Movement patterns and marine habitat associations of juvenile loggerhead sea turtles (Caretta caretta) in the southwestern Atlantic Ocean

Bycatch, or the incidental capture of non-target species, has been implicated as one of the main factors leading to population declines of many large marine vertebrates, including sea turtles. To effectively manage and conserve these long-lived species, their marine distribution, high use areas, foraging habitats, and regions of highest likelihood of interaction with fisheries must be understood. I analyzed the movements and habitat use of satellite tracked juvenile loggerhead sea turtles (Caretta caretta) in the Southwestern Atlantic Ocean, a poorly studied region with high turtle-fisheries interactions. Between July 2006 and March 2010, 27 satellite transmitters were deployed at sea on juvenile loggerheads captured as bycatch in the Uruguayan and Brazilian pelagic longline fishing vessels. I characterized the broad-scale behavioral patterns, inter-seasonal variability, and general high use areas for 26 juvenile turtles, which were tracked for 259±159 days between latitudes of 25-45°S and longitudes 35-54°W. The high use areas for the tracked turtles were over the continental shelf and slope within the Uruguayan and Brazilian Economic Exclusive Zones, and in oceanic international waters between the Rio Grande Rise and the continental slope off of southern Brazil. Diving information was available for 5 of the tagged turtles; the maximum dive depth recorded varied between 100-300m depths, and two turtles demonstrated potential bottom-feeding behaviors by diving to depths that corresponded with the bathymetry at their location. The mean sea surface temperature encountered by turtles was 19.8±2.3°C (10.21°C-28.4°C) and turtles showed an affinity for mesotrophic waters (0.458±1.012 mg/m³ chlorophyll-a). Overall, broad scale latitudinal movements of juvenile loggerheads varied by season and sea surface temperature. Because recent studies on marine megafauna movements have highlighted that ocean currents can have an important effect on movement paths, I decoupled active foraging behavior from likely passive movement of tracked juvenile loggerheads in ocean currents. Using First Passage Time analysis; a method to measure changes in movement patterns along a pathway through the environment, and generalized additive mixed models, I quantified similarities in the movement patterns and habitat "affinities" of the turtles and surface drifters in the ocean. Turtles and drifters both exhibited movement patterns that could be classified as likely "foraging behavior" at a spatial scale of 80km. This corresponds to the identified scale of eddies in the Southwestern Atlantic Ocean, which may suggest that passive movement of turtles in ocean currents largely drives their scale of search. Current velocity and sea floor depth were the most important variables correlated with both turtle and drifter movement patterns at that scale. Both turtles and drifters generally showed a negative relationship between first passage time and current velocities. Some differences between turtle and drifter behavior were evident, particularly on the continental shelf; deviations in turtle behavior from the patterns of drifters is likely indicative of active movement on the turtles part. There were no seasonal or annual effects on the fine scale movements of turtles or drifters. Interestingly, turtle search behavior was not correlated with temperature or chlorophyll a in this scale of analysis. I suggest that evaluation of drifter movements in the area of study is an important addition to satellite tracking work that attempts to identify foraging behavior in sea turtles or other large marine vertebrates that may take advantage of ocean currents for transport and feeding

Biotic and abiotic factors influencing forage fish and pelagic nekton community in the Columbia River plume (USA) throughout the upwelling season 1999–2009

Large river plumes modify coastal environments and can impact production across multiple trophic levels. From 1999 to 2009, the assemblages of forage fish, predator fish, and other pelagic nekton were monitored in coastal waters associated with the Columbia River plume. Surveys were conducted at night to target vertically migrating species, and community structure evaluated to better understand ecological interactions. Distinct inshore and offshore communities were identified during spring and summer that were correlated with ocean temperature, salinity, plume volume, and upwelling intensity. Resident euryhaline forage fish species, such as smelts, anchovy, herring, market squid, juvenile salmon, and spiny dogfish, showed a high affinity for inshore habitat and the lower salinity plume during spring. Highly migratory species, such as sardine, piscivorous hake, sharks, and mackerels, were associated with warmer, saltier waters offshore, during strong upwelling periods in summer. Overall, our study of pelagic nekton revealed that temporal dynamics in abundance and community composition were associated with seasonal abiotic phenomenon, but not interannual, large-scale oceanographic processes. Forage fish assemblages differed seasonally and spatially from the assemblages of major piscivorous predators. This finding suggests a potential role of the plume as refuge for forage fish from predation by piscivorous fish in the northern California Current.Keywords: Predator fish, Columbia River plume, California current, Community analysis, Forage fishKeywords: Predator fish, Columbia River plume, California current, Community analysis, Forage fis

‘Drivin' with your eyes closed’: Results from an international, blinded simulation experiment to evaluate spatial stock assessments

Spatial models enable understanding potential redistribution of marine resources associated with ecosystem drivers and climate change. Stock assessment platforms can incorporate spatial processes, but have not been widely implemented or simulation tested. To address this research gap, an international simulation experiment was organized. The study design was blinded to replicate uncertainty similar to a real-world stock assessment process, and a data-conditioned, high-resolution operating model (OM) was used to emulate the spatial dynamics and data for Indian Ocean yellowfin tuna (Thunnus albacares). Six analyst groups developed both single-region and spatial stock assessment models using an assessment platform of their choice, and then applied each model to the simulated data. Results indicated that across all spatial structures and platforms, assessments were able to adequately recreate the population trends from the OM. Additionally, spatial models were able to estimate regional population trends that generally reflected the true dynamics from the OM, particularly for the regions with higher biomass and fishing pressure. However, a consistent population biomass scaling pattern emerged, where spatial models estimated higher population scale than single-region models within a given assessment platform. Balancing parsimony and complexity trade-offs were difficult, but adequate complexity in spatial parametrizations (e.g., allowing time- and age-variation in movement and appropriate tag mixing periods) was critical to model performance. We recommend expanded use of high-resolution OMs and blinded studies, given their ability to portray realistic performance of assessment models. Moreover, increased support for international simulation experiments is warranted to facilitate dissemination of methodology across organizations.Peer reviewe

State of the California Current 2014-15: Impacts of the Warm-Water "Blob"

In 2014, the California Current (~28˚–48˚N) saw average, or below average, coastal upwelling and relatively low productivity in most locations, except from 38˚–43˚N during June and July. Chlorophyll-a levels were low throughout spring and summer at most locations, except in a small region around 39˚N. Catches of juvenile rockfish (an indicator of upwelling-related fish species) remained high throughout the area surveyed (32˚–43˚N). In the fall of 2014, as upwelling ceased, many locations saw an unprecedented increase in sea surface temperatures (anomalies as large as 4˚C), particularly at 45˚N due to the coastal intrusion of an extremely anomalous pool of warm water. This warm surface anomaly had been building offshore in the Gulf of Alaska since the fall of 2013, and has been referred to as the “blob.” Values of the Pacific Decadal Oscillation index (PDO) continued to climb during 2014, indicative of the increase in warm coastal surface waters, whereas the North Pacific Gyre Oscillation index (NPGO) saw a slight rebound to more neutral values (indicative of average productivity levels) during 2014. During spring 2015, the upwelling index was slightly higher than average for locations in the central and northern region, but remained below average at latitudes south of 35˚N. Chlorophyll a levels were slightly higher than average in ~0.5˚ latitude patches north of 35˚N, whereas productivity and phytoplankton biomass were low south of Pt. Conception. Catches of rockfish remained high along most of the coast, however, market squid remained high only within the central coast (36˚–38˚N), and euphausiid abundance decreased everywhere, as compared to the previous year. Sardine and anchovy were nearly absent from the southern portion of the California Current system (CCS), whereas their larvae were found off the coast of Oregon and Washington during winter for the first time in many years. Waters warmed dramatically in the southern California region due to a change in wind patterns similar to that giving rise to the blob in the broader northeast Pacific. For most of the coast, there were intrusions of species never found before or found at much higher abundances than usual, including fish, crustaceans, tunicates and other gelatinous zooplankton, along with other species often indicative of an El Niño. Thus species richness was high in many areas given the close juxtaposition of coastal upwelling-related species with the offshore warm-water intrusive or El Niño-typical taxa. Thus the California Current by 2015 appears to have transitioned to a very different state than previous observations

State of the California Current 2012–13: No Such Thing as an "Average" Year

This report reviews the state of the California Current System (CCS) between winter 2012 and spring 2013, and includes observations from Washington State to Baja California. During 2012, large-scale climate modes indicated the CCS remained in a cool, productive phase present since 2007. The upwelling season was delayed north of 42˚N, but regions to the south, especially 33˚ to 36˚N, experienced average to above average upwelling that persisted throughout the summer. Contrary to the indication of high production suggested by the climate indices, chlorophyll observed from surveys and remote sensing was below average along much of the coast. As well, some members of the forage assemblages along the coast experienced low abundances in 2012 surveys. Specifically, the concentrations of all lifestages observed directly or from egg densities of Pacific sardine, Sardinops sagax, and northern anchovy, Engraulis mordax, were less than previous years’ survey estimates. However, 2013 surveys and observations indicate an increase in abundance of northern anchovy. During winter 2011/2012, the increased presence of northern copepod species off northern California was consistent with stronger southward transport. Krill and small-fraction zooplankton abundances, where examined, were generally above average. North of 42˚N, salps returned to typical abundances in 2012 after greater observed concentrations in 2010 and 2011. In contrast, salp abundance off central and southern California increased after a period of southward transport during winter 2011/2012. Reproductive success of piscivorous Brandt’s cormorant, Phalacrocorax penicillatus, was reduced while planktivorous Cassin’s auklet, Ptychoramphus aleuticus was elevated. Differences between the productivity of these two seabirds may be related to the available forage assemblage observed in the surveys. California sea lion pups from San Miguel Island were undernourished resulting in a pup mortality event perhaps in response to changes in forage availability. Limited biological data were available for spring 2013, but strong winter upwelling coastwide indicated an early spring transition, with the strong upwelling persisting into early summer

Marine Neritic and Epipelagic Community Dynamics: An Investigation of the 'Yin' and 'Yang', No-Analog, and Refugia from a Multi-species Perspective

Changes in ocean conditions influenced by climatic fluctuations have lead to changes in individual species distributions, which alter the diversity, communities and species interactions across marine ecosystems worldwide. Assessing the species composition and identifying regions and habitats that can safeguard the persistence of biota are critically important. In this dissertation, I present multiple analyses on two long-term fishery–independent survey datasets; one along the Skagerrak coastline of southeastern Norway, and another in the epipelagic zone of the Northern California Current in the northeastern Pacific Ocean. Chapter 1 presents an overall discussion of general biodiversity, and how community ecology in marine ecosystems can be integrated into marine ecosystem based management. Chapter 2 presents an analysis of an assemblage of juvenile nearshore fishes based on nearly eight decades of highly standardized Norwegian survey records. Using multivariate statistical techniques, I (i) characterize the change in taxonomic community composition through time, (ii) determine whether there has been an increase in warm-water affinity species relative to their cold-water affinity counterparts, and (iii) characterize the temporal changes in the species functional trait assemblage. The results strongly indicate a shift toward a novel fish assemblage between the late 1990s and 2000s. The context of changes within the most recent two decades is in stark contrast to those during the 1960s and 1970s, but similar to those during the previous warm period during the 1930s and 1940s. This novel assemblage is tightly linked to the warming temperatures in the region portrayed by the increased presence of warm-water species and a higher incidence of pelagic, planktivorous species. The results indicate a clear influence of ocean temperature on the regions juvenile fish community that points to climate-mediated effects the species assemblage of important fish nursery area. Chapter 3 addresses the current interdisciplinary challenge of effectively tracking multiple facets of biodiversity of the marine ecosystem from a remote perspective with the ultimate goal of developing ecosystem indicators for management. In this study, I use generalize additive mixed models to quantify the relationship between spatially and temporally explicit community data using both in-situ and remotely sensed oceanographic data over three different months and across 10 years. From the modeling approach as well as with matchups of satellite data with species specific positive catch locations, I show the utility of using MODIS-Aqua Rrs555 data field in order to understand the distribution of higher trophic levels community data associated with freshwater input into this region. Using these community gradients projected onto satellite data, I develop a new community-level temporally and spatially explicit indicator that assesses variations in the epipelagic community. This index of community differences is useful for regional ecosystem condition reports and could be useful within a broader ecosystem based fisheries management context. Chapter 4 presents results from a study using a unique and long-term (1999-2015) standardized survey occurring in the month of June of pelagic marine and anadromous species off Oregon and Washington in the northern California Current. The objectives of this study were to identify geographic locations with a stable species compositions off of Oregon and Washington that are also relatively buffered from climate fluctuations observed over the past two decades. Specifically, I used species richness and a metric of temporal beta diversity (change in species composition) to assess locations with high species richness and community persistence relative to local and basin-scale environmental fluctuations. Also, using spatially variant generalized additive mixed models, I identified areas with species communities that are more influenced by basin-scale climatic fluctuations than others. I have identified a specific region along the continental shelf off Washington State to be a potential climate change refugia for pelagic nekton and some gelatinous taxa. This potential climate change refugia off of Washington contrasts with adjacent areas to the south (e.g. the Newport Hydrographic transect) and offshore regions that have generally lower species richness, and higher temporal change in species composition. I propose that upwelling regions with retentive topographic features, such as wide continental shelves, can function as marine refugia for pelagic fauna, whereas offshore locations are potentially more climatically sensitive and experience higher temporal change in species composition. Finally, Chapter 5 includes the main conclusions of this thesis and provides discussion of other studies that could follow

Spatial Overlap Between Forage Fishes and the Large Medusa \u3ci\u3eChrysaora fuscescens\u3c/i\u3e In the Northern California Current Region

As in many regions of the world, the shelf waters of the western United States have experienced large increases and high interannual variability in jellyfish populations in recent decades. The northern California Current (NCC) is a productive upwelling zone that is home to large populations of medusae, particularly during some years. Seasonal trawl surveys in the NCC over 13 yr have documented a substantial biomass of jellyfish consisting primarily of one species, the sea nettle Chrysaora fuscescens, with abundances generally peaking in late summer. Trophic overlap can be high in the NCC with planktivorous species such as Pacific sardines and herring that consume copepods and other zooplankton. In this study, we examine the spatial overlap and co-occurrence of C. fuscescens and Pacific herring Clupea pallasii, northern anchovy Engraulis mordax and Pacific sardine Sardinops sagax in the NCC using spatial analysis tools to determine the species that have the potential to be most affected by high jellyfish biomass and the geographic areas in which these interactions are likely to occur. Significant spatial overlap of C. fuscescens with these pelagic fishes occurred during certain months and years, although the results were highly variable. There was an overall negative relationship between the abundance of C. fuscescens and the catch of the 3 forage fishes for both June and September. End-to-end food web models show that jellyfish have a greater potential to affect production of pelagic forage fishes than the reverse

Spatial overlap between forage fishes and the large medusa Chrysaora fuscescens in the northern California Current region

As in many regions of the world, the shelf waters of the western United States have experienced large increases and high interannual variability in jellyfish populations in recent decades. The northern California Current (NCC) is a productive upwelling zone that is home to large populations of medusae, particularly during some years. Seasonal trawl surveys in the NCC over 13 yr have documented a substantial biomass of jellyfish consisting primarily of one species, the sea nettle Chrysaora fuscescens, with abundances generally peaking in late summer. Trophic overlap can be high in the NCC with planktivorous species such as Pacific sardines and herring that consume copepods and other zooplankton. In this study, we examine the spatial overlap and co-occurrence of C. fuscescens and Pacific herring Clupea pallasii, northern anchovy Engraulis mordax and Pacific sardine Sardinops sagax in the NCC using spatial analysis tools to determine the species that have the potential to be most affected by high jellyfish biomass and the geographic areas in which these interactions are likely to occur. Significant spatial overlap of C. fuscescens with these pelagic fishes occurred during certain months and years, although the results were highly variable. There was an overall negative relationship between the abundance of C. fuscescens and the catch of the 3 forage fishes for both June and September. End-to-end food web models show that jellyfish have a greater potential to affect production of pelagic forage fishes than the reverse.Keywords: Spatial overlap, Planktivores, Pelagic fishes, Scyphomedusae, Interannual variability, Seasonal variabilit

The use of mesoscale eddies by juvenile loggerhead sea turtles (Caretta caretta) in the southwestern Atlantic.

Marine animals, such as turtles, seabirds and pelagic fishes, are observed to travel and congregate around eddies in the open ocean. Mesoscale eddies, large swirling ocean vortices with radius scales of approximately 50-100 km, provide environmental variability that can structure these populations. In this study, we investigate the use of mesoscale eddies by 24 individual juvenile loggerhead sea turtles (Caretta caretta) in the Brazil-Malvinas Confluence region. The influence of eddies on turtles is assessed by collocating the turtle trajectories to the tracks of mesoscale eddies identified in maps of sea level anomaly. Juvenile loggerhead sea turtles are significantly more likely to be located in the interiors of anticyclones in this region. The distribution of surface drifters in eddy interiors reveals no significant association with the interiors of cyclones or anticyclones, suggesting higher prevalence of turtles in anticyclones is a result of their behavior. In the southern portion of the Brazil-Malvinas Confluence region, turtle swimming speed is significantly slower in the interiors of anticyclones, when compared to the periphery, suggesting that these turtles are possibly feeding on prey items associated with anomalously low near-surface chlorophyll concentrations observed in those features

Sea Turtle Bycatch Mitigation in U.S. Longline Fisheries

Capture of sea turtles in longline fisheries has been implicated in population declines of loggerhead (Caretta caretta) and leatherback (Dermochelys coriacea) turtles. Since 2004, United States (U.S.) longline vessels targeting swordfish and tunas in the Pacific and regions in the Atlantic Ocean have operated under extensive fisheries regulations to reduce the capture and mortality of endangered and threatened sea turtles. We analyzed 20+ years of longline observer data from both ocean basins during periods before and after the regulations to assess the effectiveness of the regulations. Using generalized additive mixed models (GAMMs), we investigated relationships between the probability of expected turtle interactions and operational components such as fishing location, hook type, bait type, sea surface temperature, and use of light sticks. GAMMs identified a two to three-fold lower probability of expected capture of loggerhead and leatherback turtle bycatch in the Atlantic and Pacific when circle hooks are used (vs. J hook). Use of fish bait (vs. squid) was also found to significantly reduce the capture probability of loggerheads in both ocean basins, and for leatherbacks in the Atlantic only. Capture probabilities are lowest when using a combination of circle hook and fish bait. Influences of light sticks, hook depth, geographic location, and sea surface temperature are discussed specific to species and regions. Results confirmed that in two U.S.-managed longline fisheries, rates of sea turtle bycatch significantly declined after the regulations. In the Atlantic (all regions), rates declined by 40 and 61% for leatherback and loggerhead turtles, respectively, after the regulations. Within the NED area alone, where additional restrictions include a large circle hook (18/0) and limited use of squid bait, rates declined by 64 and 55% for leatherback and loggerhead turtles, respectively. Gains were even more pronounced for the Pacific shallow set fishery, where mean bycatch rates declined by 84 and 95%, for leatherback and loggerhead turtles, respectively, for the post-regulation period. Similar management approaches could be used within regional fisheries management organizations to reduce capture of sea turtles and to promote sustainable fisheries on a global scale