Agathe Maupetit, VetAgro'Sup: *Étude de la distribution des organismes planctoniques dans le courant Ligure*. Internship contributed to

* Faillettaz R, Picheral M, Luo JY, Guigand C, Cowen RK, Irisson J-O. Imperfect automatic image classification successfully describes plankton distribution patterns. *Methods in Oceanography*, 15-16:60-77 (2018)

Alexis Deru-Denise, INP ENSE3, Grenoble: *Reconnaissance du zooplancton assistée par ordinateur*. 2012

## 5.4 Teaching

I taught 64h per year as teaching assistant during my PhD and teach over 200h per year as associate professor since 2009, mostly at Masters level. I am in charge of four teaching modules.

Instrumentation and Acquisition of Data in Oceanography (coordinator), Master 2 Sciences de la Mer, Sorbonne Univ: *Scientific cruise planning* (3h), *Databases for oceanography* (6h), *Reading and plotting data with R* (3h), *Plankton imaging* (4.5h), *Supervision of student projects* (6h)

Methods for Data Exploitation in Oceanography (coordinator), Master 2 Sciences de la Mer, Sorbonne Univ: *R for data science* (6h), *Mapping and interpolation* with practical (3+6h), *Introduction to multivariate data analysis* with practical (3+3h), *Signal processing* with practical (3+3h), *Supervision of student projects* (6h) [and previously: *Oceanographic "big" data processing* with practical (3+3h)]

Modelling of Marine Ecosystems, Master 2 Sciences de la Mer, Sorbonne Univ: class + practical for all topics, *Lagrangian models* (3+3h), *Advanced population dynamics* (3+3h), *Supervision of student projects* (3h) [and previously: *Optimal behaviour* (3+3h)]

Multivariate Statistics (coordinator), Summer school, Sorbonne Univ: class + practical for all topics, *Introduction to programming with R* (6h), *Data series* (6+6h), *Redundancy analysis* (3+3h), *Tree-based learning* (3+3h) [and previously: *Multivariate regression* (3+3h)]

Agrégation SVTU, Sorbonne Univ: *Behavioural Ecology* (8h), *Sexual selection* (4h), "Leçons" (supervision of lectures by students; 5h).

Plankton diversity, Summer school, Sorbonne Univ: *Ichthyoplankton diversity*, with practical (3h)

Exploited marine resources (co-coordinator), Master 2 Sciences de la Mer, Sorbonne Univ: *Ichthyoplankton ecology*, with modelling practical (3+3h)

Introduction to modelling, Master 1 Sciences de la Mer, Sorbonne Univ: *Introduction to population dynamics* (4h)
2009-2018 Response of plankton to environmental changes, Master 2, Sciences de la Mer, Sorbonne Univ: *Ichthyoplankton's response to its environment* (3h)

2016-2017 Biological processes in the ocean, Master 1 Sciences de la Mer, Sorbonne Univ: *Connectivity of marine populations*, with modelling practical (6h)

2014-2016 Research education, License Biologie, Sorbonne Univ: *Scientific communication* (7h), *Connectivity and marine reserves* (7h)

2012-2016 Coordinator of a student and professor exchange program between the oceanography departments of Univ Pierre et Marie Curie and of the Rosenstiel School of Marine and Atmospheric Sciences or Univ Miami (PUF-funded project).

2015 Graduate courses, RSMAS, Univ Miami: Multivariate Statistics, similar to the one taught at Sorbonne Univ (above) but adapted to the graduate program at RSMAS.

2013 Graduate courses, RSMAS, Univ Miami: *Ichthyoplankton response to physical forcings* (3h)

2009-2015 GIS and spatial processes, Master 2, Sciences de la Mer, Sorbonne Univ: *Introduction to R* (3h), *Species distribution modelling* (3h)

2009-2010 Introduction to modelling for conservation, Master 2, Sciences de la Mer, Sorbonne Univ: *Modelling population dynamics* (8h)

2005-2008 Agrégation SVTU, Univ Montpellier: *The ecology of sociality* (8h)

2004-2008 Biology, License pluridisciplinaire 3, Univ Perpignan: 60h of classes on general biology (from cell processes to environmental sciences); I was coordinator of the biology curriculum, taught most classes and graded all exams

2006-2007 Reef Ecology, EPHE/Univ Perp: *Hydrodynamics, modelling and larval flux* (3h)

2002-2006 Master 1 Ecology, École Normale Supérieure/Univ Pierre Marie Curie: *Bifurcation analysis* (6h), *Interspecific relationships* (3h)

## 5.5 Community activities

2019-... Leader of team COMPutational PLankton Ecology (COMPLEx; 10 permanent staff, 10 contract staff), Laboratoire d'Océanographie de Villefranche (LOV).

Member of the European Marine Board panel on Big Data.

Chair of the International Council for the Exploration of the Sea (ICES) working group on Machine Learning for Marine Sciences (WGMLEARN).

2013-... Member of the board of the Société Française d'Écologie et d'Évolution (French Society for Ecology and Evolution).
Leader of team Processus dans les Ecosystèmes Pélagiques (PEPS; 19 per-manent staff, 15 contract staff), Laboratoire d'Océanographie de Ville-franche (LOV). 2016-2018

Panel member of the Commission Nationale de la Flotte Côtière (CNFC). 2015-2018

Coordinator of the ecosystem observation actions at Observatoire Océan-ologique de Villefranche. 2013-2017

Reviewer for Aquatic Biology, Canadian Journal of Fisheries and Aqua-tic Sciences, Coral Reefs, Ecology Letters, Ecological Complexity, Estu-arine Coastal and Shelf Science, Global Change Biology, ICES Journal of Marine Science, Ichthyological Research, Integrative and Comparative Biology, Interface Focus, Journal of Plankton Research, Journal of Statist-ical Software, Limnology and Oceanography: Methods, Marine Biology, Nature Communications, PCI Ecology, PeerJ, PLoS ONE, The R Journal.

Reviewer or panel member for Agence Nationale de la Recherche (ANR), Belspo, CNRS (INSU, LEFE and GMMC), Fondation pour la Recherche sur la Biodiversité (FRB), Haut Conseil de l'Évaluation de la Recherche et de l'Enseignement Supérieur (HCÉRES), Institut Français de Recher-che pour l'Exploitation de la MER (IFREMER), National Geographic, Re-search Foundation - Flanders (FWO), Sorbonne Université.
<figure><img src="image_51.png" /></figure>
Bibliography

[1] Hjort J. Fluctuations in the Great Fisheries of Northern Europe Viewed in the Light of Biological Research. *Rapp P-V Réun Cons Perm Int Explor Mer* **20**, 1–228 (1914).

[2] Cowen RK, Gawarkiewicz G, Pineda J, Thorrold SR, Werner FE. Population Connectivity in Marine Systems: An Overview. *Oceanography* **20**, 14–21 (2007).

[3] Sale PF. Reef Fish Communities: Open Nonequilibrial Systems. In *The Ecology of Fishes on Coral Reefs*, Academic Press, San Diego, California, USA, 564–598 (1991).

[4] Cushing DH. The Natural Regulation of Fish Populations. *Sea fisheries research* 399–412 (1974).

[5] Roberts CM. Connectivity and Management of Caribbean Coral Reefs. *Science* **278**, 1454–1457 (1997).

[6] Leis JM, Sweatman HPA, Reader SE. What the Pelagic Stages of Coral Reef Fishes Are Doing out in Blue Water: Daytime Field Observations of Larval Behavioural Capabilities. *Aust J Mar Fresh Res* **47**, 401–411 (1996).

[7] Leis JM. Are Larvae of Demersal Fishes Plankton or Nekton? *Adv Mar Biol* **51**, 57–141 (2006).

[8] Stobutzki IC, Bellwood DR. An Analysis of the Sustained Swimming Abil-
ities of Pre- and Post-Settlement Coral Reef Fishes. *Journal of Experimental
Marine Biology and Ecology* **175**, 275–286 (1994).

[9] Leis JM, Hay AC, Trnski T. In Situ Ontogeny of Behaviour in Pelagic Larvae of Three Temperate, Marine, Demersal Fishes. *Marine Biology* **148**, 655–669 (2005).

[10] Stemmann L, Prieur L, Legendre L, Taupier-Letage I, Picheral M, Guidi L, Gorsky G. Effects of Frontal Processes on Marine Aggregate Dynamics and Fluxes: An Interannual Study in a Permanent Geostrophic Front (NW Mediterranean). *Journal of Marine Systems* **70**, 1–20 (2008).

[11] Paris CB, Guigand CM, Irisson JO, Fisher R, D'Alessandro E. Orientation With No Frame of Reference (OWNFOR): A Novel System to Observe and
Quantify Orientation in Reef Fish Larvae. In *Caribbean Connectivity: Implications for Marine Protected Area Management. Proceedings of a Special Symposium*, 9-11 November 2006, 59th Annual Meeting of the Gulf and Caribbean Fisheries Institute, Belize City, Belize, Grober-Dunsmore R, Keller BD, eds. U.S. Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Sanctuary Program, Silver Spring, MD (2008), Marine Sanctuaries Conservation Series ONMS-08-07, 52-62.

[12] Irisson JO, Guigand C, Paris CB. Detection and Quantification of Marine Larvae Orientation in the Pelagic Environment. *Linnology and Oceanography: Methods* 7, 664-672 (2009).

[13] Paris CB, Atema J, Irisson JO, Kingsford M, Gerlach G, Guigand CM. Reef Odor: A Wake up Call for Navigation in Reef Fish Larvae. *PLoS ONE* 8, e72808 (2013).

[14] Leis JM, Paris CB, Irisson JO, Yerman MN, Siebeck UE. Orientation of Fish Larvae in Situ Is Consistent among Locations, Years and Methods, but Variables with Time of Day. *Marine Ecology Progress Series* 505, 193-208 (2014).

[15] Irisson JO, Paris CB, Leis JM, Yerman MN. With a Little Help from My Friends: Group Orientation by Larvae of a Coral Reef Fish. *PLoS ONE* 10, e0144060 (2015).

[16] Simons AM. Many Wrongs: The Advantage of Group Navigation. *Trends Ecol Evol* 19, 453-455 (2004).

[17] Couzin ID, Krause J, Franks NR, Levin SA. Effective Leadership and Decision-Making in Animal Groups on the Move. *Nature* 433, 513-516 (2005).

[18] Faillettaz R, Blandin A, Paris CB, Koubbi P, Irisson JO. Sun-Compass Orientation in Mediterranean Fish Larvae. *PLoS ONE* 10, e0135213 (2015).

[19] Batschelet E. *Circular Statistics in Biology*. Academic Press, London (1981).

[20] Miller TJ. Contribution of Individual-Based Coupled Physical-Biological Models to Understanding Recruitment in Marine Fish Populations. *Marine Ecology Progress Series* 347, 127-138 (2007).

[21] North E, Gallego A, Petitgas P. Manual of Recommended Practices for Modelling Physical-Biological Interactions during Fish Early Life. *ICES Coop Res Rep* 295 (2009).

[22] Irisson JO, Leis JM, Paris CB, Browman H. Biological Processes: Behaviour and Settlement. In *Manual of Recommended Practices for Modelling Physical-Biological Interactions during Fish Early Life*, North E, Gallego A, Petitgas P, eds., ICES Cooperative Research Report, vol. 295, 42-59 (2009).

[23] Faillettaz R, Durand E, Paris CB, Koubbi P, Irisson JO. Swimming Speeds of Mediterranean Settlement-Stage Fish Larvae Nuance Hjort's Aberrant Drift Hypothesis. *Linnology and Oceanography* 63, 509-523 (2018).

[24] Faillettaz R, Paris CB, Irisson JO. Larval Fish Swimming Behavior Alters Dispersal Patterns from Marine Protected Areas in the North-Western Mediterranean Sea. *Frontiers in Marine Science* 5, 97 (2018).
[25] MacArthur RH, Pianka ER. On Optimal Use of a Patchy Environment. *The American Naturalist* **100**, 603–609 (1966).

[26] Perry G, Pianka ER. Animal Foraging: Past, Present and Future. *Trends in Ecology and Evolution* **12**, 360–364 (1997).

[27] Houde ED. Comparative Growth, Mortality, and Energetics of Marine Fish Larvae: Temperature and Implied Latitudinal Effects. *Fisheries Bulletin* **87**, 471–495 (1989).

[28] Houde ED. Emerging from Hjort's Shadow. *J Northw Atl Fish Sci* **41**, 53–70 (2008).

[29] Irisson JO, LeVan A, De Lara M, Planes S. Strategies and Trajectories of Coral Reef Fish Larvae Optimizing Self-Recruitment. *Journal of Theoretical Biology* **227**, 205–218 (2004).

[30] Lett C, Ayata SD, Huret M, Irisson JO. Biophysical Modelling to Investigate the Effects of Climate Change on Marine Populations Dispersal and Connectivity. *Progress in Oceanography* **87**, 106–112 (2010).

[31] Munday PL. Climate Change and Coral Reef Connectivity. *Coral Reefs* **28**, 379–395 (2009).

[32] Bellman R. The Theory of Dynamic Programming. *Bulletin of the American Mathematical Society* **60**, 503–515 (1954).

[33] Doty MS, Oguri M. The Island Mass Effect. *ICES Journal of Marine Science: Journal du Conseil* **22**, 33–37 (1956).

[34] Luo JY, Grassian B, Tang D, Irisson JO, Greer AT, Guigand CM, McClatchie S, Cowen RK. Environmental Drivers of the Fine-Scale Distribution of a Gelatinous Zooplankton Community across a Mesoscale Front. *Marine Ecology Progress Series* **510**, 129–149 (2014).

[35] Brun P, Payne MR, Kiørboe T. Trait Biogeography of Marine Copepods—an Analysis across Scales. *Ecology letters* **19**, 1403–1413 (2016).

[36] Fiksen Ø, Giske J. Vertical Distribution and Population Dynamics of Copepods by Dynamic Optimization. *ICES Journal of Marine Science: Journal du Conseil* **52**, 483–503 (1995).

[37] Banse K. On the Vertical Distribution of Zooplankton in the Sea. *Progress in oceanography* **2**, 53–125 (1964).

[38] Wiebe PH, Burt KH, Boyd SH, Morton AW. A Multiple Opening/Closing Net and Environmental Sensing System for Sampling Zooplankton. *Journal of Marine Research* **34**, 313–326 (1976).

[39] Hirata T, Aiken J, Hardman-Mountford N, Smyth TJ, Barlow RG. An Absorption Model to Determine Phytoplankton Size Classes from Satellite Ocean Colour. *Remote Sensing of Environment* **112**, 3153–3159 (2008).

[40] Hirzel AH, Lay GL. Habitat Suitability Modelling and Niche Theory. *Journal of Applied Ecology* **45**, 1372–1381 (2008).
[41] Cuzin-Roudy J, Irisson JO, Penot F, Kawaguchi S, Vallet C. Chapter 6.9 Southern Ocean Euphausiids. In *Biogeographic Atlas of the Southern Ocean*, De Broyer C, Koubbi P, Griffiths HJ, Raymond B, Udekem d'Acoz C, et al, eds., Scientific Committee on Antarctic Research, Cambridge, 309-320 (2014).

[42] Duhamel G, Hulley PA, Causse R, Koubbi P, Vacchi M, Pruvost P, Vigetta S, Irisson JO, Mormede S, Belchier M, Dettai A, Detrich HW, Gutt J, Jones CD, Kock KH, Lopez Abellan LJ, Van de Putte A. Chapter 7 Biogeographic Patterns of Fish. In *Biogeographic Atlas of the Southern Ocean*, De Broyer C, Koubbi P, Griffiths HJ, Raymond B, Udekem d'Acoz C, et al, eds., Scientific Committee on Antarctic Research, 328-362 (2014).

[43] Reygondeau G, Irisson JO, Ayata SD, Gasparini S, Benedetti F, Albouy C, Hattab T, Guieu C, Koubbi P. Definition of the Mediterranean Eco-Regions and Maps of Potential Pressures in These Eco-Regions. *Delivrable* 1.6, PERSEUS (2014).

[44] Benedetti F, Guilhaumon F, Adloff F, Ayata SD. Investigating Uncertainties in Zooplankton Composition Shifts under Climate Change Scenarios in the Mediterranean Sea. *Ecography* 41, 345-360 (2018).

[45] Longhurst AR. *Ecological Geography of the Sea*. Elsevier (2010).

[46] Reygondeau G, Guieu C, Benedetti F, Irisson JO, Ayata SD, Gasparini S, Koubbi P. Biogeochemical Regions of the Mediterranean Sea: An Objective Multidimensional and Multivariate Environmental Approach. *Progress in Oceanography* 151, 138-148 (2017).

[47] Oliver MJ, Glenn S, Kohut JT, Irwin AJ, Schofield OM, Moline MA, Bissett WP. Bioinformatic Approaches for Objective Detection of Water Masses on Continental Shelves. *Journal of Geophysical Research: Oceans* 109 (2004).

[48] Yeung KY, Haynor DR, Ruzzo WL. Validating Clustering for Gene Expression Data. *Bioinformatics* 17, 309-318 (2001).

[49] Josse J, Pagès J, Husson F. Multiple Imputation in Principal Component Analysis. *Advances in data analysis and classification* 5, 231-246 (2011).

[50] Cleveland RB, Cleveland WS, McRae JE, Terpenning I. STL: A Seasonal-Trend Decomposition Procedure Based on Loess. *Journal of Official Statistics* 6, 3-73 (1990).

[51] Steltzer H, Post E. Seasons and Life Cycles. *Science* 324, 886-887 (2009).

[52] Giorgi F. Climate Change Hot-Spots. *Geophysical Research Letters* 33 (2006).

[53] Grosjean P, Picheral M, Warembourg C, Gorsky G. Enumeration, Measurement, and Identification of Net Zooplankton Samples Using the ZOOSCAN Digital Imaging System. *ICES Journal of Marine Science: Journal du Conseil* 61, 518-525 (2004).

[54] Villéger S, Mason NW, Mouillot D. New Multidimensional Functional Diversity Indices for a Multifaceted Framework in Functional Ecology. *Ecology* 89, 2290-2301 (2008).
[55] Legendre P, Legendre L. *Numerical Ecology*. Elsevier (2012).

[56] Rosenzweig ML, Abramsky Z. How Are Diversity and Productivity Related? In *Species Diversity in Ecological Communities*, University of Chicago Press, 52–65 (1993).

[57] McIntyre A. *Life in the World's Oceans: Diversity, Distribution, and Abundance*. John Wiley & Sons (2010).

[58] Lecailleur G. The "CARE" (Collect by Artificial Reef Eco-Friendly) System as a Method of Producing Farmed Marine Animals for the Aquarium Market: An Alternative Solution to Collection in the Wild. *SPC Live Reef Fish Information Bulletin* **12**, 17–20 (2004).

[59] Faillettaz R, Voué R, Crec'hriou R, Garsi LH, Lecailleur G, Agostini S, Lencant P, Irisson JO. Spatio-Temporal Patterns of Larval Fish Settlement in the Northwestern Mediterranean Sea. *Mar. Ecol. Prog. Ser.* **650**, 153–173 (2020).

[60] Victor BC. Recruitment and Population Dynamics of a Coral Reef Fish. *Science* **219**, 419–420 (1983).

[61] Koenker R. *Quantile Regression*, vol. 38. Cambridge University Press (2005).

[62] Chen K, Ying Z, Zhang H, Zhao L. Analysis of Least Absolute Deviation. *Biometrika* **95**, 107–122 (2008).

[63] Linton O, Whang YJ. The Quantilogram: With an Application to Evaluating Directional Predictability. *Journal of Econometrics* **141**, 250–282 (2007).

[64] Giraldo C, Mayzaud P, Tavernier E, Irisson JO, Penot F, Becciu J, Chartier A, Boutoute M, Koubbi P. Lipid Components as a Measure of Nutritional Condition in Fish Larvae (Pleuragramma Antarcticum) in East Antarctica. *Marine Biology* **160**, 877–887 (2013).

[65] Talec A, Philistin M, Ferey F, Walenta G, Irisson JO, Bernard O, Sciandra A. Effect of Gaseous Cement Industry Effluents on Four Species of Microalgae. *Bioresource Technology* **143**, 353–359 (2013).

[66] Howes EL, Stemmann L, Assailly C, Irisson JO, Dima M, Bijma J, Gattuso JP. Pteropod Time Series from the North Western Mediterranean (1967-2003): Impacts of pH and Climate Variability. *Marine Ecology Progress Series* **531**, 193–206 (2015).

[67] Ezzat L, Towle E, Irisson JO, Langdon C, Ferrier-Pagès C. The Relationship between Heterotrophic Feeding and Inorganic Nutrient Availability in the Scleractinian Coral T. Reniformis under a Short-Term Temperature Increase. *Linnology and Oceanography* **61**, 89–102 (2016).

[68] Jean M, Irisson JO, Gras G, Bouchand F, Simo D, Duran C, Perronne C, Mulleman D, Bernard L, Dinh A. Diagnostic Delay of Pyogenic Vertebral Osteomyelitis and Its Associated Factors. *Scandinavian Journal of Rheumatology* **46**, 64–68 (2017).
[69] Labrousse S, Vacquié-Garcia J, Heerah K, Guinet C, Sallée JB, Authier M, Picard B, Roquet F, Bailleul F, Hindell M. Winter Use of Sea Ice and Ocean Water Mass Habitat by Southern Elephant Seals: The Length and Breadth of the Mystery. *Progress in Oceanography* **137**, 52–68 (2015).

[70] Labrousse S, Sallée JB, Fraser AD, Massom RA, Reid P, Sumner M, Guinet C, Harcourt R, Mcmahon C, Bailleul F. Under the Sea Ice: Exploring the Relationship between Sea Ice and the Foraging Behaviour of Southern Elephant Seals in East Antarctica. *Progress in oceanography* **156**, 17–40 (2017).

[71] Labrousse S, Sallée JB, Fraser AD, Massom RA, Reid P, Hobbs W, Guinet C, Harcourt R, McMahon C, Authier M. Variability in Sea Ice Cover and Climate Elicit Sex Specific Responses in an Antarctic Predator. *Scientific reports* **7**, 43236 (2017).

[72] Biard T, Stemmann L, Picheral M, Mayot N, Vandromme P, Hauss H, Gor-
sky G, Guidi L, Kiko R, Not F. In Situ Imaging Reveals the Biomass of Giant
Protists in the Global Ocean. *Nature* **532**, 504 (2016).

[73] Dumollard R, Minc N, Salez G, Aicha SB, Bekkouche F, Hebras C, Besnardeau L, McDougall A. The Invariant Cleavage Pattern Displayed by Ascidian Embryos Depends on Spindle Positioning along the Cell's Longest Axis in the Apical Plane and Relies on Asynchronous Cell Divisions. *eLife* (2017).

[74] Gattuso JP, Magnan AK, Bopp L, Cheung WWL, Duarte CM, Hinkel J, Mcleod E, Micheli F, Oschlies A, Williamson P, Billé R, Chalastani V, Gates RD, Irisson JO, Middelburg JJ, Poertner HO, Rau G. Ocean Solutions to Address Climate Change and Its Effects on Marine Ecosystems. *Frontiers in Marine Science* **5**, 337 (2018).

[75] Sukhovich A, Irisson JO, Simons FJ, Ogé A, Hello Y, Deschamps A, Nolet G. Automatic Discrimination of Underwater Acoustic Signals Generated by Teleseismic P-waves: A Probabilistic Approach. *Geophysical Research Letters* **38** (2011).

[76] Sukhovich A, Bonnieux S, Hello Y, Irisson JO, Simons FJ, Nolet G. Seismic Monitoring in the Oceans by Autonomous Floats. *Nature Communications* **6**, 8027 (2015).

[77] Wickham H. *Ggplot2: Elegant Graphics for Data Analysis*. Springer-Verlag New York Inc (2009).

[78] De Broyer C, Koubbi P, Griffiths H, Grant SA. *Biogeographic Atlas of the Southern Ocean*. Scientific Committee on Antarctic Research Cambridge (2014).

[79] Beaugrand G, Lenoir S, Ibañez F, Manté C. A New Model to Assess the Probability of Occurrence of a Species, Based on Presence-Only Data. *Marine Ecology Progress Series* **424**, 175–190 (2011).

[80] Behrenfeld MJ, Randerson JT, McClain CR, Feldman GC, Los SO, Tucker CJ, Falkowski PG, Field CB, Frouin R, Esaias WE. Biospheric Primary Production during an ENSO Transition. *Science* **291**, 2594–2597 (2001).
[81] Volk T, Hoffert MI. Ocean Carbon Pumps: Analysis of Relative Strengths and Efficiencies in Ocean-Driven Atmospheric CO2 Changes. *The carbon cycle and atmospheric CO2: natural variations Archean to present* 32, 99–110 (1985).

[82] Frederiksen M, Edwards M, Richardson AJ, Halliday NC, Wanless S. From Plankton to Top Predators: Bottom-up Control of a Marine Food Web across Four Trophic Levels. *Journal of Animal Ecology* 75, 1259–1268 (2006).

[83] Thiel M, Macaya EC, Acuna E, Arntz WE, Bastias H, Brokordt K, Camus PA, Castilla JC, Castro LR, Cortes M. The Humboldt Current System of Northern and Central Chile: Oceanographic Processes, Ecological Interactions and Socioeconomic Feedback. *Oceanography and marine biology: an annual review* (2007).

[84] Hays GC, Richardson AJ, Robinson C. Climate Change and Marine Plankton. *Trends in ecology & evolution* 20, 337–344 (2005).

[85] Beaugrand G. Monitoring Pelagic Ecosystems Using Plankton Indicators. *ICES Journal of Marine Science* 62, 333–338 (2005).

[86] De Vargas C, Audic S, Henry N, Decelle J, Mahé F, Logares R, Lara E, Berney C, Le Bescot N, Probert I. Eukaryotic Plankton Diversity in the Sunlit Ocean. *Science* 348, 1261–1265 (2015).

[87] Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum JR, Coelho LP, Espinoza JCI, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S, Tara Oceans Consortium Coordinators, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, de Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G. Plankton Networks Driving Carbon Export in the Oligotrophic Ocean. *Nature* 532, 465–470 (2016).

[88] Russakovsky O, Deng J, Su H, Krause J, Satheesh S, Ma S, Huang Z, Karpathy A, Khosla A, Bernstein M. ImageNet Large Scale Visual Recognition Challenge. *International journal of computer vision* 115, 211–252 (2015).

[89] Krizhevsky A, Sutskever I, Hinton GE. Imagenet Classification with Deep Convolutional Neural Networks. In *Advances in Neural Information Processing Systems* (2012), 1097–1105.

[90] LeCun Y, Bengio Y, Hinton G. Deep Learning. *Nature* 521, 436 (2015).

[91] Elith J, Graham CH, Anderson RP, Dudík M, Ferrier S, Guisan A, Hijmans RJ, Huettmann F, Leathwick JR, Lehmann A, Li J, Lohmann LG, Loiselle BA, Manion G, Moritz C, Nakamura M, Nakazawa Y, Overton JM, Peterson AT, Phillips SJ, Richardson K, Scachetti-Pereira R, Schapire RE, Soberón J, Williams S, Wisz MS, Zimmermann NE. Novel Methods Improve Prediction of Species' Distributions from Occurrence Data. *Ecography* 29, 129–151 (2006).

[92] Uhlmann D, Schlimpeet O, Uhlmann W. Automated Phytoplankton Analysis by a Pattern Recognition Method. *Internationale Revue der gesamten Hydrobiologie und Hydrographie* 63, 575–583 (1978).
[93] Graham B. Spatially-Sparse Convolutional Neural Networks. arXiv:1409.6070 [cs] (2014).

[94] Graham B. Fractional Max-Pooling. arXiv:1412.6071 [cs] (2014).

[95] Luo JY, Irisson JO, Graham B, Guigand C, Sarafraz A, Mader C, Cowen RK. Automated Plankton Image Analysis Using Convolutional Neural Networks. *Limnology and Oceanography: Methods* **16**, 814–827 (2018).

[96] Szegedy C, Vanhoucke V, Ioffe S, Shlens J, Wojna Z. Rethinking the Inception Architecture for Computer Vision. In *Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition* (2016), 2818–2826.

[97] Malde K, Kim H. Beyond Image Classification: Zooplankton Identification with Deep Vector Space Embeddings. arXiv:1909.11380 [cs] (2019).

[98] Elineau A, Desnos C, Jalabert L, Olivier M, Romagnan JB, Brandao M, Lombard F, Llopis N, Courboulès J, Caray-Counil L, Serranito B, Irisson JO, Picheral M, Gorsky G, Stemmann L. ZooScanNet: Plankton Images Captured with the ZooScan. https://doi.org/10.17882/55741 (2018).

[99] Bakkum P, Skadron K. Accelerating SQL Database Operations on a GPU with CUDA. In *Proceedings of the 3rd Workshop on General-Purpose Computation on Graphics Processing Units*. ACM (2010), 94–103.

[100] Zhu X, Bain M. B-CNN: Branch Convolutional Neural Network for Hierarchical Classification. arXiv preprint arXiv:1709.09890 (2017).

[101] Ronneberger O, Fischer P, Brox T. U-Net: Convolutional Networks for Bio-medical Image Segmentation. arXiv:1505.04597 [cs] (2015).

[102] Badrinarayanan V, Kendall A, Cipolla R. SegNet: A Deep Convolutional Encoder-Decoder Architecture for Image Segmentation. *IEEE Transactions on Pattern Analysis and Machine Intelligence* **39**, 2481–2495 (2017).

[103] He K, Gkioxari G, Dollár P, Girshick R. Mask R-CNN. arXiv:1703.06870 [cs] (2018).

[104] Ibarbalz FM, Henry N, Brandão MC, Martini S, Busseni G, Byrne H, Coelho LP, Endo H, Gasol JM, Gregory AC. Global Trends in Marine Plankton Diversity across Kingdoms of Life. *Cell* **179**, 1084–1097 (2019).

[105] Lévy M, Franks PJS, Smith KS. The Role of Submesoscale Currents in Structuring Marine Ecosystems. *Nat Commun* **9**, 1–16 (2018).

[106] Mahadevan A. The Impact of Submesoscale Physics on Primary Productivity of Plankton. *Annu. Rev. Mar. Sci.* **8**, 161–184 (2016).

[107] Ohman MD, Powell JR, Picheral M, Jensen DW. Mesozooplankton and Particulate Matter Responses to a Deep-Water Frontal System in the Southern California Current System. *J Plankton Res* **34**, 815–827 (2012).

[108] Greer AT, Cowen RK, Guigand CM, Hare JA. Fine-Scale Planktonic Habitat Partitioning at a Shelf-Slope Front Revealed by a High-Resolution Imaging System. *Journal of Marine Systems* **142**, 111–125 (2015).
[109] Schmid MS, Cowen RK, Robinson K, Luo JY, Briseño-Avena C, Sponaugle S. Prey and Predator Overlap at the Edge of a Mesoscale Eddy: Fine-Scale, in-Situ Distributions to Inform Our Understanding of Oceanographic Processes. *Scientific Reports* **10**, 1–16 (2020).

[110] Greer AT, Cowen RK, Guigand CM, McManus MA, Sevadjian JC, Timmerman AHV. Relationships between Phytoplankton Thin Layers and the Fine-Scale Vertical Distributions of Two Trophic Levels of Zooplankton. *J Plankton Res* **35**, 939–956 (2013).

[111] Bertrand A, Grados D, Colas F, Bertrand S, Capet X, Chaigneau A, Vargas G, Mousseigne A, Fablet R. Broad Impacts of Fine-Scale Dynamics on Seascape Structure from Zooplankton to Seabirds. *Nat Commun* **5**, 1–9 (2014).

[112] Snyder S, Franks PJS, Talley LD, Xu Y, Kohin S. Crossing the Line: Tunas Actively Exploit Submesoscale Fronts to Enhance Foraging Success. *Limnology and Oceanography Letters* **2**, 187–194 (2017).

[113] Lombard F, Boss E, Waite AM, Vogt M, Uitz J, Stemmann L, Sosik HM, Schulz J, Romagnan JB, Picheral M, Pearlman J, Ohman MD, Niehoff B, Möller KO, Miloslavich P, Lara-Lpez A, Kudela R, Lopes RM, Kiko R, Karp-Boss L, Jaffe JS, Iversen MH, Irisson JO, Fennel K, Hauss H, Guidi L, Gorsky G, Giering SLC, Gaube P, Gallager S, Dubelaar G, Cowen RK, Carlotti F, Briseño-Avena C, Berline L, Benoit-Bird K, Bax N, Batten S, Ayata SD, Artigas LF, Appeltans W. Globally Consistent Quantitative Observations of Planktonic Ecosystems. *Frontiers in Marine Science* **6** (2019).

[114] Cowen RK, Guigand CM. In Situ Ichthyoplankton Imaging System (ISIIS): System Design and Preliminary Results. *Limnology and Oceanography: Methods* **6**, 126–132 (2008).

[115] Ohman MD, Davis RE, Sherman JT, Grindley KR, Whitmore BM, Nickels CF, Ellen JS. Zooglider: An Autonomous Vehicle for Optical and Acoustic Sensing of Zooplankton. *Limnology and Oceanography: Methods* **17**, 69–86 (2019).

[116] Picheral M, Guidi L, Stemmann L, Karl DM, Iddaoud G, Gorsky G. The Underwater Vision Profiler 5: An Advanced Instrument for High Spatial Resolution Studies of Particle Size Spectra and Zooplankton. *Limnology and Oceanography: Methods* **8**, 462–473 (2010).

[117] Faillettaz R, Picheral M, Luo JY, Guigand C, Cowen RK, Irisson JO. Imperfect Automatic Image Classification Successfully Describes Plankton Distribution Patterns. *Methods in Oceanography* **15–16**, 60–77 (2016).

[118] Cailleton C, Desnos C, Jalabert L, Elineau A, Stemmann L, Ayata SD, Irisson JO. Morphological Diversity Increases with Oligotrophy along a Zooplankton Time Series. In *SFEcologie* 2018. Rennes (2018).

[119] Hu MK. Visual Pattern Recognition by Moment Invariants. *IRE transactions on information theory* **8**, 179–187 (1962).

[120] Jaffe JS, Franks PJS, Roberts PLD, Mirza D, Schurgers C, Kastner R, Boch A. A Swarm of Autonomous Miniature Underwater Robot Drifters for Exploring Submesoscale Ocean Dynamics. *Nat Commun* **8**, 1–8 (2017).
[121] Fu LL, Chelton DB, Le Traon PY, Morrow R. Eddy Dynamics from Satellite Altimetry. *Oceanography* **23**, 14–25 (2010).

[122] Alvain S, Moulin C, Dandonneau Y, Loisel H. Seasonal Distribution and Succession of Dominant Phytoplankton Groups in the Global Ocean: A Satellite View. *Global Biogeochemical Cycles* **22** (2008).

[123] Basedow SL, McKee D, Lefering I, Gislason A, Daase M, Trudnowska E, Egeland ES, Choquet M, Falk-Petersen S. Remote Sensing of Zooplankton Swarms. *Scientific reports* **9**, 686 (2019).

[124] Jónasdóttir SH, Visser AW, Richardson K, Heath MR. Seasonal Copepod Lipid Pump Promotes Carbon Sequestration in the Deep North Atlantic. *Proceedings of the National Academy of Sciences* **112**, 12122–12126 (2015).

[125] Jean N, Burke M, Xie M, Davis WM, Lobell DB, Ermon S. Combining Satellite Imagery and Machine Learning to Predict Poverty. *Science* **353**, 790–794 (2016).

[126] Aurell E, Boffetta G, Crisanti A, Paladin G, Vulpiani A. Predictability in the Large: An Extension of the Concept of Lyapunov Exponent. *Journal of Physics A: Mathematical and General* **30**, 1 (1997).

[127] d'Ovidio F, De Monte S, Alvain S, Dandonneau Y, Lévy M. Fluid Dynamical Niches of Phytoplankton Types. *Proceedings of the National Academy of Sciences* **107**, 18366–18370 (2010).

[128] Huntley ME, Gonzalez A, Zhu Y, Zhou M, Irigoien X. Zooplankton Dynamics in a Mesoscale Eddy-Jet System off California. *Marine Ecology Progress Series* **201**, 165–178 (2000).
<figure><img src="image_52.png" /></figure>
Résumé

Ma carrière scientifique a commencé par l'étude du comportement des larves de poissons. J'ai prouvé qu'elles nagent à des vitesses non-négligeables, s'orientent, notamment en fonction de l'azimut solaire, et s'orientent mieux en groupe que seules. Quand ces capacités comportementales sont introduites dans des modèles Lagrangiens de dispersion, elles influencent les patrons spatiaux de recrutement, réduisant souvent les distances de dispersion.

Je me suis également intéressé à la distribution tridimensionnelle de ces larves et du plancton associé. Ces études ont montré que, dans les structures à mésoéchelle, une très haute résolution spatio-temporelle est nécessaire pour parvenir à détecter des patrons clairs dans la distribution des organismes ou les associations entre taxa.

À plus large échelle, je me suis ensuite intéressé à la biogéographie d'espèces pélagiques. Dans un atlas de l'océan Austral, la modélisation de la niche écologique d'espèces de poissons et de krill a souligné la forte influence des fronts circumantarctiques. Les travaux de régionalisation de la Méditerranée ont montré que des communautés spécifiques d'organismes pélagiques exploitent la zone de gradient entre les bassins Est et Ouest. La comparaisons entre diverses régionalisations de cette région a permis d'identifier des zones, de stabilité ou de fort gradient, cohérentes quelles que soit les caractéristiques des masses d'eau considérées.

Enfin, j'ai contribué à l'effort d'observation à long terme mené à Villefranche-sur-Sermer, notamment en mettant en place un système de centralisation et visualisation des données récoltées. L'exploitation de ces données a confirmé que la Méditerranée est une zone où le changement climatique est prononcé, que l'oligotrophisation associée résulte en une diversification des organismes zooplanctoniques et que le recrutement des poissons côtiers est cohérent spatialement mais extrêmement sporadique temporellement.

Le point commun entre ces activités apparemment disparates est l'utilisation d'outils numériques pour répondre à des questions écologiques. Mon projet de recherche est également focalisé sur des approches "computationnelles", telles que l'apprentissage machine, qui combine de nombreux calculs unitaires pour reconnaitre des structures dans de grandes masses de données. Ces données sont maintenant disponibles pour l'étude du plancton, notamment grâce à de nouveaux instruments d'imagerie. Je commencerai par poursuivre mes efforts actuels vers l'automatisation de l'identification d'organismes planctoniques sur des images. En utilisant ces nouveaux outils instrumentaux et logiciels, il deviendra possible de décrire la distribution spatio-temporelle du plancton à la même, haute, résolution que son environnement biogéochimique. Cela permettra d'étudier leurs intéractions dans les structures à submésoéchelle, qui sont primordiales pour la dynamique de ces organismes à plus grande échelle. Enfin, à cette grande échelle, les satellites permettent d'avoir une vision synoptique de la couche de surface des océans. Je propose d'utiliser les corrélations spatio-temporelles locales dans données qu'ils récoltent pour décrire, et prédire à l'échelle globale, la structure des communautés de zooplancton.