Effects of Physical Barriers on Genetic Variation of Populations of Stone Lapping Minnow, Garra cambodgiensis (Tirant, 1884), in Wa River, Nan Province, Thailand
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Published:
Apr 2, 2018
Keywords:
Garra cambodgiensis physical barriers gene flow upper Nan River basin genetic impact
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Abstract
Physical barriers within streams and rivers can lead to population fragmentation of fish species, and results in some undesirable genetic consequences. This study evaluated the impacts of three physical barriers (one large waterfall and two small concrete weirs) on genetic variation of Garra cambodgiensis, a small-bodied (4-10 cm) cyprinid native to Southeast Asia, and widely distributed in headwater streams of the Chao Phraya and Mekong river systems. In the upper Nan River drainage basin, especially in the Wa River, the populations are threatened by high fishing pressure and rapid habitat change. We analyzed five polymorphic microsatellite loci for 191 samples, which were collected during November-December 2016, from six locations: above and below Sapun Waterfall (SPA and SPB) in Pun Stream, Nakham Dam (NKA and NKB) in Mang Stream and Sawanua Dam (SWA and SWB) in Wa River. The sample above Sapan Waterfall (SPA) was most genetically distinct from other samples (FST = 0.097 - 0.307) and had the lowest genetic diversity. For the remaining samples, samples above and below the weirs were genetically similar (FST = 0.051 for SWA-SWB; 0.024 for NKA-NKB). STRUCTURE analysis suggested unequal admixture between the Nakham Dam and Sawanua Dam samples, suggesting some restrictions to downstream migration. The results suggest that a large barrier (>10 m high) has a significant impact on genetic differentiation, while smaller concrete weirs (< 5 m high) cause few genetic differences among populations. The barrier size should be an important consideration for the design of fish friendly structures.
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Jaisuk, C., & Senanan, W. (2018). Effects of Physical Barriers on Genetic Variation of Populations of Stone Lapping Minnow, Garra cambodgiensis (Tirant, 1884), in Wa River, Nan Province, Thailand. Journal of Fisheries and Environment, 42(1), 53–65. Retrieved from https://li01.tci-thaijo.org/index.php/JFE/article/view/104289
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References
1. Aljanabi, S.M. and I. Martinez. 1997. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Research 25:4692-4693.
2. Beneteau, L.C., E.N. Mandrak and D.D. Heath. 2009. The effects of river barriers and range expansion of the population genetic structure and stability in Greenside Darter (Etheostoma blennioides) populations. Conservation Genetic 10:477-487.
3. Chakraborty, R., M.R. Srinivasan and P.S. Daiger. 1992. Evaluation of Standard Error and Confidence Interval of Estimated Multilocus Genotype Probabilities, and Their Implications in DNA Forensics. The American Journal of Human Genetics 52:60-70.
4. Chapuis, M.P. and A. Estoup. 2007. Microsatellite Null Alleles and Estimation of Population Differentiation. Molecular Biology and Evolution 24:621-631.
5. Crooks, S. and W.P. Shaw. 2016. Isolation by distance and non-identical patterns of gene flow within two river populations of the freshwater fish Rutilus rutilus (L. 1758). Conservation Genetic 17:861-874.
6. Dempster, P.A., M.N. Laird and B.D. Rubin. 1977. Maximum Likelihood from Incomplete Data via the EM Algorithm. Journal of the Royal Statistical Society 39:1-38.
7. Di Rienzo, A., A.C. Peterson, J.C. Garza, A.M. Valdes, M. Slatkin and N.B. Freimer. 1994. Mutational processes of simple-sequence repeat loci in human populations. Proceedings of the National Academy of Sciences of the United States of America 91:3166-3170.
8. Do, C., R.S. Waples, D. Peel, G.M. Macbeth, B.J. Tillett and J.R. Ovenden. 2014. NeEstimator v2: reimplementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Molecular Ecology Resources 14:209-214.
9. Earl, D.A. and B.M. VonHoldt. 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4: 359-361.
10. Excoffier, L., G. Laval and S. Schneider. 2006. Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1:47-50.
11. Excoffier, L. and H.E.L. Lischer. 2010. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10:564-567.
12. Evanno, G., S. Regnaut and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14:2611-2620.
13. Francis, R.M. 2016. POPHELPER: An R package and web app to analyse and visualize population structure. Molecular Ecology Resources 17:27-32.
14. Frankham, R., J.D. Ballou and D.A. Briscore. 2010. Population Fragmentation. Introduction to conservation genetics. Cambridge University Press, United Kingdom. 618 p.
15. Goudet, J. 2001. FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available: www2.unil.ch/popgen/softwares/fstat.html.
16. Hansen, M.M., M. T. Limborg, A. Ferchaud and J. Pujolar. 2014. The effects of Medieval dams on genetic divergence and demographic history in brown trout populations. BMC Evolutionary Biology 14:1-14.
16. Hubisz, M.J., D. Falush, M. Stephens and J.K. Pritchard. 2009. Inferring weak population structure with the assistance of sample group information. Molecular Ecology Resources 9: 1322-1332.
17. Jaisuk, C., A. Lothongkham, J. Keereelang and S. Sriyam. 2014. Development of microsatellite primers for native fish and applications to population genetic studies of native fish in Nan River. Rajabhat Journal of Sciences, Humanities and Social Sciences 14:23-33.
18. Kamvar, Z.N., J.F. Tabima and N.J. Grunwald. 2014. Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2:281. 2: e281. DOI 10.7717/Peerj.281
19. Kirchner, S., T. Weinmaier, T. Rattei, H. Sattmann and L. Kruckenhauser. 2014. Characterization of 19 new microsatellite loci for the Omani barb Garra barreimiae from 454 sequences. BMC Research Notes 7:522. DOI 10.1186/1756-0500-7-522.
20. Ligaray, M., H. Kom, S. Sthiannopkao, S. Lee, K.H. Cho and J. H. Kim. 2015. Assessment on hydrologic response by climate change in the Chao Phraya River basin, Thailand. Water 7: 6892-6909.
21. Nei, M. 1978. Estimation of average heterozygosity and genetic distance for small number of individuals. Genetics 89:583-590.
22. Neville, H.M., J.B. Dunham and M.M. Peacock. 2006. Landscape attributes and life history variability shape genetic structure of trout populations in a stream network. Landscape Ecology 21:901-916.
23. Neville, M.H., J. Dunham, A. Rosenberger, A. Umek and B. Nelson. 2009. Influences of wildfire, Habitat Size, and Connectivity on Trout in Headwater Streams Revealed by Patterns of Genetic Diversity. Transactions of the American Fisheries Society 138:1314-1327.
24. Peakall, R. and P.E. Smouse. 2006. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6:288-295.
25. Pilger, T.J., K.B. Gido, D.L. Propst, J.E. Whitney and T.F. Turner. 2017. River network architecture, genetic effective size, and distributional patterns predict differences in genetic structure across species in a dryland stream fish community. Molecular Ecology 26: 2687–2697.
26. Piry, S., G. Luikart and J.M. Cornuet. 1999. BOTTLENECK: a computer program for detecting recent reductions in the effective population size using allele frequency data. Journal of Heredity 90:502-503.
27. Pritchard, J.K., M. Stephens and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
28. Rice, W.R. 1989. Analyzing tables of statistical test. Evolution 43:223-225.
29. Roberts, J.H., P.L. Angermeier and E.M. Hallerman. 2013. Distance, dams and drift: what structures populations of an endangered, benthic stream fish? Freshwater Biology 58 (10): 2050-2064. DOI:10.1111/fwb.12190.
30. Rousset, F. 2008. GENEPOP’007: a complete re-implementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources 8:103-106.
31. Sterling, K.A., D.H. Reed, B.P. Noonan and M.L.Jr. Warren. 2012. Genetic effects of habitat fragmentation and population isolation on Etheostoma raneyi (Percidae). Conservation Genetic 13:859-872.
32. Su, W.L., Z.Z. Liu, T.C. Wang, Z. Zhen, Y.A. Liu, Q.W. Tang and Q.J. Yang. 2013. Isolation and characterization of polymorphic microsatellite markers in the fish Garra orientalis (oriental sucking barb). Conservation Genetic Resource 5:231-233.
33. Van Oosterhout, C., W.F. Hutchinson, D.P.M. Will and P. Shipley. 2004. MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4:535-538.
34. Wang, J. 2016. A comparison of single-sample estimators of effective population sizes from genetic marker data. Molecular Ecology 25:4692-711.
35. Weir, B.S. 1996. Genetic data analysis II. Sunderland, MA: Sinauer Associates, Inc.
36. Yamamoto, S., K. Morita, I. Koizumi and K. Maekawa. 2004. Genetic differentiation of white-spotted charr (Salvelinus leucomaenis) populations after habitat fragmentation: Spatial-temporal changes in gene frequencies. Conservation Genetics 5:529-538.
37. Yamamoto, S., K. Maekawa, T. Tamate, I. Koizumi, K. Hasegawa and H. Kubota. (2006). Genetic evaluation of translocation in artificially isolated populations of white-spotted charr (Salvelinus leucomaenis). Fisheries Research 78: 352-358.
38. Zhao, L., E.L. Chenoweth, J. Liu and Q. Liu. 2016. Effects of dam structures on genetic diversity of freshwater fish Sinibrama macrops in Min River, China. Biochemical Systematics and Ecology 68:216-222.
2. Beneteau, L.C., E.N. Mandrak and D.D. Heath. 2009. The effects of river barriers and range expansion of the population genetic structure and stability in Greenside Darter (Etheostoma blennioides) populations. Conservation Genetic 10:477-487.
3. Chakraborty, R., M.R. Srinivasan and P.S. Daiger. 1992. Evaluation of Standard Error and Confidence Interval of Estimated Multilocus Genotype Probabilities, and Their Implications in DNA Forensics. The American Journal of Human Genetics 52:60-70.
4. Chapuis, M.P. and A. Estoup. 2007. Microsatellite Null Alleles and Estimation of Population Differentiation. Molecular Biology and Evolution 24:621-631.
5. Crooks, S. and W.P. Shaw. 2016. Isolation by distance and non-identical patterns of gene flow within two river populations of the freshwater fish Rutilus rutilus (L. 1758). Conservation Genetic 17:861-874.
6. Dempster, P.A., M.N. Laird and B.D. Rubin. 1977. Maximum Likelihood from Incomplete Data via the EM Algorithm. Journal of the Royal Statistical Society 39:1-38.
7. Di Rienzo, A., A.C. Peterson, J.C. Garza, A.M. Valdes, M. Slatkin and N.B. Freimer. 1994. Mutational processes of simple-sequence repeat loci in human populations. Proceedings of the National Academy of Sciences of the United States of America 91:3166-3170.
8. Do, C., R.S. Waples, D. Peel, G.M. Macbeth, B.J. Tillett and J.R. Ovenden. 2014. NeEstimator v2: reimplementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Molecular Ecology Resources 14:209-214.
9. Earl, D.A. and B.M. VonHoldt. 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4: 359-361.
10. Excoffier, L., G. Laval and S. Schneider. 2006. Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1:47-50.
11. Excoffier, L. and H.E.L. Lischer. 2010. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10:564-567.
12. Evanno, G., S. Regnaut and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14:2611-2620.
13. Francis, R.M. 2016. POPHELPER: An R package and web app to analyse and visualize population structure. Molecular Ecology Resources 17:27-32.
14. Frankham, R., J.D. Ballou and D.A. Briscore. 2010. Population Fragmentation. Introduction to conservation genetics. Cambridge University Press, United Kingdom. 618 p.
15. Goudet, J. 2001. FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available: www2.unil.ch/popgen/softwares/fstat.html.
16. Hansen, M.M., M. T. Limborg, A. Ferchaud and J. Pujolar. 2014. The effects of Medieval dams on genetic divergence and demographic history in brown trout populations. BMC Evolutionary Biology 14:1-14.
16. Hubisz, M.J., D. Falush, M. Stephens and J.K. Pritchard. 2009. Inferring weak population structure with the assistance of sample group information. Molecular Ecology Resources 9: 1322-1332.
17. Jaisuk, C., A. Lothongkham, J. Keereelang and S. Sriyam. 2014. Development of microsatellite primers for native fish and applications to population genetic studies of native fish in Nan River. Rajabhat Journal of Sciences, Humanities and Social Sciences 14:23-33.
18. Kamvar, Z.N., J.F. Tabima and N.J. Grunwald. 2014. Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2:281. 2: e281. DOI 10.7717/Peerj.281
19. Kirchner, S., T. Weinmaier, T. Rattei, H. Sattmann and L. Kruckenhauser. 2014. Characterization of 19 new microsatellite loci for the Omani barb Garra barreimiae from 454 sequences. BMC Research Notes 7:522. DOI 10.1186/1756-0500-7-522.
20. Ligaray, M., H. Kom, S. Sthiannopkao, S. Lee, K.H. Cho and J. H. Kim. 2015. Assessment on hydrologic response by climate change in the Chao Phraya River basin, Thailand. Water 7: 6892-6909.
21. Nei, M. 1978. Estimation of average heterozygosity and genetic distance for small number of individuals. Genetics 89:583-590.
22. Neville, H.M., J.B. Dunham and M.M. Peacock. 2006. Landscape attributes and life history variability shape genetic structure of trout populations in a stream network. Landscape Ecology 21:901-916.
23. Neville, M.H., J. Dunham, A. Rosenberger, A. Umek and B. Nelson. 2009. Influences of wildfire, Habitat Size, and Connectivity on Trout in Headwater Streams Revealed by Patterns of Genetic Diversity. Transactions of the American Fisheries Society 138:1314-1327.
24. Peakall, R. and P.E. Smouse. 2006. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6:288-295.
25. Pilger, T.J., K.B. Gido, D.L. Propst, J.E. Whitney and T.F. Turner. 2017. River network architecture, genetic effective size, and distributional patterns predict differences in genetic structure across species in a dryland stream fish community. Molecular Ecology 26: 2687–2697.
26. Piry, S., G. Luikart and J.M. Cornuet. 1999. BOTTLENECK: a computer program for detecting recent reductions in the effective population size using allele frequency data. Journal of Heredity 90:502-503.
27. Pritchard, J.K., M. Stephens and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
28. Rice, W.R. 1989. Analyzing tables of statistical test. Evolution 43:223-225.
29. Roberts, J.H., P.L. Angermeier and E.M. Hallerman. 2013. Distance, dams and drift: what structures populations of an endangered, benthic stream fish? Freshwater Biology 58 (10): 2050-2064. DOI:10.1111/fwb.12190.
30. Rousset, F. 2008. GENEPOP’007: a complete re-implementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources 8:103-106.
31. Sterling, K.A., D.H. Reed, B.P. Noonan and M.L.Jr. Warren. 2012. Genetic effects of habitat fragmentation and population isolation on Etheostoma raneyi (Percidae). Conservation Genetic 13:859-872.
32. Su, W.L., Z.Z. Liu, T.C. Wang, Z. Zhen, Y.A. Liu, Q.W. Tang and Q.J. Yang. 2013. Isolation and characterization of polymorphic microsatellite markers in the fish Garra orientalis (oriental sucking barb). Conservation Genetic Resource 5:231-233.
33. Van Oosterhout, C., W.F. Hutchinson, D.P.M. Will and P. Shipley. 2004. MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4:535-538.
34. Wang, J. 2016. A comparison of single-sample estimators of effective population sizes from genetic marker data. Molecular Ecology 25:4692-711.
35. Weir, B.S. 1996. Genetic data analysis II. Sunderland, MA: Sinauer Associates, Inc.
36. Yamamoto, S., K. Morita, I. Koizumi and K. Maekawa. 2004. Genetic differentiation of white-spotted charr (Salvelinus leucomaenis) populations after habitat fragmentation: Spatial-temporal changes in gene frequencies. Conservation Genetics 5:529-538.
37. Yamamoto, S., K. Maekawa, T. Tamate, I. Koizumi, K. Hasegawa and H. Kubota. (2006). Genetic evaluation of translocation in artificially isolated populations of white-spotted charr (Salvelinus leucomaenis). Fisheries Research 78: 352-358.
38. Zhao, L., E.L. Chenoweth, J. Liu and Q. Liu. 2016. Effects of dam structures on genetic diversity of freshwater fish Sinibrama macrops in Min River, China. Biochemical Systematics and Ecology 68:216-222.