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At least 73 records · Page 4Linked to original sources

Investigation of hurricane Ivan using the coupled ocean-atmosphere-wave-sediment transport (COAWST) model

The coupled ocean–atmosphere–wave–sediment transport (COAWST) model is used to hindcast Hurricane Ivan (2004), an extremely intense tropical cyclone (TC) translating through the Gulf of Mexico. Sensitivity experiments with increasing complexity in ocean–atmosphere–wave coupled exchange processes are performed to assess the impacts of coupling on the predictions of the atmosphere, ocean, and wave environments during the occurrence of a TC. Modest improvement in track but significant improvement in intensity are found when using the fully atmosphere–ocean-wave coupled configuration versus uncoupled (e.g., standalone atmosphere, ocean, or wave) model simulations. Surface wave fields generated in the fully coupled configuration also demonstrates good agreement with in situ buoy measurements. Coupled and uncoupled model-simulated sea surface temperature (SST) fields are compared with both in situ and remote observations. Detailed heat budget analysis reveals that the mixed layer temperature cooling in the deep ocean (on the shelf) is caused primarily by advection (equally by advection and diffusion).

Ocean Dynamics↗

Are threatened seabird colonies of the Pacific Ocean genetically vulnerable? The case of the red-tailed tropicbird, Phaethon rubricauda, as a model species

Oceanic seabirds have suffered population declines and extirpations due to human disturbance and still face multiple threats. Here, we assessed the potential genetic vulnerability of the red-tailed tropicbird, Phaethon rubricauda , a seabird species threatened by human disturbance and listed as ‘least concern’ by the IUCN. Using Single Nucleotide Polymorphisms (SNPs) we evaluated the genetic population structure of the red-tailed tropicbird throughout the Pacific Ocean using samples from 132 individuals from six islands. We sampled individuals from islands without human-related disturbance (non-impacted islands) and with human-related disturbance (impacted islands). Results of genome-wide SNP analyses were consistent with previous results using mitochondrial DNA sequences analyses. Genetic diversity did not differ between impacted and non-impacted islands, and low inbreeding estimates were detected for all colonies. The SNPs analyses confirmed a pattern of isolation by distance and significant inter-regional (Chile, Australasia, and Hawaiʻi) genetic structure, but revealed greater differentiation of tropicbirds in Hawaiʻi compared with Chile and Australasia. Within regions, our results further indicated significant differentiation between Rapa Nui and Salas & Gómez Island (Chile), and between Meyer and Phillip islands (Australasia) that was not detected using mitochondrial DNA analyses. Within Hawaiʻi, we found a lack of significant genetic differentiation between Oʻahu and Kauaʻi, separated by 200 km. Our findings indicated that red-tailed tropicbird colonies are at genetic risk due to limited dispersal among colonies which may reduce the fitness of the species in the long-term. We suggest that red-tailed tropicbird colonies are vulnerable to future population declines because recovery through immigration from other islands may be limited by geographic distance. Conservation actions will help preserve genetic diversity and discrete populations for this native seabird at colonies throughout the Pacific.

Biodiversity and Conservation↗

A comparison of deep-sea coral and sponge species distribution models and the impact of ocean currents in the Southern California Bight

Deep-sea corals and sponges (DSCS) are signature taxa of deep-water habitats, but ecological mechanisms that drive their geographic distributions can be difficult to uncover due to the challenges of surveying deep-water ecosystems and limited oceanographic data. A comparison of species distribution models was made for three DSCS ( Antipathes dendochristos, Plumarella longispina, and an unidentified sponge morphotype known as Porifera #2), two of which are associated with young-of-the-year and adult rockfish taxa ( Sebastes spp.). Models were built using generalized additive models (GAMs) that accounted for spatial autocorrelation. These models were compared to Maxent models, a commonly used method. All models utilized bathymetrically derived variables (including depth, slope, and Bathymetric Position Index) and output from a coupled physical-biogeochemical ocean model (including current direction and magnitude, food abundance, and dissolved oxygen). Direction of benthic ocean currents played an important role in predictions, pointing to large-scale ecological processes that may determine presence of DSCS. GAMs outperformed Maxent models and predicted more ecologically interpretable patterns. Additionally we quantified the predicted amount of suitable habitat that is currently located within some protected areas of the Southern California Bight and show that many hot spots occur outside protected areas. Given the importance of DSCS for multiple demersal fish species of commercial or conservation concerns, this research provides valuable information that natural resource managers can use as a tool in the Southern California Bight.

California↗

SPEAR: The next generation GFDL modeling system for seasonal to multidecadal prediction and projection

We document the development and simulation characteristics of the next generation modeling system for seasonal to decadal prediction and projection at the Geophysical Fluid Dynamics Laboratory (GFDL). SPEAR ( S eamless System for P rediction and EA rth System R esearch) is built from component models recently developed at GFDL—the AM4 atmosphere model, MOM6 ocean code, LM4 land model, and SIS2 sea ice model. The SPEAR models are specifically designed with attributes needed for a prediction model for seasonal to decadal time scales, including the ability to run large ensembles of simulations with available computational resources. For computational speed SPEAR uses a coarse ocean resolution of approximately 1.0° (with tropical refinement). SPEAR can use differing atmospheric horizontal resolutions ranging from 1° to 0.25°. The higher atmospheric resolution facilitates improved simulation of regional climate and extremes. SPEAR is built from the same components as the GFDL CM4 and ESM4 models but with design choices geared toward seasonal to multidecadal physical climate prediction and projection. We document simulation characteristics for the time mean climate, aspects of internal variability, and the response to both idealized and realistic radiative forcing change. We describe in greater detail one focus of the model development process that was motivated by the importance of the Southern Ocean to the global climate system. We present sensitivity tests that document the influence of the Antarctic surface heat budget on Southern Ocean ventilation and deep global ocean circulation. These findings were also useful in the development processes for the GFDL CM4 and ESM4 models.

Journal of Advances in Modeling Earth Systems↗

Analysis of ocean dynamics during the impact of Hurricane Matthew using ocean-atmosphere coupling

The main goal of this investigation is to improve the understanding of ocean-atmosphere coupling during hurricanes. The present work involves the integration of the ocean-atmosphere coupled components of the Coupled Ocean-Atmosphere-Wave-Sediment Transport Modeling System in the Very Short Term Prediction System (SisPI). Three experiments are performed: First, using a dynamic sea surface temperature, consistent with the daily updated atmospheric model Weather Research and Forecast (SisPI); second, using the Regional Oceanic Modeling System and third, using a dynamic coupling between the atmospheric and the oceanic models. The coupled system improves the tracks of the hurricane simulations respect to the SisPI. The use of the oceanic model allows a more detailed representation of the sea surface temperature. Using the coupled model, a more precise diurnal cycle of the surface net heat fluxes is obtained.

Cuban Journal of Meteorology (Revista Cubana de Me↗

From the oceans to the cloud: Opportunities and challenges for data, models, computation and workflows

Advances in ocean observations and models mean increasing flows of data. Integrating observations between disciplines over spatial scales from regional to global presents challenges. Running ocean models and managing the results is computationally demanding. The rise of cloud computing presents an opportunity to rethink traditional approaches. This includes developing shared data processing workflows utilizing common, adaptable software to handle data ingest and storage, and an associated framework to manage and execute downstream modeling. Working in the cloud presents challenges: migration of legacy technologies and processes, cloud-to-cloud interoperability, and the translation of legislative and bureaucratic requirements for “on-premises” systems to the cloud. To respond to the scientific and societal needs of a fit-for-purpose ocean observing system, and to maximize the benefits of more integrated observing, research on utilizing cloud infrastructures for sharing data and models is underway. Cloud platforms and the services/APIs they provide offer new ways for scientists to observe and predict the ocean’s state. High-performance mass storage of observational data, coupled with on-demand computing to run model simulations in close proximity to the data, tools to manage workflows, and a framework to share and collaborate, enables a more flexible and adaptable observation and prediction computing architecture. Model outputs are stored in the cloud and researchers either download subsets for their interest/area or feed them into their own simulations without leaving the cloud. Expanded storage and computing capabilities make it easier to create, analyze, and distribute products derived from long-term datasets. In this paper, we provide an introduction to cloud computing, describe current uses of the cloud for management and analysis of observational data and model results, and describe workflows for running models and streaming observational data. We discuss topics that must be considered when moving to the cloud: costs, security, and organizational limitations on cloud use. Future uses of the cloud via computational sandboxes and the practicalities and considerations of using the cloud to archive data are explored. We also consider the ways in which the human elements of ocean observations are changing – the rise of a generation of researchers whose observations are likely to be made remotely rather than hands on – and how their expectations and needs drive research towards the cloud. In conclusion, visions of a future where cloud computing is ubiquitous are discussed.

Frontiers in Marine Science↗

Comparing a quasi-3D to a full 3D nearshore circulation model: SHORECIRC and ROMS

Predictions of nearshore and surf zone processes are important for determining coastal circulation, impacts of storms, navigation, and recreational safety. Numerical modeling of these systems facilitates advancements in our understanding of coastal changes and can provide predictive capabilities for resource managers. There exists many nearshore coastal circulation models, however they are mostly limited or typically only applied as depth integrated models. SHORECIRC is an established surf zone circulation model that is quasi-3D to allow the effect of the variability in the vertical structure of the currents while maintaining the computational advantage of a 2DH model. Here we compare SHORECIRC to ROMS, a fully 3D ocean circulation model which now includes a three dimensional formulation for the wave-driven flows. We compare the models with three different test applications for: (i) spectral waves approaching a plane beach with an oblique angle of incidence; (ii) monochromatic waves driving longshore currents in a laboratory basin; and (iii) monochromatic waves on a barred beach with rip channels in a laboratory basin. Results identify that the models are very similar for the depth integrated flows and qualitatively consistent for the vertically varying components. The differences are primarily the result of the vertically varying radiation stress utilized by ROMS and the utilization of long wave theory for the radiation stress formulation in vertical varying momentum balance by SHORECIRC. The quasi-3D model is faster, however the applicability of the fully 3D model allows it to extend over a broader range of processes, temporal, and spatial scales.

Ocean Modelling↗

Implementation of the vortex force formalism in the coupled ocean-atmosphere-wave-sediment transport (COAWST) modeling system for inner shelf and surf zone applications

The coupled ocean-atmosphere-wave-sediment transport modeling system (COAWST) enables simulations that integrate oceanic, atmospheric, wave and morphological processes in the coastal ocean. Within the modeling system, the three-dimensional ocean circulation module (ROMS) is coupled with the wave generation and propagation model (SWAN) to allow full integration of the effect of waves on circulation and vice versa. The existing wave-current coupling component utilizes a depth dependent radiation stress approach. In here we present a new approach that uses the vortex force formalism. The formulation adopted and the various parameterizations used in the model as well as their numerical implementation are presented in detail. The performance of the new system is examined through the presentation of four test cases. These include obliquely incident waves on a synthetic planar beach and a natural barred beach (DUCK' 94); normal incident waves on a nearshore barred morphology with rip channels; and wave-induced mean flows outside the surf zone at the Martha's Vineyard Coastal Observatory (MVCO). Model results from the planar beach case show good agreement with depth-averaged analytical solutions and with theoretical flow structures. Simulation results for the DUCK' 94 experiment agree closely with measured profiles of cross-shore and longshore velocity data from and . Diagnostic simulations showed that the nonlinear processes of wave roller generation and wave-induced mixing are important for the accurate simulation of surf zone flows. It is further recommended that a more realistic approach for determining the contribution of wave rollers and breaking induced turbulent mixing can be formulated using non-dimensional parameters which are functions of local wave parameters and the beach slope. Dominant terms in the cross-shore momentum balance are found to be the quasi-static pressure gradient and breaking acceleration. In the alongshore direction, bottom stress, breaking acceleration, horizontal advection and horizontal vortex forces dominate the momentum balance. The simulation results for the bar/rip channel morphology case clearly show the ability of the modeling system to reproduce horizontal and vertical circulation patterns similar to those found in laboratory studies and to numerical simulations using the radiation stress representation. The vortex force term is found to be more important at locations where strong flow vorticity interacts with the wave-induced Stokes flow field. Outside the surf zone, the three-dimensional model simulations of wave-induced flows for non-breaking waves closely agree with flow observations from MVCO, with the vertical structure of the simulated flow varying as a function of the vertical viscosity as demonstrated by Lentz et al. (2008).

Ocean Modelling↗

Wave-current interaction between Hurricane Matthew wave fields and the Gulf Stream

Hurricanes interact with the Gulf Stream in the South Atlantic Bight (SAB) through a wide variety of processes, which are crucial to understand for prediction of open-ocean and coastal hazards during storms. However, it remains unclear how waves are modified by large-scale ocean currents under storm conditions, when waves are aligned with the storm-driven circulation and tightly coupled to the overlying wind field. Hurricane Matthew (2016) impacted the US southeast coast, causing extensive coastal change due to large waves and elevated water levels. The hurricane traveled on the continental shelf parallel to the SAB coastline, with the right side of the hurricane directly over the Gulf Stream. Using the Coupled Ocean Atmosphere Wave Sediment Transport Modeling System, we investigate wave-current interaction between Hurricane Matthew and the Gulf Stream. The model simulates ocean currents and waves over a grid encompassing the US east coast, with varied coupling of the hydrodynamic and wave components to isolate the effect of the currents on the waves, and the effect of the Gulf Stream relative to storm-driven circulation. The Gulf Stream modifies the direction of the storm-driven currents beneath the right side of the hurricane. Waves transitioned from following currents that result in wave lengthening, through negative current gradients that result in wave steepening and dissipation. Wave-current interaction over the Gulf Stream modified maximum coastal total water levels, and changed incident wave directions at the coast by up to 20°, with strong implications for the morphodynamic response and stability of the coast to the hurricane.

East Coast, Gulf Coast↗

DNA and dispersal models highlight constrained connectivity in a migratory marine megavertebrate

Population structure and spatial distribution are fundamentally important fields within ecology, evolution, and conservation biology. To investigate pan-Atlantic connectivity of globally endangered green turtles ( Chelonia mydas ) from two National Parks in Florida, USA, we applied a multidisciplinary approach comparing genetic analysis and ocean circulation modeling. The Everglades (EP) is a juvenile feeding ground, whereas the Dry Tortugas (DT) is used for courtship, breeding, and feeding by adults and juveniles. We sequenced two mitochondrial segments from 138 turtles sampled there from 2006-2015, and simulated oceanic transport to estimate their origins. Genetic and ocean connectivity data revealed northwestern Atlantic rookeries as the major natal sources, while southern and eastern Atlantic contributions were negligible. However, specific rookery estimates differed between genetic and ocean transport models. The combined analyses suggest that post-hatchling drift via ocean currents poorly explains the distribution of neritic juveniles and adults, but juvenile natal homing and population history likely play important roles. DT and EP were genetically similar to feeding grounds along the southern US coast, but highly differentiated from most other Atlantic groups. Despite expanded mitogenomic analysis and correspondingly increased ability to detect genetic variation, no significant differentiation between DT and EP, or among years, sexes or stages was observed. This first genetic analysis of a North Atlantic green turtle courtship area provides rare data supporting local movements and male philopatry. The study highlights the applications of multidisciplinary approaches for ecological research and conservation.

Florida↗

Modeling transport and deposition of the Mekong River sediment

A Coupled Wave–Ocean–SedimentTransport Model was used to hindcast coastal circulation and fine sedimenttransport on the Mekong shelf in southeastern Asian in 2005. Comparisons with limited observations showed that the model simulation captured the regional patterns and temporal variability of surface wave, sea level, and suspended sediment concentration reasonably well. Significant seasonality in sedimenttransport was revealed. In summer, a large amount of fluvial sediments was delivered and deposited near the MekongRiver mouth. In the following winter, strong ocean mixing, and coastal current lead to resuspension and southwestward dispersal of a small fraction of previously deposited sediments. Model sensitivity experiments (with reduced physics) were performed to investigate the impact of tides, waves, and remotely forced ambient currents on the transport and dispersal of the fluvial sediment. Strong wave mixing and downwelling-favorable coastal current associated with the more energetic northeast monsoon in the winter season are the main factors controlling the southwestward along-shelf transport.

Mekong River↗

Assessing first-order emulator inference for physical parameters in nonlinear mechanistic models

We present an approach for estimating physical parameters in nonlinear models that relies on an approximation to the mechanistic model itself for computational efficiency. The proposed methodology is validated and applied in two different modeling scenarios: (a) Simulation and (b) lower trophic level ocean ecosystem model. The approach we develop relies on the ability to predict right singular vectors (resulting from a decomposition of computer model experimental output) based on the computer model input and an experimental set of parameters. Critically, we model the right singular vectors in terms of the model parameters via a nonlinear statistical model. Specifically, we focus our attention on first-order models of these right singular vectors rather than the second-order (covariance) structure.

Journal of Agricultural, Biological, and Environme↗

Revised budget for the oceanic uptake of anthropogenic carbon dioxide

Tracer-calibrated models of the total uptake of anthropogenic CO 2 by the world's oceans give estimates of about 2 gigatonnes carbon per year 1 , significantly larger than a recent estimate 2 of 0.3-0.8 Gt C yr -1 for the synoptic air-to-sea CO 2 influx. Although both estimates require that the global CO 2 budget must be balanced by a large unknown terrestrial sink, the latter estimate implies a much larger terrestrial sink, and challenges the ocean model calculations on which previous CO 2 budgets were based. The discrepancy is due in part to the net flux of carbon to the ocean by rivers and rain, which must be added to the synoptic air-to-sea CO 2 flux to obtain the total oceanic uptake of anthropogenic CO 2 . Here we estimate the magnitude of this correction and of several other recently proposed adjustments to the synoptic air-sea CO 2 exchange. These combined adjustments minimize the apparent inconsistency, and restore estimates of the terrestrial sink to values implied by the modelled oceanic uptake.

Nature↗

Impact of SST and surface waves on Hurricane Florence (2018): A coupled modeling investigation

Hurricane Florence (2018) devastated the coastal communities of the Carolinas through heavy rainfall that resulted in massive flooding. Florence was characterized by an abrupt reduction in intensity (Saffir-Simpson Category 4 to Category 1) just prior to landfall and synoptic-scale interactions that stalled the storm over the Carolinas for several days. We conducted a series of numerical modeling experiments in coupled and uncoupled configurations to examine the impact of sea surface temperature (SST) and ocean waves on storm characteristics. In addition to experiments using a fully coupled atmosphere-ocean-wave model, we introduced the capability of the atmospheric model to modulate wind stress and surface fluxes by oceanwaves through data from an uncoupled wave model. We examined these experiments by comparing track, intensity, strength, SST, storm structure, wave height, surface roughness, heat fluxes, and precipitation in order to determine the impacts of resolving ocean conditions with varying degrees of coupling. We found differences in the storm’s intensity and strength, with the best correlation coefficient of intensity (r=0.89) and strength (r=0.95) coming from the fully-coupled simulations. Further analysis into surface roughness parameterizations added to the atmospheric model revealed differences in the spatial distribution and magnitude of the largest roughness lengths. Adding ocean andwave features to the model further modified the fluxes due to more realistic cooling beneath the stormwhich in turn modified the precipitation field. Our experiments highlight significant differences in how air-sea processes impact hurricane modeling. The storm characteristics of track, intensity, strength, and precipitation at landfall are crucial to predictability and forecasting of future landfalling hurricanes.

Weather and Forecasting↗

Modelling the enigmatic Late Pliocene Glacial Event - Marine Isotope Stage M2

The Pliocene Epoch (5.2 to 2.58 Ma) has often been targeted to investigate the nature of warm climates. However, climate records for the Pliocene exhibit significant variability and show intervals that apparently experienced a cooler than modern climate. Marine Isotope Stage (MIS) M2 (~ 3.3 Ma) is a globally recognisable cooling event that disturbs an otherwise relatively (compared to present-day) warm background climate state. It remains unclear whether this event corresponds to significant ice sheet build-up in the Northern and Southern Hemisphere. Estimates of sea level for this interval vary, and range from modern values to estimates of 65 m sea level fall with respect to present day. Here we implement plausible M2 ice sheet configurations into a coupled atmosphere–ocean climate model to test the hypothesis that larger-than-modern ice sheet configurations may have existed at M2. Climate model results are compared with proxy climate data available for M2 to assess the plausibility of each ice sheet configuration. Whilst the outcomes of our data/model comparisons are not in all cases straight forward to interpret, there is little indication that results from model simulations in which significant ice masses have been prescribed in the Northern Hemisphere are incompatible with proxy data from the North Atlantic, Northeast Arctic Russia, North Africa and the Southern Ocean. Therefore, our model results do not preclude the possibility of the existence of larger ice masses during M2 in the Northern or Southern Hemisphere. Specifically they are not able to discount the possibility of significant ice masses in the Northern Hemisphere during the M2 event, consistent with a global sea-level fall of between 40 m and 60 m. This study highlights the general need for more focused and coordinated data generation in the future to improve the coverage and consistency in proxy records for M2, which will allow these and future M2 sensitivity tests to be interrogated further.

Global and Planetary Change↗

Development of a two-stage life cycle model to inform the Trap and Haul Program for Coho salmon in the Lewis River, Washington

Restoration of salmon populations in the upper Lewis River Basin depends on a trap-and-haul program owing to the Lewis River Hydroelectric Project (Project) operated by PacifiCorp and Cowlitz PUD (Utilities), which has been a barrier to salmon passage since the 1930s. Thus, sustaining the Coho salmon ( Oncorhynchus kisutch ) population upstream of the Project currently depends on two fundamental factors: (1) the collection of upstream migrating adult Coho salmon at Merwin Dam, the lower most dam within the Project, and transporting them by truck to spawn above Swift Dam, the upper most dam within the Project; and (2) the collection of out-migrating juvenile Coho salmon at the downstream collection facility at Swift Dam for transport and release below the Project. The reintroduction program began once the downstream collection facility at Swift Dam was commissioned in late-2012 with the first year of transport data being collected in 2013. Over the past decade, the Utilities have been collecting data on juvenile outmigrants and adult fish returns at the dams. The need to construct a life cycle model for Lewis River anadromous fish was identified by the Lewis River Aquatic Technical Subgroup, with the understanding that many years (>15) of data collection are needed to adequately measure the life cycle production of coho salmon. Use of past data to construct models could help inform future data collection and provide a framework that can be updated annually to measure trap and haul program performance within a life cycle context (Note: Data are not currently available from PacifiCorp. Contact organization Chris Karchesky for further information). Because Coho salmon can live as long as five years, estimating demographic parameters for Coho salmon populations over their life cycle requires at least 10 or more years of data collection. Over the past decade, PacifiCorp has been collecting data on fish collection efficiency and the numbers of adult and juvenile salmon transported around the Lewis River dams, providing sufficient data to formulate a life cycle model that can guide future data collection efforts and provide preliminary information to resource managers The goal of the statistical life cycle model was to estimate annual production and survival during two critical life-stage transitions (1) the freshwater production from escapement of adults released upstream of Swift Dam, and the collection of downstream migrating juveniles at the passage facility at Swift Dam, and (2) the smolt-to-adult survival from the time of collection at Swift Dam to their return as adults. We used the Beverton-Holt stock-recruitment model to estimate juvenile production from the number of spawners. This approach allowed us to test for density dependence at current spawner abundances while estimating annual productivity, defined as the number of juveniles produced per spawner at low spawner abundance. Productivity was then expressed as a function of the number of juveniles collected and transported downstream of the Project. Because juvenile Fish Collection Efficiency (FCE) directly affects the number of juveniles that survive to continue downstream migration, FCE is a primary determinant of fish production. Consequently, the modeling framework is well suited to evaluate the performance of trap and haul programs within a life cycle context. The objectives of this study were to: (1) gather and collate available data on adult and juvenile Coho salmon at Merwin and Swift dams, (2) quantify adult escapement, juvenile abundance, and the age at outmigration and adult return, (3) describe, formulate, and fit the integrated population model (IPM) to the data, and (4) summarize our findings, identify data gaps, and identify potential opportunities for future studies that could provide information used to improve model estimation and inference. Our key findings were: (1) over and above the number of spawning females, FCE was the primary factor affecting productivity of Coho salmon above Swift Dam, (2) smolt-to-adult return (SAR) rates were relatively high considering that harvest was included in the estimate, averaging about 4.5% and ranging as high as 12.9%, and (3) juvenile capacity upriver of Swift Dam was difficult to estimate due to the limited range in spawning females over the time series of data, suggesting the model may be improved by collecting data at higher spawner abundances. In addition, by including FCE in the model, we estimated that the median pre-collection productivity, defined as the number of juveniles produced per spawner when FCE = 1, was 64 juveniles per spawner. Because this two-stage life cycle model partitions factors that affect fish production in river versus the ocean, the model estimates should help inform fishery managers about the overall role that fish collection at Swift Dam plays in the recovery and sustainability of Lewis River Coho salmon. By providing the model with (1) more years of data, (2) higher numbers of spawning females, and (3) data on age at juvenile migration in relation to age at adult return greater certainty in the estimates of capacity and SAR can be attained. Ultimately, information provided by the model can assist in the evaluation and continued improvement of the current trap and haul program to support anadromous fishes in the Lewis River Basin.

BioRxiv↗

Development of a two-stage lifecycle model to inform the trap-and-haul program for Oncorhynchus kisutch (coho salmon) in the Lewis River, Washington

Restoration of salmon populations in the upper Lewis River Basin, Washington, depends on a trap-and-haul program owing to the Lewis River Hydroelectric Project (hereinafter referred to as “Project”) operated by PacifiCorp and Cowlitz Public Utilities District (hereinafter referred to as “Utilities”), which has been a barrier to salmon passage since the 1930s. Thus, sustaining the Oncorhynchus kisutch (Walbaum, 1792; coho salmon) population upstream from the Project currently depends on two fundamental factors: (1) the collection of upstream migrating adult coho salmon at Merwin Dam, the lowermost dam within the Project, and transporting them by truck to spawn above Swift Dam, the uppermost dam within the Project; and (2) the collection of out-migrating juvenile coho salmon at the downstream collection facility at Swift Dam for transport and release below the Project. The reintroduction program began once the downstream collection facility at Swift Dam was commissioned in late 2012, with the first year of transport data being collected in 2013. Over the past decade, the Utilities have been collecting data on juvenile outmigrants and adult fish returns at the dams. The need to construct a lifecycle model for Lewis River anadromous fish was identified by the Lewis River Aquatic Technical Subgroup, with the understanding that many years (more than 15 years) of data collection are needed to adequately measure the lifecycle production of salmon. The U.S. Geological Survey was contracted to develop and apply the model to past data at the Lewis River dams to help inform future data collection and provide a framework that can be updated annually to measure trap-and-haul program performance within a lifecycle context. Because coho salmon can live as long as 5 years, estimating demographic parameters for coho salmon populations over their lifecycle requires at least 10 or more years of data collection. Over the past decade, PacifiCorp has been collecting data on fish collection efficiency and the numbers of adult and juvenile salmon transported around the Lewis River dams, making this an ideal time to formulate a lifecycle model that can guide future data collection efforts and provide preliminary information to resource managers. The goal of the statistical lifecycle model is to estimate annual production and survival during two critical life-stage transitions: (1) the freshwater production from escapement of adults released upstream from Swift Dam, and the collection of downstream migrating juveniles at the downstream passage facility at Swift Dam; and (2) the smolt-to-adult survival from the time of collection at Swift Dam to their return as adults. We used the Beverton-Holt stock-recruitment model to estimate juvenile production from the number of spawners (Beverton and Holt, 1957). This approach allowed us to test for density dependence at current spawner abundances while estimating annual productivity, defined as the number of juveniles produced per spawner at low spawner abundance. Productivity was then expressed as a function of the number of juveniles collected and transported downstream from the Project. Because juvenile fish collection efficiency (FCE) directly affects the number of juveniles that survive to continue downstream migration, FCE is a primary determinant of fish production. Consequently, the modeling framework is well suited to evaluate the performance of trap-and-haul programs within a lifecycle context. The objectives of this study were to (1) gather and collate available data on adult and juvenile coho salmon at Merwin and Swift Dams; (2) quantify adult escapement, juvenile abundance, and the age at outmigration and adult return; (3) describe, formulate and fit the integrated population model to the data; and (4) summarize our findings, identify data gaps, and identify opportunities for future studies that could improve model estimation and inference. Our key findings were: (1) over and above the number of spawning females, FCE was the primary factor affecting productivity of coho salmon above Swift Dam; (2) smolt-to-adult return (SAR) rates were relatively high considering that harvest was included in the estimate, averaging about 4.5 percent and ranging as high as 12.9 percent; and (3) juvenile capacity upstream from Swift Dam was difficult to estimate due to the limited range in spawning females over the time series of data, suggesting the model may be improved by collecting data at higher spawner abundances. In addition, by including FCE in the model, we estimated that the median pre-collection productivity, defined as the number of juveniles produced per spawner when FCE=1, was 64 juveniles per spawner. Because the two-stage lifecycle model partitions factors that affect fish production in rivers versus the ocean, the model estimates may help inform fishery managers about the overall role that fish collection at Swift Dam plays in the recovery and sustainability of Lewis River coho salmon. By providing the model with (1) more years of data, (2) higher numbers of spawning females, and (3) data on age at juvenile migration in relation to age at adult return, greater certainty in the estimates of capacity and SAR can be attained. Ultimately, information provided by the model may assist in the evaluation and continued improvement of the current trap-and-haul program to support anadromous fishes in the Lewis River Basin.

Washington↗

Predicting connectivity of green turtles at Palmyra Atoll, central Pacific: a focus on mtDNA and dispersal modelling

Population connectivity and spatial distribution are fundamentally related to ecology, evolution and behaviour. Here, we combined powerful genetic analysis with simulations of particle dispersal in a high-resolution ocean circulation model to investigate the distribution of green turtles foraging at the remote Palmyra Atoll National Wildlife Refuge, central Pacific. We analysed mitochondrial sequences from turtles ( n = 349) collected there over 5 years (2008–2012). Genetic analysis assigned natal origins almost exclusively (approx. 97%) to the West Central and South Central Pacific combined Regional Management Units. Further, our modelling results indicated that turtles could potentially drift from rookeries to Palmyra Atoll via surface currents along a near-Equatorial swathe traversing the Pacific. Comparing findings from genetics and modelling highlighted the complex impacts of ocean currents and behaviour on natal origins. Although the Palmyra feeding ground was highly differentiated genetically from others in the Indo-Pacific, there was no significant differentiation among years, sexes or stage-classes at the Refuge. Understanding the distribution of this foraging population advances knowledge of green turtles and contributes to effective conservation planning for this threatened species.

Journal of the Royal Society Interface↗