Register      Login
Marine and Freshwater Research Marine and Freshwater Research Society
Advances in the aquatic sciences
RESEARCH ARTICLE

Rapid age estimation of longnose skate (Raja rhina) vertebrae using near-infrared spectroscopy

Morgan B. Arrington https://orcid.org/0000-0002-1885-7294 A C , Thomas E. Helser B * , Irina M. Benson B * , Timothy E. Essington A , Mary Elizabeth Matta B * and André E. Punt A
+ Author Affiliations
- Author Affiliations

A School of Aquatic and Fishery Sciences, University of Washington, 1122 Boat Street, Seattle, WA 98195, USA.

B Resource Ecology and Fisheries Management Division, Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 7600 Sand Point Way NE, Seattle, WA 98115, USA.

C Corresponding author. Email: marringt@uw.edu

Marine and Freshwater Research 73(1) 71-80 https://doi.org/10.1071/MF21054
Submitted: 13 February 2021  Accepted: 30 July 2021   Published: 23 September 2021

Abstract

There is a paucity of age data for chondrichthyan fishes owing, in large part, to limitations in traditional age estimation methods. Fourier transform near-infrared (FT-NIR) spectroscopy has shown promise as an alternative, more efficient method for acquiring age data from chondrichthyans. However, studies are limited to sharks in the southern hemisphere. We explored FT-NIR spectroscopy to predict age for a batoid species in the northern hemisphere. The longnose skate (Raja rhina) is one of a small number of batoids for which annual band periodicity in vertebral centra has been validated, allowing for traditional age estimation and making it an ideal candidate for this study. We fit a multivariate partial least-square predictive model between FT-NIR spectra collected from vertebral centra and traditional age estimates, and tested model predictive skill by using external validation. Using FT-NIR spectroscopy, we were able to predict age for longnose skates between the ages of 1 and 14 years with precision and bias near equal to those of traditional methods in less than a quarter of the time. These results support potential for FT-NIR spectroscopy to increase the amount of age data available for assessments used to inform the conservation and management of this sensitive group of species.

Keywords: elasmobranchs, fisheries, marine, modelling.


References

Arrington, M. B. (2020). Growth and maturity of Longnose Skates (Raja rhina) along the North American West Coast. M.Sc. Thesis, University of Washington, Seattle, WA, USA.

Baumann, P. (2020). simplerspec: soil and plant spectroscopic model building and prediction. R package version 0.1.0.9001. Available at https://github.com/philipp-baumann/simplerspec.

Baykal, D., Irrechukwu, O., Lin, P., Fritton, K., Spencer, R. G., and Pleshko, N. (2010). Nondestructive assessment of engineered cartilage constructs using near-infrared spectroscopy. Applied Spectroscopy 64, 1160–1166.
Nondestructive assessment of engineered cartilage constructs using near-infrared spectroscopy.Crossref | GoogleScholarGoogle Scholar | 20925987PubMed |

Brown, C. D., Vega-Montoto, L., and Wentzell, P. D. (2000). Derivative preprocessing and optimal corrections for baseline drift in multivariate calibration. Applied Spectroscopy 54, 1055–1068.
Derivative preprocessing and optimal corrections for baseline drift in multivariate calibration.Crossref | GoogleScholarGoogle Scholar |

Cailliet, G. M. (1990). Elasmobranch age determination and verification: an updated review. In ‘Elasmobranchs as Living Resources: Advances in the Biology, Ecology, Systematics, and the Status of the Fisheries. Proceedings of the Second United States–Japan Workshop’. 9–14 December 1987, Honolulu, HI, USA. NOAA Technical Report NMFS 90. (Eds H. L. Pratt, S. H. Gruber, and T. Taniuchi.) pp. 157–165. (US Department of Commerce.)

Cailliet, G. M., and Goldman, K. J. (2004). Age determination and validation in Chondrichthyan fishes. In ‘Biology of Sharks and Their Relatives’. (Eds J. C. Carrier, J. A. Musick, and M. R. Heithaus.) pp. 399–447. (CRC Press: Boca Raton, FL, USA.)

Cailliet, G. M., Smith, W. D., Mollet, H. F., and Goldman, K. J. (2006). Age and growth studies of chondrichthyan fishes: the need for consistency in terminology, verification, validation, and growth function fitting. Environmental Biology of Fishes 77, 211–228.
Age and growth studies of chondrichthyan fishes: the need for consistency in terminology, verification, validation, and growth function fitting.Crossref | GoogleScholarGoogle Scholar |

Campana, S. E. (2001). Accuracy, precision and quality control in age determination, including a review of the use and abuse of age validation methods. Journal of Fish Biology 59, 197–242.
Accuracy, precision and quality control in age determination, including a review of the use and abuse of age validation methods.Crossref | GoogleScholarGoogle Scholar |

Chang, W. Y. B. (1982). A statistical method for evaluating the reproducibility of age determination. Canadian Journal of Fisheries and Aquatic Sciences 39, 1208–1210.
A statistical method for evaluating the reproducibility of age determination.Crossref | GoogleScholarGoogle Scholar |

Couture, J. J., Singh, A., Rubert-Nason, K. F., Serbin, S. P., Lindroth, R. L., and Townsend, P. A. (2016). Spectroscopic determination of ecologically relevant plant secondary metabolites. Methods in Ecology and Evolution 7, 1402–1412.
Spectroscopic determination of ecologically relevant plant secondary metabolites.Crossref | GoogleScholarGoogle Scholar |

Dulvy, N. K., Fowler, S. L., Musick, J. A., Cavanagh, R. D., Kyne, P. M., Harrison, L. R., Carlson, J. K., Davidson, L., Fordham, S. V., Francis, M. P., Pollock, C. M., Simpfendorfer, C. A., Burgess, G. H., Carpenter, K. E., Compagno, L., Ebert, D. A., Gibson, C., Heupel, M. R., Livingstone, S. R., Sanciangco, J. C., Stevens, J. D., Valenti, S., and White, W. T. (2014). Extinction risk and conservation of the world’s sharks and rays. eLife 3, e00590.
Extinction risk and conservation of the world’s sharks and rays.Crossref | GoogleScholarGoogle Scholar | 24448405PubMed |

Elkabouss, K., Kacimi, M., Ziyad, M., Ammar, S., and Bozon-Verduraz, F. (2004). Cobalt-exchanged hydroxyapatite catalysts: magnetic studies, spectroscopic investigations, performance in 2-butanol and ethane oxidative dehydrogenations. Journal of Catalysis 226, 16–24.
Cobalt-exchanged hydroxyapatite catalysts: magnetic studies, spectroscopic investigations, performance in 2-butanol and ethane oxidative dehydrogenations.Crossref | GoogleScholarGoogle Scholar |

Farrugia, T. J. (2017). Interdisciplinary assessment of the skate fishery in the Gulf of Alaska. Ph.D. Thesis, University of Alaska Fairbanks, Fairbanks, AK, USA.

Fowler, S. L., Cavanagh, R. D., Camhi, M., Burgess, G. H., Cailliet, G. M., Fordham, S. V., Simpfendorfer, C. A., and Musick, J. A. (2005). ‘Sharks, Rays and Chimaeras: The Status of the Chondrichthyan Fishes.’ IUCN/SSC Shark Specialist Group. (IUCN: Gland, Switzerland; and Cambridge, UK.)

Gburski, C. M., Gaichas, S. K., and Kimura, D. K. (2007). Age and growth of big skate (Raja binoculata) and longnose skate (R. rhina) in the Gulf of Alaska. Environmental Biology of Fishes 80, 337–349.
Age and growth of big skate (Raja binoculata) and longnose skate (R. rhina) in the Gulf of Alaska.Crossref | GoogleScholarGoogle Scholar |

Gertseva, V., Matson, S., Taylor, I., Bizzarro, J., and Wallace, J. (2019). ‘Stock Assessment of the Longnose Skate (Beringraja rhina) in State and Federal Waters off California, Oregon and Washington.’ (Pacific Fishery Management Council: Portland, OR, USA.)

Heino, M., and Dieckmann, U. (2008). Detecting fisheries-induced life-history evolution: an overview of the reaction-norm approach. Bulletin of Marine Science 83, 69–93.

Helser, T. E., Benson, I., Erickson, J., Healy, J., Kastelle, C., and Short, J. A. (2018). 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, 1–10.

Hoenig, J. M., Morgan, M. J., and Brown, C. A. (1995). Analysing differences between two age determination methods by tests of symmetry. Canadian Journal of Fisheries and Aquatic Sciences 52, 364–368.
Analysing differences between two age determination methods by tests of symmetry.Crossref | GoogleScholarGoogle Scholar |

Keller, A. K., Wallace, J. R., and Methot, R. D. (2017). ‘The Northwest Fisheries Science Center’s West Coast Groundfish Bottom Trawl Survey: History, Design, and Description.’ NOAA Technical Memorandum NMFS-NWFSC-136. (US Department of Commerce.)

Kerr, L. A., and Campana, S. E. (2014). Chemical composition of fish hard parts as a natural marker of fish stocks. In ‘Stock Identification Methods’. 2nd edn. (Eds S. X. Cadrin, L. A. Kerr, and S. Mariani.) pp. 205–234. (Academic Press: San Diego, CA, USA.)

King, J. R., and McFarlane, G. A. (2003). Marine fish life history strategies: applications to fishery management. Fisheries Management and Ecology 10, 249–264.
Marine fish life history strategies: applications to fishery management.Crossref | GoogleScholarGoogle Scholar |

King, J. R., Helser, T., Gburski, C., Ebert, D. A., Cailliet, G., and Kastelle, C. R. (2017). Bomb radiocarbon analyses validate and inform age determination of longnose skate (Raja rhina) and big skate (Beringraja binoculata) in the North Pacific Ocean. Fisheries Research 193, 195–206.
Bomb radiocarbon analyses validate and inform age determination of longnose skate (Raja rhina) and big skate (Beringraja binoculata) in the North Pacific Ocean.Crossref | GoogleScholarGoogle Scholar |

Kucheryavskiy, S. (2020). mdatools – R package for chemometrics. Chemometrics and Intelligent Laboratory Systems 198, 103937.
mdatools – R package for chemometrics.Crossref | GoogleScholarGoogle Scholar |

Lai, H. L., and Gunderson, D. R. (1987). Effects of ageing errors on estimates of growth, mortality and yield per recruit for walleye pollock (Theragra chalcogramma). Fisheries Research 5, 287–302.
Effects of ageing errors on estimates of growth, mortality and yield per recruit for walleye pollock (Theragra chalcogramma).Crossref | GoogleScholarGoogle Scholar |

Lorenzen, K., and Enberg, K. (2002). Density-dependent growth as a key mechanism in the regulation of fish populations: evidence from among-population comparisons. Proceedings of the Royal Society London B: Biological Sciences 269, 49–54.
Density-dependent growth as a key mechanism in the regulation of fish populations: evidence from among-population comparisons.Crossref | GoogleScholarGoogle Scholar |

Matta, M. E., Black, B. A., and Wilderbuer, T. K. (2010). Climate-driven synchrony in otolith growth-increment chronologies for three Bering Sea flatfish species. Marine Ecology Progress Series 413, 137–145.
Climate-driven synchrony in otolith growth-increment chronologies for three Bering Sea flatfish species.Crossref | GoogleScholarGoogle Scholar |

Matta, M. E., Tribuzio, C. A., Ebert, D. A., Goldman, K. J., and Gburski, C. M. (2017). Age and growth of elasmobranchs and applications to fisheries management and conservation in the Northeast Pacific Ocean. Advances in Marine Biology 77, 179–220.
Age and growth of elasmobranchs and applications to fisheries management and conservation in the Northeast Pacific Ocean.Crossref | GoogleScholarGoogle Scholar | 28882214PubMed |

Matta, M. E., Helser, T. E., and Black, B. A. (2018). Intrinsic and environmental drivers of growth in an Alaskan rockfish: an Otolith biochronology approach. Environmental Biology of Fishes 101, 1571–1587.
Intrinsic and environmental drivers of growth in an Alaskan rockfish: an Otolith biochronology approach.Crossref | GoogleScholarGoogle Scholar |

McBride, R. (2015). Diagnosis of paired age agreement: a simulation of accuracy and precision effects. ICES Journal of Marine Science 72, 2149–2167.
Diagnosis of paired age agreement: a simulation of accuracy and precision effects.Crossref | GoogleScholarGoogle Scholar |

McClure, W., Crowell, B., Stanfield, D., Mohapatra, S., Morimoto, S., and Batten, G. (2002). Near infrared technology for precision environmental measurements: Part 1. Determination of nitrogen in green-and dry-grass tissue. Journal of Near Infrared Spectroscopy 10, 177–185.
Near infrared technology for precision environmental measurements: Part 1. Determination of nitrogen in green-and dry-grass tissue.Crossref | GoogleScholarGoogle Scholar |

Natanson, L. J., Skomal, G. B., Hoffman, S. L., Porter, M. E., Goldman, K. J., and Serra, D. (2018). Age and growth of sharks: do vertebral band pairs record age? Marine and Freshwater Research 69, 1440–1452.
Age and growth of sharks: do vertebral band pairs record age?Crossref | GoogleScholarGoogle Scholar |

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 (Lutjanus 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 (Lutjanus 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 |

Pistevos, J. C. A., Nagelkerken, I., Rossi, T., Olmos, M., and Connell, S. D. (2015). Ocean acidification and global warming impair shark hunting behaviour and growth. Scientific Reports 5, 16293.
Ocean acidification and global warming impair shark hunting behaviour and growth.Crossref | GoogleScholarGoogle Scholar |

Punt, A. E., Smith, D. C., KrusicGolub, K., and Roberston, S. (2008). Quantifying age-reading error for use in fisheries stock assessments, with application to species in Australia’s southern and eastern scalefish and shark fishery. Canadian Journal of Fisheries and Aquatic Sciences 65, 1991–2005.
Quantifying age-reading error for use in fisheries stock assessments, with application to species in Australia’s southern and eastern scalefish and shark fishery.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 |

Rinnan, A., van den Berg, F., and Engelsen, S. B. (2009). Review of the most common pre-processing techniques for near-infrared spectra. Trends in Analytical Chemistry 28, 1201–1222.
Review of the most common pre-processing techniques for near-infrared spectra.Crossref | GoogleScholarGoogle Scholar |

Robins, J. B., Wedding, B. B., Wright, C., Grauf, S., Sellin, M., Fowler, A., Saunders, T., and Newman, S. J. (2015). ‘Revolutionising Fish Ageing: Using Near Infrared Spectroscopy to Age Fish.’ (Department of Agriculture, Fisheries and Forestry: Brisbane, Qld, Australia.)

Roggo, Y., Chalus, P., Maurer, L., Lema-Martinez, C., Edmond, A., and Jent, N. (2007). A review of near infrared spectroscopy and chemometrics in pharmaceutical technologies. Journal of Pharmaceutical and Biomedical Analysis 44, 683–700.
A review of near infrared spectroscopy and chemometrics in pharmaceutical technologies.Crossref | GoogleScholarGoogle Scholar | 17482417PubMed |

Savitzky, A., and Golay, M. J. E. (1964). Smoothing and differentiation of data by simplified least squares procedures. Analytical Chemistry 36, 1627–1639.
Smoothing and differentiation of data by simplified least squares procedures.Crossref | GoogleScholarGoogle Scholar |

Shelton, A. O., and Mangel, M. (2012). Estimating von Bertalanffy parameters with individual and environmental variations in growth. Journal of Biological Dynamics 6, 3–30.
Estimating von Bertalanffy parameters with individual and environmental variations in growth.Crossref | GoogleScholarGoogle Scholar | 22882022PubMed |

Stokes, K., and Law, R. (2000). Fishing as an evolutionary force. Marine Ecology Progress Series 208, 307–309.

Thompson, J. E. (2005). Age, growth and maturity of the Longnse Skate (Raja rhina) for the US West Coast and sensitivity to fishing impacts. M.Sc. Thesis, State University, OR, USA.

Vance, C. K., Tolleson, D. R., Kinoshita, K., Rodriguez, J., and Foley, W. J. (2016). Near infrared spectroscopy in wildlife and biodiversity. Journal of Near Infrared Spectroscopy 24, 1–25.
Near infrared spectroscopy in wildlife and biodiversity.Crossref | GoogleScholarGoogle Scholar |

Wedding, B. B., Forrest, A. J., Wright, C., Grauf, S., Exley, P., and Poole, S. E. (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 |

Wold, S., Ruhe, A., Wold, H., and Dunn, W. J. (1984). The collinearity problem in linear regression. The Partial least squares (PLS) approach to generalized inverses. Society for Industrial and Applied Mathematics 5, 735–743.
The collinearity problem in linear regression. The Partial least squares (PLS) approach to generalized inverses.Crossref | GoogleScholarGoogle Scholar |

Wright, C., Wedding, B. B., Grauf, S., and Whybird, O. J. (2021). Age estimation of barramundi (Lates calcarifer) over multiple seasons from the southern Gulf of Carpentaria using FT-NIR spectroscopy. Marine and Freshwater Research 72, 12–34.