Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene




Abstract. Basith A, Abinawanto, Kusrini E, Yasman. 2021. Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene. Biodiversitas 22: 4282-4290. Groupers populations in Indonesia, particularly from Madura Island, East Java are indicated to be over-fished, thereby requiring data collection of more accurate genetic resources as an important step for grouper conservation. A total of 14 samples of the Epinepheplus groupers were obtained from the fish landing port on Madura Island. The 617 bp CO1 gene sequence was utilized for genetic diversity analysis and phylogenetic tree reconstruction. Genetic diversity is based on the value of haplotype diversity (Hd) and nucleotide diversity (?). Reconstruction of the phylogenetic tree includes neighbor-joining (NJ) implementing K2P substitution model, while maximum likelihood (ML) is conducted by implementing HKY+G+I substitution model, both of which were evaluated by employing a bootstrap of 1000 replications. Analysis of genetic distance between species indicated that the farthest distance between E. heniochus and E. fasciatus was 0.189, while the closest distance between E. erythrurus and E. ongus was 0.099. Intrapopulation genetic diversity indicated a high value with details of Hd=0.978 and ?=0.12107. Furthermore, NJ and ML phylogenetic tree demonstrated similar topology in the observed Epinephelus spp. obtained from Madura Island grouped into 7 clades, that is Epinephelus coioides, E. bleekeri, E. areolatus, E. erythrurus, E. heniochus, E. fasciatus, and E. ongus.


Akmal S, Fadlian, R, Prismayanti, A. Rahayu, S. 2019. Population structure of caught fish in Madura Strait waters. J Trop Fish. Manag 3(1):16-23.
Alcantara, SG & Yambot, AV 2016. DNA barcoding of commercially important Grouper species (Perciformes, Serranidae) in the Philippines. Mitochondrial DNA A DNA Mapp Seq Anal 27 (6): 3837-3845.
Amorim P, Sousa P, Jardim E, Azevedo M, Menezes GM. 2020. Length-frequency data approaches to evaluate snapper and grouper fisheries in the Java Sea, Indonesia. Fish Res 229:1-15.
Ariyanti Y, Farajallah, A. 2019. Species confirmation of juvenile cloudy grouper, Epinephelus erythrurus (Valencinennes, 1828), based on morphological analysis and partial CO1 gene sequencing. Biodiversitas 20 (3): 914-921.
Aziz NMA, Esa Y, Arshad A. 2016. DNA barcoding and phylogenetic analysis of Malaysian grouper (Subfamily Epinephelinae) using mitochondrial cytochrome c oxidase I (COI) gene. J Environ Biol 37: 725-733.
Basheer VS, Vineesh N, Bineesh KK, Kumar RG, Mohitha C, Venu S, Kathirvelpandian A, Gopalakrishnan A, Jena JK. 2017. Mitochondrial signatures for identification of grouper species from Indian waters. Mitochondrial DNA Part A 28 (4): 451-457
Basith A, Abinawanto A, Kusrini E. Yasman Y. 2021. Species inventories and conservation status of groupers (family Serranidae) from Madura Island, East Java, Indonesia. AIP Conf Proc 2331: 050021-1-050021-7.
Cracraft J, Helm-Bychowski K. 1991. Parsimony and phylogenetic inference using DNA sequences: some methodological strategies. In Phylogenetic Analysis of DNA Sequences. M. Miyanmoto and J. Cracraft (Eds.). Oxford Univ. Press, New York.
Crandall ED, Frey MA, Grosberg RK. Barber PH. 2008. Contrasting demographic history and phylogeographical patterns in two Indo-Pacific Gastropods. Mol Ecol 17: 611–626.
Craig MT, Graham RT, Torres RA, Hyde JR, Freitas MO, Ferreira BP, Hostim-Silva M, Gerhardinger LC, Bertoncini AA, Robertson DR. 2009. "How many species of goliath grouper are there? Cryptic genetic divergence in a threatened marine fish and the resurrection of a geopolitical species." Endanger Species Res 7 (3): 167–174.
Darwin C, Pamulapati P, Gatreddi S. 2020. Taxonomic validation of Areolate grouper, Epinephelus areolatus (Perciformes: Serranidae) along the Nizampatnam coast, India. J Appl Biol Biotechnol 8 (4): 7-15.
Deepti VI, Kandula S, Khedkar GD. 2018. DNA barcoding of five species of groupers (Pisces: Serranidae) of Visakhapatnam, central eastern coast of India. Mitochondrial DNA Part A 29 (5): 659-663.
Dogan I & Dogan N. 2016. Genetic distance measures: review. Turkiye Klinikleri J Biostat 8 (1): 87-93.
Durand JD, Pham MH, Tran TTV, Hoang DH, Vo QV. 2020. Sorting the wheat from the chaff: a review of BINs associated with groupers of Vietnam and the implications for species identification from DNA barcoding. Mar Biodivers 50 (3): 1-23.
Felsenstein J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791.
Ferguson A, Taggart JB, Prodhöl PA, McMeel O, Thompson C, Stone C, McGinnity P, Hynes RA. 1995. The application of molecular markers to the study and conservation of fish population, with special references to Salmo. J Fish Biol 47 (Suppl. A): 103-112.
Hall, TA 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41: 95-98.
Hasegawa M, Kishino H, Yano T. 1985. Dating the human-ape split by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160-174.
He B, Lai T, Peng Z, Wang X, Pan L. 2013. Complete mitogenome of the areolate grouper Epinephelus areolatus (Serranidae, Epinephelinae). Mitochondrial DNA 24 (5):498–500.
Heemstra PC, Randall JE. 1993. FAO species catalogue. Vol.16. Groupers of the world (Family Serranidae, Subfamily Epinephelinae). An annotated and illustrated catalogue of the grouper, rockcod, hind, coral grouper and lyretail species known to date. Rome (IT): Food and Agriculture Organization of the United Nations.
Jefri E, Zamani NP, Subhan B, Madduppa HH. 2015. Molecular phylogeny inferred from mitochondrial DNA of the Grouper Epinephelus spp. In Indonesia collected from local fish market. Biodiversitas, 16 (2): 254-263
Kamal MM, Hakim AA, Butet NA, Fitrianingsih Y, Astuti R. 2019. Authentication of grouper species based on the MT-CO1 gene marker from Peukan Bada Waters, Aceh. J Trop Biol 19 (2): 116-123. [Indonesian]
Khasanah M, Nurdin N, Sadovy Y, Jompa J. 2019. Management of the Grouper Export Trade in Indonesia. Rev Fish Sci Aquac 28:1-15.
Madduppa HH, Agus SB, Farhan AR, Suhendra D, Subhan B. 2012. Fish biodiversity in coral reefs and lagoons at the Maratua Island, East Kalimantan. Biodiversitas 13:145-150.
Manel S, Guerin PE, Mouillot D, Blanchet S, Velez L, Albouy C, Pellissier L. 2020. Global determinants of freshwater and marine fish genetic diversity. Nat Comm 11(692): 1-9.
Mignon-Grasteau S, Boissy A, Bouix J, Faure JM, Fisher AD, Hinch GN, Jensen P, Le Neindre P, Mormède P, Prunet P, Vandeputte M, Beaumont C. 2005. Genetics of adaptation and domestication in livestock. Livest Prod Sci 93(1): 3-14.
Muhsoni FF. 2008. Characteristics of capture fisheries in Madura waters. Engineering 1(1):17-31
Muldoon G, Sadovy YJ, Shea S, Tam I, Welford R, Whitfort A. 2016. Mostly legal, but not sustainable how airlines can support sustainable trade in live reef food fish. Hong Kong: ADM Capital Foundation Report.
Nei M, Kumar S. 2000. Molecular evolution and phylogenetics. New York: Oxford University Press.
Nei M. 1972. Genetic distance between populations. Am Nat 106: 283-292.
Nei M. 1987. Molecular Evolutionary Genetics. New York: Columbia University Press.
Noikotr K, Chaveerach A, Pinthong K, Tanomtong A, Sudmoon R, Tanee T. 2013. RAPD and barcode analysis of groupers of the Genus Epinephelus. Genet Mol Res 12 (4): 5721-5732.
Qu M, Tang W, Liu Q, Wang D, Ding S. 2018. Genetic diversity within grouper species and a method for interspecific hybrid identification using DNA barcoding and RYR3 marker. Mol Phylogenet Evol 121: 46-51.
Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A. DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Mol Biol Evol 34 (12): 3299-3302.
Song H, Buhay JE, Whiting MF, Crandall KA. 2008. Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. PNAS 105 (36): 13486-13491.
Sukandar, Handayani M, Dewi CSU, Harsindhi CJ, Maulana AW, Supriyadi, Bahroni A. 2016. Profile of coastal villages in East Java Province volume III (Madura Islands). Surabaya: Marine, Coastal, and Supervision of the Department of Fisheries and Marine Affairs of East Java Province. [Indonesian]
Tapilatu RF, Tururaja TS, Sipriyadi, Kusuma AB. 2021. Molecular phylogeny reconstruction of grouper (Serranidae: Epinephelinae) at northern part of Bird's Head Seascape-Papua Inferred from COI Gene. Fish Aquat Sci 24 (5): 181-190.
Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22 (22): 4673-80.
Ward RD, Hanner R, Hebert PDN. 2009. The campaign to DNA barcode all fishes, FISH-BOL. J Fish Biol 74: 329-356.
Waugh J. 2007. DNA barcoding in animal species: progress, potential, and pitfalls. BioEssays 29: 188-197.

Most read articles by the same author(s)

1 2 3 > >>