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138 Oceanography vs. behaviour Initialisation of a channel with a uniform geostrophic flow the current has to be vertically sheared, and horizontally uniform. The former is meant to reproduce vertical shear observed in the field and is an important feature of the model in relation to the vertical swimming behaviour of larvae 196 (see also previous chapter). The latter is requested to prevent anomalous behaviour of larvae that would seek low speed areas near the boundaries for example. The two configurations consisted of (1) an isolated cylindrical island surrounded by a uniform eastward current and (2) a promontory on the southern side of a channel embedded in an eastward current (Figure 6.9), both of which represent idealised versions of common coastal features. To initialise such current field, the zonal flow is defined by a density gradient both meridional and vertical. Details of the formulas used for the definition of the flow are given in Dong et al. 219 . Therefore, the flow is geostrophic and the entire model domain is initialised with the same flow. For both cases the model domain is a zonal channel (200 × 100 km) and the horizontal resolution is 500 m. The model is discretised with 20 layers vertically. In case (1), the flow is maintained constant at the four domain boundaries using relaxation toward the initial flow Figure 6.9 Bathymetry of the two model systems: circular island at the top, promontory at the bottom. Distances are in metres and distances in the vertical dimension are exaggerated twenty times. Shading is proportional to depth.
Oriented swimming and passive advection 139 and density fields as well as radiation boundary conditions of type specified and Orlansky. The former constrains the field to be equal to the initial field at the boundary and the latter allows perturbation to leave the domain. In case (2) the same boundary conditions are applied at three of the boundaries, whereas the southern boundary is treated as a wall. The solid boundary around the island and along the southern wall has a zero-normal and no-slip flow implemented through a standard land-mask algorithm 265 . The surface momentum, heat flux, and freshwater flux are set to zero. The bottom stress applied is linearly proportional to the horizontal bottom velocity with a friction coefficient of 2.0·10 -4 m s -1 . In configuration (1), the centre of the island is located one-fourth of the domain away from the upstream boundary and in the middle of the meridional range. The island diameter is 20 km, and the water depth is 500 m, well below the incoming shear and stratification layers (Figure 6.9, top). The current is maximum at the surface (20 cm s -1 ) and null at the bottom. Flow regimes consist of the formation of an anticyclonic and a cyclonic eddy respectively north and south of the island (Figure 6.10). Once the wake eddies are well formed, mutual advection among them governs their motion, along with downstream advection by the mean wake flow. A return flow is present in the lee of the island. Vertically, the eddy decreases quickly with depth, just like the incoming current. However, the peak of the returning flow in the wake is located at the depth of 100 m, the top of the stratification. In case (2), the promontory is gaussian-like, 16.5 km wide, extruding from a linear sloping bottom. Depth at the southern boundary is 20 m and decreases to 500 m at the northern boundary (Figure 6.9, bottom). The vertical shear in the current is identical to the island case (current speed = 20 cm s -1 at the surface, zero at the bottom, and 12 cm s -1 at 100 m). The promontory creates a jet at its tip and a region of reduced or even returning flow behind it. This generates a meridional shear in the lee of the cape that contributes to the formation of anticyclonic eddies that are carried in the wake of the promontory (Figure 6.11). In the shallow water region, east of the promontory near the southern boundary, current speed is also reduced within the depth range of interest for the advection of larvae (0-100 m, see Figure 6.11). Vortex street in the wake of a deep-ocean island Anticyclonic eddies shed by a promontory Simple advection scheme and its justification The grid of the biological model is regular in all directions, including the vertical, the mesh size is 500 m in the horizontal and 25 m in the vertical, and the dimensions are 150 km × 80 km × 100 m. Hence, before advecting particles, the speed field is cropped to the dimensions of the biological model and interpolated from the 500 m × 500 m and σ-coordinate Arakawa-C grid of the ROMS to the 500 m × 500 m × 25 m regular biological grid using 4 th order polynomial interpolation with special masking conditions for the topography (the speeds around Interpolate current field
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À mon étoile.
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vi Résumé La plupart des organism
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viii Abstract Most demersal marine
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x Table des matières 1.3.3 Simple
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xii Table des matières 6.2.3 Examp
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xiv Liste des figures 4.6 Distribut
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Liste des tableaux 1.1 Potential or
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2 Introduction La survie des larves
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4 Introduction Limitation par le re
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6 Introduction Les courants déterm
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8 Introduction où m est le taux de
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10 Introduction biologique simple.
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12 Introduction Le milieu lui-même
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14 Introduction Figure I.6 Schémat
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16 Introduction obstacles technique
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18 Introduction Figure I.8 Prédict
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20 Introduction I.5 La biologie des
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22 Introduction du fonctionnement d
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24 Introduction L’objectif de cet
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26 Behaviour in models 1.1 Introduc
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28 Behaviour in models Using mean p
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30 Behaviour in models 1.3 Vertical
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32 Behaviour in models . . . bring
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34 Behaviour in models of measured
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36 Behaviour in models Additive dis
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38 Behaviour in models In situ stud
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40 Behaviour in models Operational
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42 Behaviour in models Effects on p
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44 Behaviour in models begins is no
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46 Behaviour in models 1.10 Conclus
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48 Larvae orientation in situ Diver
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50 Larvae orientation in situ . . .
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52 Larvae orientation in situ optio
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54 Larvae orientation in situ if >
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56 Larvae orientation in situ Table
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58 Larvae orientation in situ that
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60 Larvae orientation in situ 2.A A
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62 Behaviour of settling fishes at
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Chapter 4 Biophysical correlates in
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Methods 71 4.2 Methods 4.2.1 Sampli
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Methods 73 Three rotations were com
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Methods 75 test really focuses on w
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Results 77 Figure 4.3 Mean of insta
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Results 79 Figure 4.5 Perspective v
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Results 81 Table 4.1 Abundances of
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Results 83 Figure 4.8 Distribution
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Results 85 Figure 4.10 Concentratio
Page 105 and 106: Discussion 87 Figure 4.11 Compariso
Page 107 and 108: Discussion 89 But the most likely e
Page 109 and 110: Acknowledgements 91 This evidence a
Page 111 and 112: Chapter 5 Ontogenetic vertical “m
Page 113 and 114: The statistical analysis of vertica
Page 119 and 120: Methods 101 80, 55, 30 m (Figure 4.
Page 121 and 122: Methods 103 same station were likel
Page 123 and 124: Results 105 Figure 5.2 Univariate r
Page 125 and 126: Results 107 5.4.3 Ontogenetic shift
Page 127 and 128: Results 109 Figure 5.5 Violin plot
Page 129 and 130: Discussion 111 5.5 Discussion 5.5.1
Page 131 and 132: Discussion 113 expression of differ
Page 133 and 134: Chapter 6 Oceanography vs. behaviou
Page 135 and 136: Introduction 117 a good description
Page 137 and 138: A general modelling framework for l
Page 145 and 146: The balance between feeding and pre
Page 155: Oriented swimming and passive advec
Page 159 and 160: Oriented swimming and passive advec
Page 179 and 180: General discussion 161 such integra
Page 181 and 182: General discussion 163 6.5.2 Why se
Page 183 and 184: General discussion 165 such as the
Page 185 and 186: General discussion 167 energeticall
Page 187: Acknowledgements 169 Therefore: •
Page 190 and 191: 172 Conclusion Un environnement pé
Page 192 and 193: 174 Conclusion global sur la connec
Page 194 and 195: 176 Conclusion l’intérêt est po
Page 196 and 197: 178 Conclusion La différence entre
Page 198 and 199: 180 Conclusion Mieux décrire la di
Page 200 and 201: 182 Conclusion Comme tout comportem
Page 202 and 203: 184 Undescribed Chaetodonthidae Fig
Page 204 and 205: 186 Undescribed Chaetodonthidae Fig
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188 Bibliographie [12] Cushing DH.
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190 Bibliographie [39] Johnson MW.
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192 Bibliographie [71] Paris CB, Co
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194 Bibliographie [99] Lara MR. Mor
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196 Bibliographie [127] Masuda R, S
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198 Bibliographie [157] Holbrook SJ
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200 Bibliographie [187] Bowen B, Ba
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202 Bibliographie [218] Oxenford HA
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204 Bibliographie [246] Wellington
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206 Bibliographie [276] Sargent RC,
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208 Bibliographie [308] Greenberg D
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210 Remerciements solides pour ces
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212 Remerciements tri des larves de
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214 Remerciements Évidemment, tout
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