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USGS2022

California Deepwater Investigations and Groundtruthing (Cal DIG) I, volume 3 — Benthic habitat characterization offshore Morro Bay, California

Coastal and Marine Ecological Classification Standard (CMECS) geoform, substrate, and biotic component geographic information system (GIS) products were developed for the U.S. Exclusive Economic Zone (U.S. EEZ) of south-central California in the region of Santa Lucia Bank motivated by interest in development of offshore wind-energy capacity and infrastructure. The Bureau of Ocean Energy Management (BOEM), in coordination with the State of California and many other members of the California Task Force, issued calls for information in 2018 for the study area offshore of Morro Bay, California. The study area is in depths of 500 to 1,200 meters (m) and adjacent to a decommissioned nuclear power plant with a developed electric grid connection, and in an area of high wind resource. BOEM is the lead agency responsible for planning and leasing in the U.S. EEZ and funded this project to assess baseline conditions of, and the potential effects on, the seafloor environment. This project, carried out by the U.S. Geological Survey (USGS), resulted in three reports: one on biological analysis of seafloor video data, one on analysis of the geologic framework and hazards, and this report on seafloor habitat. The study area consists of 8,424 square kilometers (km 2 ) of multibeam echo sounder (MBES) data acquired during five surveys from 2016 to 2019. Remotely operated vehicle (ROV) video was acquired in 2019 to supervise the classification of the MBES data into habitats. Derivatives of the MBES data were classified into 16 unique biotopes, 6 substrate types, 28 modifier groups, and 22 geoforms. The study area substrate is predominantly soft sediment (mud and fine sand) covering 7,804 km 2 (92.7 percent) of the area. Mixed substrate areas on rocky banks, channel scarps, and the shelf break comprise 404 km 2 (4.8 percent) of the study area. Hard substrate areas are found predominantly on the tops and flanks of banks and on bank ridges that separate canyons incising the banks. Hard substrates comprise 211 km 2 of the study area (2.5 percent). After the bathymetry and backscatter raster images (rasters) were classified, manual editing was also done to remove noise artifacts. This effort was not completely successful and there are numerous erroneous small areas in the rasters that have been passed on to the CMECS polygon product. Nearly 120,000 annotations of organisms and their habitat were made from 25 video transects selected from 185 hours of ROV video. In total, 2,714 km 2 of seafloor were successfully assigned to biotopes. Some biotopes were assigned to separate areas spatially distant from the transects that define the biotope. Expected relations between physical habitat and biota such as the number of species and the substrate induration and rugosity were verified. Slope is typically a predictive variable and was used in the classification of habitat, but the ground truth used for biotic component analysis included very little steeply sloping area. Ground-truth ROV operations were reduced by the sea state; additional ground truth could improve the biotic results and increase confidence in the spatial distribution of classifications reported here.

California↗

USGS2021

Egg retention of high-latitude sockeye salmon (Oncorhynchus nerka) in the Pilgrim River, Alaska, during the Pacific marine heatwave of 2014–2016

Ocean and freshwater conditions can influence spawning success of Pacific salmon ( Oncorhynchus spp.) by governing the energy content of fish at the start of and during the spawning migration. Ocean conditions determine the energy stores of fish at the freshwater entry, while freshwater conditions determine how quickly stored energy is depleted as individuals migrate to spawning grounds in natal rivers and lakes. We assessed the occurrence of sockeye salmon ( Oncorhynchus nerka ) egg retention (failure to deposit eggs) in a high-latitude (~ 65°N) watershed that has a large, inter-annual variation in the number of returning adults. We also explored relationships between ocean and freshwater conditions with egg retention of female sockeye salmon. The proportion of females with egg retention (> 50 eggs) varied by threefold (12 to 36%) across years (2013 to 2020) and was related to ocean conditions represented by the North Pacific Index (NPI). Egg retention was more common in years with low NPI values (a stronger Aleutian Low) in association with the Pacific marine heatwave of 2014–2016 that disrupted food webs. This initial study contains the first empirical data observing the influence of ocean conditions on egg retention for any Pacific salmon population. The lack of any relationship between egg retention and freshwater temperatures was consistent with water temperatures primarily occurring below thresholds associated with heat stress related mortality (< 18 °C). Understanding the amount of egg retention and how environmental drivers influence egg retention within Pacific salmon populations provides insights for managers assessing the number of successful spawners and helps refine escapement-based management efforts.

Alaska↗

USGS2015

California State Waters Map Series — Drakes Bay and vicinity, California

In 2007, the California Ocean Protection Council initiated the California Seafloor Mapping Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, marine benthic habitats, and geology within the 3-nautical-mile limit of California’s State Waters. The CSMP approach is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar data, acoustic backscatter, seafloor video, seafloor photography, high-resolution seismic-reflection profiles, and bottom-sediment sampling data. The map products display seafloor morphology and character, identify potential marine benthic habitats, and illustrate both the surficial seafloor geology and shallow (to about 100 m) subsurface geology. The Drakes Bay and Vicinity map area is located in northern California, about 30 km north of San Francisco and about 65 km south of Fort Ross. The map area is in the northern part of the Gulf of the Farallones National Marine Sanctuary, and it includes all or parts of four California Marine Protected Areas. The largely undeveloped onshore part of the map area, which occupies much of the southern and southeastern parts of the Point Reyes peninsula, is used primarily for grazing, as well as recreation, as it is home to the Point Reyes National Seashore. The triangular Point Reyes peninsula, which lies completely west of the San Andreas Fault Zone, is bounded by the steep terrain of Inverness Ridge along its northeastern margin, Tomales Point at its northernmost tip, Point Reyes at its southwesternmost point, and Bolinas at its southern end. The landscape in between includes (from southeast to northwest) the sandy beaches along Drakes Bay, the estuaries of Drakes Estero and Estero de Limantour, and the long, windswept Point Reyes Beach, which is backed by an extensive dune field. The seafloor in the map area generally extends from the shoreline to water depths of about 40 to 50 m, except for the area south of the Point Reyes headland where water depths reach 60 to 70 m. This bathymetric gradient south and west of the Point Reyes headland is related to north-side-up motion along the Point Reyes Fault Zone. Except for the bathymetric gradient across the Point Reyes Fault Zone, the bedrock platform in the nearshore and inner shelf areas (50 to 60 m depth) is relatively flat (less than 1.0°) and is overlain by sand-sized to coarser grained sediment. Finer grained sediments are found in water depths greater than 60 m south of the Point Reyes headland, but they also extend into shallower (less than 40 m) water within Drakes Bay. Surficial and shallow sediments were deposited in the last about 21,000 years during the approximately 125-m sea-level rise that followed the last major lowstand associated with the Last Glacial Maximum, at which time the entire Drakes Bay and Vicinity map area was emergent and the shoreline was about 30 km south and west of the present-day shoreline. Tectonic influences that impact the shelf morphology and geology in the map area are related to local faulting, folding, uplift, and subsidence. Offshore of the Point Reyes headland, granitic basement rocks are offset vertically about 1.4 km along the Point Reyes Fault Zone; this uplift, combined with west-side-up offset on the San Andreas Fault Zone, has resulted in uplift of the Point Reyes peninsula and the adjacent shelf. Late Pleistocene uplift of marine terraces on the southern Point Reyes peninsula suggests active deformation of offshore structures west of the San Andreas Fault Zone. Pervasive stratal thinning within inferred uppermost Pliocene and Pleistocene deposits above the west strand of the Point Reyes Fault Zone suggests Quaternary active shortening of the curvilinear, northeast- to north-dipping Point Reyes Fault Zone. Lack of clear deformation in the uppermost Pleistocene and Holocene deposits suggests that activity along the Point Reyes Fault Zone has ceased or slowed since about 21,000 years ago. Seafloor habitats in the Drakes Bay and Vicinity map area range from unconsolidated continental-shelf sediment to hard substrate. Rocky-shelf outcrops and rubble are considered to be promising potential habitats for rockfish and lingcod, both of which are recreationally and commercially important species. Circulation over the continental shelf in the map area is dominated by the southward-flowing California Current, the eastern limb of the North Pacific Gyre. Associated upwelling brings cool, nutrient-rich waters to the surface, resulting in high biological productivity. The current flow generally is southeastward during the spring and summer; however, during the fall and winter, the otherwise persistent northwest winds are sometimes weak or absent, causing the California Current to move farther offshore and the Davidson Current, a weaker, northward-flowing countercurrent, to become active. Sediment transport in the map area largely is controlled by surface waves and tidal currents in the nearshore and, at depths greater than 20 to 30 m, by tidal and subtidal currents. In the map area, nearshore littoral drift of sand and coarse sediment is to the south, owing to the dominant west-northwest swell direction, and scour from large waves and tidal currents removes and redistributes sediment over large areas of the inner shelf. Tidal currents are particularly strong over the shelf in the map area, and they dominate the current regime in the nearshore. Further offshore, bottom currents generally flow to the northwest, distributing finer grained sediment accordingly.

California↗

USGS1984

Geochemistry of a naturally occurring massive marine gas hydrate

During Deep Sea Drilling Project (DSDP) Leg 84 a core 1 m long and 6 cm in diameter of massive gas hydrate was unexpectedly recovered at Site 570 in upper slope sediment of the Middle America Trench offshore of Guatemala. This core contained only 5–7% sediment, the remainder being the solid hydrate composed of gas and water. Samples of the gas hydrate were decomposed under controlled conditions in a closed container maintained at 4°C. Gas pressure increased and asymptotically approached the equilibrium decomposition pressure for an ideal methane hydrate, CH 4 .5-3/4H 2 O, of 3930 kPa and approached to this pressure after each time gas was released, until the gas hydrate was completely decomposed. The gas evolved during hydrate decomposition was 99.4% methane, ∼0.2% ethane, and ∼0.4% CO 2 . Hydrocarbons from propane to heptane were also present, but in concentrations of less than 100 p.p.m. The carbon-isotopic composition of methane was −41 to −44 permil(( 0 00 "> 000 ), relative to PDB standard. The observed volumetric methane/water ratio was 64 or 67, which indicates that before it was stored and analyzed, the gas hydrate probably had lost methane. The sample material used in the experiments was likely a mixture of methane hydrate and water ice. Formation of this massive gas hydrate probably involved the following processes: (i) upward migration of gas and its accumulation in a zone where conditions favored the growth of gas hydrates, (ii) continued, unusually rapid biological generation of methane, and (iii) release of gas from water solution as pressure decreased due to sea level lowering and tectonic uplift.

Middle America Trench↗

USGS2010

Shifting microbial community structure across a marine terrace grassland chronosequence, Santa Cruz, California

Changes in the biomass and structure of soil microbial communities have the potential to impact ecosystems via interactions with plants and weathering minerals. Previous studies of forested long-term (1000s – 100,000s of years) chronosequences suggest that surface microbial communities change with soil age. However, significant gaps remain in our understanding of long-term soil microbial community dynamics, especially for non-forested ecosystems and in subsurface soil horizons. We investigated soil chemistry, aboveground plant productivity, and soil microbial communities across a grassland chronosequence (65,000–226,000 yrs old) located near Santa Cruz, CA. Aboveground net primary productivity (ANPP) initially increased to a maximum and then decreased for the older soils. We used polar lipid fatty acids (PLFA) to investigate microbial communities including both surface (<0.1 m) and subsurface (≥0.2 m) soil horizons. PLFAs characteristic of Gram-positive bacteria and actinobacteria increased as a fraction of the microbial community with depth while the fungal fraction decreased relative to the surface. Differences among microbial communities from each chronosequence soil were found primarily in the subsurface where older subsurface soils had smaller microbial community biomass, a higher proportion of fungi, and a different community structure than the younger subsurface soil. Subsurface microbial community shifts in biomass and community structure correlated with, and were likely driven by, decreasing soil P availability and Ca concentrations, respectively. Trends in soil chemistry as a function of soil age led to the separation of the biological (≤1 m depth) and geochemical (>1 m) cycles in the old, slowly eroding landscape we investigated, indicating that this separation, commonly observed in tropical and subtropical ecosystems, can also occur in temperate climates. This study is the first to investigate subsurface microbial communities in a long-term chronosequence. Our results highlight connections between soil chemistry and both the aboveground and belowground parts of an ecosystem.

California↗

USGS1993

Inorganic geochemistry of domed peat in Indonesia and its implication for the origin of mineral matter in coal

The inorganic geochemistry of three domed ombrogenous peat deposits in Riau and West Kalimantan provinces, Indonesia, was investigated as a possible modern analogue for certain types of low-ash, low-sulfur coal. Mineral matter entering the deposits is apparently limited to small amounts from the allogenic sources of dryfall, rainfall, and diffusion from substrate pore water. In the low-ash peat in the interior of the deposits, a large portion of the mineral matter is authigenic and has been mobilized and stabilized by hydrological, chemical, and biological processes and conditions. Ash yield and sulfur content are low through most of the peat deposits and average 1.1% and 0.14%, respectively, on a moisture-free basis. Ash and sulfur contents only exceed 5% and 0.3%, respectively, near the base of the deposits, with maximum concentrations of 19.9% ash and 0.56% sulfur. Peat water in all three deposits has a low pH, about 4 units, and low dissolved cation concentration, averaging 14 ppm. Near the base, in the geographic interior of each peat deposit, pH is about two units higher and dissolved cation concentration averages 110 ppm. Relative concentrations of the inorganic constituents vary, resulting in chemical facies in the peat. In general, Si, Al, and Fe are the abundant inorganic constituents, although Mg, Ca, and Na dominate in the middle horizon in the geographic interior of coastal peat deposits. The composition of the three deposits reported in this paper indicates that domed ombrogenous peat deposits will result in low ash and sulfur coal, probably less than 10% ash and 1% sulfur, even if marine rocks are laterally and vertically adjacent to the coal.

Special Paper of the Geological Society of America↗

USGS2003

Arthrophycus in the Silurian of Alabama (USA) and the problem of compound trace fossils

Arthrophycus brongniartii (Harlan, 1832) is common in marginal-marine deposits in the Silurian Red Mountain Formation of Alabama. The ichnospecies, the second to be named in North America, is revived and emended after long disuse. Transitional forms to Rusophycus isp. and other morphologic evidence indicate that the maker of Arthrophycus was an arthropod, perhaps a trinucleine (raphiophorid?) trilobite. Interconnection of Arthrophycus and Nereites biserialis, as well as intergradation of Arthrophycus with Cruziana aff. quadrata, Phycodes flabellum, and Asterosoma ludwigae, indicate that these Red Mountain trace fossils were made by the same species of arthropod. Possible relationships with Arthrophycus alleghaniensis (Harlan, 1831) in the Silurian belt from Ontario to Tennessee are also explored. Ichnofamily Arthrophycidae Schimper, 1879 is emended. The ichnofamily is interpreted as chiefly the work of arthropods. Arthrophycus and other trace fossils from the Silurian of Alabama constitute a test case to build criteria for recognizing the members of complexes of trace fossils. In general, criteria such as interconnection of different forms, intergradation among unconnected forms, similarity of size, similarity of morphologic elements, and co-occurrence should be examined in order to determine the biologic and ethologic interrelationships of trace fossils. ?? 2003 Elsevier Science B.V. All rights reserved.

Palaeogeography, Palaeoclimatology, Palaeoecology↗

USGS2015

Evaluating unsupervised methods to size and classify suspended particles using digital in-line holography

Substantial information can be gained from digital in-line holography of marine particles, eliminating depth-of-field and focusing errors associated with standard lens-based imaging methods. However, for the technique to reach its full potential in oceanographic research, fully unsupervised (automated) methods are required for focusing, segmentation, sizing and classification of particles. These computational challenges are the subject of this paper, in which we draw upon data collected using a variety of holographic systems developed at Plymouth University, UK, from a significant range of particle types, sizes and shapes. A new method for noise reduction in reconstructed planes is found to be successful in aiding particle segmentation and sizing. The performance of an automated routine for deriving particle characteristics (and subsequent size distributions) is evaluated against equivalent size metrics obtained by a trained operative measuring grain axes on screen. The unsupervised method is found to be reliable, despite some errors resulting from over-segmentation of particles. A simple unsupervised particle classification system is developed, and is capable of successfully differentiating sand grains, bubbles and diatoms from within the surf-zone. Avoiding miscounting bubbles and biological particles as sand grains enables more accurate estimates of sand concentrations, and is especially important in deployments of particle monitoring instrumentation in aerated water. Perhaps the greatest potential for further development in the computational aspects of particle holography is in the area of unsupervised particle classification. The simple method proposed here provides a foundation upon which further development could lead to reliable identification of more complex particle populations, such as those containing phytoplankton, zooplankton, flocculated cohesive sediments and oil droplets.

Journal of Atmospheric and Oceanic Technology↗

USGS1972

Biological data on PCBs in animals other than man

SUMMARY: Polychlorinated biphenyls have become ubiquitous in the world ecosystem in quantities similar to those of DDE. Experimental studies have shown that PCBs have a toxicity to mallards, pheasants, bobwhite quail, coturnix quail, red-winged blackbirds, starlings, cowbirds, and grackles that is of the same order as the toxicity of DDE to these species. Overt signs of poisoning also are similar to those caused by compounds of the DDT group. Toxic effects of DDE and Aroclor 1254 to coturnix chicks were additive, but not synergistic. PCBs containing higher percentages of chlorine are more toxic to birds than those containing lower percentages. PCBs of foreign manufacture contained contaminants to an extent that greatly increased their toxicity. Residues of PCBs in the brains of birds killed by these compounds measure in the hundreds of parts per million. PCBs may have contributed to mortality of some birds in the field. Toxicity to insects of PCBs of different degrees of chlorination is the reverse of the pattern in birds: the lower chlorinations are more toxic to insects. PCBs enhanced the toxicity of dieldrin and DDT to insects. Shrimp are very sensitive to PCBs and most will die as a result of 20-day exposure to a concentration of 5 ppb. PCBs also inhibit shell growth of oysters. Crabs are less sensitive; all accumulate residues to many times the concentrations in the water, and a test with crabs showed that they lost the residues very slowly. Growth of certain species of marine diatoms was experimentally inhibited by PCBs, but algae were not affected. The small marine crustacean, Gammarus, is sensitive to PCBs in concentrations of thousandths to tenths of a part per billion. Exposure to 5 ppb of Aroclor 1254 caused mortality of two species of fish in 14-45 days. Onset of death was delayed and was accompanied by fungus-like lesions. Rainbow trout were quickly killed by terphenyls at 10 ppb under normal oxygen conditions and at 2 ppb with reduced oxygen. Metabolic changes of PCBs have been suggested by environmental observations of different isomeric patterns in animals of different trophic levels. Quantitative differences also are pronounced, with magnifications of hundreds to thousands of times. Laboratory studies have shown no metabolic changes of PCBs by crabs and shrimps, minimal changes by fish, and pronounced changes by birds. PCBs induce microsomal enzyme activity in birds. Exposure to PCBs increased the susceptibility of mallard ducklings to duck hepatitis virus. Offspring of pheasants whose parents received high dosages of PCBs made poor choices in visual cliff tests. Egg production and hatching after pipping also were affected. Migratory restlessness was increased in English robins exposed to PCBs. Long-term studies of the reproductive effects of Aroclor 1254 on mallards and bobwhite quail and of Aroclor 1254 plus DDE on quail showed no significant differences from controls. In studies of chickens, however, egg production and hatchability were impaired by high doses of Aroclor 1254 and by low doses of Aroclor 1242. Statistical evaluations of the role that different chemicals may play in thinning eggshells of brown pelicans showed that DDE residues correlate better with shell thinning than do residues of dieldrin or PCBs, confirming observations with cormorants and white pelicans.

Book chapter↗

USGS2003

A stable carbon isotope and biological marker study of Polish bituminous coals and carbonaceous shales

Biological marker and carbon isotopic compositions of coals and carbonaceous shales from the Upper Carboniferous strata of the Upper Silesian (USCB), Lower Silesian (LSCB), and Lublin (LCB) coal basins were determined to assess depositional conditions and sources of the organic matter. n-Alkane, sterane, and isoprenoid distribution, and carbon isotope ratios are consistent with an origin from higher plants. In some cases, pristane/phytane (Pr/Ph) ratios of carbonaceous shales (roof and floor shales) are < 1.0, while the associated coals have high ratios (??? 1.0). This suggests that reducing conditions prevailed during deposition of the shales, but a period of oxidizing conditions accompanied deposition of the coals. Steranes present in coal extracts are dominated by the 14??(H)17??(H)20R C29 stereoisomers, typical, but not conclusive, of higher plant origin. Carbonaceous shales exhibit a wider range of sterane composition, suggesting local, significant input of algal organic matter. Significant amounts of benzohopanes and gammacerane are present in some coals. Although benzohopanes are present at least in small amounts in samples from many different environments, they have been reported to occur most commonly in marine environments. The present study seems to provide the first example where benzohopanes have been reported in significant amounts in terrestrial organic matter. Gammacerane is abundant in rocks or sediments deposited in carbonate or highly saline marine environments. The finding of high gammacerane concentrations in the coals expands the depositional settings in which it has been observed and questions its utility as an independent indicator of hypersaline carbonate environments. Stable carbon isotope composition of coals, and type III kerogen in carbonaceous shales as well as correlation of stable carbon isotope composition of saturated and aromatic hydrocarbons in carbonaceous shales from both the USCB and the LSCB indicate terrigenous origin. Bitumens are always co-genetic with associated coals and kerogens. Isotopic data reveal that Sofer's genetic classification of oils is not applicable to organic matter in coals. ?? 2003 Elsevier B.V. All rights reserved.

International Journal of Coal Geology↗

USGS2021

Heatwave-induced synchrony within forage fish portfolio disrupts energy flow to top pelagic predators

During the Pacific marine heatwave of 2014–2016, abundance and quality of several key forage fish species in the Gulf of Alaska were simultaneously reduced throughout the system. Capelin ( Mallotus catervarius ), sand lance ( Ammodytes personatus ), and herring ( Clupea pallasii ) populations were at historically low levels, and within this community abrupt declines in portfolio effects identify trophic instability at the onset of the heatwave. Although compensatory changes in age‐structure, size, growth or energy content of forage fish were observed to varying degrees among all these forage fish, none were able to fully mitigate adverse impacts of the heatwave, which likely included both top‐down and bottom‐up forcing. Notably, changes to the demographic structure of forage fish suggested size‐selective removals typical of top‐down regulation. At the same time, zooplankton community structure may have driven bottom‐up regulation as copepod community structure shifted towards smaller, warm‐water species, and euphausiid biomass was reduced owing to the loss of cold‐water species. Mediated by these impacts on the forage fish community, an unprecedented disruption of the normal pelagic food web was signaled by higher trophic level disruptions during 2015–2016, when seabirds, marine mammals, and groundfish experienced shifts in distribution, mass mortalities, and reproductive failures. Unlike decadal‐scale variability underlying ecosystem regime shifts, the heatwave appeared to temporarily overwhelm the ability of the forage fish community to buffer against changes imposed by warm water anomalies, thereby eliminating any ecological advantages that may have accrued from having a suite of coexisting forage species with differing life history compensations.

Alaska↗

USGS2012

A review of the key genetic tools to assist imperiled species conservation: analyzing West Indian manatee populations

Managers faced with decisions on threatened and endangered wildlife populations often are lacking detailed information about the species of concern. Integration of genetic applications will provide management teams with a better ability to assess and monitor recovery efforts on imperiled species. The field of molecular biology continues to progress rapidly and many tools are currently available. Presently, little guidance is available to assist researchers and managers with the appropriate selection of genetic tools to study the status of wild manatee populations. We discuss several genetic tools currently employed in the application of conservation genetics, and address the utility of using these tools to determine population status to aid in conservation efforts. As an example, special emphasis is focused on the endangered West Indian manatee (Order Sirenia). All four extant species of sirenians are imperiled throughout their range, predominately due to anthropogenic sources; therefore, the need for genetic information on their population status is direly needed.

Journal of Marine Animals and Their Ecology↗

USGS2022

Alaskan Yelloweye Rockfish fecundity revealed through an automated egg count and digital imagery method

Spawning stock biomass (SSB) is often used as an index for reproductive potential (RP) in fisheries stock assessments. This method assumes that mature female biomass is proportional to total egg production and implies that (1) the fecundity–length relationship follows a cubic function or (2) relative fecundity is constant. For many marine fishes, adequate fecundity estimates to evaluate these relationships are lacking. This study estimated fecundity and fecundity relationships for Yelloweye Rockfish Sebastes ruberrimus and evaluated an automated method of counting eggs and larvae. We collected Yelloweye Rockfish ovaries ( N = 90) from the northern Gulf of Alaska, including Prince William Sound, Alaska, during 2018–2019 and used the gravimetric method and image analysis software to count eggs from digital camera images. To evaluate the speed, accuracy, and precision of the automated counting procedure, one-third of the gravimetric samples were also manually counted. Image analysis software was approximately four times faster but equally accurate and precise for fecundity estimates relative to manual counts. Fecundity ranged from 53,249 to 3.052 × 10 6 eggs (mean ± SD = 896,762 ± 699,504 eggs), and relative fecundity increased with female FL and ranged from 68 to 435 eggs/g of body weight (mean ± SD = 226 ± 87 eggs/g). The use of SSB for Yelloweye Rockfish stock assessment could underestimate the contribution to egg production by larger (>5.6-kg) females, overestimate the contribution by smaller females, and lead to biased biological reference points. This study provides critical information to more realistically model RP and improve stock assessment inputs for the development of harvest control rules for Yelloweye Rockfish. Additionally, the use of image analysis software to count eggs in digital images proved to be an effective fecundity estimation method that could be applied to other highly fecund fish species for which the time demand of manual counting methods would be prohibitive.

Alaska↗

USGS2009

Chemical weathering of a marine terrace chronosequence, Santa Cruz, California. Part II: Solute profiles, gradients and the comparisons of contemporary and long-term weathering rates

The spatial and temporal changes in hydrology and pore water elemental and 87 Sr/ 86 Sr compositions are used to determine contemporary weathering rates in a 65- to 226-kyr-old soil chronosequence formed from granitic sediments deposited on marine terraces along coastal California. Soil moisture, tension and saturation exhibit large seasonal variations in shallow soils in response to a Mediterranean climate. These climate effects are dampened in underlying argillic horizons that progressively developed in older soils, and reached steady-state conditions in unsaturated horizons extending to depths in excess of 15 m. Hydraulic fluxes (q h ), based on Cl mass balances, vary from 0.06 to 0.22 m yr -1 , resulting in fluid residence times in the terraces of 10-24 yrs. As expected for a coastal environment, the order of cation abundances in soil pore waters is comparable to sea water, i.e., Na > Mg > Ca > K > Sr, while the anion sequence Cl > NO 3 > HCO 3 > SO 4 reflects modifying effects of nutrient cycling in the grassland vegetation. Net Cl-corrected solute Na, K and Si increase with depth, denoting inputs from feldspar weathering. Solute 87 Sr/ 86 Sr ratios exhibit progressive mixing of sea water-dominated precipitation with inputs from less radiogenic plagioclase. While net Sr and Ca concentrations are anomalously high in shallow soils due to biological cycling, they decline with depth to low and/or negative net concentrations. Ca/Mg, Sr/Mg and 87 Sr/ 86 Sr solute and exchange ratios are similar in all the terraces, denoting active exchange equilibration with selectivities close to unity for both detrital smectite and secondary kaolinite. Large differences in the magnitudes of the pore waters and exchange reservoirs result in short-term buffering of the solute Ca, Sr, and Mg. Such buffering over geologic time scales can not be sustained due to declining inputs from residual plagioclase and smectite, implying periodic resetting of the exchange reservoir such as by past vegetational changes and/or climate. Pore waters approach thermodynamic saturation with respect to albite at depth in the younger terraces, indicating that weathering rates ultimately become transport-limited and dependent on hydrologic flux. Contemporary rates R solute are estimated from linear Na and Si pore weathering gradients b solute such that R solute = frac(q h , b solute ?? S v ) where S v is the volumetric surface area and ?? is the stoichiometric coefficient. Plagioclase weathering rates (0.38-2.8 ?? 10 -15 mol m -2 s -1 ) are comparable to those based on 87 Sr/ 86 Sr mass balances and solid-state Na and Ca gradients using analogous gradient approximations. In addition, contemporary solute gradients, under transport-limited conditions, approximate long-term solid-state gradients when normalized against the mass of protolith plagioclase and its corresponding aqueous solubility. The multi-faceted weathering analysis presented in this paper is perhaps the most comprehensive yet applied to a single field study. Within uncertainties of the methods used, present day weathering rates, based on solute characterizations, are comparable to average long-term past rates as evidenced by soil profiles.

Geochimica et Cosmochimica Acta↗

USGS1980

Geology and biology of Oceanographer submarine canyon.

Santonian beds more than 100 m thick are the oldest rocks collected from the canyon. Quaternary silty clay veneers the canyon walls in many places and is commonly burrowed by benthic organisms that cause extensive erosion of the canyon walls, especially in the depth zone (100-1300 m) inhabited by the crabs Geryon and Cancer. Bioerosion is minimal on high, near-vertical cliffs of sedimentary rock, in areas of continual sediment movement, and where the sea floor is paved by gravel. A thin layer of rippled, unconsolidated silt and sand is commonly present on the canyon walls and in the axis. Shelf sediments are transported from Georges Bank over the E rim and in the Canyon by the SW drift and storm currents; tidal currents and internal waves move the sediment downcanyon along the walls and axis.- from Authors

Marine Geology↗

USGS2022

Diet analysis using generalized linear models derived from foraging processes using R package mvtweedie

Diet analysis integrates a wide variety of visual, chemical, and biological identification of prey. Samples are often treated as compositional data, where each prey is analyzed as a continuous percentage of the total. However, analyzing compositional data results in analytical challenges, for example, highly parameterized models or prior transformation of data. Here, we present a novel approximation involving a Tweedie generalized linear model (GLM). We first review how this approximation emerges from considering predator foraging as a thinned and marked point process (with marks representing prey species and individual prey size). This derivation can motivate future theoretical and applied developments. We then provide a practical tutorial for the Tweedie GLM using new package mvtweedie that extends capabilities of widely used packages in R ( mgcv and ggplot2 ) by transforming output to calculate prey compositions. We demonstrate this approach and software using two examples. Tufted Puffins ( Fratercula cirrhata ) provisioning their chicks on a colony in the northern Gulf of Alaska show decadal prey switching among sand lance and prowfish (1980–2000) and then Pacific herring and capelin (2000–2020), while wolves ( Canis lupus ligoni ) in southeast Alaska forage on mountain goats and marmots in northern uplands and marine mammals in seaward island coastlines.

Ecology↗

USGS2008

Common relationships among proximate composition components in fishes

Relationships between the various body proximate components and dry matter content were examined for five species of fishes, representing anadromous, marine and freshwater species: chum salmon Oncorhynchus keta, Chinook salmon Oncorhynchus tshawytscha, brook trout Salvelinus fontinalis, bluefish Pomatomus saltatrix and striped bass Morone saxatilis. The dry matter content or per cent dry mass of these fishes can be used to reliably predict the per cent composition of the other components. Therefore, with validation it is possible to estimate fat, protein and ash content of fishes from per cent dry mass information, reducing the need for costly and time-consuming laboratory proximate analysis. This approach coupled with new methods of non-lethal estimation of per cent dry mass, such as from bioelectrical impedance analysis, can provide non-destructive measurements of proximate composition of fishes. ?? 2008 The Authors.

Journal of Fish Biology↗

USGS2006

Modeling habitat distribution from organism occurrences and environmental data: Case study using anemonefishes and their sea anemone hosts

We demonstrate the KGSMapper (Kansas Geological Survey Mapper), a straightforward, web-based biogeographic tool that uses environmental conditions of places where members of a taxon are known to occur to find other places containing suitable habitat for them. Using occurrence data for anemonefishes or their host sea anemones, and data for environmental parameters, we generated maps of suitable habitat for the organisms. The fact that the fishes are obligate symbionts of the anemones allowed us to validate the KGSMapper output: we were able to compare the inferred occurrence of the organism to that of the actual occurrence of its symbiont. Characterizing suitable habitat for these organisms in the Indo-West Pacific, the region where they naturally occur, can be used to guide conservation efforts, field work, etc.; defining suitable habitat for them in the Atlantic and eastern Pacific is relevant to identifying areas vulnerable to biological invasions. We advocate distinguishing between these 2 sorts of model output, terming the former maps of realized habitat and the latter maps of potential habitat. Creation of a niche model requires adding biotic data to the environmental data used for habitat maps: we included data on fish occurrences to infer anemone distribution and vice versa. Altering the selection of environmental variables allowed us to investigate which variables may exert the most influence on organism distribution. Adding variables does not necessarily improve precision of the model output. KGSMapper output distinguishes areas that fall within 1 standard deviation (SD) of the mean environmental variable values for places where members of the taxon occur, within 2 SD, and within the entire range of values; eliminating outliers or data known to be imprecise or inaccurate improved output precision mainly in the 2 SD range and beyond. Thus, KGSMapper is robust in the face of questionable data, offering the user a way to recognize and clean such data. It also functions well with sparse datasets. These features make it useful for biogeographic meta-analyses with the diverse, distributed datasets that are typical for marine organisms lacking direct commercial value. ?? Inter-Research 2006.

Marine Ecology Progress Series↗