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DNA barcoding and taxonomic validation of Caranx spp. larvae

Published online by Cambridge University Press:  14 April 2021

Claudia A. Silva-Segundo Open the ORCID record for Claudia A. Silva-Segundo [Opens in a new window] ,
René Funes-Rodríguez Open the ORCID record for René Funes-Rodríguez [Opens in a new window] ,
Jaime Gómez-Gutiérrez Open the ORCID record for Jaime Gómez-Gutiérrez [Opens in a new window] ,
Griselda Gallegos-Simental Open the ORCID record for Griselda Gallegos-Simental [Opens in a new window] ,
Sergio Hernández-Trujillo Open the ORCID record for Sergio Hernández-Trujillo [Opens in a new window]  and
Anidia Blanco-Jarvio Open the ORCID record for Anidia Blanco-Jarvio [Opens in a new window]
Claudia A. Silva-Segundo*
Affiliation:
Laboratorio de Bioingenieria y Ciencias Ambientales, Departamento Académico de Ingeniería en Pesquerías, Universidad Autónoma de Baja California Sur, Carretera al Sur Km 5.5, 23088, La Paz, Baja California Sur, Mexico
René Funes-Rodríguez
Affiliation:
Departamento de Plancton y Ecología Marina, Centro Interdisciplinario de Ciencias Marinas, Instituto Politécnico Nacional, Av. IPN s/n, Col. Playa Palo de Sta. Rita Sur, 23096, La Paz, Baja California Sur, Mexico
Jaime Gómez-Gutiérrez
Affiliation:
Departamento de Plancton y Ecología Marina, Centro Interdisciplinario de Ciencias Marinas, Instituto Politécnico Nacional, Av. IPN s/n, Col. Playa Palo de Sta. Rita Sur, 23096, La Paz, Baja California Sur, Mexico
Griselda Gallegos-Simental
Affiliation:
Laboratorio Nodo CIBNOR Código de Barras, Centro de Investigaciones Biológicas del Noroeste, Km 1 Carretera a San Juan de La Costa, El Comitán, 23205, La Paz, Baja California Sur, Mexico
Sergio Hernández-Trujillo
Affiliation:
Departamento de Plancton y Ecología Marina, Centro Interdisciplinario de Ciencias Marinas, Instituto Politécnico Nacional, Av. IPN s/n, Col. Playa Palo de Sta. Rita Sur, 23096, La Paz, Baja California Sur, Mexico
Anidia Blanco-Jarvio
Affiliation:
Laboratorio de Bioingenieria y Ciencias Ambientales, Departamento Académico de Ingeniería en Pesquerías, Universidad Autónoma de Baja California Sur, Carretera al Sur Km 5.5, 23088, La Paz, Baja California Sur, Mexico
*
Author for correspondence: Claudia A. Silva-Segundo, E-mail: ca.silva@uabcs.mx
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Abstract

Of the five nominal species in the genus Caranx Lacepède 1801 distributed throughout the Eastern Central Pacific, Caranx caballus and Caranx sexfasciatus are the only two that have formal fish larval descriptions based on diagnostic characteristics (morphology, meristics and pigmentation). In this study, the diagnostic characteristics of three Caranx species larvae were validated using DNA barcoding analysis cytochrome c oxidase subunit I (COI; 651 bp). For the first time, the morphological taxonomic assignation of C. caballus fish larvae was confirmed using COI gene partial sequences of adults, with a genetic similarity between 99.8–100%. However, molecular evidence demonstrated that fish larvae previously described as C. sexfasciatus had high genetic similarity (99.7–100%) and low genetic distance (<1%) to Caranx caninus adults. An undescribed larval morphotype collected in the present study genetically matched (100%) with COI sequences of C. sexfasciatus adults. The diagnostic characteristics of this new morphotype were a lack of pigmentation in the supraoccipital crest, over the gut, and at the terminal region of the gut. The combination of diagnostic characteristics and DNA barcoding evidence allowed the discrimination and validation of C. caballus, C. caninus and C. sexfasciatus larvae. The diagnostic characteristics and COI sequences of Caranx lugubris and Caranx melampygus larvae, which are also distributed in the Eastern Central Pacific, remain to be investigated.

Keywords

COIDNA barcodingEastern Central Pacificfish larvaeGulf of Californiataxonomy
Type
Research Article
Information
Journal of the Marine Biological Association of the United Kingdom , Volume 101 , Issue 2 , March 2021 , pp. 399 - 407
Copyright
Copyright © The Author(s), 2021. Published by Cambridge University Press on behalf of Marine Biological Association of the United Kingdom

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References

Ahern, ALM, Gómez-Gutiérrez, J, Aburto-Oropeza, O, Saldierna-Martínez, RJ, Johnson, AF, Harada, AE, Sánchez-Uvera, AR, Erisman, B, Castro-Arvizú, DI and Burton, RS (2018) DNA sequencing of fish eggs and larvae reveals high species diversity and seasonal changes in spawning activity in the southeastern Gulf of California. Marine Ecology Progress Series 592, 159–179.CrossRefGoogle Scholar
Allen, GR and Robertson, DR (1994) Peces del Pacífico Oriental Tropical, 2nd Edn. Mexico City: CONABIO, Agrupación Sierra Madre, CEMEX.Google Scholar
Avendaño-Ibarra, R, Aceves-Medina, G, Domínguez, E, De Silva-Dávila, R, Jiménez-Rosenberg, SPA, Urias-Leyva, H and Robinson, C (2014) Fish larvae from the Gulf of California to Colima, Mexico: an update. Check List 10, 106–121.CrossRefGoogle Scholar
Beltrán-León, BS and Ríos-Herrera, R (2000) Estadios tempranos de peces del Pacífico Colombiano (Vol. I, II) . Buenaventura, Colombia: Instituto Nacional de Pesca y Acuicultura.Google Scholar
Briggs, JC and Bowen, BW (2012) A realignment of marine biogeographic provinces with particular reference to fish distributions. Journal of Biogeography 39, 12–30.CrossRefGoogle Scholar
Camacho-Gastélum, R, Díaz-Viloria, N, Sánchez-Velasco, L, Jiménez-Rosenberg, SP and Perez-Enriquez, R (2017) Molecular identification and morphological description of Micropogonias megalops, Cynoscion othonopterus, C. reticulatus and Menticirrhus nasus larvae, collected in the upper Gulf of California during summer 2012. Mitochondrial DNA Part A 28, 416–423.CrossRefGoogle Scholar
Chang, CH, Shao, KT, Lin, HY, Chiu, YC, Lee, MY, Liu, SH and Lin, PL (2017) DNA barcodes of the native ray-finned fishes in Taiwan. Molecular Ecology Resource 17, 796–805.CrossRefGoogle ScholarPubMed
Dahruddin, H, Hutama, A, Busson, F, Sauri, S, Hanner, R, Keith, P, Hadiaty, R and Hubert, N (2017) Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species. Molecular Ecology Resource 17, 288–299.CrossRefGoogle ScholarPubMed
Delrieu-Trottin, E, Williams, JT, Pitassy, D, Driskell, A, Hubert, N, Viviani, J, Cribb, TH, Espiau, B, Galzin, R, Kulbicki, M, de Loma T, Lison, Meyer, C, Mourier, J, Mou-Tham, G, Parravicini, V, Plantard, P, Sasal, P, Siu, G, Tolou, N, Veuille, M, Weigt, L and Planes, S (2019) A DNA barcode reference library of French Polynesian shore fishes. Scientific Data 6, 1–8.CrossRefGoogle ScholarPubMed
Fahay, MP (2007) Early Stages of Fishes in the Western North Atlantic Ocean (Davis Strait, Southern Greenland and Flemish Cap to Cape Hatteras). Acipenseriformes Through Syngnathiformes (Vol. I). Dartmouth, Canada: Northwest Atlantic Fisheries Organization.Google Scholar
Fischer, W, Krupp, F, Schneider, W, Sommer, C, Carpenter, KE and Niem, VH (1995) Guía FAO para la identificación de especies para los fines de la Pesca: Pacífico Centro-Oriental (Vol. III). Rome: FAO Inter-Departmental Working Group.Google Scholar
Froese, R and Pauly, D (2021). FishBase. Caranx Lacepède, 1801. World Register of Marine Species. Available at http://www.marinespecies.org/aphia.php?p=taxdetails&id=125936 (Accessed 22 January 2021).Google Scholar
Harada, AE, Lindgren, EA, Hermsmeier, MC, Rogowski, PA, Terrill, E and Burton, RS (2015) Monitoring spawning activity in a southern California marine protected area using molecular identification of fish eggs. PLoS ONE 10, e0134647.CrossRefGoogle Scholar
Hebert, PDN and Gregory, TR (2005) The promise of DNA barcoding for taxonomy. Systematic Biology 54, 852–859.CrossRefGoogle ScholarPubMed
Hebert, PDN, Cywinska, A, Ball, SL and de Waard, JR (2003 a) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B 270, 313–321.CrossRefGoogle ScholarPubMed
Hebert, PDN, Ratnasingham, S and de Waard, JR (2003 b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London B 270, S96–S399.CrossRefGoogle ScholarPubMed
Hou, G, Chen, WT, Lu, HS, Cheng, F and Xie, SG (2018) Developing a DNA barcode library for perciform fishes in the South China Sea: species identification, accuracy and cryptic diversity. Molecular Ecology Resource 18, 137–146.CrossRefGoogle ScholarPubMed
Hubert, N, Meyer, CP, Bruggemann, HJ, Guerin, F, Komeno, RJ, Espiau, B, Causse, R, Williams, JT and Planes, S (2012) Cryptic diversity in Indo-Pacific coral-reef fishes revealed by DNA-barcoding provides new support to the centre-of-overlap hypothesis. PLoS ONE 7, e28987.CrossRefGoogle ScholarPubMed
Hui-Ling, K, Yu-Tze, W, Tai-Sheng, C, Ming-An, L, Ming-Yih, L, Kuang-Zong, C, Wen-Yu, C and Kwang-Tsao, S (2013) Evaluating the accuracy of morphological identification of larval fishes by applying DNA barcoding. PLoS ONE 8, e53451.Google Scholar
I-Shiung, C, Kwang-Tsao, S, Shao-Liang, H, Gwo-Ching, G, Yu-Chih, C and Ta-Kang, L (2013) DNA barcoding of coastal larval fish communities of Dongsha Island, South China Sea revealed by mitochondrial COI sequences. Journal of Marine Science and Technology 21, 252–257.Google Scholar
Ivanova, NV, Dewaard, JR and Hebert, PDN (2006) An inexpensive, automation friendly protocol for recovering high-quality DNA. Molecular Ecology Notes 6, 998–1002.CrossRefGoogle Scholar
Ivanova, NV, Zemlak, TS, Hanner, RH and Hebert, PDN (2007) Universal primer cocktails for fish DNA barcoding. Molecular Ecology Notes 7, 544–548.CrossRefGoogle Scholar
Jaafar, TNAM, Taylor, MI, Nor, SAM, Bruyn, Md and Carvalho, GR (2012) DNA barcoding reveals cryptic diversity within commercially exploited Indo-Malay Carangidae (Teleosteii: Perciformes). PLoS ONE 7, e49623.CrossRefGoogle Scholar
Justine, JL, Rahmouni, C, Gey, D, Schoelinck, C and Hoberg, EP (2013) The Monogenean which lost its clamps. PLoS ONE 8, e79155.CrossRefGoogle ScholarPubMed
Kearse, M, Moir, R, Wilson, A, Stones-Havas, S, Cheung, M, Sturrock, S, Buxton, S, Cooper, A, Markowitz, S, Duran, C, Thierer, T, Ashton, B, Mentjies, P and Drummond, A (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649.CrossRefGoogle ScholarPubMed
Kim, BG, Divakaran, S, Brown, CL and Ostrowski, AC (2001) Comparative digestive enzyme ontogeny in two marine larval fishes: Pacific threadfin (Polydactylus sexfilis) and bluefin trevally (Caranx melampygus). Fish Physiology and Biochemistry 24, 225–241.CrossRefGoogle 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.CrossRefGoogle ScholarPubMed
Lewis, LA, Richardson, DE, Zakharov, EV and Hanner, R (2016) Integrating DNA barcoding of fish eggs into ichthyoplankton monitoring programs. Fishery Bulletin 114, 153–165.CrossRefGoogle Scholar
Matarese, AC Jr Kendall, AW, Blood, D and Vinter, BM (1989) Laboratory Guide to Early Life Stages of Northeast Pacific Fishes. Springfield, VA: National Oceanic and Atmospheric Administration, National Marine Fisheries Center.Google Scholar
Matarese, AC, Spies, IB, Busby, MS and Orr, JW (2011) Early larvae of Zesticelus profundorum (family Cottidae) identified using DNA barcoding. Ichthyological Research 58, 170–174.CrossRefGoogle Scholar
Moser, HG (1996) The Early Stages of Fishes in the California Current Region. California Cooperative Oceanic Fisheries Investigations. Atlas 33. La Jolla, CA: Scripps Institution of Oceanography.Google Scholar
Murakami, K, James, S, Randall, JE and Suzumoto, A (2007) Two hybrids of Carangid fishes of the genus Caranx, C. ignobilis × C. melampygus and C. melampygus × C. sexfasciatus, from the Hawaiian Islands. Zoological Studies 46, 186–193.Google Scholar
Pegg, GG, Sinclair, B, Briskey, L and Aspen, WJ (2006) MtDNA barcode identification of fish larvae in the southern Great Barrier Reef, Australia. Scientia Marina 70, 7–12.CrossRefGoogle Scholar
Ratnasingham, S and Hebert, PDN (2013) A DNA-based registry for all animal species: the barcode index number (BIN) system. PLoS ONE 8, e66213.CrossRefGoogle ScholarPubMed
Reed, DL, Carpenter, KE and de Gravelle, MJ (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.CrossRefGoogle ScholarPubMed
Rozas, J, Sanchéz-DelBarrio, JC, Messenguer, X and Rozas, R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496–2497.CrossRefGoogle ScholarPubMed
Santos, SR, Xiang, Y and Tagawa, AW (2011) Population structure and comparative phylogeography of jack species (Caranx ignobilis and C. melampygus) in the high Hawaiian Islands. Journal of Heredity 102, 47–54.CrossRefGoogle Scholar
Spalding, MD, Fox, HE, Allen, GR, Davidson, N, Ferdaña, ZA, Finlayson, M, Halpern, BS, Jorge, MA, Lombana, A, Lourie, SA, Martin, KD, McManus, E, Molnar, J, Recchia, CA and Robertson, J (2007) Marine ecoregions of the world: a bioregionalization of coastal and shelf areas. Bioscience 57, 573–583.CrossRefGoogle Scholar
Steinke, D, Connell, A and Hebert, P (2016) Linking adults and immatures of South African marine fishes. Genome 59, 959–967.CrossRefGoogle ScholarPubMed
Steinke, D, Dewaard, J, Gomon, M, Johnson, J, Larson, H, Lucanus, O, Moore, G, Reader, S and Ward, R (2017) DNA barcoding the fishes of Lizard Island (Great Barrier Reef). Biodiversity Data Journal 5, e12409.CrossRefGoogle Scholar
Sumida, BY, Moser, HG and Ahlstrom, EH (1985) Descriptions of larvae of California yellowtail, Seriola lalandi, and three other carangids from the Eastern Tropical Pacific: Chloroscombrus orqueta, Caranx caballus, and Caranx sexfasciatus. California Cooperative Oceanic Fisheries Investigation Report 26, 139–159.Google Scholar
Taylor, C and Watson, W (2004) Utility of larval pigmentation to identify nearshore rockfishes of the Sebastes subgenus Pteropodus from southern California. California Cooperative Oceanic Fisheries Investigation Report 45, 113–117.Google Scholar
Templonuevo, RM, Alcantara, S, Juanico, CS and Yambot, A (2018) DNA barcoding of two commercially important fish families (Carangidae and Lutjanidae) collected from Cuyo, Palawan, Philippines. International Journal of Agricultural Technology 14, 2051–2066.Google Scholar
Thirumaraiselvi, R, Das, S, Ramanadevi, V and Thangaraj, M (2015) MtDNA barcode identification of finfish larvae from Vellar estuary, Tamilnadu, India. Notulae Scientia Biologicae 7, 16–19.CrossRefGoogle Scholar
Thomson, DA, Findley, L and Kerstitch, AN (1979) Reef Fishes of the Sea of Cortez: The Rocky-Shore Fishes of the Gulf of California. New York, NY: John Wiley and Sons.Google Scholar
Victor, BC, Hanner, R, Shivji, M, Hyde, J and Caldow, C (2009) Identification of the larval and juvenile stages of the Cubera snapper, Lutjanus cyanopterus, using DNA barcoding. Zootaxa 2215, 24–36.Google Scholar
Ward, RD and Holmes, BH (2007) An analysis of nucleotide and amino acid variability in the barcode region of cytochrome c oxidase I (cox1) in fishes. Molecular Ecology Notes 7, 899–907.CrossRefGoogle Scholar
Ward, RD, Zemlak, TS, Innes, BH, Last, PR and Hebert, PDN (2005) DNA Barcoding Australia's fish species. Philosophical Transactions of The Royal Society B 360, 1–11.CrossRefGoogle ScholarPubMed
Watson, W, Charter, S and Lawley, C (2015) Early larvae of the swordspine rockfish (Sebastes ensifer) identified by molecular methods. Fishery Bulletin 114, 135–143.CrossRefGoogle Scholar
Xu, L, Van-Damme, K, Li, H, Ji, Y, Wang, X and Du, F (2019) A molecular approach to the identification of marine fish of the Dongsha Islands (South China Sea). Fisheries Research 213, 105–112.CrossRefGoogle Scholar
Yancy, HF, Zemlak, TS, Mason, JA, Washington, JD, Tenge, BJ, Nguyen, NL, Barnett, JD, Savary, WE, Hill, WE, Moore, MM, Fry, FS, Randolph, SC, Rogers, PL and Hebert, PD (2008) Potential use of DNA barcodes in regulatory science: applications of the Regulatory Fish Encyclopedia. Journal of Food Protection 71, 210–217.CrossRefGoogle ScholarPubMed
Zhang, J and Hanner, R (2011) DNA barcoding is a useful tool for the identification of marine fishes from Japan. Biochemical Systematics and Ecology 39, 31–42.CrossRefGoogle Scholar
Zou, K, Chen, Z, Zhang, P and Li, M (2016) Mitochondrial genome of the mackerel scad Decapterus macarellus (Perciformes: Carangidae). Mitochondrial DNA Part A 27, 2151–2152.Google Scholar