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Automated flow control of a multi-lane swimming chamber for small fishes indicates species-specific sensitivity to experimental protocols

Citation

Illing, Björn et al. (2020), Automated flow control of a multi-lane swimming chamber for small fishes indicates species-specific sensitivity to experimental protocols, Dryad, Dataset, https://doi.org/10.5061/dryad.z34tmpgb7

Abstract

In fishes, swimming performance is considered an important metric to measure fitness, dispersal, and migratory abilities. Swimming performance of individual larval fishes is often integrated into models to make inferences on how environmental parameters affect population-level dynamics (e.g., connectivity). However, little information exists regarding how experimental protocols affect the swimming performance of marine fish larvae. In addition, the technical setups used to measure larval fish swimming performance often lack automation and accurate control of water quality parameters and flow velocity. In this study, we automated the control of multi-lane swimming chambers for small fishes by developing an open-source algorithm. This automation allowed us to execute repeatable flow scenarios and reduce operator interference and inaccuracies in flow velocity typically associated with manual control. Furthermore, we made structural modifications to a prior design to reduce areas of lower flow velocity. We then validated the flow dynamics of the new chambers using computational fluid dynamics and particle tracking software. The algorithm provided accurate alignment between set and measured flow velocities and we used it to test whether faster critical swimming speed (Ucrit) protocols (i.e., shorter time intervals and higher velocity increments) would increase Ucrit of early life stages of two tropical fish species (4-10 mm standard length). The Ucrit of barramundi (Lates calcarifer) and cinnamon anemonefish (Amphiprion melanopus) increased linearly with fish length, but in cinnamon anemonefish, Ucrit started to decrease upon metamorphosis. Swimming protocols using longer time intervals (>2.5 times increase) negatively affected Ucrit in cinnamon anemonefish but not in barramundi. These species-specific differences in swimming performance highlight the importance of testing suitable Ucrit protocols prior to experimentation. Automated control of flow velocity will create more accurate and repeatable data on swimming performance of larval fishes. Integrating refined measurements into individual-based models will support future research on the effects of environmental change.

Methods

Please refer to the original manuscript for details on how the data were collected.

Regarding the swimming protocol data, the ISI Web of Knowledge was searched (Clarivate Analytics, Core collection search on 19.02.2019) using the term: ((swim* OR sust* OR prolong* OR burst*OR cruis* OR routin* OR Ucrit OR endur*) AND (early life stage* OR larv*) AND (marin* OR sea* OR brack*) AND (fish* OR teleost*))). The results were manually checked and 36 papers were identified were fish were swum in multi-lane swimming chambers.

The video files show recordings of fluorescent green polyethylene buoyant particles (850-1000 µm) inside the multi-lane swimming chambers at 10 and 40 cm s-1, respectively. The original recordings were processed using a Flowtrace algorithm (see original manuscript for further details) and inverted using Sony Vegas Pro 13.0 (VEGAS Creative Software). A still of the multi-lane swimming chamber, added to the background of the videos, allowed the evaluation and tracking of individual particles in each raceway. The video of the lower velocity (10 cm s-1) is provided at the original speed, whereas the video of the higher velocity (40 cm s-1) is slowed down to 0.25x speed.

Usage Notes

In the Excel file, several sheets present the data that were used for the analyses in our study.

  • The sheet 'Modelled flow velocity' presents the modeled velocities, obtained through a computational fluid dynamics software, in the column 'velocity_modeled', all set velocity values (10 or 40 cm s-1) in the column 'velocity_set_cm_s'. The data are separated by chamber design ('chamb_design') and the section at which the velocity was modeled ('chamb_section').
  • In the sheet 'Flow control', we present results from testing the alignment of set ('FLOWSV.ValueY') versus actually measured (processed) velocities ('FLOWPV.ValueY'). The 'Interval' column represents the time interval the algorithm waited before the velocity increment was increased (by 2 cm s-1). 'Deviation' is the difference between 'FLOWSV.ValueY' and 'FLOWPV.ValueY', and represents how well the set and measured velocities aligned. 'FLOWSV.Time' and 'Time_s' stand for the duration of these tests.
  • The sheet 'Particle tracking' holds data from the experiments where we tracked fluorescent beads. 'Set_Speed_cm_s' indicates at what set velocity the flow was measured, 'Lane' represents the raceway in which the particles were tracked, 'Measurement' gives the number of the measured particle (10 per raceway), 'Nr_frames' indicates how many frames were used for tracking a particle, 'Frame_rate_frames_s' represents the frame rate used in the video recording, 'Time_s' is the time that a particle took to travel a certain distance ('Distance_cm'), 'Velocity_cm_s' is the speed of the particle, and 'Actual_Speed_cm_s' is the speed that the flow meter measured as actual speed (see ''FLOWPV.ValueY' above). 'Actual_Speed_SD' is the standard deviation of the set speed's velocity during the measurement.
  • The sheet 'Swimming protocols' holds data on critical swimming speed (Ucrit) protocols that were gained through a literature search (see Methods). 'Study_ID' refers to the study that was investigated, 'Speed_Increment_cm_s' is the velocity increase or step height measured in cm s-1,  sometimes reported as 'Speed_Increment_BL_s', where BL abbreviates body length. 'Time_Interval_min' is the step length or duration of each measurement in the Ucrit protocol. '. 'Climatic_region' represents the tested fish's regional Fishbase classification, and 'Reference' refers to the study's authors. Please note, that many studies did not presented speed increments in both cm s-1 and BL s-1.
  • In the sheet 'Swimming trials', we present data collected during experimental trials with two tropical fish species, Cinnamon anemonefish (Amphiprion melanopus) and barramundi (Lates calcarifer). 'ID', 'Date', and 'Spec' refer to the individually tested fish, the date of the trial and the tested species. 'Age_dph' is the age in days post hatch, while 'Increment_cm_s' and 'Interval_min' abbreviate the step height and length used in the Ucrit trial. 'SL_mm_mean' is the standard length in mm, measured right after the swimming trial. 'Time_start', 'Time_stop', and 'Total_Time' indicate at what time and for how long a fish was sum. 'Intervals_passed' is the number of time intervals a fish managed to swim at (required for calculating Ucrit). 'U_Last_Int_cm_s' and 'Time_Last_Int_s' are the final velocity a fish reached during the trial, and the time it spent swimming at this last velocity, respectively. These variables were used to calculate the critical swimming speed 'Ucrit_cm_s'. The column 'Notes' holds information of unusual behaviour or other occurrences.

Funding

Deutsche Forschungsgemeinschaft, Award: IL 220/2-1

Deutsche Forschungsgemeinschaft, Award: IL 220/3-1

Centre of Excellence for Coral Reef Studies, Australian Research Council

Australian Institute of Marine Science