SEASIM-NEAM: A Spatially-Explicit Agent-based SIMulator of North East Atlantic Mackerel population dynamics

In 2018 we published a spatially-explicit individual-based model (IBM) that uses satellite-derived maps of food availability and temperature to predict Northeast Atlantic mackerel (Scomber scombrus, NEAM) population dynamics. Since then, to address various ecological questions, we have extended the IBM to include additional processes and data. Throughout its development, technical documents have been provided in the form of e.g. supplementary information to published articles. However, we acknowledge that it would be difficult for potential users to collate information from separate supplementary documents and gain a full understanding of the current state of the IBM. Here, we provide a full technical specification of the latest version of our IBM. The technical specification is provided in the standard ODD (Overview, Design concepts and Details) format, and supplemented by a TRACE (TRAnsparent and Comprehensive model Evaludation) document. For the first time, we give our model the acronym SEASIM-NEAM: a Spatially-Explicit Agent-based SIMulator of North East Atlantic Mackerel population dynamics. This article supersedes previous documentation. Going forward we hope that this article will stimulate development of similar models.• This article collates improvements that have been made to SEASIM-NEAM over time.

[1]  Jared Aldstadt,et al.  Using multiple scale spatio-temporal patterns for validating spatially explicit agent-based models , 2018, Int. J. Geogr. Inf. Sci..

[2]  Uta Berger,et al.  Pattern-Oriented Modeling of Agent-Based Complex Systems: Lessons from Ecology , 2005, Science.

[3]  Chih-hao Hsieh,et al.  Using coupled fish behavior–hydrodynamic model to investigate spawning migration of Japanese anchovy, Engraulis japonicus, from the East China Sea to Taiwan , 2012 .

[4]  Volker Grimm,et al.  Effects of human‐induced prey depletion on large carnivores in protected areas: Lessons from modeling tiger populations in stylized spatial scenarios , 2019, Ecology and evolution.

[5]  J. Beddington,et al.  Mutual Interference Between Parasites or Predators and its Effect on Searching Efficiency , 1975 .

[6]  T M Yohannan,et al.  GROWTH PATTERN OF INDIAN MACKEREL , 1979 .

[7]  Teunis Jansen,et al.  Geographical expansion of Northeast Atlantic mackerel (Scomber scombrus) in the Nordic Seas from 2007 to 2016 was primarily driven by stock size and constrained by low temperatures , 2019, Deep Sea Research Part II: Topical Studies in Oceanography.

[8]  T. Dawson,et al.  Selecting thresholds of occurrence in the prediction of species distributions , 2005 .

[9]  R. Richards-Kortum,et al.  A comparison of C/B ratios from studies using receiver operating characteristic curve analysis. , 1999, Journal of clinical epidemiology.

[10]  Marten Scheffer,et al.  Super-individuals a simple solution for modelling large populations on an individual basis , 1995 .

[11]  Geir Huse,et al.  Feeding strategy of mackerel in the Norwegian Sea relative to currents, temperature, and prey , 2016 .

[12]  Teunis Jansen,et al.  Temperature affects the timing of spawning and migration of North Sea mackerel , 2011 .

[13]  M. Castonguay,et al.  Growth of juvenile Pacific mackerel, Scomber japonicus in the Gulf of California* , 1998 .

[14]  J. Herrmann,et al.  Effect of body size on the standard metabolism of horse mackerel , 2000 .

[15]  Steven F Railsback,et al.  Pattern-oriented modelling: a ‘multi-scope’ for predictive systems ecology , 2012, Philosophical Transactions of the Royal Society B: Biological Sciences.

[16]  Yanan Fan,et al.  Handbook of Approximate Bayesian Computation , 2018 .

[17]  J. M. Donley,et al.  Effects of temperature on sustained swimming performance and swimming kinematics of the chub mackerel Scomber japonicus. , 2002, The Journal of experimental biology.

[18]  Winfried Kurth,et al.  RNETLOGO: an R package for running and exploring individual‐based models implemented in NETLOGO , 2012 .

[19]  V. C. Sambilay,et al.  Interrelationships between swimming speed, caudal fin aspect ratio and body length of fishes , 1990 .

[20]  Teunis Jansen,et al.  Population Structure of Atlantic Mackerel (Scomber scombrus) , 2013, PloS one.

[21]  W. A. Dawson,et al.  The estimation of a mackerel (Scomber scombrus L.) spawning stock size by plankton survey , 1981 .

[22]  A. Webster,et al.  The energy cost of fat and protein deposition in the rat , 1977, British Journal of Nutrition.

[23]  P. D. Wallace.  Seasonal variation in fat content of mackerel (Scomber scombrus L.) caught in the western English Channel , 1991 .

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

[25]  Lawrence W. Harding,et al.  Calibration of a bioenergetics model linking primary production to Atlantic menhaden Brevoortia tyrannus growth in Chesapeake Bay , 2011 .

[26]  Imants G. Priede,et al.  Batch fecundity of Atlantic mackerel, Scomber scombrus L. , 1992 .

[27]  M. Dickey‐Collas,et al.  Life-cycle spatial patterns of small pelagic fish in the Northeast Atlantic , 2010 .

[28]  David G. Reid,et al.  Understanding mackerel migration off Scotland: Tracking with echosounders and commercial data, and including environmental correlates and behaviour , 1995 .

[29]  G. A. Steven,et al.  Contributions to the biology of the mackerel, Scomber scombrus L. III. Age and growth , 1952, Journal of the Marine Biological Association of the United Kingdom.

[30]  Geoffrey B. West,et al.  Response to Clarke and Fraser: effects of temperature on metabolic rate , 2006 .

[31]  R. Sibly,et al.  Representing the acquisition and use of energy by individuals in agent‐based models of animal populations , 2013 .

[32]  Kieran Hyder,et al.  A general approach to incorporating spatial and temporal variation in individual-based models of fish populations with application to Atlantic mackerel , 2018 .

[33]  Walter Chavin.  Signs and Symptoms: Applied Pathologic Physiology and Clinical Interpretation. , 1957 .

[34]  A. T. G. W. Eltink.  Changes in age—size distribution and sex ratio during spawning and migration of Western mackerel ( Scomber scombrus L.) , 1987 .

[35]  Knut Schmidt-Nielsen,et al.  Animal Physiology: Adaptation and Environment , 1985 .

[36]  Richard D. Methot,et al.  Estimating Natural Mortality in Stock Assessment Applications , 2011 .

[37]  Donald L. DeAngelis,et al.  A Model for Tropic Interaction , 1975 .

[38]  S. Kooijman,et al.  On the dynamics of chemically stressed populations: The deduction of population consequences from effects on individuals , 1983, Hydrobiological Bulletin.

[39]  Mark Dickey-Collas,et al.  Quantifying the influence of geography and environment on the northeast Atlantic mackerel spawning distribution , 2018 .

[40]  Ronald,et al.  GFDL’s ESM2 Global Coupled Climate–Carbon Earth System Models. Part I: Physical Formulation and Baseline Simulation Characteristics , 2012 .

[41]  R. Sibly,et al.  Simulating the summer feeding distribution of Northeast Atlantic mackerel with a mechanistic individual-based model , 2020, Progress in Oceanography.

[42]  Y. Shin,et al.  Exploring fish community dynamics through size dependent trophic interactions using a spatialized individual based model , 2001 .

[43]  U. Cotano,et al.  Growth of young-of-the-year mackerel in the Bay of Biscay , 2003 .

[44]  Steven F. Railsback,et al.  Pattern-oriented modeling of bird foraging and pest control in coffee farms , 2011 .

[45]  Teunis Jansen,et al.  Migration and Fisheries of North East Atlantic Mackerel (Scomber scombrus) in Autumn and Winter , 2012, PloS one.

[46]  Begoña Villamor,et al.  Models describing mackerel (Scomber scombrus) early life growth in the North and Northwest of the Iberian Peninsula in 2000 , 2004 .

[47]  Pablo Carrera,et al.  Nursery areas and recruitment variation of Northeast Atlantic mackerel (Scomber scombrus) , 2015 .

[48]  Peter Calow,et al.  Physiological Ecology of Animals: An Evolutionary Approach , 1986 .

[49]  William T. Peterson,et al.  Diets and selective feeding by larvae of Atlantic mackerel Scomber scombrus on zooplankton , 1984 .

[50]  Dennis Prangle,et al.  Taking error into account when fitting models using Approximate Bayesian Computation. , 2018, Ecological applications : a publication of the Ecological Society of America.

[51]  Timothy C. Lambert,et al.  Gastric emptying time and assimilation efficiency in Atlantic mackerel (Scomber scombrus) , 1985 .

[52]  F.E.J. Fry,et al.  1 – The Effect of Environmental Factors on the Physiology of Fish , 1971 .

[53]  Fran Saborido-Rey,et al.  Changes in distribution of Greenland halibut in a varying environment , 2013 .

[54]  Pierre Petitgas,et al.  A coupled movement and bioenergetics model to explore the spawning migration of anchovy in the Bay of Biscay , 2015 .

[55]  Anne L. Studholme.  Essential fish habitat source document. Atlantic mackerel, Scomber scombrus, life history and habitat characteristics , 1999 .

[56]  Keith C. Clarke,et al.  Toward Optimal Calibration of the SLEUTH Land Use Change Model , 2007, Trans. GIS.

[57]  Krista,et al.  GFDL’s ESM2 Global Coupled Climate–Carbon Earth System Models. Part II: Carbon System Formulation and Baseline Simulation Characteristics* , 2013 .

[58]  Alice S.A. Johnston,et al.  Calibration and evaluation of individual-based models using Approximate Bayesian Computation , 2015 .

[59]  Bruce Edmonds,et al.  The ODD Protocol for Describing Agent-Based and Other Simulation Models: A Second Update to Improve Clarity, Replication, and Structural Realism , 2020, J. Artif. Soc. Soc. Simul..

[60]  L. Bertalanffy,et al.  A quantitative theory of organic growth , 1938 .

[61]  W. A. Dawson,et al.  Changes in Western mackerel (Scomber scombrus) spawning stock composition during the spawning season , 1986, Journal of the Marine Biological Association of the United Kingdom.

[62]  Begoña Villamor,et al.  Spatial pattern of migration and recruitment of north east Atlantic mackerel , 2001 .

[63]  Jon Helge Vølstad,et al.  Quantifying changes in abundance, biomass, and spatial distribution of Northeast Atlantic mackerel (Scomber scombrus) in the Nordic seas from 2007 to 2014 , 2016 .

[64]  Kieran Hyder,et al.  Potential Consequences of Climate and Management Scenarios for the Northeast Atlantic Mackerel Fishery , 2020, Frontiers in Marine Science.

[65]  Diego Mendiola,et al.  Effects of temperature on development and mortality of Atlantic mackerel fish eggs , 2006 .

[66]  R. Peters.  The Ecological Implications of Body Size , 1983 .