Identification of four species of Clupeiformes (Actinopterygii) through analysis of mitochondrial DNA sequences in fishing exploitation areas of the Gulf of Nicoya, Costa Rica
DOI:
https://doi.org/10.15359/revmar.13-1.3Keywords:
Opisthonema spp., Cetengraulis sp, mtDNA, rDNA, taxonomic placementAbstract
Sardines, together with anchovies, constitute one of the most important groups in the fishery of the Gulf of Nicoya. They are consumed by large fish and seabirds; therefore, they not only suffer from fishing exploitation but also have high rates of natural mortality. Due to their commercial and ecological importance, it is necessary to have a reliable taxonomic identification of these species, mainly for the preparation of fisheries studies. Previously, the identification of fish species was based only on external morphological characteristics; however, this is not always possible due to their morphological similarity, but the combined use of morphological and genetic data based on mitochondrial genes can contribute to their accurate recognition. Historically, taxonomic studies have grouped the species O. libertate, O. medirastre and O. bulleri as members of the Opisthonema spp. complex due to their great morphological similarity, while, there are few taxonomic studies of the family Engraulidae. In the present work, species of the Opisthonema spp. complex and a species of the genus Cetengraulis sp., collected between June-December 2017, were molecularly identified by sequencing mitochondrial genes: COI, Ctyb, and 16S rRNA. The findings of the molecular data analysis confirm the identity and presence of three species of the Opisthonema spp. complex and a species of anchovy, in areas of fishing exploitation in the gulf of Nicoya, Costa Rica, information that facilitates the use and management of these fishing resources in a marine area of commercial importance for the country.
References
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol., 215(3), 403-410. https://doi.org/10.1016/S0022-2836(05)80360-2
Ardura, A., Linde, A. R., Moreira, J. C. & García-Vázquez, E. (2010). DNA barcoding for conservation and management of Amazonian commercial fish. Biol. Conserv., 143(6), 1438-43. https://doi.org/10.1016/j.biocon.2010.03.019
Baldwin, C. C., Mounts, J. H., Smith, D. G. & Weigt, L. A. (2009). Genetic identification and color descriptions of early life/history stages of Belizean Phaeoptyx and Astrapogon (Teleostei: Apogonidae) with comments on identification of adult Phaeoptyx. Zootaxa, 2008, 1-22. https://doi.org/10.11646/zootaxa.2008.1.1
Benson, D. A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., … & Sayers, E. W. (2012). GenBank. Nucleic Acids Res., 41(D1), D36-D42. https://doi.org/10.1093/nar/gks1195
Berry, F. H. & Barrett, I. (1963). Análisis de las branquiespinas y denominación del arenque de hebra Opisthonema. Inter-A. Tuna Trop. Comm. Bull., 7(2), 110-190.
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
Bloom, D. D. & Lovejoy, N. R. (2014). The evolutionary origins of diadromy inferred from a time/calibrated phylogeny for Clupeiformes (herring and allies). Proc. R. Soc. Lond. B. Biol. Sci., 281(1778), 2013-2081. https://doi.org/10.1098/rspb.2013.2081
Bussing, W. & López, M. (1994). Peces demersales y pelágicos costeros del Pacífico de Centroamérica Meridional. Guía Ilustrada. Rev. Biol. Trop., 47 (Supplemento), 47-164.
Carvalho, D. C., Oliveira, D. A., Pompeu, P. S., Leal, C. G., Oliveira, C. & Hanner, R. (2011). Deep barcode divergence in Brazilian freshwater fishes: the case of the São Francisco River basin. Mitochondrial DNA, 22(1), 80-86. https://doi.org/10.3109/19401736.2011.588214
Chakraborty, A. & Iwatsuki. Y. (2006). Genetic variation at the mitochondrial 16S rRNA gene among Trichiurus lepturus (Teleostei:Trichiuridae) from various localities: Preliminary evidence of a new species from West Coast of Africa. Hydrobiologia, 563, 501-513. https://doi.org/10.1007/s10750-006-0105-4
Darriba, D., Taboada, G. L., Doallo, R. & Posada, D. (2012). jModelTest 2: more models, new heuristics, and parallel computing. Nat. Methods, 9(8), 772. https://doi.org/10.1038/nmeth.2109
Durand, J. D., Hubert, N., Shen, K. N. & Borsa, P. (2017). DNA barcoding grey mullets. Rev. Fish. Biol. Fish., 27, 233-43. https://doi.org/10.1007/s11160-016-9457-7
FAO. Organización de las Naciones Unidas para la Alimentación y la Agricultura. (2018). El estado mundial de la pesca y la acuicultura 2018. Cumplir los objetivos de desarrollo sostenible. Italia: FAO.
Fischer, W., Krupp, F., Schneider, W., Sommer, C., Carpenter, K. E. & Miem, V. H. (1995). Guía FAO para la identificación de especies para los fines de la pesca. Pacífico Centro Oriental. Italia: FAO.
Froese, R. & Pauly, D. (2019). FishBase. World Wide Web electronic publication. https://www.fishbase.se/search.php
Goodbody-Gringley, G., Strand, E. & Pitt, J. M. (2019). Molecular characterization of nearshore baitfish populations in Bermuda to inform management. PeerJ, 7, e7244. https://doi: 10.7717/peerj.7244
Hebert, P. D., Ratnasingham, S. & de Waard, J. R. (2003). Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. R. Soc. Lond. B. Biol. Sci., 270 Suppl 1(Suppl 1), S96-S99. https://doi.org/10.1098/rsbl.2003.0025
Huelsenbeck, J. P. & Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogeny. Bioinf., 17(8), 754-755. https://doi.org/10.1093/bioinformatics/17.8.754
Ivanova, N. V., deWaard, J. R. & Hebert, P. D. N. (2006). An inexpensive automatization friendly protocol for recovering high quality DNA. Mol. Ecol. Notes, 6(4), 998-1002. https://doi.org/10.1111/j.1471-8286.2006.01428.x
Jahan, H., Akter, M., Begum, R. A. & R. Shahijahan. (2017). Identification and comparison of three carp fishes based on mitochondrial 16S rRNA gene. J. Biol. Sci., 26 (2): 167-174.
Katoh, K., Asimenos, G. & Toh, H. (2009). Multiple alignment of DNA sequences with MAFFT. In D. Posada (Ed.), Bioinformatics for DNA Sequence Analysis. Methods in Molecular Biology (Methods and Protocols) (pp. 39-64). EE. UU.: Humana Press. https://doi.org/10.1007/978-1-59745-251-9_3
Kocher, T. D., Thomas, W. K., Meyer, A., Edwards, S. V., Paabo, S., … & Wilson, A. C. (1989). Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc. Nat. Acad. Sci. U. S. A., 86(16), 6196-6200. https://doi.org/10.1073/pnas.86.16.6196
Kochzius, M., Seidel, C., Antoniou, A., Kumar, S., Campo, D., Cariani, A., ... & Blohm, D. (2010). Identifying fishes through DNA barcodes and microarrays. Plos One, 5(9), e12620. https://doi.org/10.1371/journal.pone.0012620
Lagúnez, L. & Rodríguez, F. (1992). Contribución al conocimiento genético de Opisthonema spp. del noreste de México. Inv. Mar. CICIMAR, 7(1),15-24.
Li, C. & Ortí, G. (2007). Molecular phylogeny of Clupeiformes (Actinopterygii) inferred from nuclear and mitochondrial DNA sequences. Mol. Phylogenet. Evol., 44, 386-398. https://doi.org/10.1016/j.ympev.2006.10.030
Meyer, A., Kocher, T. D., BasasibwakI, P. & Wilson, A. C. (1990). Monophyletic origin of Lake Victoria cichlid fishes suggested by mitochondrial DNA sequences. Nature, 347(6293), 550-553. https://doi.org/10.1038/347550a0
Murase, A., Angulo, A., Miyazaki, Y., Bussing, W. & López, M. (2014). Marine and estuarine fish diversity in the inner Gulf of Nicoya, Pacific coast of Costa Rica, Central America. Check List, 10(6), 1401-1413. https://www.biotaxa.org/cl/article/view/10.6.1401
Paine, M., McDowell, J. & Graves, J. (2007). Specific identification of Western Atlantic Ocean scombrids using mitochondrial DNA cytochrome c oxidase subunit I (COI) gene region sequences. Bull. Mar. Sci., 80(2), 353-367.
Palumbi, S. R. (1996). Nucleic acids II: the polymerase chain reaction. In D. M. Hillis, C. Moritz & B. K. Mable (Eds.), Molecular systematics (pp. 205-247). EE. UU.: Sinauer & Associates, Inc.
Peng, Z., He, S. & Zhang, Y. (2004). Phylogenetic relationships of glyptosternoid fishes (Siluriformes: Sisoridae) inferred from mitochondrial cytochrome b gene sequences. Mol. Phylogenet. Evol., 31(3), 979-987. https://doi.org/10.1016/j.ympev.2003.10.023
Pereira, L. H. G., Hanner, R., Foresti, F. & Oliveira, C. (2013). Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna? BMC Genet., 14, 20. https://doi.org/10.1186/1471-2156-14-20
Pérez-Enríquez, R., Díaz-Viloria, N., Cruz-Hernández, P., Aranceta-Garza, F., Gutiérrez-González, J. L., … & Max-Aguilar, A. (2016). Estudios de genética en poblaciones de abulón y sus aplicaciones en ordenamiento pesquero. Rec. Nat. Soc., 2(2), 24-39. https://doi.org/10.18846/renaysoc.2016.02.02.02.0002
Pérez-Quiñonez, C. I. (2014). Discriminación de las especies del género Opisthonema Gill, 1861 en el Sur del Golfo de California usando análisis morfométricos y genéticos. (Tesis de Maestría no publicada). Centro Interdisciplinario de Ciencias Marinas (CICIMAR), Instituto Politécnico Nacional, México.
Pérez-Quiñonez, C. I., Quiñonez-Velázquez, C. & García-Rodríguez, F. J. (2020). A simple method for the genetic identification of commercially important species in the Opisthonema genus Gill, 1861 in the southern Gulf of California. Ciencias Marinas, 46(3), 145-154. https://doi.org/10.7773/cm.v46i3.3059
Pérez-Quiñonez, C. I., Quiñonez-Velázquez, C. & García-Rodríguez, F. J. (2018). Detecting Opisthonema libertate (Günther, 1867) phenotypic stocks in northwestern coast of Mexico using geometric morphometrics based on body and otolith shape. Lat. Am. J. Aquat. Res., 46(4), 779-790. http://doi.org/10.3856/vol46-issue4-fulltext-15
Pérez-Quiñonez, C. I., Quiñonez-Velázquez, C. & García-Rodríguez, F. J. (2019). Genetic homogeneity of the Pacific thread herring (Opisthonema libertate) (Günther, 1867) in the Eastern Pacific, inferred from mtDNA sequences. Mitochondrial DNA Part A, 30(3), 517-524. https://doi.org/10.1080/24701394.2019.1570173
Pérez-Quiñónez, C. I., Quiñónez-Velázquez, C., Ramírez-Pérez, J. S, Vergara-Solana, F. J. & García-Rodríguez, F. J. (2017). Combining geometric morphometrics and genetic analysis to identify species of Opisthonema Gill, 1861 in the eastern Mexican Pacific. J. Appl. Ichthyol., 33(1), 84-92. https://doi.org/10.1111/jai.13051
QGIS. Development Team. (2018). QGIS Geographic Information System. EE. UU: Open Source Geospatial Foundation Project. http://qgis.osgeo.org
Rambaut, A. (2009). FigTree v1.4 2012-2014: Tree Figure Drawing Tool. Edinburgh. Scotland: Institute of Evolutionary Biology, University of Edinburgh. http://tree.bio.ed.ac.uk/software/figtree
Robertson, D. R. & Allen, G. R. (2002). Shore fishes of the Tropical Eastern Pacific: an Information System. Smithsonian Tropical Research Institute. http://www.neotropicalfishes.org/sftep
Rocha, A., Garber, N., Garber, A. & Stuck, K. (2005). Structure of the mitochondrial control region and flanking tRNA genes of Mugil cephalus. Hidrobiológica, 15(2), 139-149.
Rodríguez, J. A. & Gómez, K. R. (1998). Aspectos relevantes en la biología de Cetengraulis mysticetus (Günther) (Pisces: Engraulidae) en el Golfo de Nicoya, Costa Rica. Uniciencia, 15(1), 57-60.
Rodríguez-Sánchez, R. (octubre, 1985). Aspectos de dinámica poblacional en apoyo de la separación de las especies del género Opisthonema por el método de índice de densidad de branquiespinas. CalCOFI abstracts, annual, conference. EE. UU.
Soto, R. & Rodríguez, J. (1999). Dinámica poblacional de Opisthonema medirastre (Pisces: Clupeidae) en la costa Pacífica de Costa Rica. Uniciencia, 15(16), 61-64.
Stamatakis, A., Ludwig, T. & Meier, H. (2005). RAxML/III: a fast program for maximum likelihood/ based inference of large phylogenetic trees. Bioinf., 21(4), 456-463. https://doi.org/10.1093/bioinformatics/bti191
Teletchea, F. (2009). Molecular identification methods of fish species: reassessment and possible applications. Rev. Fish. Biol. Fish., 19(3), 265-293. https://doi.org/10.1007/s11160-009-9107-4
Vega‐Corrales, L. A. (2010). Evaluación poblacional del stock explotable del complejo Opisthonema (Pisces: Cupleidae) en el Golfo de Nicoya, Costa Rica. Rev. Cien. Mar. Cos., 2, 83-94. https://doi.org/10.15359/revmar.2.7
Vicente, F., Loeb, M. V., Paiva, A. C. G. D., Sampaio, C. L., Argolo, L. A. & Jacobina, U. P. (2020). Integrative systematics unveils the controversial identity of Engraulidae fishing stocks in a Neotropical estuary, northeast Brazil. Neotrop. Ichthyol., 18(4), 1-17. https://doi.org/10.1590/1982-0224-2020-0037
Wang, P., Zhao, C., Fan, S., Yan, L. & Qiu, L. (2018). The complete mitochondrial genome of Thryssa hamiltonii and phylogenetic analysis of Engraulidae (Clupeiformes; Clupeoidei). Mitochondrial DNA Part B., 3(2), 538-540. https://doi.org/10.1080/23802359.2018.1467232
Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R. & Hebert, P. D. N. (2005). DNA barcoding Australia’s fish species. Phil. Trans. R. Soc., 360(1462), 1847-1858. https://doi.org/10.1098/rstb.2005.1716
Wortley, H. & Scotland, R. (2006). The effect of combining molecular and morphological data in Published Phylogenetic Analyses. Syst. Biol., 55(4), 677-685. https://doi.org/10.1080/10635150600899798
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