Age estimation of barramundi (Lates calcarifer) over multiple seasons from the southern Gulf of Carpentaria using FT-NIR spectroscopy
C. Wright
A , B. B. Wedding B D , S. Grauf B and O. J. Whybird C
+ Author Affiliations
- Author Affiliations
A Rapid Assessment Unit, Horticulture and Forestry Science, Department of Agriculture and Fisheries, PO Box 1054, Mareeba, Qld 4880, Australia.
B Rapid Assessment Unit, Crop and Food Science, Department of Agriculture and Fisheries, PO Box 652, Cairns, Qld 4870, Australia.
C Fisheries Queensland, Department of Agriculture and Fisheries, PO Box 5396, Cairns, Qld 4870, Australia.
D Corresponding author. Email: brett.wedding@daf.qld.gov.au
Marine and Freshwater Research 72(9) 1268-1279 https://doi.org/10.1071/MF20300
Submitted: 8 October 2020 Accepted: 12 February 2021 Published: 1 April 2021
Journal Compilation © CSIRO 2021 Open Access CC BY
Abstract
The age of whole otoliths from barramundi (Lates calcarifer) obtained from the southern Gulf of Carpentaria were estimated using Fourier transform near-infrared (FT-NIR) spectroscopy. Otoliths from 1716 barramundi collected in 2006, 2009 and 2012–2015 were used in this study. Partial least-squares regression models (PLS-R) and multiple linear regression models (MLR) were developed from the diffuse reflectance spectra and the age was obtained from traditional sectioned otoliths. Calibration models were built up over consecutive years (2012–2015) by using a subset of the samples and used to predict the age of the remaining samples and samples from the following year. Results suggest that when seasonal (temporal) variability is incorporated into the calibration model, FT-NIR has the ability to predict barramundi age (validation R2 ranged from 0.73 to 0.78; RMSEP ranged from 6.92 to 7.64 months). The predicted age class was within 1 year of the reference age in over 96% of the samples. These models were also able to predict the age of otoliths from 2006 and 2009, which were retrieved from long-term storage (validation R2 ranged from 0.77 to 0.84; RMSEP ranged from 8.66 to 10.88 months). The results from this study have shown the potential for barramundi from the southern Gulf of Carpentaria to be aged quickly and accurately by using FT-NIR.
Keywords: fish ageing, otolith, spectroscopy.
References
Beamish, R. J. (1979). New information on the longevity of Pacific Ocean perch (Sebastes alutus). Journal of the Fisheries Research Board of Canada 36, 1395–1400.| New information on the longevity of Pacific Ocean perch (Sebastes alutus).Crossref | GoogleScholarGoogle Scholar |
Bellon-Maurel, V., Fernandez-Ahumada, E., Palagos, B., Roger, J. M., and McBratney, A. (2010). Critical review of chemometric indicators commonly used for assessing the quality of the prediction of soil attributes by NIR spectroscopy. Trends in Analytical Chemistry 29, 1073–1081.
| Critical review of chemometric indicators commonly used for assessing the quality of the prediction of soil attributes by NIR spectroscopy.Crossref | GoogleScholarGoogle Scholar |
Blanco, M., and Villarroya, I. (2002). NIR spectroscopy: a rapid-response analytical tool. Trends in Analytical Chemistry 21, 240–250.
| NIR spectroscopy: a rapid-response analytical tool.Crossref | GoogleScholarGoogle Scholar |
Bobelyn, E., Serban, A.-S., Nicu, M., Lammertyn, J., Nicolaï, B. M., and Saeys, W. (2010). Postharvest quality of apple predicted by NIR-spectroscopy: study of the effect of biological variability on spectra and model performance. Postharvest Biology and Technology 55, 133–143.
| Postharvest quality of apple predicted by NIR-spectroscopy: study of the effect of biological variability on spectra and model performance.Crossref | GoogleScholarGoogle Scholar |
Burns, D. A., and Ciurczak, E. W. (2001) ‘Handbook of Near-Infrared Analysis.’ 2nd edn. (Marcel Dekker: New York, NY, USA.)
Campana, S. E. (1999). Chemistry and composition of fish otoliths: pathways, mechanisms and applications. Marine Ecology Progress Series 188, 263–297.
| Chemistry and composition of fish otoliths: pathways, mechanisms and applications.Crossref | GoogleScholarGoogle Scholar |
Campana, S. E., and Thorrold, S. R. (2001). Otoliths, increments and elements: keys to a comprehensive understanding of fish populations? Canadian Journal of Fisheries and Aquatic Sciences 58, 30–38.
| Otoliths, increments and elements: keys to a comprehensive understanding of fish populations?Crossref | GoogleScholarGoogle Scholar |
Capron, X., Walczak, B., de Noord, O. E., and Massart, D. L. (2005). Selection and weighting of samples in multivariate regression model updating. Chemometrics and Intelligent Laboratory Systems 76, 205–214.
| Selection and weighting of samples in multivariate regression model updating.Crossref | GoogleScholarGoogle Scholar |
Cardinale, M., and Arrhenius, F. (2004). Application of the otolith weight–age relationship to estimate the age-structure of haddock (Melanogramus aeglefinus). Journal of Applied Ichthyolpgu 20, 470–475.
| Application of the otolith weight–age relationship to estimate the age-structure of haddock (Melanogramus aeglefinus).Crossref | GoogleScholarGoogle Scholar |
Chang, M.-Y., and Geffen, A. J. (2013). Taxonomic and geographic influences on fish otolith microchemistry. Fish and Fisheries 14, 458–492.
| Taxonomic and geographic influences on fish otolith microchemistry.Crossref | GoogleScholarGoogle Scholar |
Crook, D. A., Buckle, D. J., Allsop, Q., Baldwin, W., Saunders, T. M., Kyne, P. M., Woodhead, J. D., Maas, R., Roberts, B., and Douglas, M. M. (2017). Use of otolith chemistry and acoustic telemetry to elucidate migratory contingents in barramundi Lates calcarifer. Marine and Freshwater Research 68, 1554–1566.
| Use of otolith chemistry and acoustic telemetry to elucidate migratory contingents in barramundi Lates calcarifer.Crossref | GoogleScholarGoogle Scholar |
Davis, T. L. O. (1982). Maturity and sexuality in barramundi, Lates calcarifer (Bloch), in the Northern Territory and south-eastern Gulf of Carpentaria. Australian Journal of Marine and Freshwater Research 33, 529–545.
| Maturity and sexuality in barramundi, Lates calcarifer (Bloch), in the Northern Territory and south-eastern Gulf of Carpentaria.Crossref | GoogleScholarGoogle Scholar |
De Vries, S., and Ter Braak Cajo, J. F. (1995). Prediction error in partial least squares regression: a critique on the deviation used in the Unscrambler. Chemometrics and Intelligent Laboratory Systems 30, 239–245.
| Prediction error in partial least squares regression: a critique on the deviation used in the Unscrambler.Crossref | GoogleScholarGoogle Scholar |
Degens, E., Deuser, W., and Haedrich, R. (1969). Molecular structure and composition of fish otoliths. Marine Biology 2, 105–113.
| Molecular structure and composition of fish otoliths.Crossref | GoogleScholarGoogle Scholar |
Department of Primary Industries and Fisheries (2005). ‘Fisheries Long Term Monitoring Program Sampling Protocol – Barramundi.’ (Department of Primary Industries and Fisheries, Queensland, QI05117: Brisbane, Qld, Australia.)
Dunstan, D. J. (1959). The barramundi in Queensland waters. Division of Fisheries and Oceanography Technical Paper No. 5. CSIRO Australia.
Fearn, T. (1992). Flat or natural? A note on the choice of calibration samples. In ‘Near Infrared Spectroscopy Bridging the Gap between Data Analysis and NIR Applications’. (Eds K. I. Hildrum, T. Næs, and A. Tandberg.) pp. 61–66. (Ellis Horwood: New York, NY, USA.)
Fisheries Queensland (2020). ‘Fishery Monitoring Barramundi Ageing Protocol.’ (Department of Agriculture and Fisheries: Brisbane, Qld, Australia.)
Hale, R., and Swearer, S. E. (2008). Otolith microstructural and microchemical changes associated with settlement in the diadromous fish Galaxias maculatus. Marine Ecology Progress Series 354, 229–234.
| Otolith microstructural and microchemical changes associated with settlement in the diadromous fish Galaxias maculatus.Crossref | GoogleScholarGoogle Scholar |
Helser, T. E., Benson, I., Erickson, J., Healy, J., Kastele, C., and Short, J. A. (2019). A transformative approach to ageing fish otoliths using Fourier transform near infrared spectroscopy: a case study of eastern Bering Sea walleye pollock (Gadus chalcogrammus). Canadian Journal of Fisheries and Aquatic Sciences 76, 780–789.
| A transformative approach to ageing fish otoliths using Fourier transform near infrared spectroscopy: a case study of eastern Bering Sea walleye pollock (Gadus chalcogrammus).Crossref | GoogleScholarGoogle Scholar |
Herschel, W. (1800). Experiments on the refrangibility of the invisible rays of the sun. Philosophical Transactions of the Royal Society of London 90, 284–292.
Kalivas, J. H., Siano, G. G., Andries, E., and Goicoechea, H. C. (2009). Calibration maintenance and transfer using Tikhonov regularization approaches. Applied Spectroscopy 63, 800–809.
| Calibration maintenance and transfer using Tikhonov regularization approaches.Crossref | GoogleScholarGoogle Scholar | 19589218PubMed |
Kennard, R. W., and Stone, L. A. (1969). Computer-aided design of experiments. Technometrics 11, 137–148.
| Computer-aided design of experiments.Crossref | GoogleScholarGoogle Scholar |
Mc Dougall, A. (2004). Assessing the use of sectioned otoliths and other methods to determine the age of centropomid fish, barramundi (Lates calcarifer) (Bloch), using known-age fish. Fisheries Research 67, 129–141.
| Assessing the use of sectioned otoliths and other methods to determine the age of centropomid fish, barramundi (Lates calcarifer) (Bloch), using known-age fish.Crossref | GoogleScholarGoogle Scholar |
Mercader, M. B., and Puigdoménech, A. R. (2014). Near infrared multivariate model maintenance: the cornerstone of success. NIR News 25, 7–9.
| Near infrared multivariate model maintenance: the cornerstone of success.Crossref | GoogleScholarGoogle Scholar |
Milton, D., Halliday, I., Sellin, M., Marsh, R., Staunton-Smith, J., and Woodhead, J. (2008). The effect of habitat and environmental history on otolith chemistry of barramundi Lates calcarifer in estuarine populations of a regulated tropical river. Estuarine, Coastal and Shelf Science 78, 301–315.
| The effect of habitat and environmental history on otolith chemistry of barramundi Lates calcarifer in estuarine populations of a regulated tropical river.Crossref | GoogleScholarGoogle Scholar |
Moore, B. R., Maclaren, J., Peat, C., Anjomrouz, M., Horn, P. L., and Hoyle, S. (2019). Feasibility of automating otolith ageing using CT scanning and machine learning. Fisheries New Zealand, Wellington, New Zealand.
Morisseau, K. M., and Rhodes, C. T. (1995). Pharmaceutical Uses of Near-Infrared Spectroscopy. Drug Development and Industrial Pharmacy 21, 1071–1090.
| Pharmaceutical Uses of Near-Infrared Spectroscopy.Crossref | GoogleScholarGoogle Scholar |
Murray, I., and Williams, P. (1987). Chemical principles of near-infrared technology. In ‘Near infrared technology in the agricultural and food industries’. (Eds P. Williams and K. H. Norris.) pp. 17–34. (American Association of Cereal Chemists, Inc.: St Paul, MN, USA.)
Norris, K. H., and Hart, J. R. (1963) Proceedings of the 1963 International Symposium on Humidity and Moisture 4, 19–25
Ogle, D. H., Wheeler, P., and Dinno, A. (2020). FSA: Fisheries Stock Analysis. R package version 0.8.3. Available at https://github.com/droglenc/FSA.
Ono, K., Licandeo, R., Muradian, M. L., Cunningham, C. J., Anderson, S. C., Hurtado-Ferro, F., Johnson, K. F., McGilliard, C. R., Monnahan, C. C., Szuwalski, C. S., Valero, J. L., Vert-Pre, K. A., Whitten, A. R., and Punt, A. E. (2015). The importance of length and age composition data in statistical age-structured models for marine species. Journal of Marine Science 72, 31–43.
Ozaki, Y., McClure, W. F., and Christy, A. A. (2003). ‘Near-infrared Spectroscopy in Food Science and Technology.’ (John Wiley and Sons: New York, NY, USA.)
Passerotti, M. S., Helser, T. E., Benson, I. M., Barnett, B. K., Ballenger, J. C., Bubley, W. J., Reichert, M. J. M., and Quattro, J. M. (2020a). Age estimation of red snapper (Lujanus campechanus) using FT-NIR spectroscopy: feasibility of application to production ageing for management. ICES Journal of Marine Science 77, 2144–2156.
| Age estimation of red snapper (Lujanus campechanus) using FT-NIR spectroscopy: feasibility of application to production ageing for management.Crossref | GoogleScholarGoogle Scholar |
Passerotti, M. S., Jones, C. M., Swanson, C. E., and Quattro, J. M. (2020b). Fourier-transform near infrared spectroscopy (FT-NIRS) rapidly and non-destructively predicts daily age and growth in otoliths of juvenile red snapper Lutjanus campechanus (Poey, 1860). Fisheries Research 223, 105439.
| Fourier-transform near infrared spectroscopy (FT-NIRS) rapidly and non-destructively predicts daily age and growth in otoliths of juvenile red snapper Lutjanus campechanus (Poey, 1860).Crossref | GoogleScholarGoogle Scholar |
Radtke, R. L., and Shafer, D. J. (1992). Environmental sensitivity of fish otolith microchemistry. Australian Journal of Marine and Freshwater Research 43, 935–951.
| Environmental sensitivity of fish otolith microchemistry.Crossref | GoogleScholarGoogle Scholar |
Reeves, J. B., McCarty, G. W., and Meisinger, J. J. (1999). Near infrared reflectance spectroscopy for the analysis of agricultural soils. Journal of Near Infrared Spectroscopy 7, 179–193.
| Near infrared reflectance spectroscopy for the analysis of agricultural soils.Crossref | GoogleScholarGoogle Scholar |
Rigby, C. L., Wedding, B. B., Grauf, S., and Simpfendorfer, C. A. (2014). The utility of near infrared spectroscopy for age estimation of deepwater sharks. Deep-sea Research. Part I, Oceanographic Research Papers 94, 184–194.
| The utility of near infrared spectroscopy for age estimation of deepwater sharks.Crossref | GoogleScholarGoogle Scholar |
Rigby, C. L., Wedding, B. B., Grauf, S., and Simpfendorfer, C. A. (2016). Novel method for shark age estimation using near infrared spectroscopy. Marine and Freshwater Research 67, 537–545.
| Novel method for shark age estimation using near infrared spectroscopy.Crossref | GoogleScholarGoogle Scholar |
Robertson, S. G., and Morison, A. K. (1999). A trial of artificial neural networks for automatically estimating the age of fish. Marine and Freshwater Research 50, 73–82.
| A trial of artificial neural networks for automatically estimating the age of fish.Crossref | GoogleScholarGoogle Scholar |
Robins, J., Mayer, D. G., Staunton-Smith, J., Halliday, I., Sawynok, B., and Sellin, M. (2006). Variable growth rates of the tropical estuarine fish barramundi Lates calcarifer (Bloch) under different freshwater flow conditions. Journal of Fish Biology 69, 379–391.
| Variable growth rates of the tropical estuarine fish barramundi Lates calcarifer (Bloch) under different freshwater flow conditions.Crossref | GoogleScholarGoogle Scholar |
Robins, J. B., Wedding, B. B., Wright, C., Grauf, S., Sellin, M., Fowler, A., Saunders, T., and Newman, S. (2015). ‘Revolutionising Fish Ageing: Using Near Infrared Spectroscopy to Age Fish.’ (Department of Agriculture, Fisheries and Forestry: Brisbane, Qld, Australia.)
Saunders, T., Whybird, O., Trinnie, F., and Newman, S. (2018). Barramundi Lates calcarifer. In ‘Status of Australian fish stocks reports 2018’. (Eds Stewardson, C., Andrews, J., Ashby, C., Haddon, M., Hartmann, K., Hone, P., Horvat, P., Mayfield, S., Roelofs, A., Sainsbury, K., Saunders, T., Stewart, J., Nicol, S., and Wise, B.) (Fisheries Research and Development Corporation: Canberra, ACT, Australia.) Available at http://www.fish.gov.au/.
Secor, D. H., Dean, J. M., and Laban, E. H. (1992). Chapter 3: Otolith Removal and Preparation for Microstructural Examination. In ‘Otolith Microstructure Examination and Analysis’. Canadian Special Publication of Fisheries and Aquatic Sciences 117. (Eds D. K. Stevenson and S. E. Campana.) (Department of Fisheries and Oceans: Ottawa, Canada.)
Secor, D. H., Dean, J. M., and Campana, S. E. (1995). Recent developments in otolith research. In ‘The Belle W. Baruch Library in Marine Science’. (Ed. S. E. Campana.) pp. 19–57. (University of South Carolina Press: Columbia, SC, USA.)
Shenk, J. S., Workman, J. J., and Westerhaus, M. O. (2001). Application of NIR spectroscopy to agricultural products. In ‘Handbook of Near-Infrared Analysis’. (Eds D. A. Burnes and E. W. Ciurczak.) pp. 419–474. (Marcel Dekker: New York, USA.)
Stork, C. L., and Kowalski, B. R. (1999). Weighting schemes for updating regression models – a theoretical approach. Chemometrics and Intelligent Laboratory Systems 48, 151–166.
| Weighting schemes for updating regression models – a theoretical approach.Crossref | GoogleScholarGoogle Scholar |
Streipert, S., Filar, J., Robins, J. B., and Whybird, O. (2019). Stock assessment of the barramundi (Lates calcarifer) fishery in Queensland, Australia. May 2019. Technical Report, State of Queensland, Australia.
Stuart, I. G., and McKillup, C. (2002). The use of sectioned otoliths to age barramundi (Lates calcarifer) (Bloch, 1790) [Centropomidae]. Hydrobiologia 479, 231–236.
| The use of sectioned otoliths to age barramundi (Lates calcarifer) (Bloch, 1790) [Centropomidae].Crossref | GoogleScholarGoogle Scholar |
Tabouret, H., Lord, C., Bareille, G., Pecheyran, C., Monti, D., and Keith, P. (2011). Otolith microchemistry in Sicydium punctatum: indices of environmental condition changes after recruitment. Aquatic Living Resources 24, 369–378.
| Otolith microchemistry in Sicydium punctatum: indices of environmental condition changes after recruitment.Crossref | GoogleScholarGoogle Scholar |
Walsh, K., Golic, M., and Greensill, C. (2004). Sorting of fruit using near infrared spectroscopy: application to a range of fruit and vegetables for soluble solids and dry matter content. Journal of Near Infrared Spectroscopy 12, 141–148.
| Sorting of fruit using near infrared spectroscopy: application to a range of fruit and vegetables for soluble solids and dry matter content.Crossref | GoogleScholarGoogle Scholar |
Walsh, K. B., Blasco, J. B., Zude-Sasse, M., and Sun, X. (2020). Visible-NIR ‘point’ spectroscopy in postharvest fruit and vegetable assessment: the science behind three decades of commercial use. Postharvest Biology and Technology 168, 111246.
| Visible-NIR ‘point’ spectroscopy in postharvest fruit and vegetable assessment: the science behind three decades of commercial use.Crossref | GoogleScholarGoogle Scholar |
Wedding, B. B., Forrest, A. J., Wright, C., Grauf, S., and Exley, P. (2014). A novel method for the age estimation of saddletail snapper (Lutjanus malabaricus) using Fourier transform–near infrared (FT-NIR) spectroscopy. Marine and Freshwater Research 65, 894–900.
| A novel method for the age estimation of saddletail snapper (Lutjanus malabaricus) using Fourier transform–near infrared (FT-NIR) spectroscopy.Crossref | GoogleScholarGoogle Scholar |
Winkler, A. C., Duncan, M. I., Farthing, M. W., and Potts, W. M. (2019). Sectioned or whole otoliths? A global review of hard structure preparation techniques used in ageing sparid fishes. Reviews in Fish Biology and Fisheries 29, 605–611.
| Sectioned or whole otoliths? A global review of hard structure preparation techniques used in ageing sparid fishes.Crossref | GoogleScholarGoogle Scholar |
Zhang, F., Zhang, R., Wang, W., Yang, Y., Li, L., Xiong, Y., and Kang, Q. (2019). Ridge regression combined with model complexity analysis for near infrared (NIR) spectroscopic model updating. Chemometrics and Intelligent Laboratory Systems 195, 103896.
| Ridge regression combined with model complexity analysis for near infrared (NIR) spectroscopic model updating.Crossref | GoogleScholarGoogle Scholar |
