Dissertation - HQ

Methods 73
Three rotations were completed in a row and a fourth one was done
after a 4 days break.
4.2.2 Treatment of samples and data
In the laboratory, fish larvae were sorted out of the MOCNESS samples
and reef fishes were identified to the lowest possible taxonomic level, under
a stereomicroscope. Larvae were identified using various books 172–175
and articles. When in doubt, the specimen was photographed and pictures
were commented by several experts in the field, through an online
photography database b . When clear morphological characteristics were
discernible but that it was still impossible to relate the specimen to a
single genus, larvae were catalogued in morphological groups within
a family. The ontogenetic stage of each individual was classified as
pre-flexion (notochord completely straight), flexion (notochord bent but
caudal fin not yet fully formed), post-flexion (notochord flexed at ca.
90º and caudal fin fully formed). A few Bongo samples were processed
through a ZOOSCAN 176 for broad taxonomic identification and detection
of size classes. This data is still being processed at the Scripps
Institution of Oceanography, San Diego, and will not be used here.
Outliers in CTD profiles near the surface (0-50 m) were filtered
out using techniques based on the median absolute deviation 177 . Then,
each portion was linearly interpolated on a 1 m resolution vertical
coordinate. Finally, the profile for each station was computed as the
mean between the descending and ascending portions of the MOCNESS
tows to better represent the mean conditions at the sampling station. To
detect the depth of the thermo-, halo-, and pycnocline the profiles were
first approximated by a smoothing spline. Then, a 15 m tall moving
window was used to compute the standard deviation of the value of
interest from surface to bottom. The middle points of the windows in
which the standard deviation of the temperature, salinity or density
were maximal were taken as the depths of the thermocline, halocline,
and pycnocline respectively. The fluorometry maxima (a proxy for the
chlorophyll maxima) were identified on smoothed fluorometry profiles
and their depths were recorded.
ADCP measurements are highly variable inherently and particularly
with the setting we used. In addition, the ship drifted during the
measurement and its movement needed to be suppressed from the
speeds measured. To avoid outlying values, the start and end time bins
were discarded and the intermediate values were filtered following
the method of Paris et al. 178 . ADCP measurements were taken at 18 s
intervals. Ship drift was computed within 22 s intervals centred on
each ACDP measurement, to smooth instantaneous variability. Drift
distance was computed from start and end DGPS positions assuming
Visual identification
of fish larvae
CTD and ADCP data
need to be cleaned
and interpolated
b http://cbetm.univ-perp.fr/larvae/. The database is now open for consultation
and the pictures and comments are placed under a Creative Commons Attribution-Share
Alike 3.0 Licence.