Phylogenetic analysis of transparent gobies in three Sumatran lakes, inferred from mitochondrial Cytochrome Oxidase I (COI) gene
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Abstract. Roesma DI, Tjong DH, Aidil DR. 2020. Phylogenetic analysis of transparent gobies in three Sumatran lakes, inferred from mitochondrial Cytochrome Oxidase I (COI) gene. Biodiversitas 21: 43-48. The transparent gobies fish found in three lakes in Sumatra island is known as Rinuak fish (in Maninjau Lake and Singkarak Lake, West Sumatra, Indonesia) or Badar fish (in Siais Lake, North Sumatra, Indonesia), and are morphologically very similar to the Gobiopterus brachypterus. The phylogenetic study was carried out by analyzing 619 base pairs of the mitochondrial DNA cytochrome oxidase subunit I (COI) gene in 12 fish individuals from the three lakes. Rinuak and Badar fish in three populations have four haplotypes. The sequence divergences in and between populations are very low (0.0-0.5%). This value indicates that Rinuak and Badar fish are the same species with low genetic diversity. The phylogenetic tree illustrates that this fish belongs to the group of Gobiidae and a sister taxon from G. brachypterus.
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References
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Agorreta A, San Mauro D, Schliewen U, Van Tassell JL, Kovacic M, Zardoya R, Ruber L. 2013. Molecular Phylogenetics of Gobioidei and Phylogenetic Placement of European Gobies. Molecular Phylogenetics and Evolution 69: 619-633
Akihito A, Iwata T, Kobayashi T, Ikeo K, Imanishi T, Ono H, Umehara Y, Hamamatsu C, Sugiyama K, Ikeda Y, Sakamoto K, Fumihito A, Ohno S, Gojobori T. 2000. Evolutionary of Gobioid Fishes based upon a Phylogenetic Analysis of Mitochondrial Cytochrome b Genes. Gene 259: 5-15.
Aquilino SVL, Tango JM, Fontanilla IKC, Pagulayan RC, Basiao ZU, Ong PS, Quilang JP. 2011. DNA barcoding of the ichthyofauna of Taal Lake, Philippines. Molecular Ecology Resources 11: 612-619.
Aquino LMG, Tango JM, Canoy RJC, Fontanilla IKC, Basiao ZU, Ong PS, Quilang JP. 2011. DNA Barcoding of Fishes of Laguna de Bay, Philippines. Mitochondrial DNA 22(4): 143–153.
Arisuryanti T. Hasan RL, Koentjana JP. 2018. Genetic Identification of Two Mudskipper Species (Pisces: Gobiidae) from Bogowonto Lagoon (Yogyakarta, Indonesia) using COI Mitochondrial Gene as a DNA Barcoding Marker. AIP Conference Proceedings 2002: 020068-1-020068-7.
Astuti T, Yusra, Mardiah A. 2016. Studi Mutu Ikan Rinuak (Psilopsis Sp) Olahan di Danau Maninjau, Kecamatan Tanjung Raya Kabupaten Agam Sumatera Barat. (Quality Study of Processed Rinuak fish (Psilopsis Sp.) in Maninjau Lake, Tanjung Raya District, Agam Regency, West Sumatra). Katalisator 1(1). DOI: 10.22216/jk.v1i1.982.
Aurich HJ. 1938. Intern. Rev. Hydrobiol. xxxviii: 125-183.
Brown WM, George MJr, Wilson AC. 1979. Rapid Evolution of Animal Mitochondrial DNA. Proceedings of the National Academy of Sciences of the United States America 76: 1967-1971.
Burland TG. 2000. DNA STAR’s Lasergene Sequence Analysis Software. Methods Mol Biol 132: 71-91.
Cailliet GM, Love MS, Ebeling AW. 1986. Fishes. A Field and Laboratory Manual on Their Structure, Identification and Natural History. Edn1, Vol. I Waveland Press, Inc.
Chandra KF. 2012. Identifikasi Kesamaan Genetik Antara Ikan Lempuk Gobiopterus Spp. di Ranu Grati dengan Gobiopterus brachypterus Berdasarkan Sekuen Gen 12s rRNA. (Identification of Genetic Similarities between Gobiopterus Spp. in Ranu Grati Lake with Gobiopterus brachypterus based on 12s rRNA Gene). [Thesis]. Brawijaya University, Malang. [Indonesian].
Froese R, Pauly D. 2004. Fishbase. A Global Information System on Fishes. [Online]. www.fishbase.org.
Hall TA. 1999. Bio Edit: A user-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT. Nucleic Acid Symposium Series 41: 95-98.
Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM, 2004. Identification of Birds through DNA Barcodes. PLoS Biology 2:e312.
Hora SL. 1934. Rees. Indian Mus. xxxvi: 483-490.
Hubert N, Hanner R, Holm E, Mandrak N, Taylor E. 2008. Identifying Canadian Freshwater Fishes through DNA Barcodes. PLoS One 3: e2490.
Jeon HB, Choi SH, Suk HY. 2012. Exploring the Utility of Partial Cytochrome C Oxidase Subunit-1 for DNA Barcoding of Gobies. Anim. Syst. Evol. Divers 28(4): 269-278.
Jin XX, Wang R, Wei T, Tang D, Xu T. 2014. Complete Mitochondrial Genome Sequence of Tridentiger bifasciatus and Tridentiger barbatus (Perciformes, Gobiidae): A Mitogenomic Perspective on the Phylogenetic Relationships of Gobiidae. Mol Biol Rep DOI 10.1007/s11033-014-3768-3.
Johns GC, Avise JC, 1998. A Comparative Summary of Genetic Distances in the Vertebrates from the Mitochondrial Cytochrome b Gene. Molecular Biology and Evolution 15: 1481-1490.
Kartavtsev YP. 2011. Divergence at Cyt-b and Co-I mtDNA Genes on Different Taxonomic Levels and Genetics of Speciation in Animals. Mitochondrial DNA 22: 55-65. https://doi. org/10.3109/1940 1736.2011.588215.
Kartavtsev YP. 2013. Sequence Diversity at Cyt-b and Co-I mtDNA Genes in Animal Taxa Proved Neo-Darwinism. J. Phylogenetics Evol Biol 1. https://doi.org/10.4172/2329-90 02.1000120.
Keith P, Galewski T, Cattaneo-Berrebi G, Hoareau T, Berrebi P. 2005. Ubiquity of Sicyopterus lagocephalus (Teleostei: Gobioidei) and Phylogeography of the Genus Sicyopterus in the Indo-Pacific Area Inferred from Mitochondrial Cytochrome b Gene. Mol Phylogenet Evol 37: 721–732.
Kottelat M, Whitten AJ, Kartikasari SN, Wiejoatmodjo S. 1993. Freshwater Fishes of Western Indonesia and Sulawesi.Periplus Eds. (HK) Ltd., and EMDI: Indonesia, Singapore.
Kottelat M. 2013. The Fishes of the Inland Waters of Southeast Asia: A Catalogue and Core Bibliography of the Fishes Known To Occur In Freshwaters, Mangroves and Estuaries. The Raffles Bulletin of Zoology. Supplement 27: 1-663.
Koumans FP. 1931. Prelim. Revision Genera Gobioid Fish: 1-174.
McDowall RM, David BO. 2008. Gobiopterus in New Zealand (Teleostei: Gobiidae), with Observations on Sexual Dimorphism, New Zealand. Journal of Marine and FreshwaterResearch 42(3): 325-331. DOI: 10.1080/00 288330809509960.
McGlashan DJ, Hughes JM. 2001. Low levels of Genetic Differentiation Among Populations of the Freshwater Fish Hypseleotris compressa (Gobiidae: Eleotridinae): Implications for its Biology, Population Connectivity and History. Heredity 86: 222-233.
Mukerji DD. 1936. Recs. Indian Mus. xxxviii: 9-13.
Munro ISR. 1949. A New Genus and Species of Transparent Gobioid Fish from Australia. Annals and Magazine of Natural History: Series 12 2(15): 229-240. DOI: 10.1080/00222934908653984.
Nelson JS. 2006. Fishes of the world. 4th ed. John Wiley and Sons, Hoboken, NJ: 1-601.
Olii AH, Sahami FM, Hamzah SN, Pasisingi N.2019. Molecular Approach to Identify Gobioid Fishes, “Nike” and “Hundala” (Local Name), from Gorontalo Waters, Indonesia. Online Journal of Biological Sciences (1): 51-56. DOI: 10.3844/Ojbsci.201951.56.
Ott G. 2011. First Records of Gobiopterus brachypterus and Mugilogobiustigrinus from Sri Lanka (Teleostei, Perciformes, Gobiidae: Gobionellinae). Bull. Fish BioI 13(1/2): 71-75.
Periwaldi RAP. 2012. Studi Morfologi Ikan Badar Danau Siais Sumatera Utara Dan Ikan Rinuak Danau Maninjau Sumatera Barat. (Morphological Study of Badar Fish in Siais Lake, North Sumatra and Rinuak Fish in Maninjau Lake, West Sumatra). [Thesis]. Andalas University, Padang. [Indonesian]
Pezold F, 1993. Evidence for a Monophyletic Gobiinae. Copeia : 634-643.
Pfeil VDF. 2009. The Fishes of the Batang Hari drainage, Sumatra, with Description of Six New Species. Ichthyol. Explor. Freshwaters 20(1): 13-69.
Roesma, D. I., Santoso, P. 2010. Fishes in Lake Siais and adjoining rivers of the Angkola-Siondop wilderness forest ecosystem, North Sumatra, Sumatra, Indonesia. In: Yanuar A. (ed.). A Biological Assessment of the Angkola-Siondop Wilderness Forest Ecosystem, Northwestern Sumatra, Indonesia. Conservation International-Indonesia. 84–91 (Unpublished).
Roesma DI, Tjong DH, Munir W, Aidil DR. 2018. New Record Species of Puntius (Pisces: Cyprinidae) from West Sumatra based on Cytochrome Oxidase I Gene. International Journal on Advanced Science Engineering Information Technol 8(1): 250-256.
Roesma DI, Tjong DH, Karlina W, Aidil DR. 2019. Taxonomy Confirmation of Puntius cf. binotatus from Gunung Tujuh Lake, Jambi, Indonesia based on Cytochrome Oxidase-I (COI) Gene. Biodiversitas 20(1)
Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R. 2003. DnaSP, DNA Polymorphism Analyses by the Coalescent and Other Methods. Bioinformatics 19: 2496-2497. https:// doi.org /10. 1093/ bioinformatics/btg359.
Sodhi NS, Brook, BW. 2006. Southeast Asian Biodiversity in Crisis. Cambridge University Press, Cambridge.
Taillebois L, Castelin M, Lord C, Chabarria R, DettaI A, Keith P. 2014. New Sicydiinae Phylogeny (Teleostei: Gobioidei) inferred from Mitochondrial and Nuclear Genes: Insights on Systematics and Ancestral Areas. Molecular Phylogenetics and Evolution 70: 260-271.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA 6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol Biol Evol 30: 2725–2729.
Thacker CE. 2009. Phylogeny of Gobioidei and Placement within Acanthomorpha, with a New Classification and Investigation of Diversification and Character Evolution. Copeia 1: 93-104.
Thacker CE. 2015. Biogeography of Goby Lineages (Gobiiformes: Gobioidei): Origin, Invasions and Extinction throughout the Cenozoic. Journal of Biogeography 42: 1615-1625.
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The Clustal X Windows Interface: Flexible Strategies for Multiple Sequence Alignment Aided by Quality Analysis Tools. Nuclead Acids Research 24: 4876-4882.
Tornabene L, Ahmadia G, Berumen M, Smith D, Jompa J, Pezold F. 2013. Evolution of Microhabitat Association and Morphology in A Diverse Group of Cryptobenthic Coral Reef Fishes (Teleostei: Gobiidae: Eviota). Molecular Phylogenetics and Evolution 66: 391-400.
Wang ZD, Liao J, Huang CQ, Long SS, Zhang S, Guo YS, Liu L, Liu CW. 2017. Significant Genetic Differentiation of Gobiopterus lacustris, a Newly Recorded Transparent Goby in China. Mitochondrial DNA Part A DOI: 10.1080/24701394.2017.1357712.
Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA Barcoding Australia’s Fish Species. Philos Trans R Soc B 360: 1847-1857.
Ward RD, Holmes BH. 2007. An Analysis of Nucleotide and Amino Acid Variability in the Barcode Region of Cytochrome C Oxidase I (CO1) in fishes. Molecular Ecology Notes. Molecular Ecology Notes 7: 899-907.
Agorreta A, San Mauro D, Schliewen U, Van Tassell JL, Kovacic M, Zardoya R, Ruber L. 2013. Molecular Phylogenetics of Gobioidei and Phylogenetic Placement of European Gobies. Molecular Phylogenetics and Evolution 69: 619-633
Akihito A, Iwata T, Kobayashi T, Ikeo K, Imanishi T, Ono H, Umehara Y, Hamamatsu C, Sugiyama K, Ikeda Y, Sakamoto K, Fumihito A, Ohno S, Gojobori T. 2000. Evolutionary of Gobioid Fishes based upon a Phylogenetic Analysis of Mitochondrial Cytochrome b Genes. Gene 259: 5-15.
Aquilino SVL, Tango JM, Fontanilla IKC, Pagulayan RC, Basiao ZU, Ong PS, Quilang JP. 2011. DNA barcoding of the ichthyofauna of Taal Lake, Philippines. Molecular Ecology Resources 11: 612-619.
Aquino LMG, Tango JM, Canoy RJC, Fontanilla IKC, Basiao ZU, Ong PS, Quilang JP. 2011. DNA Barcoding of Fishes of Laguna de Bay, Philippines. Mitochondrial DNA 22(4): 143–153.
Arisuryanti T. Hasan RL, Koentjana JP. 2018. Genetic Identification of Two Mudskipper Species (Pisces: Gobiidae) from Bogowonto Lagoon (Yogyakarta, Indonesia) using COI Mitochondrial Gene as a DNA Barcoding Marker. AIP Conference Proceedings 2002: 020068-1-020068-7.
Astuti T, Yusra, Mardiah A. 2016. Studi Mutu Ikan Rinuak (Psilopsis Sp) Olahan di Danau Maninjau, Kecamatan Tanjung Raya Kabupaten Agam Sumatera Barat. (Quality Study of Processed Rinuak fish (Psilopsis Sp.) in Maninjau Lake, Tanjung Raya District, Agam Regency, West Sumatra). Katalisator 1(1). DOI: 10.22216/jk.v1i1.982.
Aurich HJ. 1938. Intern. Rev. Hydrobiol. xxxviii: 125-183.
Brown WM, George MJr, Wilson AC. 1979. Rapid Evolution of Animal Mitochondrial DNA. Proceedings of the National Academy of Sciences of the United States America 76: 1967-1971.
Burland TG. 2000. DNA STAR’s Lasergene Sequence Analysis Software. Methods Mol Biol 132: 71-91.
Cailliet GM, Love MS, Ebeling AW. 1986. Fishes. A Field and Laboratory Manual on Their Structure, Identification and Natural History. Edn1, Vol. I Waveland Press, Inc.
Chandra KF. 2012. Identifikasi Kesamaan Genetik Antara Ikan Lempuk Gobiopterus Spp. di Ranu Grati dengan Gobiopterus brachypterus Berdasarkan Sekuen Gen 12s rRNA. (Identification of Genetic Similarities between Gobiopterus Spp. in Ranu Grati Lake with Gobiopterus brachypterus based on 12s rRNA Gene). [Thesis]. Brawijaya University, Malang. [Indonesian].
Froese R, Pauly D. 2004. Fishbase. A Global Information System on Fishes. [Online]. www.fishbase.org.
Hall TA. 1999. Bio Edit: A user-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT. Nucleic Acid Symposium Series 41: 95-98.
Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM, 2004. Identification of Birds through DNA Barcodes. PLoS Biology 2:e312.
Hora SL. 1934. Rees. Indian Mus. xxxvi: 483-490.
Hubert N, Hanner R, Holm E, Mandrak N, Taylor E. 2008. Identifying Canadian Freshwater Fishes through DNA Barcodes. PLoS One 3: e2490.
Jeon HB, Choi SH, Suk HY. 2012. Exploring the Utility of Partial Cytochrome C Oxidase Subunit-1 for DNA Barcoding of Gobies. Anim. Syst. Evol. Divers 28(4): 269-278.
Jin XX, Wang R, Wei T, Tang D, Xu T. 2014. Complete Mitochondrial Genome Sequence of Tridentiger bifasciatus and Tridentiger barbatus (Perciformes, Gobiidae): A Mitogenomic Perspective on the Phylogenetic Relationships of Gobiidae. Mol Biol Rep DOI 10.1007/s11033-014-3768-3.
Johns GC, Avise JC, 1998. A Comparative Summary of Genetic Distances in the Vertebrates from the Mitochondrial Cytochrome b Gene. Molecular Biology and Evolution 15: 1481-1490.
Kartavtsev YP. 2011. Divergence at Cyt-b and Co-I mtDNA Genes on Different Taxonomic Levels and Genetics of Speciation in Animals. Mitochondrial DNA 22: 55-65. https://doi. org/10.3109/1940 1736.2011.588215.
Kartavtsev YP. 2013. Sequence Diversity at Cyt-b and Co-I mtDNA Genes in Animal Taxa Proved Neo-Darwinism. J. Phylogenetics Evol Biol 1. https://doi.org/10.4172/2329-90 02.1000120.
Keith P, Galewski T, Cattaneo-Berrebi G, Hoareau T, Berrebi P. 2005. Ubiquity of Sicyopterus lagocephalus (Teleostei: Gobioidei) and Phylogeography of the Genus Sicyopterus in the Indo-Pacific Area Inferred from Mitochondrial Cytochrome b Gene. Mol Phylogenet Evol 37: 721–732.
Kottelat M, Whitten AJ, Kartikasari SN, Wiejoatmodjo S. 1993. Freshwater Fishes of Western Indonesia and Sulawesi.Periplus Eds. (HK) Ltd., and EMDI: Indonesia, Singapore.
Kottelat M. 2013. The Fishes of the Inland Waters of Southeast Asia: A Catalogue and Core Bibliography of the Fishes Known To Occur In Freshwaters, Mangroves and Estuaries. The Raffles Bulletin of Zoology. Supplement 27: 1-663.
Koumans FP. 1931. Prelim. Revision Genera Gobioid Fish: 1-174.
McDowall RM, David BO. 2008. Gobiopterus in New Zealand (Teleostei: Gobiidae), with Observations on Sexual Dimorphism, New Zealand. Journal of Marine and FreshwaterResearch 42(3): 325-331. DOI: 10.1080/00 288330809509960.
McGlashan DJ, Hughes JM. 2001. Low levels of Genetic Differentiation Among Populations of the Freshwater Fish Hypseleotris compressa (Gobiidae: Eleotridinae): Implications for its Biology, Population Connectivity and History. Heredity 86: 222-233.
Mukerji DD. 1936. Recs. Indian Mus. xxxviii: 9-13.
Munro ISR. 1949. A New Genus and Species of Transparent Gobioid Fish from Australia. Annals and Magazine of Natural History: Series 12 2(15): 229-240. DOI: 10.1080/00222934908653984.
Nelson JS. 2006. Fishes of the world. 4th ed. John Wiley and Sons, Hoboken, NJ: 1-601.
Olii AH, Sahami FM, Hamzah SN, Pasisingi N.2019. Molecular Approach to Identify Gobioid Fishes, “Nike” and “Hundala” (Local Name), from Gorontalo Waters, Indonesia. Online Journal of Biological Sciences (1): 51-56. DOI: 10.3844/Ojbsci.201951.56.
Ott G. 2011. First Records of Gobiopterus brachypterus and Mugilogobiustigrinus from Sri Lanka (Teleostei, Perciformes, Gobiidae: Gobionellinae). Bull. Fish BioI 13(1/2): 71-75.
Periwaldi RAP. 2012. Studi Morfologi Ikan Badar Danau Siais Sumatera Utara Dan Ikan Rinuak Danau Maninjau Sumatera Barat. (Morphological Study of Badar Fish in Siais Lake, North Sumatra and Rinuak Fish in Maninjau Lake, West Sumatra). [Thesis]. Andalas University, Padang. [Indonesian]
Pezold F, 1993. Evidence for a Monophyletic Gobiinae. Copeia : 634-643.
Pfeil VDF. 2009. The Fishes of the Batang Hari drainage, Sumatra, with Description of Six New Species. Ichthyol. Explor. Freshwaters 20(1): 13-69.
Roesma, D. I., Santoso, P. 2010. Fishes in Lake Siais and adjoining rivers of the Angkola-Siondop wilderness forest ecosystem, North Sumatra, Sumatra, Indonesia. In: Yanuar A. (ed.). A Biological Assessment of the Angkola-Siondop Wilderness Forest Ecosystem, Northwestern Sumatra, Indonesia. Conservation International-Indonesia. 84–91 (Unpublished).
Roesma DI, Tjong DH, Munir W, Aidil DR. 2018. New Record Species of Puntius (Pisces: Cyprinidae) from West Sumatra based on Cytochrome Oxidase I Gene. International Journal on Advanced Science Engineering Information Technol 8(1): 250-256.
Roesma DI, Tjong DH, Karlina W, Aidil DR. 2019. Taxonomy Confirmation of Puntius cf. binotatus from Gunung Tujuh Lake, Jambi, Indonesia based on Cytochrome Oxidase-I (COI) Gene. Biodiversitas 20(1)
Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R. 2003. DnaSP, DNA Polymorphism Analyses by the Coalescent and Other Methods. Bioinformatics 19: 2496-2497. https:// doi.org /10. 1093/ bioinformatics/btg359.
Sodhi NS, Brook, BW. 2006. Southeast Asian Biodiversity in Crisis. Cambridge University Press, Cambridge.
Taillebois L, Castelin M, Lord C, Chabarria R, DettaI A, Keith P. 2014. New Sicydiinae Phylogeny (Teleostei: Gobioidei) inferred from Mitochondrial and Nuclear Genes: Insights on Systematics and Ancestral Areas. Molecular Phylogenetics and Evolution 70: 260-271.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA 6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol Biol Evol 30: 2725–2729.
Thacker CE. 2009. Phylogeny of Gobioidei and Placement within Acanthomorpha, with a New Classification and Investigation of Diversification and Character Evolution. Copeia 1: 93-104.
Thacker CE. 2015. Biogeography of Goby Lineages (Gobiiformes: Gobioidei): Origin, Invasions and Extinction throughout the Cenozoic. Journal of Biogeography 42: 1615-1625.
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The Clustal X Windows Interface: Flexible Strategies for Multiple Sequence Alignment Aided by Quality Analysis Tools. Nuclead Acids Research 24: 4876-4882.
Tornabene L, Ahmadia G, Berumen M, Smith D, Jompa J, Pezold F. 2013. Evolution of Microhabitat Association and Morphology in A Diverse Group of Cryptobenthic Coral Reef Fishes (Teleostei: Gobiidae: Eviota). Molecular Phylogenetics and Evolution 66: 391-400.
Wang ZD, Liao J, Huang CQ, Long SS, Zhang S, Guo YS, Liu L, Liu CW. 2017. Significant Genetic Differentiation of Gobiopterus lacustris, a Newly Recorded Transparent Goby in China. Mitochondrial DNA Part A DOI: 10.1080/24701394.2017.1357712.
Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA Barcoding Australia’s Fish Species. Philos Trans R Soc B 360: 1847-1857.
Ward RD, Holmes BH. 2007. An Analysis of Nucleotide and Amino Acid Variability in the Barcode Region of Cytochrome C Oxidase I (CO1) in fishes. Molecular Ecology Notes. Molecular Ecology Notes 7: 899-907.
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