Removing observational noise from fisheries-independent time series data using ARIMA models

Abundance indices derived from fishery-independent surveys typically exhibit much higher interannual variability than is consistent with the within-survey variance or the life history of a species. This extra variability is essentially observation noise (i.e. measurement error); it probably reflects environmentally driven factors that affect catchability over time. Unfortunately, high observation noise reduces the ability to detect important changes in the underlying population abundance. In our study, a noise-reduction technique for uncorrelated observation noise that is based on autoregressive integrated moving average (ARIMA) time series modeling is investigated. The approach is applied to 18 time series of finfish abundance, which were derived from trawl survey data from the U.S. northeast continental shelf. Although the a priori assumption of a random-walk-plus-uncorrelated-noise model generally yielded a smoothed result that is pleasing to the eye, we recommend that the most appropriate ARIMA model be identified for the observed time series if the smoothed time series will be used for further analysis of the population dynamics of a species.

Variability in supply and cross-shelf transport of pink shrimp (Farfantepenaeus duorarum) postlarvae into western Florida Bay

The variability in the supply of pink shrimp (Farfantepenaeus duorarum) postlarvae and the transport mechanisms of planktonic stages were investigated with field data and simulations of transport. Postlarvae entering the nursery grounds of Florida Bay were collected for three consecutive years at channels that connect the Bay with the Gulf of Mexico, and in channels of the Middle Florida Keys that connect the southeastern margin of the Bay with the Atlantic Ocean. The influx of postlarvae in the Middle Florida Keys was low in magnitude and varied seasonally and among years. In contrast, the greater postlarval influx occurred at the northwestern border of the Bay, where there was a strong seasonal pattern with peaks in influx from July through September each year. Planktonic stages need to travel up to 150 km eastward between spawning grounds (northeast of Dry Tortugas) and nursery grounds (western Florida Bay) in about 30 days, the estimated time of planktonic development for this species. A Lagrangian trajectory model was developed to estimate the drift of planktonic stages across the SW Florida shelf. The model simulated the maximal distance traveled by planktonic stages under various assumptions of behavior. Simulation results indicated that larvae traveling with the instantaneous current and exhibiting a diel behavior travel up to 65 km and 75% of the larvae travel only 30 km. However, the eastward distance traveled increased substantially when a larval response to tides was added to the behavioral variable (distance increased to 200 km and 85% of larvae traveled 150 km). The question is, when during larval development, and where on the shallow SW Florida shelf, does the tidal response become incorporated into the behavior of pink shrimp.

Results of bottom trawl surveys carried out in Vietnamese waters (20-200 m) in 1996-1997

Bottom trawl surveys were conducted in the southwest monsoon season in 1996 (survey 1) and in the northeast monsoon season in 1996-97 (survey 2) throughout Vietnamese waters. The surveys mainly covered the depth zone 50-200 m but in the northeast monsoon season the depth zone 20-50 m was included in the northern and southern areas. Overall, 273 trawl hauls were conducted. The total biomass for Vietnamese waters in the depth zone 20-200 m was estimated at 700 000 t . Biomass estimates are given for the most abundant species. A relatively higher mean catch-per-unit effort (CPUE) was obtained from survey 2 than from survey 1 and in partcular at depth ranges 50-100 and 100-200 m in south Vietnam. Overall, the dominant families were Monacanthidae (34%), Carangidae (15%), Trichiuridae (9%) and Synodontidae (6%).

Age and growth estimates of the thorny skate (Amblyraja radiata) in the western Gulf of Maine

The northwest Atlantic population of thorny skates (Amblyraja radiata) inhabits an area that ranges from Greenland and Hudson Bay, Canada, to South Carolina. Despite such a wide range, very little is known about most aspects of the biology of this species. Recent stock assessment studies in the northeast United States indicate that the biomass of the thorny skate is below the threshold levels mandated by the Sustainable Fisheries Act. In order to gain insight into the life history of this skate, we estimated age and growth for thorny skates, using vertebral band counts from 224 individuals ranging in size from 29 to 105 cm total length (TL). Age bias plots and the coefficient of variation indicated that our aging method represents a nonbiased and precise approach for the age assessment of A. radiata. Marginal increments were significantly different between months (Kruskal-Wallis P<0.001); a distinct trend of increasing monthly increment growth began in August. Age-at-length data were used to determine the von Bertalanffy growth parameters for this population: L∞ = 127 cm (TL) and k= 0.11 for males; L∞ = 120 cm (TL) and k= 0.13 for females. The oldest age estimates obtained for the thorny skate were 16 years for both males and females, which corresponded to total lengths of 103 cm and 105 cm, respectively.

An Historical Review of Sebastes Taxonomy and Systematics

Following the initial description of a species of Sebastes from the Atlantic in the late 1700’s, in the late 1800’s the incredible taxonomic diversity of the genus began to be recognized as more species were discovered in northeast Pacific waters. With over 100 species, most of them from the North Pacific, the genus Sebastes (rockfishes) now presents taxonomic problems at every level. For example, although early efforts to understand relationships among the species resulted in the erection of several subgenera, those and more recent efforts remain largely unsuccessful. Also, the position of the genus within the order Scorpaeniformes, as well as the limits of the genus and the validity of some species are all unresolved. This paper examines the worldwide history and status of taxonomic studies on Sebastes, and reviews the 23 subgenera that have been erected over the years. This review of research, which includes morphological and genetic studies, provides a framework against which to evaluate studies using new genetic techniques.

Review of a Small-scale Pelagic Longline Fishery off Northeastern Brazil

The annual catches of four small longliners operating off northeast Brazil from 1983 to 1997 were examined across different areas and locations. The total catch comprised tunas (30%), sharks (54%), billfishes (12%), and other fish species (4%). Fishing strategy and annual composition of catches showed large spatial and temporal variabilities with the dominant catches alternating among yellowfin tuna, Thunnus albacares; gray sharks, Carcharhinus spp.; and blue shark, Prionace glauca. Catches of blue and gray sharks showed a significant interaction among seamounts, with gray sharks occurring in maximum abundance around those seamounts that had relatively deep summits and low-sloping depth profiles. Results are discussed in terms of the various factors that may have influenced distribution of effort.

Foreword and Acknowledgments: Woods Hole Laboratory Centennial

The year 1985 was one of celebration for the Woods Hole Laboratory of the National Marine Fisheries Service's Northeast Fisheries Center. The reason was the one hundredth anniversary of the completion and occupation of the first facility in the world dedicated to marine fisheries research. Spencer Fullerton Baird, Assistant Secretary of the Smithsonian Institution, and newly appointed first Commissioner of the nascent U.S. Commission of Fish and Fisheries visited Woods Hole in the summer of 1871 to establish a base from which to begin the investigations mandated by Congress when they established the "Fish Commission." During the following three summers (1872-74), operations were conducted from several other localities along the New England coast. During the course of those four years Baird determined that Woods Hole offered the most suitable natural and physical amenities for the investigations being conducted by the Fish Commission at that time, and for those envisioned for the future. The base for Commission operations was returned to Woods Hole in the summer of 1875 and has remained there ever since, through times fair and foul and several agency changes.

PICES Press, Vol. 18, No. 1, Winter 2010

•Major Outcomes from the 2009 PICES Annual Meeting: A Note from the Chairman (pp. 1-3, 8) •PICES Science – 2009 (pp. 4-8) •2009 PICES Awards (pp. 9-10) •New Chairmen in PICES (pp. 11-15) •PICES Interns (p. 15) •The State of the Western North Pacific in the First Half of 2009 (pp. 16-17, 27) •The State of the Northeast Pacific in 2009 (pp. 18-19) •The Bering Sea: Current Status and Recent Events (pp. 20-21) •2009 PICES Summer School on “Satellite Oceanography for the Earth Environment” (pp. 22-25) •2009 International Conference on “Marine Bioinvasions” (pp. 26-27) •A New PICES Working Group Holds Workshop and Meeting in Jeju Island (pp. 28-29) •The Second Marine Ecosystem Model Inter-comparison Workshop (pp. 30-32) •ICES/PICES/UNCOVER Symposium on “Rebuilding Depleted Fish Stocks – Biology, Ecology, Social Science and Management Strategies” (pp. 33-35) •2009 North Pacific Synthesis Workshop (pp. 36-37) •2009 PICES Rapid Assessment Survey (pp. 38-40)

PICES Press, Vol. 18, No. 2, Summer 2010

•The 2010 Inter-sessional Science Board Meeting: A Note from the Science Board Chairman (pp. 1-3) •2010 Symposium on “Effects of Climate Change on Fish and Fisheries” (pp. 4-11) •2009 Mechanism of North Pacific Low Frequency Variability Workshop (pp. 12-14) •The Fourth China-Japan-Korea GLOBEC/IMBER Symposium (pp. 15-17, 23) •2010 Sendai Ocean Acidification Workshop (pp. 18-19, 31) •2010 Sendai Coupled Climate-to-Fish-to-Fishers Models Workshop (pp. 20-21) •2010 Sendai Salmon Workshop on Climate Change (pp. 22-23) •2010 Sendai Zooplankton Workshop (pp. 24-25, 28) •2010 Sendai Workshop on “Networking across Global Marine Hotspots” (pp. 26-28) •The Ocean, Salmon, Ecology and Forecasting in 2010 (pp. 29, 44) •The State of the Northeast Pacific during the Winter of 2009/2010 (pp. 30-31) •The State of the Western North Pacific in the Second Half of 2009 (pp. 32-33) •The Bering Sea: Current Status and Recent Events (pp. 34-35, 39) •PICES Seafood Safety Project: Guatemala Training Program (pp. 36-39) •The Pacific Ocean Boundary Ecosystem and Climate Study (POBEX) (pp. 40-43) •PICES Calendar (p. 44)

PICES Press, Vol. 19, No. 1, Winter 2011

•2010 PICES Science: A Note from the Former Science Board Chairman (pp. 1-4) •2010 PICES Awards (pp. 5-7) •The First Year of FUTURE: A Progress Report (pp. 8-13) •New Chairmen in PICES (pp. 14-19) •Pacific Ocean Interior Carbon Data Synthesis, PACIFICA, in Progress (pp. 20-23) •2011 PICES Calendar (p. 23) •Ecosystems 2010: Global Progress on Ecosystem-based Fisheries Management (pp. 24-26) •PICES 2010 Rapid Assessment Survey (pp. 27-29) •PICES Workshop on “An Introduction to Rapid Assessment Survey Methodologies for Application in Developing Countries” (pp. 30-31) •The State of the Western North Pacific in the First Half of 2010 (pp. 32-34) •PICES Interns (p. 34) •The State of the Bering Sea in 2010 (pp. 35-37) •The State of the Northeast Pacific in 2010 (pp. 38-40)

PICES Press, Vol. 19, No. 2, Summer 2011

•The 2011 Inter-sessional Science Board Meeting: A Note from Science Board Chairman (pp. 1-4) •Indicators for Status and Change within North Pacific Marine Ecosystems: A FUTURE Workshop (pp. 5-8) •PICES Calendar (p. 8) •2011 ESSAS Open Science Meeting (pp. 9-13) •The 5th Zooplankton Production Symposium (pp. 14-17) •Workshop on "Individual-Based Models of Zooplankton” (pp. 18-21) •New Book Release on the 100th Anniversary of the T/S Osharu Maru (p. 21) •Workshop on “Advances in Genomic and Molecular Studies of Zooplankton” (pp. 22-24) •Workshop on “Updates and Comparisons of Zooplankton Time Series” (pp. 25-27) •Workshop on “Impacts of Ocean Acidification on Zooplankton” (pp. 28-29) •Workshop on “Automated Visual Plankton Identification” (p. 30) •Professor Plum in the Dining Room with a Knife (p. 31) •PICES and ICES on the River Elbe (p. 32) •The State of the Western North Pacific in the Second Half of 2010 (pp. 33-34) •The Bering Sea: Current Status and Recent Events (pp. 35-37) •Northeast Pacific News (pp. 38-39) •PICES Advice on Marine Ecology at a Canadian Judicial Inquiry (p. 40)

PICES Press, Vol. 20, No. 1, Winter 2012

•2011 PICES Science: A Note from the Science Board Chairman (pp. 1-6) •2011 PICES Awards (pp. 7-9) •Beyond the Terrible Disaster of the Great East Japan Earthquake (pp. 10-12) •A New Era of PICES-ICES Scientific Cooperation (p. 13) •New PICES Jellyfish Working Group Formed (pp. 14-15) •PICES Working Group on North Pacific Climate Variability (pp. 16-18) •Final U.S. GLOBEC Symposium and Celebration (pp. 19-25) •2011 PICES Rapid Assessment Survey (pp. 26-29) •Introduction to Rapid Assessment Survey Methodologies for Detecting Non-indigenous Marine Species (pp. 30-31) •The 7th International Conference on Marine Bioinvasions (pp. 32-33) •NOWPAP/PICES/WESTPAC Training Course on Remote Sensing Data Analysis (pp. 34-36) •PICES-2011 Workshop on “Trends in Marine Contaminants and their Effects in a Changing Ocean” (pp. 37-39) •The State of the Western North Pacific in the First Half of 2011 (pp. 40-42) •Yeosu Symposium theme sessions (p. 42) •The Bering Sea: Current Status and Recent Events (pp. 43-44) •News of the Northeast Pacific Ocean (pp. 45-47) •Recent and Upcoming PICES Publications (p. 47) •New leadership for the PICES Fishery Science Committee (p. 48)

PICES Press, Vol. 21, No. 1, Winter 2013

•2012 PICES Science: A Note from the Science Board Chairman (pp. 1-6) ◾2012 PICES Awards (pp. 7-9) ◾GLOBEC/PICES/ICES ECOFOR Workshop (pp. 10-15) ◾ICES/PICES Symposium on “Forage Fish Interactions” (pp. 16-18) ◾The Yeosu Declaration, the Yeosu Declaration Forum and the Yeosu Project (pp. 19-23) ◾2013 PICES Calendar (p. 23) ◾Why Do We Need Human Dimensions for the FUTURE Program? (pp. 24-25) ◾New PICES MAFF-Sponsored Project on “Marine Ecosystem Health and Human Well-Being” (pp. 26-28) ◾The Bering Sea: Current Status and Recent Trends (pp. 29-31) ◾Continuing Cool in the Northeast Pacific Ocean (pp. 32, 35) ◾The State of the Western North Pacific in the First Half of 2012 (pp. 33-35) ◾New Leadership in PICES (pp. 36-39)

PICES Press, Vol. 21, No. 2, Summer 2013

•The 2013 Inter-sessional Science Board Meeting: A Note from the Science Board Chairman (pp. 1-4) •ICES/PICES Workshop on Global Assessment of the Implications of Climate Change on the Spatial Distribution of Fish and Fisheries (pp. 5-8) •PICES participates in a Convention on Biological Diversity Regional Workshop (pp. 9-11) •Social and Economic Indicators for Status and Change within North Pacific Ecosystems (pp. 12-13) •The Fourth International Jellyfish Bloom Symposium (pp. 14-15) •Workshop on Radionuclide Science and Environmental Quality in the North Pacific (pp. 16-17) •PICES-MAFF Project on Marine Ecosystem Health and Human Well-Being: Indonesia Workshop (pp. 18-19) •Socioeconomic Indicators for United States Fisheries and Fishing Communities (pp. 20-23) •Harmful Algal Blooms in a Changing World (pp. 24-25, 27) •Enhancing Scientific Cooperation between PICES and NPAFC (pp. 26-27) •Workshop on Marine Biodiversity Conservation and Marine Protected Areas in the Northwest Pacific (pp. 28-29) •The State of the Western North Pacific in the Second Half of 2012 (pp. 30-31) •Stuck in Neutral in the Northeast Pacific Ocean (pp. 32-33) •The Bering Sea: Current Status and Recent Trends (pp. 34-36) •For your Bookshelf (p. 37) •Howard Freeland takes home Canadian awards (p. 38)

Climatic factors associated with phytoplankton community succession during and after the 1977 drought for the San Francisco Bay-Delta Estuary [abstract]

Principal coordinates analysis and multiple regression analysis were used to determine the environmental factors associated with the decline in phytoplankton production during and after the 1977 drought for the San Francisco Bay-Delta Estuary. Physical, chemical and biological data were collected semimonthly or monthly during the spring-summer between 1973 and 1982 from 15 sampling sites located throughout the Bay-Delta. A decline in phytoplankton community diversity and density during the 1977 drought and subsequent years (1978 through 1981) was described using principal coordinates analysis. The best multiple regression which described the changes in phytoplankton community succession contained the variables water temperature, wind velocity and ortho-phosphate concentration. Together these variables accounted for 61 percent of the variation in the phytoplankton community among years described by principal coordinates analysis. An increase in water temperature, wind velocity and ortho-phosphate concentration within the Bay-Delta, beginning in June 1976 and continuing through 1981, was demonstrated using weighted moving averages. From the strong association between phytoplankton community succession and climatic variables it was hypothesized that the decline in phytoplankton production during and after the 1977 drought was associated with climatic changes within the northeast Pacific.