Applying Bayesian spatiotemporal models to fisheries bycatch in the Canadian Arctic

Understanding and reducing the incidence of accidental bycatch, particularly for vulnerable species such as sharks, is a major challenge for contemporary fisheries management. Here we establish integrated nested Laplace approximations (INLA) and stochastic partial differential equations (SPDE) as two powerful tools for modelling patterns of bycatch through time and space. These novel, computationally fast approaches are applied to fit zero-inflated hierarchical spatiotemporal models to Greenland shark (Somniosus microcephalus) bycatch data from the Baffin Bay Greenland halibut (Reinhardtius hippoglossoides) gillnet fishery. Results indicate that Greenland shark bycatch is clustered in space and time, varies significantly from year to year, and there are both tractable factors (number of gillnet panels, total Greenland halibut catch) and physical features (bathymetry) leading to the high incidence of Greenland shark bycatch. Bycatch risk could be reduced by limiting access to spatiotemporal hotspots or by ...

[1]  E. K. Pikitch,et al.  Ecosystem-Based Fishery Management , 2004, Science.

[2]  S. Campana,et al.  Movements of Arctic and northwest Atlantic Greenland sharks (Somniosus microcephalus) monitored with archival satellite pop-up tags suggest long-range migrations , 2015 .

[3]  Jun Yan,et al.  Gaussian Markov Random Fields: Theory and Applications , 2006 .

[4]  C. Orphanides,et al.  Estimating the risk of loggerhead turtle Caretta caretta bycatch in the US mid-Atlantic using fishery-independent and -dependent data , 2013 .

[5]  C. McClellan,et al.  Using telemetry to mitigate the bycatch of long-lived marine vertebrates. , 2009, Ecological applications : a publication of the Ecological Society of America.

[6]  D. Holland,et al.  Identifying ecological and fishing drivers of bycatch in a U.S. groundfish fishery. , 2013, Ecological applications : a publication of the Ecological Society of America.

[7]  G. Baker,et al.  Characterizing seabird bycatch in the eastern Australian tuna and billfish pelagic longline fishery in relation to temporal, spatial and biological influences. , 2010 .

[8]  J. Brodziak,et al.  Model selection and multimodel inference for standardizing catch rates of bycatch species: a case study of oceanic whitetip shark in the Hawaii-based longline fishery , 2013 .

[9]  H. Rue,et al.  Approximate Bayesian inference for hierarchical Gaussian Markov random field models , 2007 .

[10]  Juan Freire,et al.  Identifying and mapping local bycatch hotspots of loggerhead sea turtles using a GIS-based method: implications for conservation , 2013 .

[11]  S. Garcia The ecosystem approach to fisheries : issues, terminology, principles, institutional foundations, implementation and outlook , 2003 .

[12]  E. Melvin,et al.  Estimates of seabird incidental catch by pelagic longline fisheries in the South Atlantic Ocean , 2013 .

[13]  Sara Martino,et al.  Animal Models and Integrated Nested Laplace Approximations , 2013, G3: Genes, Genomes, Genetics.

[14]  Anne Cuzol,et al.  Hierarchical Bayesian modelling with habitat and time covariates for estimating riverine fish population size by successive removal method , 2008 .

[15]  A. Boustany,et al.  Spatio-temporal management of fisheries to reduce by-catch and increase fishing selectivity: Spatio-temporal by-catch management , 2011 .

[16]  S. Carpenter,et al.  Ecological forecasts: an emerging imperative. , 2001, Science.

[17]  C. Wikle Hierarchical Models in Environmental Science , 2003 .

[18]  Ransom A. Myers,et al.  Hierarchical Bayesian models of length-specific catchability of research trawl surveys , 2001 .

[19]  Y‐M. Yeh,et al.  Impact of Taiwanese distant water longline fisheries on the Pacific seabirds: finding hotspots on the high seas , 2011 .

[20]  D. Frierson,et al.  Bycatch mitigation assessment for sharks caught in coastal anchored gillnets , 2009 .

[21]  S. Jiménez,et al.  Seabird bycatch in the Southwest Atlantic: interaction with the Uruguayan pelagic longline fishery , 2009, Polar Biology.

[22]  Rebecca Lewison,et al.  Modeling spatial patterns in fisheries bycatch: improving bycatch maps to aid fisheries management. , 2008, Ecological applications : a publication of the Ecological Society of America.

[23]  Bradley P. Carlin,et al.  Bayesian measures of model complexity and fit , 2002 .

[24]  F. Douvere The importance of marine spatial planning in advancing ecosystem-based sea use management , 2008 .

[25]  Josh M. London,et al.  Bayesian Inference for Animal Space Use and Other Movement Metrics , 2011 .

[26]  J. S. Christiansen,et al.  Arctic marine fishes and their fisheries in light of global change , 2013, Global change biology.

[27]  C. Orphanides Protected Species Bycatch Estimating Approaches: Estimating Harbor Porpoise Bycatch in U.S. Northwestern Atlantic Gillnet Fisheries , 2010 .

[28]  Penelope Vounatsou,et al.  Bayesian analysis of zero inflated spatiotemporal HIV/TB child mortality data through the INLA and SPDE approaches: Applied to data observed between 1992 and 2010 in rural North East South Africa , 2013, Int. J. Appl. Earth Obs. Geoinformation.

[29]  D. Damalas,et al.  Modeling environmental, spatial, temporal, and operational effects on blue shark by‐catches in the Mediterranean long‐line fishery , 2009 .

[30]  Catherine A Calder,et al.  Accounting for uncertainty in ecological analysis: the strengths and limitations of hierarchical statistical modeling. , 2009, Ecological applications : a publication of the Ecological Society of America.

[31]  P. Wade Bayesian Methods in Conservation Biology , 2000 .

[32]  P. Barlow,et al.  Evaluating methods for estimating rare events with zero-heavy data: a simulation model estimating sea turtle bycatchin the pelagic longline fishery , 2012 .

[33]  D. L. Alverson,et al.  By-Catch: Problems and Solutions , 2000 .

[34]  Leonhard Held,et al.  Gaussian Markov Random Fields: Theory and Applications , 2005 .

[35]  Rebecca L. Lewison,et al.  Understanding impacts of fisheries bycatch on marine megafauna , 2004 .

[36]  M. Skern-Mauritzen,et al.  Estimated bycatch of harbour porpoise (Phocoena phocoena) in two coastal gillnet fisheries in Norway, 2006–2008. Mitigation and implications for conservation , 2013 .

[37]  Justin M. J. Travis,et al.  Fitting complex ecological point process models with integrated nested Laplace approximation , 2013 .

[38]  Kung-Sik Chan,et al.  Spatial fisheries ecology: Recent progress and future prospects , 2008 .

[39]  M. Ortiz,et al.  Alternative error distribution models for standardization of catch rates of non-target species from a pelagic longline fishery: billfish species in the Venezuelan tuna longline fishery , 2004 .

[40]  Brendan A. Wintle,et al.  The Use of Bayesian Model Averaging to Better Represent Uncertainty in Ecological Models , 2003 .

[41]  B. Worm,et al.  The Conservation of the Greenland Shark (Somniosus microcephalus): Setting Scientific, Law, and Policy Coordinates for Avoiding a Species at Risk , 2013 .

[42]  S. J. Cripps,et al.  Defining and estimating global marine fisheries bycatch , 2009 .

[43]  Finn Lindgren,et al.  Bayesian Spatial Modelling with R-INLA , 2015 .

[44]  P. Leung,et al.  A Bayesian hierarchical model for modeling white shrimp (Litopenaeus vannamei) growth in a commercial shrimp farm , 2010 .

[45]  L. Harden,et al.  Using spatial and behavioral data to evaluate the seasonal bycatch risk of diamondback terrapins Malaclemys terrapin in crab pots , 2012 .

[46]  Mihoko Minami,et al.  Modeling shark bycatch: The zero-inflated negative binomial regression model with smoothing , 2007, Fisheries Research.

[47]  S. Bograd,et al.  Predicting bycatch hotspots for endangered leatherback turtles on longlines in the Pacific Ocean , 2014, Proceedings of the Royal Society B: Biological Sciences.

[48]  M. MacNeil,et al.  Biology of the Greenland shark Somniosus microcephalus. , 2012, Journal of fish biology.

[49]  Sylvia Richardson,et al.  A comparison of Bayesian spatial models for disease mapping , 2005, Statistical methods in medical research.

[50]  H. Rue,et al.  Spatio-temporal modeling of particulate matter concentration through the SPDE approach , 2012, AStA Advances in Statistical Analysis.

[51]  William N. Venables,et al.  GLMs, GAMs and GLMMs: an overview of theory for applications in fisheries research , 2004 .

[52]  Leonhard Held,et al.  Posterior and Cross-validatory Predictive Checks: A Comparison of MCMC and INLA , 2010 .

[53]  Patrick Brown,et al.  Spatial modelling of lupus incidence over 40 years with changes in census areas , 2012 .

[54]  Hugh P Possingham,et al.  Zero tolerance ecology: improving ecological inference by modelling the source of zero observations. , 2005, Ecology letters.

[55]  W. Tobler A Computer Movie Simulating Urban Growth in the Detroit Region , 1970 .

[56]  C. Amante,et al.  ETOPO1 arc-minute global relief model : procedures, data sources and analysis , 2009 .

[57]  Andrew C. Parnell,et al.  Disentangling spatio-temporal processes in a hierarchical system: a case study in fisheries discards , 2013 .

[58]  Finn Lindgren,et al.  Bayesian computing with INLA: New features , 2012, Comput. Stat. Data Anal..

[59]  J. Moore,et al.  A Bayesian uncertainty analysis of cetacean demography and bycatch mortality using age-at-death data. , 2008, Ecological applications : a publication of the Ecological Society of America.

[60]  BrodziakJon,et al.  Model selection and multimodel inference for standardizing catch rates of bycatch species: a case study of oceanic whitetip shark in the Hawaii-based longline fishery , 2013 .

[61]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[62]  Michael Höhle,et al.  Ecological analysis of social risk factors for Rotavirus infections in Berlin, Germany, 2007–2009 , 2012, International Journal of Health Geographics.

[63]  P. Sullivan,et al.  Hierarchical modeling of bycatch rates of sea turtles in the western North Atlantic , 2008 .

[64]  Mevin B Hooten,et al.  Forest species diversity reduces disease risk in a generalist plant pathogen invasion. , 2011, Ecology letters.

[65]  J. Browder,et al.  Modeling Low Rates of Seabird Bycatch in the U.S. Atlantic Longline Fishery , 2011 .

[66]  D. Conesa,et al.  Estimation and prediction of the spatial occurrence of fish species using Bayesian latent Gaussian models , 2013, Stochastic Environmental Research and Risk Assessment.

[67]  Louise Matthews,et al.  Geographic determinants of reported human Campylobacter infections in Scotland , 2010, BMC public health.

[68]  H. Rue,et al.  An explicit link between Gaussian fields and Gaussian Markov random fields: the stochastic partial differential equation approach , 2011 .

[69]  R. Spieler,et al.  Serological Changes Associated with Gill-Net Capture and Restraint in Three Species of Sharks , 2001 .

[70]  H. Rue,et al.  Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations , 2009 .

[71]  P. Diggle,et al.  Model‐based geostatistics , 2007 .