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At least 19 recordsLinked to original sources
USGS2021

Genetics as a tool for conservation and management of West Indian manatee populations in Brazil

A study conducted by the National Center for Research and Conservation of Aquatic Mammals (CMA), United States Geological Survey Wetland and Aquatic Research Center, and partner researchers found that the marine Antillean manatee ( Trichechus manatus manatus ) has low genetic diversity in regions where there are territorial interfaces with the Amazonian manatee ( Trichechus inunguis ). The study was published as an article in the journal, Frontiers in Marine Science.

Sirenews↗
USGS2002

Comparison of stomach contents of haddock (Melanogrammus aeglefinus) from the 1981 and 1991 North Sea International Stomach Sampling Projects

This study analyses data from over 20 000 haddock stomachs collected during the 1981 and 1991 Stomach Sampling Projects of the North Sea. Sampling was within the framework of the Multispecies Virtual Population Analysis (MSVPA) for fisheries stock assessment. In 1981 stomachs were collected to calculate input feeding parameters from main predators. During 1991 the sampling exercise was repeated to test stability of the parameters in the region. We investigate stability of haddock stomach content weight between years accounting for ontogenic, spatial and temporal variations within the scope of the survey resolution. Analysis using generalized linear and additive models is performed for weight of the stomach content including and excluding empty stomachs and also for proportion of stomachs without food. Results indicate that haddock stomach contents varied significantly between years, quarters and North Sea roundfish areas. Content weights were overall higher in 1981 than in 1991. In 1981 levels were high from spring to fall and in 1991 mostly in spring. During both years levels were lowest in the central North Sea and in winter. Most of the deviance in modelling the stomach weight is explained by the length of the predator. Stomachs sampled in 1981 were most frequently empty in spring and those sampled in 1991 in winter. In both years, proportions decreased with fish length except in winter when levels increased. Proportion of empty stomachs was highest in the central region of the North Sea. Most of the proportion variation is explained by quarterly fluctuation. Variation of content weight can be related to prey composition found in the stomachs. High stomach contents are generally associated with high contribution of fish prey to the total stomach content, mainly sandeels. We propose that sandeels were more vulnerable to predation in 1981 than in 1991 due to colder temperatures. ?? 2002 International Council for the Exploration of the Sea. Published by Elsevier Science Ltd.

ICES Journal of Marine Science↗
USGS2016

Dynamic reusable workflows for ocean science

Digital catalogs of ocean data have been available for decades, but advances in standardized services and software for catalog search and data access make it now possible to create catalog-driven workflows that automate — end-to-end — data search, analysis and visualization of data from multiple distributed sources. Further, these workflows may be shared, reused and adapted with ease. Here we describe a workflow developed within the US Integrated Ocean Observing System (IOOS) which automates the skill-assessment of water temperature forecasts from multiple ocean forecast models, allowing improved forecast products to be delivered for an open water swim event. A series of Jupyter Notebooks are used to capture and document the end-to-end workflow using a collection of Python tools that facilitate working with standardized catalog and data services. The workflow first searches a catalog of metadata using the Open Geospatial Consortium (OGC) Catalog Service for the Web (CSW), then accesses data service endpoints found in the metadata records using the OGC Sensor Observation Service (SOS) for in situ sensor data and OPeNDAP services for remotely-sensed and model data. Skill metrics are computed and time series comparisons of forecast model and observed data are displayed interactively, leveraging the capabilities of modern web browsers. The resulting workflow not only solves a challenging specific problem, but highlights the benefits of dynamic, reusable workflows in general. These workflows adapt as new data enters the data system, facilitate reproducible science, provide templates from which new scientific workflows can be developed, and encourage data providers to use standardized services. As applied to the ocean swim event, the workflow exposed problems with two of the ocean forecast products which led to improved regional forecasts once errors were corrected. While the example is specific, the approach is general, and we hope to see increased use of dynamic notebooks across the geoscience domains.

Journal of Marine Science and Engineering↗
USGS2026

The USGS Rotating X-ray Computed Tomography (RXCT) Coral-Core Archive: Scope, access, and standardization

We announce the U.S. Geological Survey (USGS) Rotating X-ray Computed Tomography (RXCT) Coral-Core Archive, a digital resource derived from ~400 coral reef cores curated at the USGS Pacific and St. Petersburg Coastal and Marine Science Centers. The archive de-livers calibrated 3-D image volumes that enable reproducible values of skeletal density, linear extension, and calcification from decadal-to-centennials scale records of coral growth and bioerosion. Cross-study comparability within the archive is supported by a unified RXCT workflow that minimizes imaging artifacts. This includes rejecting im-age-intensity–density regressions with r² < 0.95, back-calculating standard densities to verify a ±10% target precision, and confirming that band-averaged density values fall within published species- and site-specific ranges. Given global coral-reef decline and the rarity of physical archives, we release data under FAIR (Findable, Accessible, Interopera-ble, Reusable) principles. Calibrated imagery and scan metadata are distributed through CoralCache/CoralCT for analysis (DeCarlo et al., 2025), while core locations and collection metadata are published through the USGS Geologic Core and Sample Database (DOI: 10.5066/F7319TR3) with links to CT slice imagery in a USGS ScienceBase repository (DOI: 10.5066/P139Y9H4). This archive provides a powerful dataset for evaluating environ-mental controls on coral growth, establishing restoration baselines, and improving coastal-hazard assessments in the face of global coral-reef declines.

American Somoa, Guam, Florida, Hawaii, U.S. Virgin↗
USGS2018

Projected 21st century coastal flooding in the Southern California Bight. Part 1: Development of the third generation CoSMoS model

Due to the effects of climate change over the course of the next century, the combination of rising sea levels, severe storms, and coastal change will threaten the sustainability of coastal communities, development, and ecosystems as we know them today. To clearly identify coastal vulnerabilities and develop appropriate adaptation strategies due to projected increased levels of coastal flooding and erosion, coastal managers need local-scale hazards projections using the best available climate and coastal science. In collaboration with leading scientists world-wide, the USGS designed the Coastal Storm Modeling System (CoSMoS) to assess the coastal impacts of climate change for the California coast, including the combination of sea-level rise, storms, and coastal change. In this project, we directly address the needs of coastal resource managers in Southern California by integrating a vast range of global climate change projections in a thorough and comprehensive numerical modeling framework. In Part 1 of a two-part submission on CoSMoS, methods and the latest improvements are discussed, and an example of hazard projections is presented.

Journal of Marine Science and Engineering↗
USGS2014

Advances in a distributed approach for ocean model data interoperability

An infrastructure for earth science data is emerging across the globe based on common data models and web services. As we evolve from custom file formats and web sites to standards-based web services and tools, data is becoming easier to distribute, find and retrieve, leaving more time for science. We describe recent advances that make it easier for ocean model providers to share their data, and for users to search, access, analyze and visualize ocean data using MATLAB® and Python®. These include a technique for modelers to create aggregated, Climate and Forecast (CF) metadata convention datasets from collections of non-standard Network Common Data Form (NetCDF) output files, the capability to remotely access data from CF-1.6-compliant NetCDF files using the Open Geospatial Consortium (OGC) Sensor Observation Service (SOS), a metadata standard for unstructured grid model output (UGRID), and tools that utilize both CF and UGRID standards to allow interoperable data search, browse and access. We use examples from the U.S. Integrated Ocean Observing System (IOOS®) Coastal and Ocean Modeling Testbed, a project in which modelers using both structured and unstructured grid model output needed to share their results, to compare their results with other models, and to compare models with observed data. The same techniques used here for ocean modeling output can be applied to atmospheric and climate model output, remote sensing data, digital terrain and bathymetric data.

Journal of Marine Science and Engineering↗
USGS1999

The evolutionary history of steelhead ( Oncorhynchus mykiss ) along the US Pacific Coast: Developing a conservation strategy using genetic diversity

Changes in genetic variation across a species range may indicate patterns of population structure resulting from past ecological and demographic events that are otherwise difficult to infer and thus provide insight into evolutionary development. Genetic data is used, drawn from 11 microsatellite loci amplified from anadromous steelhead ( Oncorhynchus mykiss ) sampled throughout its range in the eastern Pacific Ocean, to explore population structure at the southern edge in California. Steelhead populations in this region represent less than 10% of their reported historic abundance and survive in very small populations found in fragmented habitats. Genetic data derived from three independent molecular systems (allozymes, mtDNA, and microsatellites) have shown that the southernmost populations are characterized by a relatively high genetic diversity. Two hypothetical models supporting genetic population substructure such as observed were considered: (1) range expansion with founder-flush effects and subsequent population decline; (2) a second Pleistocene radiation from the Gulf of California. Using genetic and climatic data, a second Pleistocene refugium contributing to a southern ecotone seems more feasible. These data support strong conservation measures based on genetic diversity be developed to ensure the survival of this uniquely diverse gene pool.

ICES Journal of Marine Science↗
USGS2000

Photographic evaluation of the impacts of bottom fishing on benthic epifauna

The gravel sediment habitat on the northern edge of Georges Bank (East coast of North America) is an important nursery area for juvenile fish, and the site of a productive scallop fishery. During two cruises to this area in 1994 we made photographic transects at sites of varying depths that experience varying degrees of disturbance from otter trawling and scallop dredging. Differences between sites were quantified by analyzing videos and still photographs of the sea bottom. Videos were analyzed for sediment types and organism abundance. In the still photos, the percentages of the bottom covered by bushy, plant-like organisms and colonial worm tubes (Filograna implexa) were determined, as was the presence/absence of encrusting bryozoa. Non-colonial organisms were also identified as specifically as possible and sediment type was quantified. Significant differences between disturbed and undisturbed areas were found for the variables measured in the still photos; colonial epifaunal species were conspicuously less abundant at disturbed sites. Results from the videos and still photos were generally consistent although less detail was visible in the videos. Emergent colonial epifauna provide a complex habitat for shrimp, polychaetes, brittle stars and small fish at undisturbed sites. Bottom fishing removes this epifauna, thereby reducing the complexity and species diversity of the benthic community. (C) 2000 International Council for the Exploration of the Sea.

Georges Bank↗
USGS2024

Improved efficient physics-based computational modeling of regional wave-driven coastal flooding for reef-lined coastlines

Coastal flooding affects low-lying communities worldwide and is expected to increase with climate change, especially along reef-lined coasts, where wave-driven flooding is particularly prevalent. However, current regional modeling approaches are either insufficient or too computationally expensive to accurately assess risks in these complex environments. This study introduces and validates an improved computationally efficient and physics-based approach to compute dynamic wave-driven regional flooding on reef-lined coasts. We coupled a simplified-physics flood model (SFINCS) with a one-dimensional wave transformation model (XBeach-1D). To assess the performance of the proposed approach, we compared its results with results from a fully resolving two-dimensional wave transformation model (XBeach-2D). We applied this approach for a range of storms and sea-level rise scenarios for two contrasting reef-lined coastal geomorphologies: one low relief area and one high relief area. Our findings reveal that SFINCS coupled with XBeach-1D generates flood extents comparable to those produced by XBeach-2D, with a hit rate of 92%. However, this method tends to underpredict the flood extent of weaker, high-frequency storms and overpredict stronger, low-frequency storms. Across scenarios, our approach overpredicted the mean flood water depth, with a positive bias of 7 cm and root mean square difference of 15 cm. Offering approximately 100 times greater computational efficiency than its two-dimensional XBeach counterpart, this flood modeling technique is recommended for wave-driven flood modeling in scenarios with high computational demands, such as modeling numerous scenarios or undertaking detailed regional-scale modeling.

Journal of Marine Science & Engineering↗
USGS1989

Seasonal and annual variation in the diet of Atlantic cod ( Gadus morhua ) in relation to the abundance of capelin ( Mallotus villosus ) off eastern Newfoundland, Canada

The importance of capelin as prey for cod has long been known (Thompson, 1943; and see Lilly (1987) for a review); however, no studies have been conducted on how the highly dynamic seasonal and yearly variations in capelin abundance affect cod diet. We studied the occurrence of capelin in cod stomachs in relation to the relative abundance of capelin at Witless Bay, Newfoundland (47°15’N 52°46’W), during June, July and August, 1982-1984. The mean number of capelin per stomach and the per cent occurrence of stomachs containing capelin were determined for each collection of stomachs. A total of 680 stomachs were examined. Cod were sampled from those caught in gillnets by fishermen and averaged 66 cm ± 8 (s.d.) in 1983 and 62 cm ± 8 (s.d.) in 1984. Relative abundance of capelin in the local habitat was determined by conducting hydroacoustic surveys around Gull Island in Witless Bay, the same area where cod were collected for stomach content analysis. Only hydroacoustic surveys conducted within three days of cod stomach collections were analyzed. Further details of hydroacoustic surveys including quantifications of acoustic echograms are described in Piatt (1989).

Newfoundland↗
USGS1991

Seasonal abundance and vertical distribution of capelin ( Mallotus villosus ) in relation to water temperature at a coastal site off eastern Newfoundland

The seasonal abundance and vertical distribution of capelin in relation to water temperature have been investigated by conducting repeated hydroacoustic surveys at a coastal site off eastern Newfoundland. Water temperatures were warmer in 1983 than in 1984 as indicated by the earlier appearance and greater depth of the seasonal thermocline. Correspondingly, schools of capelin appeared earlier, were more abundant, and extended deeper in the water column in 1983 than in 1984. Most capelin were found between the surface and the 5°C isotherm. In both years, initial peaks of capelin abundance occurred when nearshore water temperatures increased from about 0-1 ° C to above 6 ° C and, at or near, periods of maximum tidal oscillation. Short-term variations in the depth of the 5 ° C isotherm were related to nearshore wind-induced upwelling events. Annual variations corresponded to the volume of cold (>0 ° C) water and sea-ice transported south by the Labrador Current.

Newfoundland↗
USGS2020

Regional ocean models indicate changing limits to biological invasions in the Bering Sea

Minimal vessel traffic and cold water temperatures are believed to limit non-indigenous species (NIS) in high-latitude ecosystems. We evaluated whether suitable conditions exist in the Bering Sea for the introduction, survival, and reproduction of NIS. We compiled temperature and salinity thresholds of known NIS and compared these to ocean conditions projected during two study periods: current (2003-2012) and mid-century (2030-2039). We also explored patterns of vessel traffic and connectivity for U.S. Bering Sea ports. We found the southeastern Bering Sea had suitable conditions for the year-round survival of 80% of NIS assessed (n=42). However, only 52% of NIS had conditions suitable for reproduction or development (n=25). Conditions north of 58° N that include sub-zero winter water temperatures were unsuitable for the survival and reproduction of most NIS. While mid-century models predicted a northward expansion of suitable conditions, conditions for reproduction remained marginal. Within the highly suitable southeastern Bering Sea is the port of Dutch Harbor, which received the most vessel arrivals and ballast water discharge in the U.S. Bering Sea. Our findings illustrate the potential vulnerability of a commercially important subarctic ecosystem and highlight the need to consider NIS reproductive and developmental life phases when evaluating limits to their establishment.

ICES Journal of Marine Science↗
USGS2020

Dynamics of lake trout production in the main basin of Lake Huron

To inform lake trout (Salvelinus namaycush) fishery management in Lake Huron that has undergone rapid ecosystem changes, we quantified lake trout production dynamics by coupling age-structured stock assessment and fish bioenergetics models. Our approach revealed the connection between piscivore production and prey consumption, included growth compensation to reproduction losses, and allowed comparisons between long-term dynamics of fishery harvests and fish production. We found that despite the collapse of alewives, a major non-native pelagic prey fish, lake trout production appeared to be sustainable. To a certain degree, the effect of recent recruitment declines on lake trout production was offset by release of harvest pressure from subadult lake trout, and reduction of fishing and sea lamprey induced mortality on adult lake trout. Evidence for sustainability also included the finding that no changes in average ratios of annual production to beginning-of-the-year biomass. Juvenile P:B ratio remained as high as 2.1. The effect of growth declines on adult and subadult production was offset by reduction in population mortality. Body growth and condition did not continue to decline when lake trout became more and more reliant on round goby as food, and the dynamics of total consumption of prey fish continued to be recipient controlled.

Lake Huron↗
USGS2020

Advancements towards selective barrier passage by automatic species identification: Applications of deep convolutional neural networks on images of dewatered fish

Invasive species negatively affect enterprises such as fisheries, agriculture, and international trade. In the Laurentian Great Lakes Basin, threats include invasive sea lamprey ( Petromyzon marinus ) and the four major Chinese carps. Barriers have proven to be an effective mechanism for managing invasive species but are detrimental in that they also limit the migration of desirable, native species. Fish passage technologies that selectively pass desirable species while blocking undesirable species are needed. Key to an automated selective barrier passage system is a high precision fish classifier to assign fish to be passed or blocked. Presented is an evaluation of two classifiers developed using images of partially dewatered fish captured from a commercial, high-speed camera array. For a lamprey vs. non-lamprey classification task, an ensemble prediction approach achieved near perfect accuracy on both a validation and test dataset. For a species classification task for 13 species found in the Great Lakes region, an ensemble prediction approach achieved accuracies of 96% and 97% on a validation and test dataset, respectively. Both prediction approaches were based on deep convolutional neural networks constructed using transfer learning and image augmentation. The study provides an important proof-of-concept for the viability in fully automated, selective fish passage systems.

Illinois, Michigan,Ohio↗
USGS2021

South Africa's experimental fisheries closures and recovery of the endangered African penguin

In a scientifically-transformative project, South Africa implemented a decade-long field experiment to understand how fisheries may be affecting its most iconic seabird, the African penguin Spheniscus demersus. This unique effort prohibits the take of anchovy and sardine within relatively small areas around four African penguin breeding colonies, two in the Benguela upwelling ecosystem and two in the adjacent Agulhas region. For the Benguela, fisheries closures within the birds’ primary foraging range increased their breeding productivity and perhaps reduced parental foraging efforts, indicating that the fisheries are competing with the birds for food. Results were less clear for foraging behaviour in the Agulhas, but no data on breeding success were collected there. The African penguin is endangered, its population continues to decline, and fisheries closures have been demonstrated to improve demographic traits that contribute to population growth. Therefore, given the critical status of the species, fisheries closures should be maintained, at least at Dassen Island where the population has great capacity to expand and support other nearby colonies. Continuing or implementing corresponding fisheries closures in the Agulhas region is also warranted, as well as creating and testing the value of pelagic closed areas during the non-breeding season when the penguins disperse widely across these ecosystems. These management actions would increase penguin food supplies and may help to meet societal goals of halting the decline of the penguin population, as well as maintaining the economic and cultural services provided by fisheries and ecotourism.

Agulhas, Benguela, Dassen Island↗
USGS2022

African penguins and localized fisheries management: Response to Butterworth and Ross-Gillespie

We present a response to Butterworth and Ross-Gillespie's (2022) comment on our perspectives on how forage fish fisheries are impacting the endangered African penguin ( Sphenicus demersus ), and corresponding management options. Butterworth and Ross-Gillespie overstate model uncertainties and downplay the clear ecological and conservation significance of the fisheries closure experiment. We demonstrate that their criticism of “pseudo-replication” is weak, and not in line with their own analyses nor with the interpretations of many international scientific review panels commissioned by the government of South Africa to evaluate experimental results. Their comment does not alter our fundamental conclusions that forage fisheries operating near penguin breeding colonies compete with the birds for food resources, are detrimental to the penguin's population health, and are impeding recovery. Given that sardines are depleted (DFFE, 2021) and the African penguin is approaching a conservation crisis, we reiterate our position that continuing the precautionary approach of closures at the local scale of central-place foraging penguins is warranted to facilitate their population growth under fisheries management goals to conserve and maintain ecosystem functions.

ICES Journal of Marine Science↗
USGS2023

Temporal, environmental, and demographic correlates of Ichthyophonus sp. infections in mature Pacific herring populations

Causes of population collapse and failed recovery often remain enigmatic in marine forage fish like Pacific herring ( Clupea pallasii ) that experience dramatic population oscillations. Diseases such as ichthyophoniasis are hypothesized to contribute to these declines, but lack of long-term datasets frequently prevents inference. Analysis of pathogen surveillance and population assessment datasets spanning 2007–2019 indicate that the age-based prevalence estimate of Ichthyophonus infection was, on average, 54% greater among a collapsed population of Pacific herring (Prince William Sound, Alaska, USA) as compared to a nearby population (Sitka Sound, Alaska, USA) that is relatively robust. During the study years, the age-based infection prevalence ranged from 14 to 44% in Prince William Sound and 5 to 33% in Sitka Sound. At both sites, the age-based infection prevalence declined over time, with an average decrease of 7% per year. Statistical analyses indicated that infection prevalence between the two populations was reduced by regional factors affecting both sites, and that these factors were independent of herring density. Infection prevalence in both populations was positively correlated with herring age and negatively correlated with the Pacific Decadal Oscillation. This study demonstrates how synthesis of environmental, stock assessment, and disease assessment data can be leveraged to elucidate epidemiological trends in diseases of wild fish.

ICES Journal of Marine Science↗
USGS2024

Reconstructing half a century of coregonine recruitment reveals species-specific dynamics and synchrony across the Laurentian Great Lakes

Understanding how multiple species and populations vary in their recruitment dynamics can elucidate the processes driving recruitment across space and time. Lake Whitefish ( Coregonus clupeaformis ) and Cisco ( C. artedi ) are socioecologically important fishes across their range; however, many Laurentian Great Lakes populations have experienced declining, poor, or sporadic recruitment in recent decades. We integrated catch and age data from 38 long-term surveys across each of the Great Lakes and Lake Simcoe, resulting in a combined time series spanning 1960–2019. We estimated Lake Whitefish and Cisco year-class strength (YCS) in each lake using longitudinal mixed-effects regressions of relative cohort abundance. We subsequently quantified interspecific, spatial, and temporal synchrony in YCS using correlation and dynamic factor analyses. Lake Whitefish YCS was positively spatially synchronous on average, and YCS in all six lakes was elevated during the 1980s–1990s. In contrast, Cisco YCS was sporadic, not spatially synchronous, and highly variable around long-term, lake-specific means. YCS was not synchronous between species in any lake. Collectively, our analyses demonstrate that these species exhibit differential recruitment dynamics that may be regulated by species-specific factors. Results from this study can be leveraged in future research on the causes and consequences of cross-species, cross-basin recruitment variability.

Laurentian Great Lakes↗