The Jawa and Bali Island Marine Fish Molecular Identification to Improve 12S rRNA-tRNA Valin-16S rRNA Partial Region Sequences on the GenBank Database

Antoro S, Na-Nakorn U, Koedprang W (2006) Study of genetic diversity of orange-spotted grouper, Epinephelus coioides, from Thailand and Indonesia using microsatellite markers. Mar Biotechnol 8:17–26

Arai, T., Aoyama, J., Limbong, D. & Tsukamoto, K. 1999. Species composition and inshore migration of the tropical eels Anguilla spp. recruiting to the estuary of the Poigar River, Sulawesi Island. Marine Ecology Progress Series, 299–303

Ariyanti Y (2012) Aplikasi DNA Barcode pada Penentuan Spesies Ikan Danau Laut Tawar, Nangroe Aceh Darussalam

Baldwin CC, Mounts JH, Smith DG, Weigt LA (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

Bellwood DR, Meyer CP (2009) Endemism and evolution in the coral triangle: a call for clarity. J Biogeogr 36:2010–2012

Bernardi G, Vagelli A (2004) Population structure in Banggai cardinalfish, Pterapogon kauderni, a coral reef species lacking a pelagic larval phase. Mar Biol 145:803–810

Bernardi G, Holbrook SJ, Schmitt RJ (2001) Gene flow at three spatial scales in a coral reef fish, the three-spot dascyllus, Dascyllus trimaculatus. Mar Biol 138:457–465

Boore JL, Medina M, Rosenberg LA (2004) Complete sequences of the highly rearranged molluscan mitochondrial genomes of the scaphopod Graptacme eborea and the bivalve Mytilus edulis. Mol Biol Evol 21:1492–1503

Carreras-Carbonell J, Pascual M, Macpherson E (2007) A review of the Tripterygion tripteronotus (Risso, 1810) complex, with a description of a new species from the Mediterranean Sea (Teleostei: Tripterygiidae). Sci Mar 71:75–86

Cawthorn D-M, Steinman HA, Witthuhn RC (2012) Evaluation of the 16s and 12s rrna genes as universal markers for the identification of commercial fish species in south africa. Gene 491:40–48

Chow S, Ueno Y, Toyokawa M, Oohara I, Takeyama H (2009) Preliminary analysis of length and GC content variation in the ribosomal first internal transcribed spacer (ITS1) of marine animals. Mar Biotechnol 11:301–306

Collette B, Carpenter K, Polidoro B, Juan-Jordá M, Boustany A, Die D, Elfes C, Fox W, Graves J, Harrison L (2011) High value and long life—double jeopardy for tunas and billfishes. Science 333:291–292

Comitini S, Hardjolukito S (1986) Economic benefits and costs of alternative arrangements for tuna fisheries development in the exclusive economic zone: the case of Indonesia. Ocean management 10:37–55

Croce O, Lamarre M, Christen R (2006) Querying the public databases for sequences using complex keywords contained in the feature lines. BMC bioinformatics 7:45

Dahruddin H, Hutama A, Busson F, Sauri S, Hanner R, Keith P, Hadiaty R, Hubert N (2017) Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species. Mol Ecol Resour 17:288–299

Das S, Deb B (2015) DNA barcoding of fungi using ribosomal ITS marker for genetic diversity analysis: a review. Int J Pure Appl Biosci 3:160–167

DJPT (2011) Statistika Perikanan Tangkap Indonesia 2010. Kementrian Kelautan dan Perikanan, Jakarta

Douady CJ, Dosay M, Shivji MS, Stanhope MJ (2003) Molecular phylogenetic evidence refuting the hypothesis of Batoidea (rays and skates) as derived sharks. Mol Phylogenet Evol 26:215–221

Dulvy NK, Baum JK, Clarke S, Compagno LJ, Cortés E, Domingo A, Fordham S, Fowler S, Francis MP, Gibson C (2008) You can swim but you can't hide: the global status and conservation of oceanic pelagic sharks and rays. Aquat Conserv Mar Freshwat Ecosyst 18:459–482

Giusti A, Armani A, Sotelo CG (2017) Advances in the analysis of complex food matrices: species identification in surimi-based products using next generation sequencing technologies. PLoS One 12:1–18

Handy SM, Deeds JR, Ivanova NV, Hebert PD, Hanner RH, Ormos A, Weigt LA, Moore MM, Yancy HF (2011) A single-laboratory validated method for the generation of DNA barcodes for the identification of fish for regulatory compliance. J AOAC Int 94:201–210

Hubert N, Hanner R, Holm E, Mandrak NE, Taylor E, Burridge M, Watkinson D, Dumont P, Curry A, Bentzen P (2008) Identifying Canadian freshwater fishes through DNA barcodes. PLoS One 3:e2490

Hubert N, Wibowo A, Busson F, Caruso D, Sulandari S, Nafiqoh N, Pouyaud L, Rüber L, Avarre J-C, Herder F (2015) DNA barcoding Indonesian freshwater fishes: challenges and prospects. DNA Barcodes 3:144–169

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 Journal of Biological Diversity:16

Johnson WE, O’Brien SJ (1997) Phylogenetic reconstruction of the Felidae using 16S rRNA and NADH-5 mitochondrial genes. J Mol Evol 44:S98–S116

Kohno H, Ordonio-Aguilar RS, Ohno A, Taki Y (1997) Why is grouper larval rearing difficult?: an approach from the development of the feeding apparatus in early stage larvae of the grouper, Epinephelus coioides. Ichthyol Res 44:267–274

Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

Lakra W, Verma M, Goswami M, Lal KK, Mohindra V, Punia P, Gopalakrishnan A, Singh K, Ward RD, Hebert P (2011) DNA barcoding Indian marine fishes. Mol Ecol Resour 11:60–71

Lebonah D, Dileep A, Chandrasekhar K, Sreevani S, Sreedevi B, Pramoda Kumari J (2014) DNA barcoding on bacteria: a review. Advances in Biology 2014

Lourie SA, Vincent AC (2004) A marine fish follows Wallace's line: the phylogeography of the three-spot seahorse (Hippocampus trimaculatus, Syngnathidae, Teleostei) in Southeast Asia. J Biogeogr 31:1975–1985

Lowe-Mcconnell R (1969) Speciation in tropical freshwater fishes. Biol J Linn Soc 1:51–75

Macey JR, Papenfuss TJ, Kuehl JV, Fourcade HM, Boore JL (2004) Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences. Mol Phylogenet Evol 33:22–31

Madduppa HH, Timm J, Kochzius M (2014) Interspecific, spatial and temporal variability of self-recruitment in anemonefishes. PLoS One 9:e90648

Meyer CP, Paulay G (2005) DNA barcoding: error rates based on comprehensive sampling. PLoS Biol 3:e422

Minamoto T, Uchii K, Takahara T, Kitayoshi T, Tsuji S, Yamanaka H, Doi H (2017) Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio. Mol Ecol Resour 17:324–333

Mitchell JK, Hellberg RS (2016) Use of the mitochondrial control region as a potential DNA mini-barcoding target for the identification of canned tuna species. Food Anal Methods 9:2711–2720

Mitcheson D, Sadovy Y, Liu M (2008) Functional hermaphroditism in teleosts. Fish Fish 9:1–43

Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Minamoto T, Yamamoto S, Yamanaka H, Araki H (2015) MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. R Soc Open Sci 2:150088

Morris AV, Roberts CM, Hawkins JP (2000) The threatened status of groupers (Epinephelinae). Biodivers Conserv 9:919–942

Muchlisin ZA, Thomy Z, Fadli N, Sarong MA, Siti-Azizah MN (2013) DNA barcoding of freshwater fishes from Lake Laut Tawar, Aceh Province. Indonesia Acta ichthyologica et piscatoria 43

Pavan-KUMAR A, Gireesh-Babu P, Babu PS, Jaiswar A, Krishna VH, Prasasd KP, Chaudhari A, Raje S, Chakraborty S, Krishna G (2014) Molecular phylogeny of elasmobranchs inferred from mitochondrial and nuclear markers. Mol Biol Rep 41:447–457

Pepe T, Trotta M, DI Marco I, Anastasio A, Bautista JM, Cortesi ML (2007) Fish species identification in surimi-based products. J Agric Food Chem 55:3681–3685

Prehadi, P., Sembiring, A., Kurniasih, E. M., Rahmad, R., Arafat, D., Subhan, B. & Madduppa, H. H. 2014. DNA barcoding and phylogenetic reconstruction of shark species landed in Muncar fisheries landing site in comparison with Southern Java fishing port. Biodiversitas Journal of Biological Diversity, 16

Puebla O (2009) Ecological speciation in marine v. freshwater fishes. J Fish Biol 75:960–996

Rocha L, Bowen B (2008) Speciation in coral-reef fishes. J Fish Biol 72:1101–1121

Roy D, Docker M, Hehanussa P, Heath D, Haffner G (2004) Genetic and morphological data supporting the hypothesis of adaptive radiation in the endemic fish of Lake Matano. J Evol Biol 17:1268–1276

Sadovy de Mitcheson Y, Craig MT, Bertoncini AA, Carpenter KE, Cheung WW, Choat JH, Cornish AS, Fennessy ST, Ferreira BP, Heemstra PC (2013) Fishing groupers towards extinction: a global assessment of threats and extinction risks in a billion dollar fishery. Fish Fish 14:119–136

Seehausen O, Wagner CE (2014) Speciation in freshwater fishes. Annu Rev Ecol Evol Syst 45:621–651

Sembiring A, Pertiwi NPD, Mahardini A, Wulandari R, Kurniasih EM, Kuncoro AW, Cahyani ND, Anggoro AW, Ulfa M, Madduppa H (2015) DNA barcoding reveals targeted fisheries for endangered sharks in Indonesia. Fish Res 164:130–134

Sevilla RG, Diez A, Norén M, Mouchel O, Jérôme M, Verrez-Bagnis V, van Pelt H, Favre-krey L, Krey G, Consortium TF (2007) Primers and polymerase chain reaction conditions for DNA barcoding teleost fish based on the mitochondrial cytochrome b and nuclear rhodopsin genes. Mol Ecol Notes 7:730–734

Sharp GD (1996) Oceanography of the Indonesian archipelago and adjacent areas. The Fish Resources of Western Indonesia ICLARM Stud Rev, Baseline Studies of Biodiversity, p 321

Thomsen PF, Kielgast J, Iversen LL, Møller PR, Rasmussen M, Willerslev E (2012a) Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS One 7:e41732

Thomsen PF, Kielgast J, Iversen LL, Wiuf C, Rasmussen M, Gilbert MTP, Orlando L, Willerslev E (2012b) Monitoring endangered freshwater biodiversity using environmental DNA. Mol Ecol 21:2565–2573

Wafar M, Venkataraman K, Ingole B, Khan SA, Lokabharathi P (2011) State of knowledge of coastal and marine biodiversity of Indian Ocean countries. PLoS One 6:e14613

Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PD (2005) DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society of London B: Biological Sciences 360:1847–1857

Wilcox TM, Mckelvey KS, Young MK, Jane SF, Lowe WH, Whiteley AR, Schwartz MK (2013) Robust detection of rare species using environmental DNA: the importance of primer specificity. PLoS One 8:e59520

Winterbottom R, Hanner RH, Burridge M, Zur M (2014) A cornucopia of cryptic species-a DNA barcode analysis of the gobiid fish genus Trimma (Percomorpha, Gobiiformes). ZooKeys 79

Zhang J-B, Hanner R (2011) DNA barcoding is a useful tool for the identification of marine fishes from Japan. Biochem Syst Ecol 39:31–42