DNA barcoding of marine fishes from Saudi Arabian waters of the Gulf.
Indo-Pacific Ocean
Saudi Arabia
biodiversity assessment
ichtyofauna
molecular species delimitation
Journal
Journal of fish biology
ISSN: 1095-8649
Titre abrégé: J Fish Biol
Pays: England
ID NLM: 0214055
Informations de publication
Date de publication:
Nov 2019
Nov 2019
Historique:
received:
18
03
2019
accepted:
29
08
2019
pubmed:
31
8
2019
medline:
17
3
2020
entrez:
31
8
2019
Statut:
ppublish
Résumé
We used the cytochrome oxidase subunit I (coI) gene DNA to barcode 117 endemic Gulf and cosmopolitan Indo-West Pacific fish species belonging to 54 families and 13 orders. Novel DNA barcodes were provided for 18 fish species (Trachinocephalus sp., Nematalosa sp., Herklotsichthys lossei, Upeneus doriae, Trachurus indicus, Apogonichthyoides taeniatus, Verulux cypselurus, Favonigobius sp., Suezichthus gracilis, Sillago sp., Brachirus orientalis, Pegusa sp., Lepidotrigla bispinosa, Lepidotrigla sp., Grammoplites suppositus, Hippichthys sp., Paramonacanthus sp. and Triacanthus sp.). The species delimitation analysis, conducted with Poisson tree processes- Bayesian PTP (PTP-bPTP) and nucleotide-divergence-threshold (NDT) models), found 137 and 119 entities respectively. Overall, NDT method, neighbour-joining species tree and the prior taxonomic assessment provided similar results. Among the 54 families considered, only 10 (Ariommatidae, Ephippidae, Leiognathidae, Nemipteridae, Plotosidae, Pomacanthidae, Pomacentridae, Priacanthidae and Rachycentridae) showed the occurrence of molecular diagnostic pure characters. The DNA barcoding database developed during this study will help ichthyologists to identify and resolve the taxonomic ambiguities they may encounter with the fishes occurring in The Gulf and throughout the region.
Substances chimiques
Electron Transport Complex IV
EC 1.9.3.1
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1286-1297Subventions
Organisme : Water, Research Institute, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
Informations de copyright
© 2019 The Fisheries Society of the British Isles.
Références
Appeltans, W., Ahyong, S. T., Anderson, G., Angel, M. V., Artois, T., Bailly, N., … Costello, M. J. (2012). The magnitude of global marine species diversity. Current Biology, 22, 2189-2202.
Bariche, M., Torres, M., Smith, C., Sayar, N., Azzurro, E., Baker, R., & Bernardi, G. (2015). Red Sea fishes in the Mediterranean Sea: A preliminary investigation of a biological invasion using DNA barcoding. Journal of Biogeography, 42, 2363-2373.
Beech, M. J. (2004). In the land of Ichthyophagi: Modelling fish exploitation in The Gulf and Gulf of Oman from the 5th millennium B.C. to the Late Islamic period. Oxford: Archeopress.
Bingpeng, X., Heshan, L., Zhilan, Z., Chunguang, W., Yanguo, W., & Jianjun, W. (2018). DNA barcoding for identification of fish species in the Taiwan Strait. PLoS One, 13(6), e0198109. https://doi.org/10.1371/journal.pone.0198109.
Brewer, P. G., A. P. Fleer, D. K. Shafer & C. L. Smith, 1987. Chemical oceanographic data from the Persian Gulf and Gulf of Oman, WHOI Technical Report WHOI-78-37. 105 pp.
Brown, S. D. J., Collins, R. A., Boyer, S., Lefort, M.-C., Malumbres-Olarte, J., Vink, C. J., & Cruickshank, R. H. (2012). Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding. Molecular Ecology Resources, 12, 562-565.
Carpenter, K. E., Krupp, F., Jones, D. A., & Zajonz, U. (1997). FAO species identification field guide for fishery purposes. The living marine resources of Kuwait, Eastern Saudi Arabia, Bahrain, Qatar and The United Arab Emirates. Rome: FAO.
Clark, P. U., Dyke, A. S., Shakun, J. D., Carlson, A. E., Clark, J., Wohlfarth, B., … McCabe, A. M. (2009). The last glacial maximum. Science, 325, 710-714.
Emery, K. O. (1956). Sediments and water of the Persian Gulf. The American Association of Petroleum Geologists Bulletin, 40, 2354-2383.
Fischer, W., & Bianchi, G. (1984). FAO species identification sheets for fishery purposes. Western Indian Ocean (fishing area 51). Prepared and printed with the support of the Danish International Development Agency (DANIDA) (Vol. 1-6). Rome: FAO.
Grandcourt, E. (2012). Reef fish and fisheries in the Gulf. In B. M. Riegl & S. J. Purkis (Eds.), Coral reefs of the Gulf: Adaptation to climatic extremes (Vol. 3, pp. 127-161). Netherlands: Springer.
Hajibabaei, M., deWaard, J. R., Ivanova, N. V., Ratnasingham, S., Dooh, R. T., Kirk, S. L., … Hebert, P. D. N. (2005). Critical factors for assembling a high volume of DNA barcodes. Philosophical Transactions of the Royal Society B, 360, 1959-1967.
Hanebuth, T. J. J., Stattegger, K., & Bojanowski, A. (2009). Termination of the last glacial maximum sea level lowstand: The Sunda-Shelf data revisited. Global and Planetary Change, 66, 76-84.
Hebert, P. D. N., Cywinska, A., Ball, S. L., & de Ward, J. R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society B, 270, 313-322.
Hebert, P. D. N., Penton, E. H., Burns, J. M., Janzen, D. H., & Hallwachs, W. (2004a). Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences of the United States of America, 101, 14812-14817.
Hebert, P. D. N., Stoeckle, M. Y., Zemlak, T. S., & Francis, C. M. (2004b). Identification of birds through DNA barcodes. PLoS One, 2, 1657-1663.
Hogg, I. D., & Hebert, P. D. N. (2004). Biological identification of springtails (Collembola: Hexapoda) from the Canadian Arctic, using mitochondrial DNA barcodes. Canadian Journal of Zoology, 82, 749-754.
Hubert, N., Hanner, R., Holm, E., Mandrak, N. E., & Taylor, E. (2008). Identifying Canadian freshwater fishes through DNA barcodes. PLoS One, 3, e2490.
Hunter, J. R. (1983). Aspects of the dynamics of the residual circulation of the Arabian Gulf. In H. G. Gade, A. Edwards, & H. Svendson (Eds.), Coastal oceanography (pp. 31-42). New York: Plenum.
Isari, S., Pearman, J. K., Casas, L., Michell, C. T., Curdia, J., Berumen, M. L., & Irigoien, X. (2017). Exploring the larval fish community of the central Red Sea with an integrated morphological and molecular approach. PLoS One, 12(8), e0182503.
Jörger, K. M., & Schrödl, M. (2013). How to describe a cryptic species? Practical challenges of molecular taxonomy. Frontiers in Zoology, 10, 59.
Keskin, E., & Atar, H. H. (2013). DNA barcoding commercially important fish species of Turkey. Molecular Ecology Resources, 13, 788-797.
Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111-120.
Krupp, F., Almarri, M., Zajonz, U., Carpenter, K. E., Almatar, S., & Zetzsche, H. (2000). Twelve new records of fishes from the Gulf. Fauna of Arabia, 18, 323-335.
Lakra, W. S., Goswami, M., & Gopalakrishnan, A. (2009). Molecular identification and phylogenetic relationships of seven Indian Sciaenids (Pisces: Perciformes, Sciaenidae) based on 16S rRNA and cytochrome oxidase subunit I mitochondrial genes. Molecular Biology Reports, 36, 831-839.
Lakra, W. S., Verma, M. S., Goswami, M., Lal, K. K., Mohindra, V., Punia, P., … Hebert, P. (2011). DNA barcoding Indian marine fishes. Molecular Ecology Resources, 11, 60-71.
Lambeck, K. (1996). Shoreline reconstructions for the Persian Gulf since the last glacial maximum. Earth and Planetary Science Letters, 142, 43-57.
Landi, M., Dimech, M., Arculeo, M., Biondo, G., Martins, R., Corneiro, M., … Costa, F. O. (2014). DNA Barcoding for species assignment: The case of Mediterranean marine fishes. PLoS One, 9(9), e106135.
Lara, A., de Leon, J. L. P., Rodriguez, R., Casane, D., Cote, G., Bernatchez, L., et al. (2010). DNA barcoding of Cuban freshwater fishes: Evidence for cryptic species and taxonomic conflicts. Molecular Ecology Resources, 10(3), 421-430.
Malakar, A. K., Lakra, W. S., Goswami, M., Singh, M., & Mishra, R. M. (2012). Molecular identification of three Ompok species using mitochondrial coI gene. Mitochondrial DNA, 23(1), 20-24.
Moritz, C., & Cicero, C. (2004). DNA barcoding: Promise and pitfalls. PLoS One, 2, e354.
Paradis, E., Claude, J., & Strimmer, K. (2004). APE: Analyses of phylogenetics and evolution in R language. Bioinformatics, 20(2), 289-290. https://doi.org/10.1093/bioinformatics/btg412.
Peltier, W. R., & Fairbanks, R. G. (2006). Global glacial ice volume and last glacial maximum duration from an extended Barbados Sea level record. Quaternary Science Reviews, 25, 3322-3337.
Price, A. R. G. (1993). The Gulf: Human impacts and management initiatives. Marine Pollution Bulletin, 27, 17-27.
Rabaoui, L., Lin, Y.-J., Maneja, R. H., Qurban, M. A., Abdurahiman, P., Premlal, P., … 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.
Rabaoui, L., Lin, Y.-J., Qurban, M. A., Maneja, R. H., Franco, J., Joydas, T. V., … Roa-Ureta, R. H. (2015). Patchwork of oil and gas facilities in Saudi waters of The Gulf has the potential to enhance local fisheries production. ICES Journal of Marine Science, 72, 2398-2408.
Randall, J. E. (1995). Coastal fishes of Oman (p. 439). Honolulu, Hawaii: University of Hawaii Press.
Ratnasingham, S., & Hebert, P. D. N. (2007). BOLD: The barcode of life data system (http://www.barcodinglife.org). Molecular Ecology Notes, 7, 355-364.
Reynolds, R. M. (1993). Physical oceanography of the Persian Gulf, Strait of Hormuz and the Gulf of Oman -- results from the Mt Mitchell expedition. Marine Pollution Bulletin, 27, 35-59.
Ronquist, F., Teslenko, M., van derMark, P., Ayres, D. L., Darling, A., Höhna, S., … Huelsenbeck, J. P. (2012). MrBayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61, 539-542.
Saitou, N., & Nei, M. (1987). The neighbor-joining method: A new method for reconstruction of phylogenetic trees. Molecular Biology and Evolution, 4, 406-425.
Scarpa, F., Cossu, P., Delogu, V., Lai, T., Sanna, D., Leasi, F., … Casu, M. (2017a). Molecular support for morphology-based family-rank taxa: The contrasting cases of two families of Proseriata (Platyhelminthes). Zoologica Scripta, 46(6), 753-766.
Scarpa, F., Cossu, P., Lai, T., Sanna, D., Curini-Galletti, M., & Casu, M. (2016). Meiofaunal cryptic species challenge species delimitation: The case of the Monocelis lineata (Platyhelminthes: Proseriata) species complex. Contribtions to Zoology, 85(2), 121-143.
Scarpa, F., Cossu, P., Sanna, D., Lai, T., Casu, M., & Curini-Galletti, M. (2017b). New insights on the genus Otoplana Du Plessis, 1889 (Platyhelminthes: Proseriata), with description of two new species from the Canary Islands. Marine Biodiversity. https://doi.org/10.1007/s12526-017-0785-1.
Schmidt, H. A., Strimmer, K., Vingron, M., & von Haeseler, A. (2002). TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics, 18, 502-504.
Schmidt, H. A., & von Haeseler, A. (2012). Phylogenetic inference using maximum likelihood methods. In P. Lemey, M. Salemi, & A. M. Vandamme (Eds.), The phylogenetic handbook (5th ed., pp. 181-209). Cambridge: Cambridge University Press.
Shen, Y., Guan, L., Wang, D., & Gan, X. (2016). DNA barcoding and evaluation of genetic diversity in Cyprinidae fish in the midstream of the Yangtze River. Ecology and Evolution, 6(9), 2702-2713.
Sievers, F., & Higgins, D. G. (2014). Clustal Omega. Current Protocols in Bioinformatics, 48, 1.25.1-1.25.33.
Smith, P. J., McVeagh, S. M., & Steinke, D. (2008). DNA barcoding for the identification of smoked fish products. Journal of Fish Biology, 72, 464-471.
Soininen, E. M., Valentini, A., Coissac, E., Miquel, C., Gielly, L., Brochmann, C., … Taberlet, P. (2009). Analysing diet of small herbivores: The efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures. Frontiers in Zoology, 6, 16.
Steinke, D., Vences, M., Salzburger, W., & Meyer, A. (2005). TaxI: A software tool for DNA barcoding using distance methods. Philosophical Transactions of the Royal Society B, 360, 1847-1857.
Strimmer, K., & Von Haeseler, A. (1996). Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies. Molecular Biology and Evolution, 13(7), 964-969.
Tang, C. T., Leasi, F., Obertegger, U., Kieneke, A., Barraclough, T. G., et al. (2012). The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna. Proceedings of the Natural Academy of Sciences, 109, 16208-16212.
Trivedi, S., Affan, R., Alessa, A. H. A., Ansari, A. A., Dhar, B., Mahadani, P., & Ghosh, S. K. (2014). DNA barcoding of Red Sea fishes from Saudi Arabia - the first approach. DNA Barcodes, 2, 17-20.
Ward, R. D., Hanner, R., & Hebert, P. D. N. (2009). The campaign to DNA barcode all fishes, FISH-BOL. Journal of Fish Biology, 74(2), 329-356.
Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R., & Hebert, P. D. (2005). DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society B, 360, 1847-1857.
White, S. T., A. M. Al-Suwailem & E. Vivekanandan, 2008. The marine capture fisheries of the Saudi Arabian Gulf. Research Institute, King Fahd University of Petroleum & Minerals. KFUPM/RI, July 2008G. 31 pp.
Yeates, D. K., Seago, A., Nelson, L., Cameron, S. L., Joseph, L., & Trueman, J. W. H. (2011). Integrative taxonomy, or iterative taxonomy? Systematic Entomology, 36, 209-217.
Zhang, D. X., & Hewitt, G. M. (1996). Nuclear integrations: Challenges for mitochondrial DNA markers. Trends in Ecology and Evolution, 11(6), 247-251 PMID: 21237827.
Zhang, J., Kapli, P., Pavlidis, P., & Stamatakis, A. (2013). A general species delimitation method with applications to phylogenetic placements. Bioinformatics, 29, 2869-2876.