Genetic diversity among the endemic barb Barbodes tumba (Teleostei: Cyprinidae) populations from Mindanao, Philippines

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Onaya P. Abdulmalik-Labe
Jonas P. Quilang


Barbodes tumba is an important fishery resource in Lake Lanao and nearby areas in Mindanao, Philippines. It is one of only two remaining endemic cyprinids out of 20 endemic species originally reported in the lake. In this study, specimens were obtained from fishermen and fish vendors from the lake and from three other sites in Mindanao, namely, Nunungan Lake in Lanao del Norte, Dagoyanan Lake in Lanao del Sur, and Pulangi River in Bukidnon. Eighty-seven haplotypes were recovered from the 122 complete mitochondrial DNA control region sequences analysed. All four populations showed high levels of haplotype (0.662–0.976) and nucleotide (0.552–2.736 %) diversities. Pairwise FST values showed high genetic divergence between populations. Maximum likelihood tree and median-joining network showed geographic separation of Bukidnon population from the three other populations. Lanao Lake specimens also formed a distinct group, which clustered with nine specimens from Dagoyanan Lake. All the other specimens from Dagoyanan clustered with specimens from Nunungan Lake. Despite the high intra- and inter-population genetic variation found in the species, its populations need to be protected and managed so that it will not suffer the same fate as that of the other endemic cyprinids which are now reported to be extinct.

Article Details

Author Biographies

Onaya P. Abdulmalik-Labe, Biology Department, College of Natural Sciences and Mathematics, Mindanao State University, Marawi City, Philippines

Biology Department Instructor

Jonas P. Quilang, Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, Philippines

Institute of Biology, University of the Philippines, Diliman

Associate Professor


Altschul, S.F., W. Gish, W. Miller, E.W. Myers & D.J. Lipman (1990). Basic local alignment search tool. Journal of Molecular Biology 215: 403–410.

Bandelt, H., P. Forster & A. Röhl (1999). Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16(1): 37–48.

Boonkusol, D. & W. Tongbai (2016). Genetic variation of striped snakehead fish (Channa striata) in river basin of Central Thailand inferred from mtDNA COI gene sequences analysis. Journal of Biological Sciences 16(1-2): 37–43.

Brooks, J.L. (1950). Speciation in ancient lakes (concluded). The Quarterly Review of Biology 25(2): 131–176.

Cek, S., N. Bromage, C. Randall & K. Rana (2001). Oogenesis, hepatosomatic and gonadosomatic indexes, and sex ratio in rosy barb (Puntius conchonius). Turkish Journal of Fisheries and Aquatic Sciences 1(1): 33–41.

Darriba, D., G.L. Taboada, R. Doallo & D. Posada (2012). jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9(8): 772.

Escudero, P.E. (1994). Lake Lanao fisheries: problems and recommendations. The Philippine Biota 27(1): 8–18.

Excoffier, L. & H.E. Lischer (2010). Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10(3): 564–567.

Fowler, H.W. (1933). Descriptions of new fishes obtained 1907 to 1910, chiefly in the Philippine Islands and adjacent seas. Proceedings of the Academy of Natural Sciences of Philadelphia 85: 233–367.

Frey, G. (1969). A limnological reconnaissance of Lake Lanao. Internationale Vereinigung für Theoretische und Angewandte Limnologie: Verhandlungen 17(2): 1090–1102.

Fu, Y.X. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147(2): 915–925.

Grant, W.A.S. & B.W. Bowen (1998). Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. Journal of Heredity 89(5): 415–426.

Greenwood, P.H. (1984). What is a species flock? pp13–20. In: Echelle, A.E. & I. Kornfield (eds.). Evolution of Fish Species Flocks. University of Maine Press, Orono, 257pp.

Harpending, H.C. (1994). Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Human Biology 66(4): 591–600.

Hasegawa, M., H. Kishino & T.A. Yano (1985). Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22(2): 160–174.

Herre, A.W.C.T. (1924). Distribution of true fresh-water fishes in the Philippines I. The Philippine Cyprinidae. Philippine Journal of Science 24(3): 249–307.

Herre, A.W.C.T. (1926). Two new fishes from Lake Lanao. Philippine Journal of Science 29(4): 499–502.

Herre, A.W.C.T. (1932). Five new Philippine fishes. Copeia 1932(3): 139–142.

Herre, A.W.C.T. (1953). Checklist of Philippine fishes. Washington, DC: United States Government Printing Office, 977pp.

Hoff-Olsen, P., B. Mevag, E. Staalstrom, B. Hovde, T. Egeland & B. Olaisen (1999). Extraction of DNA from decomposed human tissue: An evaluation of five extraction methods for short tandem repeat typing. Forensic Science International 105: 171–183.

Ismail, G.B. & P.T. Escudero (2011).Threatened fishes of the world: Puntius lindog Herre, 1924 (Cyprinidae). Environmental Biology of Fishes 91(1): 117–118.

Ismail, G.B., D.B. Sampsom & D.L. Noakes (2014). The status of Lake Lanao endemic cyprinids (Puntius species) and their conservation. Environmental Biology of Fishes 97(4): 425–434.

Kornfield, I. (1982). Report from Mindanao. Copeia 1982(2): 493–495.

Kornfield, I. & K.E. Carpenter (1984). Cyprinids of Lake Lanao, Philippines: taxonomic validity, evolutionary rates and speciation scenarios, pp. 69–84. In: Echelle, A.E., I. Kornfield (eds.). Evolution of Fish Species Flocks. University of Maine Press, Orono, 257pp.

Kumar, S., Stecher, G. & K. Tamura (2016). MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33(7): 1870–1874.

Leigh, J.W. & D. Bryant (2015). PopART: Full-feature software for haplotype network construction. Methods in Ecology and Evolution 6(9): 1110–1116.

Librado, S.P. & L.J.A. Rozas (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11): 1451–1452.

Miller, S.A., D.D. Dykes & H.F.R.N. Polesky (1988). A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Research 16(3): 1215.

Myers, G.S. (1960). The endemic fish fauna of Lake Lanao, and the evolution of higher taxonomic categories. Evolution 14(3): 323–333.

Ray, N., M. Currat & L. Excoffier (2003). Intra-deme molecular diversity in spatially expanding populations. Molecular Biology and Evolution 20(1): 76–86.

Rogers, A.R. & H. Harpending (1992). Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9(3): 552–569.

Sanguila, W.M., A. Rosales, B. Tabaranza Jr. & S. Mohamad (1975). Notes on the food habits of Puntius sirang and Glossogobius giuris. Mindanao Journal 1: 3–11.

Schneider, S. & L. Excoffier (1999). Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics 152(3): 1079–1089.

Staden, R., K.F. Beal & J.K. Bonfield (2000). The Staden package, 1998. Methods in Molecular Biology 132: 115–130.

Tan, M.T.C., J.C. Jumawan & J.P. Quilang (2016). Low genetic diversity in Clarias macrocephalus Günther, 1864 (Siluriformes: Claridae) populations in the Philippines and its implications for conservation and management. Journal of Threatened Taxa 8(6): 8849–8859.

Targonska, K. & D. Kucharczyk (2012). Reproduction of the model fish: Rosy barb (Puntius conchonius), under controlled conditions. Polish Journal of Natural Sciences 27(2): 215–227.

Thompson, J.D., D.G. Higgins & T.J. Gibson (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22(22): 4673–4680.

Untergasser, A., I. Cutcutache, T. Koressaar, J. Ye, B.C. Faircloth, M. Remm & S.G. Rozen (2012). Primer3-new capabilities and interfaces. Nucleic Acids Research 40(15): e115.

Villaluz, D.K. (1966). The Lake Lanao fisheries and their conservation. Bureau of Printing, Manila, 53pp.

Wang, J.P., K.C. Hsu & T.Y. Chiang (2000). Mitochondrial DNA phylogeography of Acrossocheilus paradoxus (Cyprinidae) in Taiwan. Molecular Ecology 9(10): 1483–1494.

Wood, C.E. (1966). Two species of Cyprinidae from north central Mindanao. Philippine Journal of Science 95: 411–423.

World Conservation Monitoring Centre. (1996). Barbodes tumba. The IUCN Red List of Threatened Species 1996: e. T18902A8677864. Retrieved on 07 October 2017.