposed adding nutrients (phosphorus) to its “pollutant of concern” list in 2002, given that excessive nutrients were causing impairments in nearshore waters. Since that time, scientists have highlighted the “shunting” of nutrients to the nearshore (Hecky et al. 2004), owing to the ability of invasive dreissenid mussels to capture some portion of allochthonous phosphorus that enters the lake through tributaries. These changes are believed to increase productivity in the nearshore, reflected in increased benthic and pelagic primary production and nuisance Cladophora (Auer et al. 2010). Whether increases in primary productivity lead to concomitant increases for secondary (by zooplankton) and tertiary (by fish) production remains largely untested. Hence, understanding the distribution and abundance of nutrients and biota (e.g., zooplankton, fish) across a nearshore to offshore gradient was identified as a Cooperative Science and Monitoring Initiative (CSMI) priority in 2015. Increased understanding of the Lake Michigan nearshore will also facilitate the development of a Nearshore Strategy by the LAMP, which is called for in the 2012 Great Lakes Water Quality Agreement. Working collaboratively with Environmental Protection Agency (EPA) and National Oceanic and Atmospheric Administration (NOAA), United States Geological Survey (USGS) described the distribution of nutrients and biota across nearshore to offshore transects in 2015 (see Appendix 1). At each transect, we sampled the food web at three sites with differing bottom depths: 18 m, 46 m, and 91-110 m. We purposefully chose transects near tributaries of varying total phosphorus (TP) input (see Figure 1, Dolan and Chapra 2012): three transects that were not associated with any large tributary where total phosphorus would be loaded (Waukegan IL, Frankfort MI, Sturgeon Bay WI), three transects adjacent to tributaries presumed to be relatively low loaders of TP (Pere Marquette MI, Root WI, Muskegon MI), and three transects adjacent to tributaries presumed to be relatively high loaders of TP (St. Joseph MI, Kalamazoo MI, Manitowoc WI). USGS estimated chlorophyll concentrations, zooplankton, Mysis , larval fish, and juvenile and adult fish seasonally (April/May, July, October/November) at eight of these transects (all but Muskegon).

Illinois, Michigan, Wisconsin↗
USGS2020

How and why is the timing and occurrence of seasonal migrants in the Gulf of Maine changing due to climate?

Plants and animals undergo certain recurring life-cycle events, such as migrations between summer and winter habitats or the annual blooming of plants. Known as phenology, the timing of these events is very sensitive to changes in climate (and changes in one species’ phenology can impact entire food webs and ecosystems). Shifts in phenology have been described as a “fingerprint” of the temporal and spatial responses of wildlife to climate change impacts. Thus, phenology provides one of the strongest indicators of the adaptive capacity of organisms (or the ability of organisms to cope with future environmental conditions). In this study, researchers are exploring how the timing and occurrence of a number of highly migratory marine animals is changing due to a series of climatic and ecological shifts. First, using existing long-term historical data series, they will determine the direction and magnitude of how migration, abundance, or other phenological factors have changed for marine mammals, sea turtles, and fishes that migrate into the Gulf of Maine on a seasonal basis. Because marine animals are inherently difficult to detect, the team will apply dynamic occupancy models to evaluate seasonal migration patterns and habitat use across multiple habitats in the Gulf of Maine region. The project team will also synthesize regional information on a key, ecologically-important prey fish, sandlance, whose timing and abundance is a strong predictor of the occurrence and behavior of predator species targeted in this study as well as a range of other regional fish and wildlife of conservation and management concern. Results from this component of the project will identify coastal fish and wildlife species that are relatively more or less able to adapt and thus potentially vulnerable to climate change; determine the likely primary drivers of those changes; and identify data gaps and future monitoring needs. Ultimately, this information will be available and useful for regional coastal management and adaptation decisions that will allow managers to effectively plan for the future. In a second component of the project, researchers will focus specifically on changes in migration patterns of the endangered North Atlantic right whale. While shifts in the distribution and time of recurring life events are adaptive responses that may help species cope with climate impacts, they can also lead to changes in how species interact with humans. The North Atlantic right whale is one of the most endangered whale species on the planet. In the North Atlantic Ocean, ship strikes and entanglements with commercial fishing gear represent fatal threats to right whales. Recent reports suggest that North Atlantic right whale migration patterns have changed. Many researchers posit that shifts in migration are responsible for recent increases in the overlap between right whales and human activities, especially fishing. To help understand how changes in right whale movements and behaviors may overlap with ship traffic, and thus put the animals at risk of encountering vessels, we will combine right whale habitat models with ship traffic maps. The end result will be a set of maps identifying risk levels.

Gulf of Maine↗