Genetic diversity and population structure of Prochilodus costatus and Prochilodus argenteus preceding dam construction in the Paraopeba River, São Francisco River Basin, Minas Gerais, Brazil

Tatiana M. Barroca, Fábio P. Arantes, Bárbara F. Magalhães, Flávia F. Siqueira, Carolina C. R. Horta, Isabella F. Pena, Jorge A. Dergam, Evanguedes Kalapothakis

Departamento de Biologia Animal, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Vi?osa, Vi?osa, Brazil.
Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
Programa de Pós-Gradua??o em Zoologia de Vertebrados, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil.

DOI: 10.4236/ojgen.2012.22017                

Abstract

Curimat?-pioa (Prochilodus costatus) and curimat?-pacu (Prochilodus argenteus) are migratory fish species endemic to the S?o Francisco River Basin in Brazil. Both species play important roles in local fisheries and ecology in the Paraopeba River. A dam was recently constructed on this river and to help in the development and conservation programs, we characterized the genetic variation of both species before dam construction. Complex hypervariable repeats micro-satellite was used to asses genetic variation for both species within and between the five collection sites in order to detect population substructuring. Nucleotide substitutions and insertion/deletion polymorphisms (indels) resulted in 35 P. costatus haplotypes (sample size = 89) and 22 P. argenteus haplotypes (sample size = 32). Significant genetic diversity and population differentiation was detected between five sampling sites for both species. Therefore, each of the five sites should be regarded as a group comprising significant genetic differences in species conservation and maintenance plans. Comparing these results to genetic diversity measures after dam construction will be critical for future management in this region.

Keywords

Freshwater Fish; Complex Hypervariable Repeats Microsatellite; Genetic Diversity; Population Structure

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	Castro, R.M.C. and Vari, R.P. (2003) Prochilodontidae (Fannel mouth characiforms). In: Reis, R.E., Kullander, S.O. and Ferraris, C.J. Jr., Eds., Checklist of the Fresh-water Fishes of South and Central America, Porto Alegre, 65-70.
[2]	Welcomme, R.L. (1979) Fisheries ecology of floodplain rivers. Logman Group Limited, London.
[3]	Bonetto, A.A. (1986) Fish of the Paraná system. In: Davies, B.R. and Walker, K.F., Eds., The Ecology of River Systems, Dordrecht, 573-588.
[4]	CESP (1996) Aspectos limnológicos, ictiológicos e pes- queiros de reservatórios da CESP no período de 1986 a 1994. CESP S?o Paulo, Série Pesquisa e Desenvolvimento, S?o Paulo.
[5]	Agostinho, A.A., Vazzoler, A.E.A. de M., Gomes, L.C. and Okada, E.K. (1993) Estratificación y comportamiento de Prochilodus scrofa em distintas fases del ciclo de vida, em la planície de inunda??o del alto rio Paraná y embalse de Itaipu, Paraná, Brasil. Revue d’Hydrobiolgie Tropicale, 26, 79-90.
[6]	Darnell, R.M. (1961) Trophic spectrum of an estuarine community based upon studies of Lagoon Pontchartrain, Louisiana. Ecology, 42, 552-568. doi:10.2307/1932242.
[7]	Darnell, R.M. (1964) Organic detritus in relation to secondary production in aquatic communities. Stuttgart, 15, 462-470.
[8]	Flecker, A.S. (1996) Ecosystem engineering by a dominant detritivore in a diverse tropical stream. Ecology, 77, 1845-1854. doi:10.2307/2265788.
[9]	CETEC (Funda??o Centro Tecnológico de Minas Gerais) (1983) Diagnóstico ambiental do Estado de Minas Gerais. Série de publica??es técnicas/SPT, 010, Minas Gerais.
[10]	Drumond, G.M., Martins, C.S., Machado, A.B.M., Sebaio, F.A. and Antonini, Y. (2005) Biodiversidade em Minas Gerais: um atlas para sua conserva??o. 2nd Edition, Funda??o Biodiversitas, Belo Horizonte.
[11]	Alves, C.B.M. (2007) Evaluation of fish passage through the Igarapé Dam Fish Ladder. Neotropical Ichthyology, 5, 233-236. doi:10.1590/S1679-62252007000200019.
[12]	Poke, F.S., Vaillancourt, R.E., Potts, B.M. and Reid, J.B. (2005) Genomic research in Eucalyptus. Genetica, 125, 79-101. doi:10.1007/s10709-005-5082-4
[13]	Avise, J.C. (1987) Intraspecific phylogeography: The mitochondrial DNA bridge between population genetics and systematic. Annual Review of Ecology and Systematics, 18, 489-522. doi:10.1146/annurev.es.18.110187.002421
[14]	Parker, P.G., Snow, A.A., Schug, M.D., Booton, G.C. and Fuerst, P.A. (1998) What molecules can tell us about populations: Choosing and using a molecular marker. Ecology, 79, 361-382. doi:10.2307/176939
[15]	Vrijenhoek, R.C. (1998) Conservation genetics of fresh-water fish. Journal of Fish Biology, 53, 394-412. doi:10.1111/j.1095-8649.1998.tb01039.x
[16]	Yazbeck, G.M. and Kalapothakis, E. (2007) Isolation and characterization of microsatellite DNA in the piracema fish Prochilodus lineatus (Characiformes). Genetics and Molecular Research, 6, 1026-1034.
[17]	Barbosa, A.C.D.R., Galzerani, F., Corrêa, T.C., Galetti, Jr. P.M. and Hatanaka, T. (2008) Description of novel microsatellite loci in the Neotropical fish Prochilodus argenteus and cross-amplification in P. costatus and P. lineatus. Genetics and Molecular Biology, 31, 357-360. doi:10.1590/S1415-47572008000200032
[18]	Paiva, A.L.B. and Kalapothakis, E. (2008) Isolation and characterization of microsatellite loci in Pimelodus maculatus (Siluriformes: Pimelodidae). Molecular Ecology Resources, 8, 1078-1080.
[19]	Hsu, T.H., Guillén Madrid, A.G., Burridge, C.P., Cheng, H.Y. and Gwo, J.C. (2011) Resolution of the Acanthopagrus black seabream complex based on mitochondrial and amplified fragment-length polymorphism analyses. Journal of Fish Biology, 79, 1182-1192. doi:10.1111/j.1095-8649.2011.03100.x
[20]	Zane, L., Barceloni, L. and Patarnello, T. (2002) Strategies for microsatellite isolation: A review. Molecular Ecology, 11, 1-16. doi:10.1046/j.0962-1083.2001.01418.x
[21]	Urquhart, A., Kimpton, C.P. and Gill, P. (1993) Sequence variability of the tetranucleotide repeat of the human beta-actin related pseudogene H-beta-Acpsi-2 (ACTBP2) locus. Human Genetics, 92, 637-638. doi:10.1007/BF00420957
[22]	Gill, P., Kimpton, C. P., D’Aloja, E., Andersen, J. F., Bar, W., Brinkmann, B., Holgersson, S., Johnsson, V., Kloosterman, A. D., Lareu, M. V., Nellemann, L., Pfitzinger, H., Phillips, C. P., Schmitter, H., Schneider, P.M. and Stenersen, M. (1994) Report of the European DNA profiling group (ED-NAP)-towards standardisation of short tandem repeat (STR) loci. Forensic Science International, 65, 51-59. doi:10.1016/0379-0738(94)90299-2
[23]	Reid, T.M., Ingala, D.A., Kraemer, C.M., Dage, W.M., Dieckhoner, C., Fortman, J., Hodge, D.M., Johnson, K.L., Oatman, C., Schlotman, H., Schuh, C. and Baird, M.L. (2003) Distri-bution of HUMACTBP2 (SE33) alleles in three North American populations. Journal of Forensic Science, 48, 1422-1423.
[24]	Butler, J.M., Hill, C.R., Kline, M.C., Duewer, D.L., Sprecher, C.J., McLaren, R.S., Rabbach, D.R., Krenke, B.E. and Storts, D.R. (2009) The single most polymorphic STR Locus: SE33 performance in US populations. Forensic Science International: Genetics Suppliment Series, 2, 23-24. doi:10.1016/j.fsigss.2009.08.173
[25]	Neraas, L.P. and Spruell, P. (2001) Fragmentation of riverine systems: The genetic effects of dams on bull trout (Salvelinus confluentus) in the Clark Fork River system. Molecular Ecology, 10, 1153-1164. doi:10.1046/j.1365-294X.2001.01269.x
[26]	Frankham, R., Ballou, J.D. and Briscoe, D.A. (2004) A primer of conservation genetics. Cambridge University Press, Cambridge.
[27]	Reid, S.M., Wilson, C.C., Mandrak, N.E. and Carl, L.M. (2008) Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed. Conservation Genetics, 9, 531-546. doi:10.1007/s10592-007-9367-2
[28]	Sambrook, J. and Russell, D. (2001) Molecular cloning: A laboratory manual. 3rd Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
[29]	Temnykh, S., De Clerck, G., Lukashova, A., Lipovich, L., Cartinhour, S. and McCouch, S. (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon asso- ciations, and genetic marker potential. Genome Research, 11, 1441-1452. doi:10.1101/gr.184001
[30]	Ewing, B. and Green, P. (1998) Basecalling of automated sequencer traces using phred. II. Error probabilities. Genome Research, 8, 186-194.
[31]	Gordon, D., Abajian, C. and Green, P. (1998) Consed: A graphical tool for sequence finishing. Genome Research, 8, 195-202.
[32]	Rozen, S. and Skaletsky, H.J. (2000) Primer3 on the www for general users and for biologist programmers. In: Krawetz, S. and Misener, S., Eds, Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, Totowa, 365-386.
[33]	Excoffier, L. and Lischer, H.E.L. (2010) Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564-567. doi:10.1111/j.1755-0998.2010.02847.x
[34]	Excoffier, L., Smouse, P.E. and Quattro, J.M. (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics, 131, 479-491.
[35]	Mantel, N. (1967) The detection of disease clustering and a generalized regression approach. Cancer Research, 27, 209-220.
[36]	Miller, M.P. (2005) Alleles in space (AIS): Computer software for the joint analysis of interindividual spatial and genetic information. Journal of Heredity, 96, 722- 724. doi:10.1093/jhered/esi119
[37]	Schl?tterer, C. (2000) Evolutionary dynamics of microsatellite DNA. Chromosoma, 109, 365-371. doi:10.1007/s004120000089
[38]	Ellegren, H. (2004) Microsatellites: simple sequences with complex evolution. Nature Reviews Genetics, 5, 435-445. doi:10.1038/nrg1348
[39]	Chenuil, A. (2006) Choosing the right molecular markers for studying biodiversity: From molecular evolution to practical aspects. Genetica, 127, 101-120. doi:10.1007/s10709-005-2485-1
[40]	Hatanaka, T., Henrique-Silva, F. and Galetti Jr., P.M. (2006) Population substructutring in a migratory fresh- water fish Prochilodus argenteus (Characiformes, Prochilodontidae) from the S?o Francisco River. Genetica, 126, 1-7. doi:10.1007/s10709-005-1445-0
[41]	Nakatani, K., Baumgarter, G. and Cavicchioli, M. (1997) Ecologia de ovos e larvas de peixes. In: Vazzoler, A.E. A.M., Agostinho, A.A. and Hahn, N.S., Eds., A Planície de Inunda??o do Alto rio Paraná: Aspectos Físicos, Biológicos e Socioecon?micos, Maringá, 281-306.
[42]	Maggio, T., Lo Brutto, S., Garoia, F., Tinti, F. and Arculeo, M. (2009) Microsatellite analysis of red Mullus barbatus (Perciformes, Mullidae) reveals the isolation of the Adriatic Basin in the Mediterranean Sea. ICES Journal of Marine Science, 66, 1883-1891. doi:10.1093/icesjms/fsp160