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50 Larvae orientation in situ . . . together with physical data and cover a region 45 cm wide (i.e. a 600 µm pixel resolution). The video data is recorded on 80 min Mini DV tapes in SP mode. The compass records the orientation of the arena and the white marker provides a fixed reference point on the arena relative to the camera. Both are used for data calibration. Finally, an opaque plastic disc tops the frame to avoid glare from the sea’s surface on the arena. The submerged part of the OWNFOR device is attached to a set of three stainless steel bridles that connect to a 3 mm diameter line leading to the surface. This line first runs through a small float, then forms a loose buckle tied with a bungee cord, and finally attaches to a larger surface float, sold as an inflatable spherical fender. The line length can be adjusted prior to deployment in order to run experiments at different depths. The use of the sub-surface float and of the bungee cord attenuates the effect of waves on the OWNFOR apparatus below. A custom made spar-type float is attached to the surface float and houses a Global Positioning System (GPS) antenna interfaced with a GPS data logger (Geostats Inc.). The position of the device is recorded every 30 s. In addition, a mini Conductivity Temperature Density (CTD) logger from Starr-Oddi Inc. is attached to the frame and records environmental variables (temperature, salinity, and depth) every 30 seconds. After deployment, the video data is retrieved and stored on the hard drive of a computer. Analysis of such data only requires a large enough storage space to hold the videos and 1 Gb of memory to allow all the video frames to be loaded at once. The video analysis relies on software programs that are most easily installed on a Unix-like operating system. The assessment data presented here was processed on a PowerMacintosh running Mac OS 10.4 and on an HP Proliant running Debian GNU/Linux 3.0 and Fedora Core Linux 7.0. 2.2.2 Procedures Deployment Reduced crew and easy deployment The OWNFOR device’s size and shape allow deployment and recovery from a small boat using only two persons. The surface float is deployed downstream from the boat and the line is slowly paid out. The frame is lowered on its side alongside the vessel. While one person holds the frame half submerged the other places one larva inside the area. Once the specimen is inside the arena the frame is slowly released. As it sinks sideways the air escapes from the arena through the mesh. The frame slowly reaches its final depth as tension in the line causes it to align vertically in the water column. After 3-5 minutes the apparatus is stable within the current and is allowed to drift for a period of 20 minutes. The boat briefly motors a few hundred meters downstream from the surface float and the engine is shut off for the remainder of the experiment. After the experiment the surface float is approached from upstream in order to pull the instrument aboard. The specimen is retrieved from
Materials and Procedures 51 the arena and preserved in 75% Ethanol. The video camera batteries and remaining time on the tape are checked before starting a new experiment. Data analysis Typical evidence for orientation preference is directionality in the swimming bearings 90 . However, in an enclosed circular arena, a larva is restricted by the boundary, and its orientation behaviour may take two forms: (1) the larva may swim toward a preferred direction, as it would do in the open environment, then touch the boundary and swim in a non-oriented manner around the arena before heading toward its preferred direction again, in which case its average swimming direction is indicative of orientation; (2) the larva may be less active and simply stay in the region of the arena corresponding to its preferred bearing, in which case its positions are indicative of orientation. To capture and statistically quantify these behaviours a good representation of the trajectory of the larva is necessary. Raw video recordings of larval positions are corrupted by several factors: in situ images are often noisy; unexpected events may occur during the recording (e.g. adult fish swimming around the arena disturbing the study specimen); the camera usually vibrates slightly with respect to the arena; and the whole device rotates on itself (ca. 360º per 20 min). Therefore, a series of processing steps are performed to mitigate these factors and yield accurate estimates of larval trajectories from video data: sub-sampling and enhancing of video data, acquisition and calibration of trajectories, and appropriate statistical analysis (Figure 2.2). This whole process is achieved using a set of customised open source software. The raw video data comes encoded as a 30 images per second movie. The position of the specimen is detected manually (see below) with a mean imprecision of 1.7 mm. Manual detection on all frames would be laborious and error prone because 1.7 mm represents half the displacement of a larva swimming at 10 cm s -1 during 1/30 s. Instead, the video is resampled by keeping only 1 frame each 30 frames (i.e. one image per second). However, when the trajectory curves during a 1 s interval, it is estimated as a straight line. The scenario leading to the largest resampling error would be a larva swimming in small circles around the centre of the arena (the smaller the circles, the larger the angular speed and error). The theoretical case of a larva swimming regularly in a 15 cm diameter circle suggests that a 1 s resampling period is virtually error free near mean cruising speeds (5 cm s -1 258 ), and induces little relative error at higher speeds (10% at 20 cm s -1 ). To minimise anomalous data, the video is analysed only once the device drifts at the selected depth and the boat engine is turned off. Video frames are denoised using the high quality denoise filter of MPlayer 147 and the contrast and luminosity are enhanced manually Orientation shows through positions or bearings Raw video data is corrupted Video sub-sampling Video enhancements and conversion
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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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Page 20 and 21: 2 Introduction La survie des larves
Page 22 and 23: 4 Introduction Limitation par le re
Page 24 and 25: 6 Introduction Les courants déterm
Page 26 and 27: 8 Introduction où m est le taux de
Page 28 and 29: 10 Introduction biologique simple.
Page 30 and 31: 12 Introduction Le milieu lui-même
Page 32 and 33: 14 Introduction Figure I.6 Schémat
Page 34 and 35: 16 Introduction obstacles technique
Page 36 and 37: 18 Introduction Figure I.8 Prédict
Page 38 and 39: 20 Introduction I.5 La biologie des
Page 40 and 41: 22 Introduction du fonctionnement d
Page 42 and 43: 24 Introduction L’objectif de cet
Page 44 and 45: 26 Behaviour in models 1.1 Introduc
Page 46 and 47: 28 Behaviour in models Using mean p
Page 48 and 49: 30 Behaviour in models 1.3 Vertical
Page 50 and 51: 32 Behaviour in models . . . bring
Page 52 and 53: 34 Behaviour in models of measured
Page 54 and 55: 36 Behaviour in models Additive dis
Page 56 and 57: 38 Behaviour in models In situ stud
Page 58 and 59: 40 Behaviour in models Operational
Page 60 and 61: 42 Behaviour in models Effects on p
Page 62 and 63: 44 Behaviour in models begins is no
Page 64 and 65: 46 Behaviour in models 1.10 Conclus
Page 66 and 67: 48 Larvae orientation in situ Diver
Page 70 and 71: 52 Larvae orientation in situ optio
Page 72 and 73: 54 Larvae orientation in situ if >
Page 74 and 75: 56 Larvae orientation in situ Table
Page 76 and 77: 58 Larvae orientation in situ that
Page 78 and 79: 60 Larvae orientation in situ 2.A A
Page 80 and 81: 62 Behaviour of settling fishes at
Page 87 and 88: Chapter 4 Biophysical correlates in
Page 89 and 90: Methods 71 4.2 Methods 4.2.1 Sampli
Page 91 and 92: Methods 73 Three rotations were com
Page 93 and 94: Methods 75 test really focuses on w
Page 95 and 96: Results 77 Figure 4.3 Mean of insta
Page 97 and 98: Results 79 Figure 4.5 Perspective v
Page 99 and 100: Results 81 Table 4.1 Abundances of
Page 101 and 102: Results 83 Figure 4.8 Distribution
Page 103 and 104: 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
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Methods 101 80, 55, 30 m (Figure 4.
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Methods 103 same station were likel
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Results 105 Figure 5.2 Univariate r
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Results 107 5.4.3 Ontogenetic shift
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Results 109 Figure 5.5 Violin plot
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Discussion 111 5.5 Discussion 5.5.1
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Discussion 113 expression of differ
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Chapter 6 Oceanography vs. behaviou
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Introduction 117 a good description
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A general modelling framework for l
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The balance between feeding and pre
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Oriented swimming and passive advec
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General discussion 161 such integra
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General discussion 163 6.5.2 Why se
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General discussion 165 such as the
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General discussion 167 energeticall
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Acknowledgements 169 Therefore: •
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172 Conclusion Un environnement pé
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174 Conclusion global sur la connec
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176 Conclusion l’intérêt est po
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178 Conclusion La différence entre
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180 Conclusion Mieux décrire la di
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182 Conclusion Comme tout comportem
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184 Undescribed Chaetodonthidae Fig
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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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