8. Bibliography

And19

Ken H. Andersen. Fish Ecology, Evolution, and Exploitation: A New Theoretical Synthesis. Monographs in Population Biology, 2019.

AJA09

Michael J Angilletta Jr and Michael James Angilletta. Thermal adaptation: a theoretical and empirical synthesis. Oxford University Press, 2009.

APH+16

Vickery L Arcus, Erica J Prentice, Joanne K Hobbs, Adrian J Mulholland, Marc W Van der Kamp, Christopher R Pudney, Emily J Parker, and Louis A Schipper. On the temperature dependence of enzyme-catalyzed rates. Biochemistry, 55(12):1681–1688, 2016.

BDE+14

David S Boukal, Ulf Dieckmann, Katja Enberg, Mikko Heino, and Christian Jørgensen. Life-history implications of the allometric scaling of growth. Journal of Theoretical Biology, 359:199–207, 2014.

BGA+04

James H Brown, James F Gillooly, Andrew P Allen, Van M Savage, and Geoffrey B West. Toward a metabolic theory of ecology. Ecology, 85(7):1771–1789, 2004.

CTW01

Eric L Charnov, Thomas F Turner, and Kirk O Winemiller. Reproductive constraints and the evolution of life histories with indeterminate growth. Proceedings of the National Academy of Sciences, 98(16):9460–9464, 2001.

CW04

Villy Christensen and Carl J Walters. Ecopath with ecosim: methods, capabilities and limitations. Ecological modelling, 172(2-4):109–139, 2004.

Cla17

Andrew Clarke. Principles of thermal ecology: Temperature, energy and life. Oxford University Press, 2017.

Cla19

Andrew Clarke. Energy flow in growth and production. Trends in ecology & evolution, 34(6):502–509, 2019.

DFS+15

Curtis Deutsch, Aaron Ferrel, Brad Seibel, Hans-Otto Pörtner, and Raymond B Huey. Climate change tightens a metabolic constraint on marine habitats. Science, 348(6239):1132–1135, 2015.

DPS20

Curtis Deutsch, Justin L Penn, and Brad Seibel. Metabolic trait diversity shapes marine biogeography. Nature, 585(7826):557–562, 2020.

FOT+17

Caihong Fu, Norm Olsen, Nathan Taylor, Arnaud Grüss, Sonia Batten, Huizhu Liu, Philippe Verley, and Yunne-Jai Shin. Spatial and temporal dynamics of predator-prey species interactions off western Canada. ICES Journal of Marine Science, 74(8):2107–2119, 05 2017. doi:10.1093/icesjms/fsx056.

FPS+13

Caihong Fu, R Ian Perry, Yunne-Jai Shin, Jake Schweigert, and Huizhu Liu. An ecosystem modelling framework for incorporating climate regime shifts into fisheries management. Progress in oceanography, 115:53–64, 2013. doi:10.1016/j.pocean.2013.03.003.

GCW+02

James F Gillooly, Eric L Charnov, Geoffrey B West, Van M Savage, and James H Brown. Effects of size and temperature on developmental time. Nature, 417(6884):70–73, 2002.

GBB+06

Volker Grimm, Uta Berger, Finn Bastiansen, Sigrunn Eliassen, Vincent Ginot, Jarl Giske, John Goss-Custard, Tamara Grand, Simone K. Heinz, Geir Huse, Andreas Huth, Jane U. Jepsen, Christian Jørgensen, Wolf M. Mooij, Birgit Müller, Guy Pe’er, Cyril Piou, Steven F. Railsback, Andrew M. Robbins, Martha M. Robbins, Eva Rossmanith, Nadja Rüger, Espen Strand, Sami Souissi, Richard A. Stillman, Rune Vabø, Ute Visser, and Donald L. DeAngelis. A standard protocol for describing individual-based and agent-based models. Ecological Modelling, 198(1):115–126, 2006. doi:10.1016/j.ecolmodel.2006.04.023.

GBD+10

Volker Grimm, Uta Berger, Donald L. DeAngelis, J. Gary Polhill, Jarl Giske, and Steven F. Railsback. The odd protocol: a review and first update. Ecological Modelling, 221(23):2760–2768, 2010. doi:10.1016/j.ecolmodel.2010.08.019.

GRV+20

Volker Grimm, Steven F. Railsback, Christian E. Vincenot, Uta Berger, Cara Gallagher, Donald L. DeAngelis, Bruce Edmonds, Jiaqi Ge, Jarl Giske, Jürgen Groeneveld, Alice S.A. Johnston, Alexander Milles, Jacob Nabe-Nielsen, Gary Polhill, Viktoriia Radchuk, Marie-Sophie Rohwäder, Richard A. Stillman, Jan C. Thiele, and Daniel Ayllón. The odd protocol for describing agent-based and other simulation models: a second update to improve clarity, replication, and structural realism. Journal of Artificial Societies and Social Simulation, 23(2):7, 2020. doi:10.18564/jasss.4259.

GQ16

Rolf A. Groeneveld and Martin F. Quaas. Promoting selective fisheries through certification? an analysis of the PNA unassociated-sets purse seine fishery. Fisheries Research, 182:69 – 78, 2016. doi:10.1016/j.fishres.2015.10.014.

GrussSC+15

Arnaud Grüss, Michael J Schirripa, David Chagaris, Michael Drexler, James Simons, Philippe Verley, Yunne-Jai Shin, Mandy Karnauskas, Ricardo Oliveros-Ramos, and Cameron H Ainsworth. Evaluation of the trophic structure of the west florida shelf in the 2000s using the ecosystem model osmose. Journal of Marine Systems, 144:30–47, 2015. doi:10.1016/j.jmarsys.2014.11.004.

HLS+16

Ghassen Halouani, Frida Ben Rais Lasram, Yunne-Jai Shin, Laure Velez, Philippe Verley, Tarek Hattab, Ricardo Oliveros-Ramos, Frédéric Diaz, Frédéric Ménard, Melika Baklouti, Arnaud Guyennon, Mohamed Salah Romdhane, and François Le Loch. Modelling food web structure using an end-to-end approach in the coastal ecosystem of the gulf of gabes (tunisia). Ecological Modelling, 339(Supplement C):45–57, 2016. doi:10.1016/j.ecolmodel.2016.08.008.

HDGodo02

Mikko Heino, Ulf Dieckmann, and Olav Rune Godø. Measuring probabilistic reaction norms for age and size at maturation. Evolution, 56(4):669–678, 2002.

HDiazPD15

Mikko Heino, Beatriz Díaz Pauli, and Ulf Dieckmann. Fisheries-induced evolution. Annual review of ecology, evolution, and systematics, 46:461–480, 2015.

Hol59

Crawford S Holling. The components of predation as revealed by a study of small-mammal predation of the european pine sawfly1. The Canadian Entomologist, 91(5):293–320, 1959.

HJorgensen14

Rebecca E Holt and Christian Jørgensen. Climate warming causes life-history evolution in a model for atlantic cod (gadus morhua). Conservation Physiology, 2(1):cou050, 2014.

JL46

Frank H. Johnson and Isaac Lewin. The growth rate of e. coli in relation to temperature, quinine and coenzyme. Journal of Cellular and Comparative Physiology, 28(1):47–75, 1946. URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/jcp.1030280104, arXiv:https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcp.1030280104, doi:https://doi.org/10.1002/jcp.1030280104.

Koo09

Bas Kooijman. Dynamic Energy Budget Theory for Metabolic Organisation. Cambridge University Press, 3 edition, 2009. doi:10.1017/CBO9780511805400.

LDDS19

Kira Lancker, A.L. Deppenmeier, T. Demissie, and J.O. Schmidt. Climate change adaptation and the role of fuel subsidies: an empirical bio-economic modeling study for an artisanal open-access fishery. PLoS ONE, 14(8):e0220433, 2019. doi:10.1371/journal.pone.0220433.

LMN17

Sjannie Lefevre, David J McKenzie, and Göran E Nilsson. Models projecting the fate of fish populations under climate change need to be based on valid physiological mechanisms. Global Change Biology, 23(9):3449–3459, 2017.

LMN18

Sjannie Lefevre, David J McKenzie, and Göran E Nilsson. In modelling effects of global warming, invalid assumptions lead to unrealistic projections. Global change biology, 24(2):553–556, 2018.

LSA04

NP Lester, BJ Shuter, and PA Abrams. Interpreting the von bertalanffy model of somatic growth in fishes: the cost of reproduction. Proceedings of the Royal Society of London. Series B: Biological Sciences, 271(1548):1625–1631, 2004.

LW+98

Michael Lynch, Bruce Walsh, and others. Genetics and analysis of quantitative traits. Volume 1. Sinauer Sunderland, MA, 1998.

Man03

Marc Mangel. Environment and longevity: the demography of the growth rate. Population and Development Review, 29:57–70, 2003.

MEBR10

Fabian M Mollet, Bruno Ernande, Thomas Brunel, and Adriaan D Rijnsdorp. Multiple growth-correlated life history traits estimated simultaneously in individuals. Oikos, 119(1):10–26, 2010.

OR14

Ricardo Oliveros Ramos. End-to-end modelling for an ecosystem approach to fisheries in the Northern Humboldt Current Ecosystem. PhD thesis, University of Montpellier, France, 2014.

ORS17

Ricardo Oliveros-Ramos and Yunne-Jai Shin. Calibrar: an r package for fitting complex ecological models. ????, ???:???, ??? 2017.

ORVES17

Ricardo Oliveros-Ramos, Philippe Verley, Vincent Echevin, and Yunne-Jai Shin. A sequential approach to calibrate ecosystem models with multiple time series data. PROGRESS IN OCEANOGRAPHY, 151:227–244, FEB 2017. doi:10.1016/j.pocean.2017.01.002.

PDS15

Samraat Pawar, Anthony I Dell, and Van M Savage. From metabolic constraints on individuals to the dynamics of ecosystems. In Aquatic functional biodiversity, pages 3–36. Elsevier, 2015.

Portner01

H Pörtner. Climate change and temperature-dependent biogeography: oxygen limitation of thermal tolerance in animals. Naturwissenschaften, 88:137–146, 2001.

QR13

Martin F. Quaas and Till Requate. Sushi or fish fingers? seafood diversity, collapsing fish stocks and multi-species fishery management. Scandinavian Journal of Economics, 115(2):381–422, 2013. doi:10.1111/sjoe.12002.

QRS+16

Martin F. Quaas, Thorsten B. H. Reusch, Jörn O. Schmidt, Olli Tahvonen, and Rudi Voss. It is the economy, stupid! projecting the fate of fish populations using ecological-economic modeling. Global Change Biology, 22(1):264–270, 2016. doi:10.1111/gcb.13060.

QSK+18

Martin F. Quaas, Max T. Stoeven, Bernd Klauer, Thomas Petersen, and Johannes Schiller. Windows of opportunity for sustainable fisheries management: the case of Eastern Baltic cod. Environmental and Resource Economics, 70(2):323–341, 2018. doi:10.1007/s10640-017-0122-y.

QASL08

Christopher Quince, Peter A Abrams, Brian J Shuter, and Nigel P Lester. Biphasic growth in fish i: theoretical foundations. Journal of Theoretical Biology, 254(2):197–206, 2008.

Rof22

Derek Roff. The evolution of life histories: theory and analysis. New York: Chapman and Hall, 1922.

SBD+95

M. Scheffer, J.M. Baveco, D.L. DeAngelis, K.A. Rose, and E.H. van Nes. Super-individuals a simple solution for modelling large populations on an individual basis. Ecological Modelling, 80(2):161–170, 1995. doi:https://doi.org/10.1016/0304-3800(94)00055-M.

SMJF03

Lynne J Shannon, Coleen L Moloney, Astrid Jarre, and John G Field. Trophic flows in the southern benguela during the 1980s and 1990s. Journal of Marine Systems, 39(1):83–116, 2003. doi:https://doi.org/10.1016/S0924-7963(02)00250-6.

SC01

YJ Shin and P Cury. Exploring fish community dynamics through size-dependent trophic interactions using a spatialized individual-based model. AQUATIC LIVING RESOURCES, 14(2):65–80, MAR-APR 2001. doi:10.1016/S0990-7440(01)01106-8.

SC04

YJ Shin and P Cury. Using an individual-based model of fish assemblages to study the response of size spectra to changes in fishing. CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES, 61(3):414–431, MAR 2004. doi:10.1139/F03-154.

SK12

Jean-Paul Soularue and Antoine Kremer. Assortative mating and gene flow generate clinal phenological variation in trees. BMC evolutionary biology, 12(1):1–14, 2012.

Ste92

Stephen C Stearns. The evolution of life histories. Volume 249. Oxford university press Oxford, 1992.

SK86

Stephen C Stearns and Jacob C Koella. The evolution of phenotypic plasticity in life-history traits: predictions of reaction norms for age and size at maturity. Evolution, 40(5):893–913, 1986.

TQV18

Olli Tahvonen, Martin F. Quaas, and Rüdiger Voss. Harvesting selectivity and stochastic recruitment in economic models of age-structured fisheries. Journal of Environmental Economics and Management, 92:659–676, 2018. doi:10.1016/j.jeem.2017.08.011.

TFSMC+19

Yoann Thomas, Jonathan Flye-Sainte-Marie, Denis Chabot, Arturo Aguirre-Velarde, Gonçalo M. Marques, and Laure Pecquerie. Effects of hypoxia on metabolic functions in marine organisms: observed patterns and modelling assumptions within the context of dynamic energy budget (deb) theory. Journal of Sea Research, 143:231–242, 2019. Ecosystem based management and the biosphere: a new phase in DEB research. URL: https://www.sciencedirect.com/science/article/pii/S1385110118300315, doi:https://doi.org/10.1016/j.seares.2018.05.001.

TPRM17

BL Townhill, JK Pinnegar, DA Righton, and JD Metcalfe. Fisheries, low oxygen and climate change: how much do we really know? Journal of Fish Biology, 90(3):723–750, 2017.

TSSC06

M Travers, YJ Shin, L Shannon, and P Cury. Simulating and testing the sensitivity of ecosystem-based indicators to fishing in the southern benguela ecosystem. CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES, 63(4):943–956, APR 2006. doi:10.1139/1706-003.

TSJ+09

M. Travers, Y.-J. Shin, S. Jennings, E. Machu, J.A. Huggett, J.G. Field, and P.M. Cury. Two-way coupling versus one-way forcing of plankton and fish models to predict ecosystem changes in the benguela. Ecological Modelling, 220("21):3089 – 3099, 2009. Selected Papers from the Sixth European Conference on Ecological Modelling - ECEM '07, on Challenges for ecological modelling in a changing world: Global Changes, Sustainability and Ecosystem Based Management, November 27-30, 2007, Trieste, Italy. doi:10.1016/j.ecolmodel.2009.08.016.

TTSF14

M Travers-Trolet, Y-J Shin, and JG Field. An end-to-end coupled model roms-n2p2z2d2-osmose of the southern benguela foodweb: parameterisation, calibration and pattern-oriented validation. African Journal of Marine Science, 36(1):11–29, 2014. URL: 10.2989/1814232X.2014.883326, arXiv:10.2989/1814232X.2014.883326, doi:10.2989/1814232X.2014.883326.