Identification of fish families and species from the western Arabian Gulf by otolith shape analysis and factors affecting the identification process
Yu-Jia Lin A C and Khaled Al-Abdulkader B
+ Author Affiliations
- Author Affiliations
A Marine Studies Section, Center for Environment and Waters, Research Institute, King Fahd University of Petroleum and Minerals, Dhahran 31261, Eastern Province, Kingdom of Saudi Arabia.
B Environmental Protection Department, Saudi Aramco, Dhahran 31261, Eastern Province, Kingdom of Saudi Arabia.
C Corresponding author. Email: yjlin@mail.com; yjlin@kfupm.edu.sa
Marine and Freshwater Research 70(12) 1818-1827 https://doi.org/10.1071/MF18282
Submitted: 1 August 2018 Accepted: 2 April 2019 Published: 3 July 2019
Journal Compilation © CSIRO 2019 Open Access CC BY-NC-ND
Abstract
Otolith shape analysis was used to identify 16 fish species belong to 5 families from the western Arabian Gulf to construct a cost-effective method of delineating fish taxonomic groups. We further tested the factors potentially affecting the identification process, including using different dataset sources, sex, the number of candidate species, different sample sizes and different sampling procedures. No specific dataset outperformed any other in the identification of fish families and species. Using all data sources yielded the best performance. Otolith shape parameters were significantly affected by somatic length, but not by sex. The correct prediction rate declined as the number of candidate species increased. An insufficient sample size led to a reduction in correct prediction rates with increased variability. The effects of size-biased sampling were species specific and could greatly reduce the correct prediction rate if the species of interest exhibits strong allometric changes in otolith shape. Having multiple sources of data, information a priori to reduce the number of candidate species and sufficiently large sample sizes across wide size classes so as to include possible variations in otolith shape are key to the precise identification of fish families and species using otolith shape analysis.
Additional keywords: linear discriminant analysis, sampling procedure, species identification, wavelet transformation.
References
Amir, S. A., Siddiqui, P. J. A., and Masroor, R. (2014). A new sparid fish of genus Sparidentex (Perciformes: Sparidae) from coastal waters of Pakistan (North Western Indian Ocean). Pakistan Journal of Zoology 46, 471–477.Anderson, M. J., and Willis, T. J. (2003). Canonical analysis of principal coordinates: a useful method of constrained ordination for ecology. Ecology 84, 511–525.
| Canonical analysis of principal coordinates: a useful method of constrained ordination for ecology.Crossref | GoogleScholarGoogle Scholar |
Beech, M. J. (2001). In the land of the ichthyophagi: modelling fish exploitation in the Arabian Gulf and Gulf of Oman from the 5th millennium BC to the Late Islamic period. Ph.D. Thesis, University of York, York, UK.
Begg, G., Overholtz, W. J., and Munroe, N. J. (2000). The use of internal otolith morphometrics for identification of haddock (Melanogramus aeglefinus) stocks on Georges Bank. Fishery Bulletin 99, 1–14.
Cardinale, M., Doering-Arjes, P., Kastowsky, M., and Mosegaard, H. (2004). Effects of sex, stock, and environment on the shape of known-age Atlantic cod (Gadus morhua) otoliths. Canadian Journal of Fisheries and Aquatic Sciences 61, 158–167.
| Effects of sex, stock, and environment on the shape of known-age Atlantic cod (Gadus morhua) otoliths.Crossref | GoogleScholarGoogle Scholar |
Carpenter, K. E., Krupp, F., Jones, D. A., and Zajonz, U. (1997). ‘FAO Species Identification Guide for Fishery Purposes. The Living Marine Resources of Kuwait, Eastern Saudi Arabia, Bahrain, Qatar, and the United Arab Emirates.’ (Food and Agriculture Organization of the United Nations: Rome, Italy.)
Chen, K. Y., Marschall, E. A., Sovic, M. G., Fries, A. C., Gibbs, H. L., and Ludsin, S. A. (2018). assignPOP: an R package for population assignment using genetic, non‐genetic, or integrated data in a machine‐learning framework. Methods in Ecology and Evolution 9, 439–446.
| assignPOP: an R package for population assignment using genetic, non‐genetic, or integrated data in a machine‐learning framework.Crossref | GoogleScholarGoogle Scholar |
Cruz, A., and Lombarte, A. (2004). Otolith size and its relationship with colour patterns and sound production. Journal of Fish Biology 65, 1512–1525.
| Otolith size and its relationship with colour patterns and sound production.Crossref | GoogleScholarGoogle Scholar |
Frisch, A. (2004). Sex-change and gonadal steroids in sequentially hermaphroditic teleost fish. Reviews in Fish Biology and Fisheries 14, 481–499.
| Sex-change and gonadal steroids in sequentially hermaphroditic teleost fish.Crossref | GoogleScholarGoogle Scholar |
Girone, A., and Nolf, D. (2009). Fish otoliths from the Priabonian (Late Eocene) of north Italy and south-east France – their paleobiogeographical significance. Revue de Icropaléontologie 52, 195–218.
| Fish otoliths from the Priabonian (Late Eocene) of north Italy and south-east France – their paleobiogeographical significance.Crossref | GoogleScholarGoogle Scholar |
Iwatsuki, Y. (2013). Review of the Acanthopagrus latus complex (Perciformes: Sparidae) with descriptions of three new species from the Indo‐West Pacific Ocean. Journal of Fish Biology 83, 64–95.
| Review of the Acanthopagrus latus complex (Perciformes: Sparidae) with descriptions of three new species from the Indo‐West Pacific Ocean.Crossref | GoogleScholarGoogle Scholar | 23808693PubMed |
Libungan, L. A., and Pálsson, S. (2015). ShapeR: an R package to study otolith shape variation among fish populations. PLoS One 10, e0121102.
| ShapeR: an R package to study otolith shape variation among fish populations.Crossref | GoogleScholarGoogle Scholar | 26101885PubMed |
Lin, C. H., and Chang, C. W. (2012). ‘Otolith Atlas of Taiwan Fishes.’ (National Museum of Marine Biology and Aquarium: Checheng, Taiwan.)
Lin, C. H., Girone, A., and Nolf, D. (2015). Tortonian fish otoliths from turbiditic deposits in northern Italy: taxonomic and stratigraphic significance. Geobios 48, 249–261.
| Tortonian fish otoliths from turbiditic deposits in northern Italy: taxonomic and stratigraphic significance.Crossref | GoogleScholarGoogle Scholar |
Lin, C. H., Girone, A., and Nolf, D. (2016). Fish otolith assemblages from Recent NE Atlantic sea bottoms: a comparative study of palaeoecology. Palaeogeography, Palaeoclimatology, Palaeoecology 446, 98–107.
| Fish otolith assemblages from Recent NE Atlantic sea bottoms: a comparative study of palaeoecology.Crossref | GoogleScholarGoogle Scholar |
Lombarte, A., and Cruz, A. (2007). Otolith size trends in marine fish communities from different depth strata. Journal of Fish Biology 71, 53–76.
| Otolith size trends in marine fish communities from different depth strata.Crossref | GoogleScholarGoogle Scholar |
Lombarte, A., Chic, Ò., Parisi-Baradad, V., Olivella, R., Piera, J., and García-Ladona, E. (2006). A web-based environment for shape analysis of fish otoliths. The AFORO database. Scientia Marina 70, 147–152.
| A web-based environment for shape analysis of fish otoliths. The AFORO database.Crossref | GoogleScholarGoogle Scholar |
Lombarte, A., Miletić, M., Kovačić, M., Otero‐Ferrer, J. L., and Tuset, V. M. (2018). Identifying sagittal otoliths of Mediterranean Sea gobies: variability among phylogenetic lineages. Journal of Fish Biology 92, 1768–1787.
| Identifying sagittal otoliths of Mediterranean Sea gobies: variability among phylogenetic lineages.Crossref | GoogleScholarGoogle Scholar | 29756341PubMed |
Lord, C., Morat, F., Lecomte-Finiger, R., and Keith, P. (2012). Otolith shape analysis for three Sicyopterus (Teleostei: Gobioidei: Sicydiinae) species from New Caledonia and Vanuatu. Environmental Biology of Fishes 93, 209–222.
| Otolith shape analysis for three Sicyopterus (Teleostei: Gobioidei: Sicydiinae) species from New Caledonia and Vanuatu.Crossref | GoogleScholarGoogle Scholar |
Monteiro, L. R., Di Beneditto, A. P. M., Guillermo, L. H., and Rivera, L. A. (2005). Allometric changes and shape differentiation of sagitta otoliths in sciaenid fishes. Fisheries Research 74, 288–299.
| Allometric changes and shape differentiation of sagitta otoliths in sciaenid fishes.Crossref | GoogleScholarGoogle Scholar |
Nolf, D. (2013). ‘The Diversity of Fish Otoliths, Past and Present.’ (Royal Belgian Institute of Natural Sciences: Brussels, Belgium.)
Ponton, D. (2006). Is geometric morphometrics efficient for comparing otolith shape of different fish species? Journal of Morphology 267, 750–757.
| Is geometric morphometrics efficient for comparing otolith shape of different fish species?Crossref | GoogleScholarGoogle Scholar | 16526058PubMed |
Rabaoui, L., Lin, Y. J., Qurban, M. A., Maneja, R. H., Franco, J., Joydas, T. V., Panickan, P., Al-Abdulkader, K., and Roa-Ureta, R. H. (2015). Patchwork of oil and gas facilities in Saudi waters of the Arabian Gulf has the potential to enhance local fisheries production. ICES Journal of Marine Science 72, 2398–2408.
| Patchwork of oil and gas facilities in Saudi waters of the Arabian Gulf has the potential to enhance local fisheries production.Crossref | GoogleScholarGoogle Scholar |
Rabaoui, L., Lin, Y. J., Maneja, R. H., Qurban, M. A., Abdurahiman, P., Premlal, P., Al-Abdulkader, K., and Roa-Ureta, R. H. (2017). Nursery habitats and life history traits of the green tiger shrimp Penaeus semisulcatus (De Haan, 1844) in the Saudi waters of the Arabian Gulf. Fisheries Research 195, 1–11.
| Nursery habitats and life history traits of the green tiger shrimp Penaeus semisulcatus (De Haan, 1844) in the Saudi waters of the Arabian Gulf.Crossref | GoogleScholarGoogle Scholar |
Salimi, N., Loh, K. H., Dhillon, S. K., and Chong, V. C. (2016). Fully automated identification of fish species based on otolith contour: using short-time Fourier transform and discriminant analysis (STFT-DA). PeerJ 4, e1664.
| Fully automated identification of fish species based on otolith contour: using short-time Fourier transform and discriminant analysis (STFT-DA).Crossref | GoogleScholarGoogle Scholar | 26925315PubMed |
Tuset, V. M., Lozano, I. J., González, J. A., Pertusa, J. F., and García‐Díaz, M. M. (2003). Shape indices to identify regional differences in otolith morphology of comber, Serranus cabrilla (L., 1758). Journal of Applied Ichthyology 19, 88–93.
| Shape indices to identify regional differences in otolith morphology of comber, Serranus cabrilla (L., 1758).Crossref | GoogleScholarGoogle Scholar |
Tuset, V. M., Lombarte, A., and Assis, C. A. (2008). Otolith atlas for the western Mediterranean, north and central eastern Atlantic. Scientia Marina 72, 7–198.
| Otolith atlas for the western Mediterranean, north and central eastern Atlantic.Crossref | GoogleScholarGoogle Scholar |
Tuset, V. M., Farré, M., Otero-Ferrer, J. L., Vilar, A., Morales-Nin, B., and Lombarte, A. (2016). Testing otolith morphology for measuring marine fish biodiversity. Marine and Freshwater Research 67, 1037–1048.
| Testing otolith morphology for measuring marine fish biodiversity.Crossref | GoogleScholarGoogle Scholar |
Venables, W. N., and Ripley, B. D. (2002). ‘Modern Applied Statistics with S’, 4th edn. (Springer: New York, NY, USA.)
Vignon, M. (2012). Ontogenetic trajectories of otolith shape during shift in habitat use: interaction between otolith growth and environment. Journal of Experimental Marine Biology and Ecology 420–421, 26–32.
| Ontogenetic trajectories of otolith shape during shift in habitat use: interaction between otolith growth and environment.Crossref | GoogleScholarGoogle Scholar |
Wakefield, C. B., Williams, A. J., Newman, S. J., Bunel, M., Dowling, C. E., Armstrong, C. A., and Langlois, T. J. (2014). Rapid and reliable multivariate discrimination for two cryptic eteline snappers using otolith morphometry. Fisheries Research 151, 100–106.
| Rapid and reliable multivariate discrimination for two cryptic eteline snappers using otolith morphometry.Crossref | GoogleScholarGoogle Scholar |
