MESOPP Acoustic data from vessels of opportunity Deliverable Lead: CSIRO Reference: MESOPP-18-0009 Dissemination Level: Public Issue: 1. 0 Date: 2018, Dec. 03 Horizon 2020. Grant agreement No 692173 Public Acoustic data from vessels of opportunity MESOPP-18-0009 Public V1.0 2018,Dec.03 Chronology Issues Issue Date Reason for change Author 1.0 21/11/2018 First version of the document K. Haris R. Kloser 23/11/2018 Second version of the document P. Lehodey (comments on first version) 27/11/2018 Third version of the document S. Fielding (comments on first version) 30/11/2018 Fourth version of the document P. Lehodey (comments on second version) 30/11/2018 Finalized issue 1.0 K. Haris R. Kloser Distribution Company Means of distribution Names CLS Notification Citation This report can be cited as follow: Haris K., Kloser R. (2018). Acoustic data from vessels of opportunity. Report from the EU-H2020 MESOPP project, MESOPP-18-0009: 39 pp. www.mesopp.eu/documents/ 1 - 10 - GB - NT - www.mesopp.eu Copyright © MESOPP Project Consortium i.1 FORM Acoustic data from vessels of opportunity MESOPP-18-0009 Public V1.0 2018,Dec.03 List of Contents 1. Introduction ........................................................................................................................... 1 1.1. Acoustic data to biomass .......................................................................................................... 2 1.2. Ecosystem models .................................................................................................................... 3 1.3. This report................................................................................................................................. 4 2. Processed acoustic data portals .............................................................................................. 4 3. Processed acoustic data description and quality flags .............................................................. 5 4. Overview of bioacoustic metrics ............................................................................................. 9 5. Effects of data processing routines and quality checking methods ......................................... 12 5.1. Calibration............................................................................................................................... 12 5.2. Effect of motion correction .................................................................................................... 13 5.3. Data quality and effect of filters ............................................................................................. 14 5.4. Effect of secondary corrections .............................................................................................. 17 6. Limitation of single frequency data ....................................................................................... 21 7. Existing resolution of the NetCDF and limitations .................................................................. 24 8. Conclusions .......................................................................................................................... 25 9. References ........................................................................................................................... 26 Appendix A - Importance of calibration parameters .................................................................. 29 Appendix B - Secondary corrections for sound speed and absorption ........................................ 30 Appendix C - Matlab function for visualisation .......................................................................... 32 1 - 10 - GB - NT - www.mesopp.eu Copyright © MESOPP Project Consortium i.2 FORM Acoustic data from vessels of opportunity MESOPP-18-0009 Public V1.0 2018,Dec.03 List of tables and figures List of tables: Table 1. Description of variables present in a NetCDF file. ..................................................................... 8 Table 2. A brief overview of bioacoustic metrics used in the literature. .............................................. 11 List of figures: Figure 1. Example of how bioacoustics data is collected by transmitting a pulse of sound in the water that reflects off the species to produce an echogram, www.imos.org.au. .................................... 1 Figure 2. Visualisation of 38 kHz acoustic data (푆푣) collected by FV Rehua during a 4 day transit from New Zealand to Australia in August 2010. Image courtesy: Tim Ryan, CSIRO. ............................... 2 Figure 3. Flowchart showing how acoustic data is normally converted to fish biomass. ....................... 3 Figure 4. Map showing spatial coverage of processed bioacoustic transects as of 13 November 2018. (a) MESOPP project. (b) IMOS. ....................................................................................................... 5 Figure 5. Generic overview of the data processing sequence in the context of data variables present in a NetCDF file. Reproduced from Ryan et al. (2015). ................................................................... 6 Figure 6. Resolution of a NetCDF file containing processed acoustic data. ............................................. 6 Figure 7. Organization of variables present in a NetCDF file. .................................................................. 7 Figure 8. A broad classification of DSL studies. ....................................................................................... 9 Figure 9. Example of the fishing vessel (Antarctic Discovery) 38 kHz acoustic data covering the Pacific Ocean. The Longhurst oceanic biogeographical provinces are superimposed as white lines. The center part of the south Pacific highlight oligotrophic regions with low predicted productivity (blue), which is observed in general by the low mesopelagic (400–800 m depth) backscatter strength (small magenta circles) (Haris and Kloser, 2017). .......................................................... 10 Figure 10. Calibrated 퐺0 (blue) and 푆푎 corr (red) values for (a) FV Rehua and (b) Austral Leader between 2005–2015. Reproduced from Downie et al. (2018). .................................................... 12 Figure 11. Effect of motion correction on raw 38 kHz 푆푣 data collected by RV Southern Surveyor on 15 October 2013. Note the strong non-linear range dependent effect. ...................................... 13 Figure 12. Voyage track of the data presented in Figure 13. Map generated using Ocean Data View (Schlitzer, 2018). ........................................................................................................................... 14 Figure 13. Combined effects of data processing filters on raw 38 kHz 푆푣 data collected by FV San Tongariro. (a) Calibrated raw data. (b) Final processed data including secondary corrections described in the following section. ............................................................................................... 15 Figure 14. Data quality flags associated with the data presented in Figure 13. ................................... 16 Figure 15. Voyage track of the data presented in Figure 16. ................................................................ 17 Figure 16. Examples of calculated sound speed and absorption coefficient values along the 38 kHz transect from SW Indian Ocean to Mauritius. The absorption coefficients were calculated using two equations as shown in the figure. .......................................................................................... 18 1 - 7 - GB - NT - www.mesopp.eu Copyright © MESOPP Project Consortium i.3 FORM Acoustic data from vessels of opportunity MESOPP-18-0009 Public V1.0 2018,Dec.03 Figure 17. Boxplots of calculated sound speed and absorption coefficient values presented in Figure 16. .................................................................................................................................................. 19 Figure 18. The difference in 38 kHz 푆푣 before and after secondary corrections. Related percentage corrections are shown in the boxplots. Note the increasing correction with range. ................... 20 Figure 19. Voyage track of the data presented in Figure 20. Map generated using Ocean Data View (Schlitzer, 2018). ........................................................................................................................... 21 Figure 20. Multi-frequency echograms highlighting different scattering layers and functional groups. .......................................................................................................................................... 22 Figure 21. Example of multi-frequency metrics (green = 120 kHz; black = 70 kHz; red = 38 kHz; blue = 18 kHz). Average backscatter data in epipelagic (20–200 m), upper mesopelagic (200–400 m), and lower mesopelagic (400–800 m) zone. .................................................................................. 23 Figure 22. Sampling range limitation of high-frequency (120 kHz) data. .............................................. 23 Figure 23. Example echogram showing fish schools at a fine resolution. The grid lines represent existing resolution of the NetCDF file. .......................................................................................... 24 1 - 7 - GB - NT - www.mesopp.eu Copyright © MESOPP Project Consortium i.4 FORM Acoustic data from vessels of opportunity MESOPP-18-0009 Public V1.0 2018,Dec.03 Overview The underlying concept of MESOPP is the creation of a collaborative network and associated