HMMoce : an R package for improved geolocation of archival-tagged fishes using a hidden Markov method

Author Posting. © The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Methods in Ecology and Evolution 9 (2018): 1212-1220, doi:10.1111/2041-210X.12959.Electronic tagging of marine fishes is commonly achieved with archival tags that rely on light levels and sea surface temperatures to retrospectively estimate movements. However, methodological issues associated with light-level geolocation have constrained meaningful inference to species where it is possible to accurately estimate time of sunrise and sunset. Most studies have largely ignored the oceanographic profiles collected by the tag as a potential way to refine light-level geolocation estimates. Open-source oceanographic measurements and outputs from high-resolution models are increasingly available and accessible. Temperature and depth profiles recorded by electronic tags can be integrated with these empirical data and model outputs to construct likelihoods and improve geolocation estimates. The R package HMMoce leverages available tag and oceanographic data to improve position estimates derived from electronic tags using a hidden Markov approach. We illustrate the use of the model and test its performance using example blue and mako shark archival tag data. Model results were validated using independent, known tracks and compared to results from other geolocation approaches. HMMoce exhibited as much as 6-fold improvement in pointwise error as compared to traditional light-level geolocation approaches. The results demonstrated the general applicability of HMMoce to marine animals, particularly those that do not frequent surface waters during crepuscular periods.This work was funded by awards to C. Braun from the Martin Family Society of Fellows for Sustainability Fellowship at the Massachusetts Institute of Technology, the Grassle Fellowship and Ocean Venture Fund at the Woods Hole Oceanographic Institution, and the NASA Earth and Space Science Fellowship

Changes in the Distribution of Atlantic Bluefin Tuna (Thunnus thynnus) in the Gulf of Maine 1979-2005

The Gulf of Maine, NW Atlantic Ocean, is a productive, seasonal foraging ground for Atlantic bluefin tuna (Thunnus thynnus), but commercial landings of adult size classes were up to 40% below the allocated total allowable catch between 2004 to 2008 for the rod and reel, harpoon, and purse seine categories in the Gulf of Maine. Reduction in Atlantic bluefin tuna catches in the Gulf of Maine could represent a decline in spawning stock biomass, but given wide-ranging, complex migration patterns, and high energetic requirements, an alternative hypothesis is that their dispersal patterns shifted to regions with higher prey abundance or profitability, reducing availability to U.S. fishing fleets. This study fit generalized linear models to Atlantic bluefin tuna landings data collected from fishermen’s logbooks (1979-2005) as well as the distances between bluefin tuna schools and Atlantic herring (Clupea harengus), a primary prey species, to test alternative hypotheses for observed shifts in Atlantic bluefin tuna availability in the Gulf of Maine. For the bluefin model, landings varied by day of year, latitude and longitude. The effect of latitude differed by day of year and the effect of longitude differed by year. The distances between Atlantic bluefin tuna schools and Atlantic herring schools were significantly smaller (p<0.05) than would be expected from a randomly distributed population. A time series of average bluefin tuna school positions was positively correlated with the average number of herring captured per tow on Georges Bank in spring and autumn surveys respectively (p<0.01, r2=0.24, p<0.01, r2=0.42). Fishermen’s logbooks contributed novel spatial and temporal information towards testing these hypotheses for the bluefin tuna fishery

Perspectives from the water: Utilizing fisher’s observations to inform SNE/ MA windowpane science and managemen

Within fisheries, stakeholders often have varying viewpoints regarding natural marine resources, and use different sets information to evaluate their condition. Evaluating a resource with different sets of information can lead to different conclusions. Windowpane flounder (Scophthalmus aquosus) are a managed finfish species in the northwest Atlantic whose regulations have the potential to limit harvest opportunities for target species. We analyzed commercial trip and catch information from video data to understand local densities of windowpane flounder in conjunction with fisheries independent surveys. Video monitoring data from three Rhode Island commercial fisher’s vessels and fisheries independent trawl survey data were analyzed to understand the geographic distribution of the stock as well as overlap with temporary closed areas. Biomass data from the fisheries-dependent and fisheries-independent surveys were combined with a spatial-temporal model that accounted for differences in catchability among vessels and spatial autocorrelation. A separate analysis of esti-mated discard rates with observer data was also conducted to determine how the distribution of windowpane discards in Southern New England compared to the distribution of model predicted windowpane abundance. In agreement with the fishermen’s observations, the temporary closed areas were not located where the highest densities of windowpane flounder occurred. The temporary closed areas, however, were located where the highest rates of discards occurred and thus where fishing had the greatest impact on the stock. The integration of verified fishery-dependent data with the scientific surveys has the potential to create a single set of information that is trusted by all user groups

Horizontal and vertical movement patterns and habitat use of juvenile porbeagles (Lamna nasus) in the Western North Atlantic

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Skomal, G., Marshall, H., Galuardi, B., Natanson, L., Braun, C. D., & Bernal, D. Horizontal and vertical movement patterns and habitat use of juvenile porbeagles (Lamna nasus) in the Western North Atlantic. Frontiers in Marine Science, 8,(2021): 624158, https://doi.org/10.3389/fmars.2021.624158.The porbeagle (Lamna nasus) is a large, highly migratory endothermic shark broadly distributed in the higher latitudes of the Atlantic, South Pacific, and Indian Oceans. In the North Atlantic, the porbeagle has a long history of fisheries exploitation and current assessments indicate that this stock is severely overfished. Although much is known of the life history of this species, there is little fisheries-independent information about habitat preferences and ecology. To examine migratory routes, vertical behavior, and environmental associations in the western North Atlantic, we deployed pop-up satellite archival transmitting tags on 20 porbeagles in late November, 2006. The sharks, ten males and ten females ranging from 128 to 154 cm fork length, were tagged and released from a commercial longline fishing vessel on the northwestern edge of Georges Bank, about 150 km east of Cape Cod, MA. The tags were programmed to release in March (n = 7), July (n = 7), and November (n = 6) of 2007, and 17 (85%) successfully reported. Based on known and derived geopositions, the porbeagles exhibited broad seasonally-dependent horizontal and vertical movements ranging from minimum linear distances of 937 to 3,310 km and from the surface to 1,300 m, respectively. All of the sharks remained in the western North Atlantic from the Gulf of Maine, the Scotian Shelf, on George's Bank, and in the deep, oceanic waters off the continental shelf along the edge of, and within, the Gulf Stream. In general, the population appears to be shelf-oriented during the summer and early fall with more expansive offshore radiation in the winter and spring. Although sharks moved through temperatures ranging from 2 to 26°C, the bulk of their time (97%) was spent in 6-20°C. In the summer months, most of the sharks were associated with the continental shelf moving between the surface and the bottom and remaining < 200 m deep. In the late fall and winter months, the porbeagles moved into pelagic habitat and exhibited two behavioral patterns linked with the thermal features of the Gulf Stream: “non-divers” (n = 7) largely remained at epipelagic depths and “divers” (n = 10) made frequent dives into and remained at mesopelagic depths (200–1000 m). These data demonstrate that juvenile porbeagles are physiologically capable of exploiting the cool temperate waters of the western North Atlantic as well as the mesopelagic depths of the Gulf Stream, possibly allowing exploitation of prey not available to other predators.This research was funded by the Large Pelagics Research Center (Grant 06-125)

Seasonal Occurrence, Horizontal Movements, and Habitat Use Patterns of Whale Sharks (\u3ci\u3eRhincodon typus\u3c/i\u3e) in the Gulf of Mexico

In the northern Gulf of Mexico (GOM), whale sharks (Rhincodon typus) form large aggregations at continental shelf-edge banks during summer; however, knowledge of movements once they leave aggregation sites is limited. Here we report on the seasonal occurrence of whale sharks in the northern GOM based on over 800 whale shark sightings from 1989 to 2016, as well as the movements of 42 whale sharks tagged with satellite-linked and popup satellite archival transmitting tags from 2008 to 2015. Sightings data were most numerous during summer and fall often with aggregations of individuals reported along the continental shelf break. Most sharks (66%) were tagged during this time at Ewing Bank, a known aggregation site off the coast of Louisiana. Whale shark track duration ranged from three to 366 days and all tagged individuals, which ranged from 4.5 to 12.0 m in total length, remained within the GOM. Sightings data revealed that whale sharks occurred primarily in continental shelf and shelf-edge waters (81%) whereas tag data revealed the sharks primarily inhabited continental slope and open ocean waters (91%) of the GOM. Much of their time spent in open ocean waters was associated with the edge of the Loop Current and associated mesoscale eddies. During cooler months, there was a net movement southward, corresponding with the time of reduced sighting reports. Several sharks migrated to the southwest GOM during fall and winter, suggesting this region could be important overwintering habitat and possibly represents another seasonal aggregation site. The three long-term tracked whale sharks exhibited interannual site fidelity, returning one year later to the vicinity where they were originally tagged. The increased habitat use of north central GOM waters by whale sharks as summer foraging grounds and potential interannual site fidelity to Ewing Bank demonstrate the importance of this region for this species

Tracking bluefin tuna reproductive migration into the Mediterranean Sea with electronic pop-up satellite archival tags using two tagging procedures

Thirteen adult bluefin tuna were tracked with elec- tronic pop-up satellite tags during their reproductive migration towards Mediterranean spawning grounds as they entered the Strait of Gibraltar. Fish were caught in tuna traps and tagged either underwater, with the aid of a modified spear gun, or on the deck of the boat. Fish tagged on board initially showed a shallower behavior than those tagged in the water. The pattern of horizontal movements was also different between both groups. Shortly after tagging, the eight fish tagged in the water entered the Mediterranean Sea. Six of these fish reached the spawning ground located south- west of the Balearic archipelago before headin g back for the Atlantic, whereas the other two traveled far- ther east, reaching its easternmost longitudes between Formentera and Sardinia and the South Tyrrhenian Sea, respectively. In contrast, two out of the five fish tagged on board never entered the Mediterranean Sea, and another one did enter the Medi terranean when the reproductive season was already over. These results suggest an impact of the tagging procedure on the post-release behavior of bluefin tuna. Exclu ding the tags that popped-off east of the Strait of Gibra ltar, bluefin tuna stayed in the Mediterranean Sea for 22– 28 days. Analysis of the median depth indicated a shallow behavior during both day and nighttime throughout the return phase of the fish from the Mediterranean Sea to the Atlantic Ocean with the exception of the area around the Strait of Gibraltar, where they showed a deeper behavior that coincided with a marked vertical gradient in the currents.Versión del editor2,044

On the Incorporation of Psychologically-Driven 'Music' Preference Models for Music Recommendation

There are hundreds of millions of songs available to the public, necessitating the use of music recommendation systems to discover new music. Currently, such systems account for only the quantitative musical elements of songs, failing to consider aspects of human perception of music and alienating the listener’s individual preferences from recommendations. Our research investigated the relationships between perceptual elements of music, represented by the MUSIC model, with computational musical features generated through The Echo Nest, to determine how a psychological representation of music preference can be incorporated into recommendation systems to embody an individual’s music preferences. Our resultant model facilitates computation of MUSIC factors using The Echo Nest features, and can potentially be integrated into recommendation systems for improved performance

Dispersal Routes and Habitat Utilization of Juvenile Atlantic Bluefin Tuna, Thunnus thynnus, Tracked with Mini PSAT and Archival Tags

Between 2005 and 2009, we deployed 58 miniature pop-up satellite archival tags (PSAT) and 132 implanted archival tags on juvenile Atlantic bluefin tuna (age 2–5) in the northwest Atlantic Ocean. Data returned from these efforts (n = 26 PSATs, 1 archival tag) revealed their dispersal routes, horizontal and vertical movements and habitat utilization. All of the tagged bluefin tuna remained in the northwest Atlantic for the duration observed, and in summer months exhibited core-use of coastal seas extending from Maryland to Cape Cod, MA, (USA) out to the shelf break. Their winter distributions were more spatially disaggregated, ranging south to the South Atlantic Bight, northern Bahamas and Gulf Stream. Vertical habitat patterns showed that juvenile bluefin tuna mainly occupied shallow depths (mean  = 5–12 m, sd  = 15–23.7 m) and relatively warm water masses in summer (mean  = 17.9–20.9°C, sd  = 4.2–2.6°C) and had deeper and more variable depth patterns in winter (mean  = 41–58 m, sd  = 48.9–62.2 m). Our tagging results reveal annual dispersal patterns, behavior and oceanographic associations of juvenile Atlantic bluefin tuna that were only surmised in earlier studies. Fishery independent profiling from electronic tagging also provide spatially and temporally explicit information for evaluating dispersals rates, population structure and fisheries catch patterns

Spawning Behaviour and Post-spawning Migration Patterns of Atlantic Bluefin Tuna (Thunnus thynnus) Ascertained from Satellite Archival Tags

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Integrated Management and Visualization of Electronic Tag Data with Tagbase

Electronic tags have been used widely for more than a decade in studies of diverse marine species. However, despite significant investment in tagging programs and hardware, data management aspects have received insufficient attention, leaving researchers without a comprehensive toolset to manage their data easily. The growing volume of these data holdings, the large diversity of tag types and data formats, and the general lack of data management resources are not only complicating integration and synthesis of electronic tagging data in support of resource management applications but potentially threatening the integrity and longer-term access to these valuable datasets. To address this critical gap, Tagbase has been developed as a well-rounded, yet accessible data management solution for electronic tagging applications. It is based on a unified relational model that accommodates a suite of manufacturer tag data formats in addition to deployment metadata and reprocessed geopositions. Tagbase includes an integrated set of tools for importing tag datasets into the system effortlessly, and provides reporting utilities to interactively view standard outputs in graphical and tabular form. Data from the system can also be easily exported or dynamically coupled to GIS and other analysis packages. Tagbase is scalable and has been ported to a range of database management systems to support the needs of the tagging community, from individual investigators to large scale tagging programs. Tagbase represents a mature initiative with users at several institutions involved in marine electronic tagging research