Genetic diversity and population structure of the African catfish, Clarias gariepinus (Burchell, 1822) in Kenya: implication for conservation and aquaculture

James E. Barasa, Sinebongo Mdyogolo, Romulus Abila, Johannes Paul Grobler, Robert A. Skilton, Hesmari Bindeman, Moses Ndotono Njahira, Emily J. Chemoiwa, Otto G. Dangasuk, Boaz Kaunda-Arara, Erik Verheyen


African catfish, Clarias gariepinus, is an important species in aquaculture and fisheries in Kenya. Mitochondrial D-loop control region was used to determine genetic variation and population structure in samples of C. gariepinus from 10 sites including five natural populations (Lakes Victoria (LVG), Kanyaboli (LKG), Turkana (LTA), Baringo (LBA) and Jipe (LJP), and five farms (Sangoro Aquaculture Center (SAN), Sagana Aquaculture Centre (SAG), University of Eldoret Fish Farm (UoE), Kibos Fish Farm (KIB), and Wakhungu Fish Farm (WKU)) in Kenya. Similarly, samples from eight localities (four natural populations: LVG/LKG, LTA, LBA, and four farmed: SAN, SAG, KIB, UoE) were genotyped using six microsatellite DNA loci. For the D-loop control region, samples from natural sites exhibited higher numbers of haplotypes and haplotype diversities compared to farmed samples, and 88.2% of haplotypes were private. All except LJP and LTA shared haplotypes, and the highest number of shared haplotypes (8) was detected in KIB. The 68 haplotypes we found in 268 individuals grouped into five phylogenetic clades: LVG/LKG, LTA, LBA, LJP and SAG. Haplotypes of farmed C. gariepinus mostly have haplotypes typical of LVG/LKG, and some shared haplotypes of the LBA population. Microsatellite analysis showed farmed samples have higher numbers of alleles than natural samples, but higher observed and expected heterozygosity levels were found in samples of natural populations. Fifteen pair-wise comparisons had significantly different FST values. All samples were in Hardy-Weinberg equilibrium. Samples from the eight localities grouped into four genetic clusters (LVG/LKG, LTA, LBA and SAG), indicating genetically distinct populations, which should be considered for aquaculture and conservation.


mitochondrial DNA; aquaculture; African catfish; microsatellites; population structure; conservation

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Alam M.S. & Islam M.S. (2005). Population genetic structure of the major Indian carp Catla catla (Hamilton) revealed by microsatellite DNA markers. Aquaculture 246: 151–160.

Allendorf R.W. (1986). Genetic drift and the loss of alleles versus heterozygosity. Zoo Biology 5: 181–190.

Allendorf F.W. & Waples R.S. (1996). Conservation and genetics of salmonid fishes. In: Avise J.C. & Hamrick J.L. (eds) Conservation Genetics: Case Histories from Nature: 238–501. New York, Chapman and Hall.

Aloo P.A. (2003). Biological diversity of Yala swamp lakes, with special emphasis on fish species composition, in relation to changes in the Lake Victoria basin Kenya: threats and conservation measures. Biodiversity Conservation 12: 905–920.

Anene S.N. & Tianxiang G. (2007). Is the Dutch domesticated strain of Clarias gariepinus (Burchell, 1822) a hybrid? African Journal of Biotechnology 6 (8): 1072–1076.

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

Barasa J.E., Abila R., Grobler J.P., Dangasuk O.G., Njahira M.N. & Kaunda-Arara B. (2014). Genetic diversity and gene flow in Clarias gariepinus from Lakes Victoria and Kanyaboli, Kenya. African Journal of Aquatic Science 39 (3): 287–293.

Barasa J.E., Abila R., Grobler J.P., Agaba M., Chemoiwa E.J. & Kaunda-Arara B. (2016). High genetic diversity and population differentiation in Clarias gariepinus (Burchell, 1822) of Yala swamp: Evidence from mitochondrial DNA sequences. Journal of Fish Biology 89 (6): 2557–2570.

Barluenga M. & Meyer A. (2010). Phylogeography, colonization and population history of the Midas species complex (Amphilophus spp.) in the Nicaraguan crater lakes. BMC Evolutionary Biology 10: 326–346.

Beadle L.C. (1974). The Inland Waters of Tropical Africa: An Introduction to Tropical Limnology. Longman, London.

Bessem I., Verschuren D., Russell J.M., Hus J., Mees F. & Cumming B.F. (2008). Palaeolimnological evidence for widespread late 18th century drought across equatorial East Africa. Palaeogeography, Palaeoclimatology, Palaeoecology 259: 107–120.

Bruton M.N. (1988). Systematics and biology of clariid catfish. In: Hecht T., Uys W. & Brit P.J. (eds) The culture of sharptooth catfish in southern Africa. South African National Scientific Programmes Report no. 153. J.L.B. Smith Institute of Ichthyology.

Cambray J.A. & Van Der Waal B.C.W. (2006). Dutch domesticated Clarias with mixed genetic background now used in aquaculture in South Africa, with unpredictable consequences for biodiversity. African Journal of Aquatic Science 31 (1): 151–153.

Castric V., Bernatchez L., Belkhir L. & Bonhomme F. (2002). Heterozygote deficiencies in small lacustrine populations of brook charr Salvelinus fontinalis Mitchill (Pisces, Salmonidae): a test of alternative hypotheses. Heredity 89: 27–35.

Chepkirui-Boit V., Ngugi C.C., Bowman J., Oyoo E.O., Rasowo J., Bundi J.M. & Cherop L. (2011). Growth performance, survival, feed utilization and nutrient utilization of the African catfish, Clarias gariepinus co-fed Artemia and a micro-diet containing atyid shrimp (Caridina nilotica) during weaning. Aquaculture Nutrition 17: e82–e89.

Chitamwebwa D., Kamanyi J., Kayungi J., Nabbongo H., Ogolla A. & Ojuok J. (2009). The present status of the hook fishery and its impact on fish stocks of Lake Victoria. African Journal of Tropical Hydrobiology and Fisheries 12: 78–82.

Cunningham E.P. & Meghen C.M. (2001). Biological identification systems: genetic markers. Scientific and Technical Review of the Office International des Epizooties 20 (2): 491–499.

De Graaf G.J., Galemoni F. & Banzoussi B. (1995). Artificial reproduction and fingerling production of the African catfish, Clarias gariepinus in protected and unprotected ponds. Aquaculture Research 26: 233–242.

Dumont H.J. (1986). The Nile River system. In: Davis B.R. & Walkers K.F. (eds) The Ecology of River Systems: 61–74. W. Junk Publishers, Dordrecht.

Earl D.A. & Vonholdt B.M. (2012). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4: 359–361.

Eknath A.E., Tayamen M.M., Palada De-VERA M.S., Danting J.C., Reyes R.A., Dionisio E.E., Capili J.B., Bolivar H.L., Abella T.A., Circa A.V., Bentsen H.B., Gjerde B., Gjedrem T. & Pullin R.S.V. (1993). Genetic improvement of farmed tilapias: the growth performance of 8 strains of Oreochromis niloticus tested in different farm environments. Aquaculture 111: 171–188.

Evanno G., Regnaut S. & Godet J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611–2620.

Excoffier L., Laval G. & Schneider S. (2005). Arlequin: an integrated software package for population genetics data analysis. Version 3.0. Computational and Molecular Population Genetics Laboratory (CMPGL). Institute of Zoology, University of Berne, Berne (Switzerland).

Fisheries Frame Survey (2006). Implementation of a Fisheries Management Plan. In: National Report on the Lake Victoria (Kenya) EDF Project no. 8 ACP ROR 029: 8–24. Ministry of Livestock and Fisheries Development, Nairobi.

Franklin I.R. & Frankharm R. (1998). How large must populations be to retain evolutionary potential? Animal conservation 1: 69–73.

Galbusera P., Volckaert F.A.M., Hellemans B. & Ollevier F. (1996). Isolation and characterization of microsatellite markers in the African catfish, Clarias gariepinus (Burchell 1822). Molecular Ecology 5: 703–705.

Giddelo C.S., Arndt A.D. & Volckaert F.A.M. (2002). Impact of rifting and hydrography on the genetic structure of Clarias gariepinus in eastern Africa. Journal of Fish Biology 60: 1252–1266.

Goudswaard K.P.C. & Witte F. (1997). The catfish fauna of Lake Victoria after the Nile perch upsurge. Environmental Biology of Fishes 49: 21–43.

Grobler J.P., Hoffman L.C. & Prinsloo J.F. (1997). A comparison of allozyme heterozygosity and life history variables in four strains of African catfish Clarias gariepinus. South African Journal of Aquatic Science 23 (1): 31–41.

Hansen M.M., Simonsen V., Mensberg K.L.D., Sarder M.D.R.I. & Ala M.D.S. (2006). Loss of genetic variation in hatchery-reared Indian major carp. Journal of Fish Biology 69 (Supplement B): 229–241.

Hatfield T. & Schluter D. (1999). Ecological speciation in sticklebacks: environment-dependent hybrid fitness. Evolution 53: 866–873.

Hedrick P.W. & Kalinowski S.T. (2000). Inbreeding depression in conservation biology. Annual Review of Ecology and Systematics 31: 139–162.

Hogendoorn H. & Vismans M.M. (1980). Controlled propagation of the African catfish, Clarias lazera. II. Artificial reproduction. Aquaculture 21: 39–53.

Huff D.D., Miller M.L., Chizinski J.C. & Bruce V. (2011). Mixed-source reintroductions lead to out-breeding depression in second-generation descendants of a native North-American fish. Molecular Ecology 20: 4246–4258.

Izquierdo M.S., Fernandez-Palacios H. & Tacon A.G.J. (2001). Effect of brood stock nutrition on reproductive performance of fish. Aquaculture 197: 25–42.

Kaufman L. & Ochumba P. (1993). Evolutionary and conservation biology of cichlid fishes as revealed by faunal remnants in the Northern Lake Victoria. Conservation Biology 7 (3): 719–730.

Knaepkens G., Knapen D., Bervoets L., Hanfling B., Verheyen E. & Eens M. (2002). Genetic diversity and condition factor: a significant relationship in Flemish but not in German populations of the European bullhead (Cottus gobio). Heredity 89: 280–287.

Kocher T.D., Lee W.J., Soboleska H., Penman D. & Mcandrew B. (1998). A genetic linkage map of a cichlid fish, the Tilapia (Oreochromis niloticus). Genetics 148: 1225–1232.

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

Lind C.E., Brummett R.E. & Ponzoni R.W. (2012). Exploitation and conservation of fish genetic resources in Africa: issues and priorities for aquaculture development and research. Reviews in Aquaculture 4: 125–141.

Macharia S.K., Ngugi C.C. & Rasowo J. (2005). Comparative study of hatching rates of African catfish (Clarias gariepinus Burchell 1822) eggs on different substrates. NAGA, World Fish Center Quarterly 28 (3–4): 23–27.

Mcclelland E.K. & Naish K.A. (2007). What is the fitness outcome of crossing unrelated fish populations? A meta-analysis and an evaluation of future research directions. Conservation Genetics 8: 397–416.

Meyer A. (1994). DNA technology and phylogeny of fish. In: Beaumont A.R. (ed.) Molecular Systematics and Evolution of Marine Organisms: 219–248. Chapman and Hall, London.

Mkumbo O.C. & Mlaponi E. (2007). Impact of the baited hook fishery on the recovering endemic fish species in Lake Victoria. Aquatic Ecosystem Health and Management 10 (4): 458–466.

Musa S.M., Aura C.M., Ngugi C.C. & Kundu R. (2012). The effect of three different feed types on growth performance and survival of Clarias gariepinus fry reared in a hatchery. ISRN Zoology 2012: 1–6.

Nazia A.K., Suzana M., Azhar H., Nguyen Thuy T.T. & Siti Azizah M.N. (2010). No genetic differentiation between geographically isolated populations of Clarias macrocephalus in Malaysia revealed by sequences of mtDNA cytochrome b and D-loop gene regions. Journal of Applied Ichthyology 26: 568–570.

Ndiwa T.C., Nyingi D.W., Claude J. & Agnese F. (2016). Morphological variations of wild populations of Nile tilapia (Oreochromis niloticus) living in extreme environmental conditions in the Kenyan Rift-Valley. Environmental Biology of Fishes 99: 4773–485.

Ngugi C.C., Amadiva J., Veverica K.L., Bowman J., Imende S., Nyandat B. & Matolla G. (2003). On-farm trials in Kenya change attitudes of fish farmers and extensionists. Samaki News I.

Norris A.T., Bradley D.G. & Cunningham E.P. (1999). Microsatellite genetic variation between and within farmed and wild Atlantic salmon (Salmo salar) populations. Aquaculture 180: 247–264.

Nyina-Wamwiza L., Wathelet B., Richir J., Rollin X. & Kestemont P. (2010). Partial or total replacement of fish meal by local agricultural by-products in diets of juvenile African catfish: growth performance, feed efficiency and digestibility. Aquaculture Nutrition 16: 237–247.

Park S.D.E. (2001). Trypanotolerance in West African Cattle and the Population Genetic Effects of Selection. PhD Thesis, University of Dublin, Dublin.

Partridge T.C., Wood B.A. & deMenocal P.B. (1995). The influence of global climate change and regional uplift on large-mammalian evolution in East and southern Africa. In: Vrba E.S., Denton G.H., Partridge G.C. & Burckle L.H. (eds) Paleoclimate and Evolution, with Emphasis on Human Origins: 331–355. Yale University Press, London and New Haven.

Peakall R. & Smouse P.E. (2012). GenALEx 6.5. Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28: 2537–2539.

Policansky D. & Magnuson J.J. (1998). Genetics, metapopulations and ecosystem management of fisheries. Ecological Applications 8 (supplement 1): S119–S123.[S119:GMAEMO]2.0.CO;2

Ponzoni R.W. & Nguyen N.H. (2008). Foreword. In: Ponzoni R.W. & Nguyen N.H. (eds) Proceedings of a workshop on the development of a Genetic improvement programme for the African catfish, Clarias gariepinus, Accra, Ghana, 5–9th November, 2007: vi. The WorldFish Center, Penang (Malaysia).

Ponzoni R.W., Nguyeni N.H. & Khaw H.I. (2009). Genetic improvement programmes for aquaculture species in the developing countries: Prospects and challenges. In: Proceedings of the 18th Conference of the Association for Advancement of Animal breeding and Genetics, September 2011, Perth, Australia: 342–349. AAABG, Roseworthy, South Australia. Available from [accessed 8 August 2017].

Popoola M.O., Fasakin E.A. & Awopetu J.I. (2014). Genetic variability in wild and cultured populations of Clarias gariepinus using Random Amplified Polymorphic DNA (RAPD) markers. Croatian Journal of Fisheries 72 (1): 5–11.

Posada D.A. & Crandall K.A. (1998). MODELTEST: Testing the model of DNA substitution. Bioinformatics 14: 817–818.

Pritchard J.K., Stephens M. & Donnelly P. (2000). Inference of population structure using multi-locus genotype data. Genetics 155: 945–959.

Rasowo J., Auma E., Ssanyu G. & Ndunguru M. (2008). Does African catfish (Clarias gariepinus) affect rice in integrated rice-fish culture in Lake Victoria Basin, Kisumu? African Journal of Environmental Science and Technology 2 (10): 336–341.

Roodt-Wilding R., Swart B.L. & Impson N.D. (2010). Genetically distinct Dutch domesticated Clarias gariepinus used in aquaculture in southern Africa. African Journal of Aquatic Science 35: 241–249.

State Department of Fisheries (2013). Fisheries statistical Bulletin, 2013. Ministry of Agriculture, Livestock and Fisheries, Nairobi.

Sukmanomon S., Senanan W., Kapuscinski A.R. & Na-Nakorn U. (2012). Genetic diversity of feral populations of Nile tilapia (Oreochromis niloticus) in Thailand and evidence of genetic introgression. Kasetsart Journal of Natural Sciences 46: 200–216.

Sulem Y.S., Tomedi E.T., Mounchili S., Tekeng S. & Brummet R.S. (2006). Survival of Clarias gariepinus fry in earthen ponds: effects of composts and leaks. Aquaculture 260 (1–4): 139–144.

Tamura K., Dudley J., Nei M. & Kumar S. (2007). MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596–1599.

Teichert-Coddington D.R. & Smitherman D.R. (1988). Lack of response by Tilapia nilotica to mass selection for rapid early growth. Transactions of the American Fisheries Society 117: 227–300.<0297:LORBNT>2.3.CO;2

Triantafyllidis A., Abatzopoulos T.J., & Economidis P.S. (1999). Genetic differentiation and phylogenetic relationships among Greek Silurus glanis and Sirulus aristotelis populations, assessed by PCR-RFLP analysis of mitochondrial DNA segments. Heredity 82: 503–509.

Uthice S. & Benzie A.H. (2003). Gene flow and population history in high dispersal marine invertebrates: mitochondrial DNA analysis of Holothuria nobilis (Echinodermata: Holothuroidea) populations from the Indo-Pacific. Molecular Ecology 12: 2635–2648.

Van Der Bank F.H., Grobler J.P. & Du Preez H.H. (1992). A comparative biochemical genetic study of three populations of domesticated and wild African Catfish, Clarias gariepinus. Comparative Biochemistry and Physiology 101B: 387–390.

Van Der Walt L.D., Van Der Bank F.H. & Steyn G.J. (1993). The suitability of using cryopreservation of spermatozoa for the conservation of genetic diversity in African catfish, Clarias gariepinus. Comparative Biochemistry and Physiology 106 (2): 313–318.

Verschuren D., Laird K.R. & Cumming B.F. (2000). Rainfall and drought in equatorial East Africa during the past 1,100 years. Nature 403: 410–413.

Vrijenhoek R.C. (1998). Conservation genetics of freshwater fish. Journal of Fish Biology 53 (Supplement A): 394–412.

Wachirachaikarn A., Rungsin W., Srisapoome P. & Na-Nakorn U. (2009). Crossing of African Catfish, Clarias gariepinus (Burchell, 1822), strains based on strain selection using genetic diversity data. Aquaculture 290: 53–60.

Waldbieser G.C., Bosworth B.G., Nonneman D.J. & Wolters W.R. (2001). A microsatellite based genetic linkage map for channel catfish, Ictalurus punctatus. Genetics 158: 727–734.

Witte F. & Van Densen W.L.T. (1995). Fish Stocks and Fisheries of Lake Victoria: a Handbook for Field Observations. Samara Publishing Limited, Dyfed, UK.

Witte F., Goldschmidt T., Ligtvoet W., Oijen M.J.P. & Wanink J.H. (1992). Species extinction and concomitant ecological changes in Lake Victoria. Netherlands Journal of Zoology 42: 214–232.

Wright S. (1965). The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 19: 395–420.

Yue G.H., Kovacs B. & Orban L. (2003). Microsatellites from Clarias batrachus and their polymorphism in seven additional catfish species. Molecular Ecology Notes 3: 465–468.



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