Molecular evidence of three species in the Pseudocaranx dentex complex (Carangidae) in Australian waters
Douglas Bearham
A E , Myrto Robert B , Jennifer A. Chaplin B , Glenn I. Moore C , David V. Fairclough D and Andrea Bertram D
+ Author Affiliations
- Author Affiliations
A CSIRO Oceans and Atmosphere Flagship, Private Bag 5, Wembley, WA 6913, Australia.
B Centre for Fish and Fisheries Research, Veterinary and Life Sciences, Murdoch University, South Street, Murdoch, WA 6150, Australia.
C Fish Section, Department of Aquatic Zoology, Western Australian Museum, 49 Kew Street, Welshpool, WA 6106, Australia.
D Department of Primary Industries and Regional Development, Fisheries Division, Government of Western Australia, PO Box 20, North Beach, WA 6920, Australia.
E Corresponding author. Email: douglas.bearham@csiro.au
Marine and Freshwater Research 71(4) 518-531 https://doi.org/10.1071/MF18445
Submitted: 20 November 2018 Accepted: 4 June 2019 Published: 6 September 2019
Abstract
The discovery and identification of species is fundamental to the documentation, conservation and management of biodiversity. The taxonomy of the antitropical Pseudocaranx dentex complex (Carangidae) is confused and inconsistently reported. Previous morphological analyses concluded that this complex consisted of three species, namely P. sp. ‘dentex’, P. georgianus and P. dinjerra, in Australian waters. This study used genetic (COI sequence) and morphological data to evaluate the validity of this conclusion. The COI data showed the presence of three discrete lineages within this complex, which appear to correspond to the above-mentioned three species. They also suggested that P. sp. ‘dentex’ is closely related to, and possibly the same species as, P. dentex from southern Africa and the Mediterranean Sea. Also, the extent of morphological and geographical overlap between P. georgianus and P. dinjerra was greater than previously documented which, uncorrected, could lead to identification errors and present challenges for monitoring and management of harvested stocks of these species. By answering important taxonomic questions, our results will facilitate the proper interpretation of the results of past studies and the design of future studies of the P. dentex complex. They have also highlighted the value of molecular data for identifying species in morphologically conservative taxa.
References
Asgharian, H., Sahafi, H. H., Ardalan, A. A., Shekarriz, S., and Elahi, E. (2011). Cytochrome c oxidase subunit 1 barcode data of fish of the Nayband National Park in the Persian Gulf and analysis using meta-data flag several cryptic species. Molecular Ecology Resources 11, 461–472.| Cytochrome c oxidase subunit 1 barcode data of fish of the Nayband National Park in the Persian Gulf and analysis using meta-data flag several cryptic species.Crossref | GoogleScholarGoogle Scholar | 21481204PubMed |
Australian Biological Resources Study (2018). Australian Faunal Directory. (ABRS: Canberra, ACT, Australia.) Available at http://www.environment.gov.au/biodiversity/abrs/online-resources/fauna/afd/index.html [accessed 16 November 2018].
Bleeker, P. (1863). Mémoire sur les poissons de la côte de Guinée. Natuurkundige Verhandelingen van de Hollandsche Maatschappij der Wetenschappen te Haarlem (Series 2) 18, 1–136.
Bloch, M. E., and Schneider, J. G. (1801). ‘M. E. Blochii, Systema Ichthyologiae Iconibus cx Ilustratum. Post obitum auctoris opus inchoatum absolvit, correxit, interpolavit Jo. Gottlob Schneider, Saxo.’ (Sumtibus Auctoris Impressum et Bibliopolio Sanderiano Commissum: Berolini, Germany)
Cadrin, S. X., Friedland, K. D., and Waldman, J. R. (2005). Chapter 1. Stock identification methods: an overview. In ‘Stock Identification Methods: Applications in Fishery Science’. (Eds S. X. Cadrin, K. D. Friedland, J. R. Waldman, L. A. Kerr and J. Mariani.) pp. 1–5. (Elsevier Academic Press: London, UK.)
Cao, X. W., Liu, J., Chen, J., Zheng, G., Kuntner, M., and Agnarsson, I. (2016). Rapid dissemination of taxonomic discoveries based on DNA barcoding and morphology. Scientific Reports 6, 37 066.
| Rapid dissemination of taxonomic discoveries based on DNA barcoding and morphology.Crossref | GoogleScholarGoogle Scholar |
Chick, R., Roelofs, A., Green, C., Fairclough, D. V., Stewart, J., Georgeson, L., and Emery, T. (2016). Silver trevally Pseudocaranx georgianus, Pseudocaranx sp. ‘dentex’ & Pseudocaranx wrighti. Status of Australian Fish Stocks Reports. (Fisheries Research and Development Corporation: Canberra, ACT, Australia.) Available at http://www.fish.gov.au/report/58-Silver-Trevally-2016 [accessed 16 November 2018].
Darriba, D., Taboada, G. L., Doallo, R., and Posada, D. (2012). jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9, 772.
| jModelTest 2: more models, new heuristics and parallel computing.Crossref | GoogleScholarGoogle Scholar | 22847109PubMed |
DeWalt, R. (2011). DNA barcoding: a taxonomic point of view. Journal of the North American Benthological Society 30, 174–181.
| DNA barcoding: a taxonomic point of view.Crossref | GoogleScholarGoogle Scholar |
Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32, 1792–1797.
| MUSCLE: multiple sequence alignment with high accuracy and high throughput.Crossref | GoogleScholarGoogle Scholar | 15034147PubMed |
Farmer, B. M., French, D. J. W., Potter, I. C., Hesp, S. A., and Hall, N. G. (2005). Determination of biological parameters for managing the fisheries for mulloway and silver trevally in Western Australia. FRDC project number 2002/004, Centre for Fish and Fisheries Research, Murdoch University, Perth, WA, Australia.
Feng, M., McPhaden, M. J., Xie, S., and Hafner, J. (2013). La Niña forces unprecedented Leeuwin Current warming in 2011. Scientific Reports 3, 1277.
| La Niña forces unprecedented Leeuwin Current warming in 2011.Crossref | GoogleScholarGoogle Scholar | 23429502PubMed |
Fricke, R., Eschmeyer, W. N., and Laan, V. D. (2018). Catalog of fishes: genera, species, references. Available at http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp [Verified 16 November 2018].
Gardner, S. N., and Hall, B. G. (2013). When whole-genome alignments just won’t work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes. PLoS One 8, e81760.
| When whole-genome alignments just won’t work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes.Crossref | GoogleScholarGoogle Scholar | 24349125PubMed |
Gaughan, D. J., and Santoro, K. (Eds) (2018). Status reports of the fisheries and aquatic resources of Western Australia 2016/17: state of the fisheries. Department of Primary Industries and Regional Development, Perth, WA, Australia. Available at http://www.fish.wa.gov.au/Documents/sofar/status_reports_of_the_fisheries_and_aquatic_resources_2016-17.pdf [Verified 16 November 2018].
Guichenot, A. (1848). Fauna Chilena. Peces. In ‘Historia fisica y politica de Chile’. (Ed. C. Gay.) pp. 137–370. (Zoología: Santiago, Chile.)
Gunn, J. S. (1990). A revision of selected genera of the family Carangidae (Pisces) from Australian waters. Records of the Australian Museum 12, 1–77.
| A revision of selected genera of the family Carangidae (Pisces) from Australian waters.Crossref | GoogleScholarGoogle Scholar |
Hasegawa, M., Kishino, H., and Yano, T. (1985). Dating of human-ape splitting by a molecular clock of mitochiondrial DNA. Journal of Molecular Evolution 22, 160–174.
| Dating of human-ape splitting by a molecular clock of mitochiondrial DNA.Crossref | GoogleScholarGoogle Scholar | 3934395PubMed |
Hubert, N., and Hanner, R. (2015). DNA barcoding, species delineation and taxonomy: a historical perspective. DNA Barcodes 3, 44–58.
| DNA barcoding, species delineation and taxonomy: a historical perspective.Crossref | GoogleScholarGoogle Scholar |
Jordaan, A., Hayhurst, S. E., and Kling, L. J. (2006). The influence of temperature on the stage at hatch of laboratory reared Gadus morhua and implications for comparisons of length and morphology. Journal of Fish Biology 68, 7–24.
| The influence of temperature on the stage at hatch of laboratory reared Gadus morhua and implications for comparisons of length and morphology.Crossref | GoogleScholarGoogle Scholar |
Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparitive studies of nucleotide sequences. Journal of Molecular Evolution 16, 111–120.
| A simple method for estimating evolutionary rates of base substitutions through comparitive studies of nucleotide sequences.Crossref | GoogleScholarGoogle Scholar | 7463489PubMed |
Korwin-Kossakowski, M. (2008). The influence of temperature during the embryonic period on larval growth and development in carp, Cyprinus caprio L., and grass carp, Ctenopharyngodon idella (Val.): theoretical and practical aspects. Archives of Polish Fisheries 16, 231–314.
| The influence of temperature during the embryonic period on larval growth and development in carp, Cyprinus caprio L., and grass carp, Ctenopharyngodon idella (Val.): theoretical and practical aspects.Crossref | GoogleScholarGoogle Scholar |
Kumar, S., Stecher, G., and Tamura, K. (2016). MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33, 1870–1874.
| MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets.Crossref | GoogleScholarGoogle Scholar | 27004904PubMed |
Lenanton, R. C. J., Dowling, C. E., Smith, K. A., Fairclough, D. V., and Jackson, G. (2017). Potential influence of a marine heatwave on range extensions of tropical fishes in the eastern Indian Ocean: invaluable contributions from amateur observers. Regional Studies in Marine Science 13, 19–31.
| Potential influence of a marine heatwave on range extensions of tropical fishes in the eastern Indian Ocean: invaluable contributions from amateur observers.Crossref | GoogleScholarGoogle Scholar |
Lewis, P. O. (2001). A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology 50, 913–925.
| A likelihood approach to estimating phylogeny from discrete morphological character data.Crossref | GoogleScholarGoogle Scholar | 12116640PubMed |
Liu, J., Jiang, J., Song, S., Tornabene, L., Chabarria, R., Naylor, G. J. P., and Li, C. (2017). Multi-locus DNA barcoding: species identification with multilocus data. Scientific Reports 7, 16601.
| Multi-locus DNA barcoding: species identification with multilocus data.Crossref | GoogleScholarGoogle Scholar | 29192249PubMed |
Mallo, D., and Posada, D. (2016). Multilocus inference of species trees and DNA barcoding. Philosophical Transactions of the Royal Society of London – B. Biological Sciences 371, 20150335.
| Multilocus inference of species trees and DNA barcoding.Crossref | GoogleScholarGoogle Scholar | 27481787PubMed |
Mat Jaafar, T. N. A., Taylor, M. I., Nor, S. A. M., Bruyn, M. D., and Carvalho, G. R. (2012). DNA barcoding reveals cryptic diversity within commercially exploited Indo-Malay Carangidae (Teleosteii: Perciformes). PLoS One 7, e49623.
| DNA barcoding reveals cryptic diversity within commercially exploited Indo-Malay Carangidae (Teleosteii: Perciformes).Crossref | GoogleScholarGoogle Scholar |
Nei, M., and Kumar, S. (2000) ‘Molecular Evolution and Phylogenetics.’ (Oxford University Press: Oxford, UK.)
Osterhage, D., Pogonoski, J. J., Appleyard, S. A., and White, W. T. (2016). Integrated taxonomy reveals hidden diversity in northern Australian fishes: a new species of seamoth (genus Pegasus). PLoS One 11, e0149415.
| Integrated taxonomy reveals hidden diversity in northern Australian fishes: a new species of seamoth (genus Pegasus).Crossref | GoogleScholarGoogle Scholar | 26934529PubMed |
Ovenden, J. R., Berry, O., Welch, D. J., Buckworth, R. C., and Dichmont, C. M. (2015). Ocean’s eleven: a critical evaluation of the role of population, evolutionary and molecular genetics in the management of wild fisheries. Fish and Fisheries 16, 125–159.
| Ocean’s eleven: a critical evaluation of the role of population, evolutionary and molecular genetics in the management of wild fisheries.Crossref | GoogleScholarGoogle Scholar |
Reed, D. L., Carpenter, K. E., and deGravelle, M. J. (2002). Molecular systematics of the Jacks (Perciformes: Carangidae) based on mitochondrial cytochrome b sequences using parsimony, likelihood, and Bayesian approaches. Molecular Phylogenetics and Evolution 23, 513–524.
| Molecular systematics of the Jacks (Perciformes: Carangidae) based on mitochondrial cytochrome b sequences using parsimony, likelihood, and Bayesian approaches.Crossref | GoogleScholarGoogle Scholar | 12099802PubMed |
Robinson, E. A., Blagoev, G. A., Hebert, P. D. N., and Adamowicz, S. J. (2009). Prospects for using DNA barcoding to identify spiders in species-rich genera. ZooKeys 16, 27–46.
| Prospects for using DNA barcoding to identify spiders in species-rich genera.Crossref | GoogleScholarGoogle Scholar |
Ryan, K. L., Hall, N. G., Lai, E. K., Smallwood, C. B., Taylor, S. M., and Wise, B. S. (2017). Statewide survey of boat-based recreational fishing in Western Australia 2015/16. Fisheries Research Report number 287. (Department of Primary Industries and Regional Development: Perth, WA, Australia.) Available at http://www.fish.wa.gov.au/Documents/research_reports/frr287.pdf [Verified 16 November 2018].
Scacco, U., La Mesa, G., and Vacchi, M. (2010). Body morphometrics, swimming diversity and niche in demersal sharks: a comparative case study from the Mediterranean Sea. Scientia Marina 74, 37–53.
| Body morphometrics, swimming diversity and niche in demersal sharks: a comparative case study from the Mediterranean Sea.Crossref | GoogleScholarGoogle Scholar |
Sfakianakis, D. G., Leris, I., Laggis, A., and Kentouri, M. (2011). The effect of rearing temperature on body shape and meristic characters in zebrafish (Danio rerio) juveniles. Environmental Biology of Fishes 92, 197–205.
| The effect of rearing temperature on body shape and meristic characters in zebrafish (Danio rerio) juveniles.Crossref | GoogleScholarGoogle Scholar |
Smallwood, C. B., Hesp, S. A., and Beckley, L. E. (2013). Biology, stock status and management summaries for selected fish species in south-western Australia. Fisheries Research Report number 242. Western Australian Department of Fisheries, Perth, WA, Australia. Available at http://www.fish.wa.gov.au/About-Us/Publications/Pages/Fisheries-Research-Reports.aspx [Verified 16 November 2018].
Smith, P. I., Steinke, D., McMillian, P. J., Stewart, A., McVeagh, S. M., Diaz de Astalroa, J. M., Welsford, D., and Ward, R. D. (2011). DNA barcoding highlights a cryptic species of grenadier Macrourus in the Southern Ocean. Journal of Fish Biology 78, 355–365.
| DNA barcoding highlights a cryptic species of grenadier Macrourus in the Southern Ocean.Crossref | GoogleScholarGoogle Scholar |
Smith-Vaniz, W. F., and Jelks, H. L. (2006). Australian trevallies of the genus Pseudocaranx (Teleostei: Carangidae), with description of a new species from Western Australia. Memoirs of the Museum of Victoria 63, 97–106.
| Australian trevallies of the genus Pseudocaranx (Teleostei: Carangidae), with description of a new species from Western Australia.Crossref | GoogleScholarGoogle Scholar |
Strauss, R. E., and Bond, C. E. (1990). Taxonomic methods: morphology. In ‘Methods for Fish Biology’. (Eds C. B. Schreck and P. B. Moyle.) pp. 109–140. (American Fisheries Society: Bethesda, MD, USA.)
Tamura, K., Peterson, D., Peterson, N., Stecher, G., and Nei, M. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28, 2731–2739.
| MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.Crossref | GoogleScholarGoogle Scholar | 21546353PubMed |
Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R., and Herbert, P. D. N. (2005). DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society of London – B. Biological Sciences 360, 1847–1857.
| DNA barcoding Australia’s fish species.Crossref | GoogleScholarGoogle Scholar | 16214743PubMed |
Ward, R. D., Hanner, R., and Hebert, P. D. N. (2009). The campaign to DNA barcode all fishes, FISH-BOL. Journal of Fish Biology 74, 329–356.
| The campaign to DNA barcode all fishes, FISH-BOL.Crossref | GoogleScholarGoogle Scholar | 20735564PubMed |
Whitley, G. P. (1931). New names for Australian fishes. Australian Zoologist 6, 310–334.
Zemlak, T. S., Ward, R. D., Connell, A. D., Holmes, B. H., and Herbert, P. D. N. (2009). DNA barcoding reveals overlooked marine fishes. Molecular Ecology Resources 9, 237–242.
| DNA barcoding reveals overlooked marine fishes.Crossref | GoogleScholarGoogle Scholar | 21564983PubMed |
Zhang, J., and Hanner, R. (2012). Molecular approach to the identification of fish in the South China Sea. PLoS One 7, e30621.
| Molecular approach to the identification of fish in the South China Sea.Crossref | GoogleScholarGoogle Scholar | 23300923PubMed |
