Molecular Biotechnology

, Volume 44, Issue 3, pp 250–266 | Cite as

Mutational Dynamics of Microsatellites

  • Atul BhargavaEmail author
  • F. F. Fuentes


Microsatellites are a ubiquitous class of simple repetitive DNA sequences, which are widespread in both eukaryotic and prokaryotic genomes. The use of microsatellites as polymorphic DNA markers has considerably increased both in the number of studies and in the number of organisms, primarily for genetic mapping, studying genomic instability in cancer, population genetics, forensics, conservation biology, molecular anthropology and in the studies of human evolutionary history. Although simple sequence repeats have been extensively used in studies encompassing varied areas of genetics, the mutation dynamics of these genome regions is still not well understood. The present review focuses on the mutational dynamics of microsatellite DNA with special reference to mutational mechanisms and their role in microsatellite evolution.


Replication slippage Mismatch repair Homoplasy Mutational models Genome size Evolutionary dynamics 


  1. 1.
    Field, D., & Wills, C. (1998). Abundant microsatellite polymorphism in Saccharomyces cerevisiae, and the different distributions of microsatellites in eight prokaryotes and S. cerevisiae, result from strong mutation pressures and a variety of selective forces. Proceedings of the National Academy of Sciences of the United States of America, 95, 1647–1652.CrossRefGoogle Scholar
  2. 2.
    Toth, G., Gaspari, Z., & Jurka, J. (2000). Microsatellites in different eukaryotic genomes: Survey and analysis. Genome Research, 10, 967–981.CrossRefGoogle Scholar
  3. 3.
    Richard, G. F., & Pâques, F. (2000). Mini- and microsatellite expansions: The recombination connection. EMBO Reports, 11, 122–126.CrossRefGoogle Scholar
  4. 4.
    Oliveira, E. J., Padua, J. G., Zucchi, M. I., Vencovsky, R., & Vieira, M. L. C. (2006). Origin, evolution and genome distribution of microsatellites. Genetics and Molecular Biology, 29, 294–307.Google Scholar
  5. 5.
    Zane, L., Bargelloni, L., & Patarnello, T. (2002). Strategies for microsatellite isolation: A review. Molecular Ecology, 11, 1–16.CrossRefGoogle Scholar
  6. 6.
    Zwettler, D., Vieria, C. P., & Schlotterer, C. (2002). Polymorphic microsatellites in Antirrhinum (Scrophulariaceae), a genus with low levels of nuclear sequence variability. Journal of Heredity, 93, 217–221.CrossRefGoogle Scholar
  7. 7.
    Estoup, A., & Angers, B. (1998). Microsatellites and minisatellites for molecular ecology: Theoretical and empirical considerations. In G. R. Carvalho (Ed.), Advances in molecular ecology (pp. 55–86). Washington, D.C.: IOS Press.Google Scholar
  8. 8.
    Barker, G. C. (2002). Microsatellite DNA: A tool for population genetic analysis. Transactions of the Royal Society of Tropical Medicine and Hygeine, 96, S21–S24.CrossRefGoogle Scholar
  9. 9.
    Fuentes, F. F., Martinez, E. A., Hinrichsen, P. V., Jellen, E. N., & Maughan, P. J. (2009). Assessment of genetic diversity patterns in Chilean quinoa (Chenopodium quinoa Willd.) germplasm using multiplex fluorescent microsatellite markers. Conservation Genetics, 10, 369–377.CrossRefGoogle Scholar
  10. 10.
    Beckmann, J. S., & Weber, J. L. (1992). Survey of human and rat microsatellites. Genomics, 12, 627–631.CrossRefGoogle Scholar
  11. 11.
    Calderon, I., Ortega, N., Duran, S., Becerro, M., Pascual, M., & Turon, X. (2007). Finding the relevant scale: Clonality and genetic structure in a marine invertebrate (Crambe crambe, Porifera). Molecular Ecology, 16, 1799–1810.CrossRefGoogle Scholar
  12. 12.
    Andersen, D. H., Pertoldi, C., Loeschcke, V., & Scali, V. (2005). Characterization of microsatellite loci in the stick insects Bacillus rossius rossius, Bacillus rossius redtenbacheri and Bacillus whitei (Insecta: Phasmatodea). Molecular Ecology Notes, 5, 576–578.CrossRefGoogle Scholar
  13. 13.
    Sarhan, A. (2006). Isolation and characterization of five microsatellite loci in the Glanville fritillary butterfly (Melitaea cinxia). Molecular Ecology Notes, 6, 163–164.CrossRefGoogle Scholar
  14. 14.
    Rosas, P. D. A. R., Segura, E. L., & Garcia, B. A. (2007). Microsatellite analysis of genetic structure in natural Triatoma infestans (Hemiptera: Reduviidae) populations from Argentina: Its implication in assessing the effectiveness of Chagas’ disease vector control programmes. Molecular Ecology, 16, 1401–1412.CrossRefGoogle Scholar
  15. 15.
    Kenchington, E. L., Patwary, M. U., Zouros, E., & Bird, C. J. (2006). Genetic differentiation in relation to marine landscape in a broadcast-spawning bivalve mollusc (Placopecten magellanicus). Molecular Ecology, 15, 1781–1796.CrossRefGoogle Scholar
  16. 16.
    Moran, P., Teel, D. J., LaHood, E. S., Drake, J., & Kalinowski, S. (2006). Standardising multi-laboratory microsatellite data in Pacific salmon: An historical view of the future. Ecology of Freshwater Fish, 15, 597–605.CrossRefGoogle Scholar
  17. 17.
    Bucklin, K. A., Banks, M. A., & Hedgecock, D. (2007). Assessing genetic diversity of protected coho salmon (Oncorhynchus kisutch) populations in California. Canadian Journal of Fisheries and Aquatic Sciences, 64, 30–42.CrossRefGoogle Scholar
  18. 18.
    Glenn, T. C., Dessauer, H. C., & Braun, M. J. (1998). Characterization of microsatellite DNA loci in American alligators. Copeia, 3, 591–601.CrossRefGoogle Scholar
  19. 19.
    Galbusera, P., van Dongen, S., & Matthysen, E. (2000). Cross-species amplification of microsatellite primers in passerine birds. Conservation Genetics, 1, 163–168.CrossRefGoogle Scholar
  20. 20.
    Hayes, M. A., Britten, H. B., & Barzen, J. A. (2006). Extra-pair fertilizations in sandhill cranes revealed using microsatellite DNA markers. The Condor, 108, 970–976.CrossRefGoogle Scholar
  21. 21.
    Sainudiin, R., Durrett, R. T., Aquadro, C. F., & Nielsen, R. (2004). Microsatellite mutation models insights from a comparison of humans and chimpanzees. Genetics, 168, 383–395.CrossRefGoogle Scholar
  22. 22.
    Pinto, L. R., Vieiria, L. R., Souze, C. L., Jr, & Souza, A. P. (2003). Reciprocal recurrent selection effects on the genetic structure of tropical maize populations assessed at microsatellite loci. Genetics and Molecular Biology, 26, 355–364.CrossRefGoogle Scholar
  23. 23.
    Odeny, D. A., Jayashree, B., Ferguson, M., Crouch, J., & Gebhardt, J. (2007). Development, characterization and utilization of microsatellite markers in pigeonpea. Plant Breeding, 126, 130–136.CrossRefGoogle Scholar
  24. 24.
    Christopher, M., Mace, E., Jordan, D., David, R., Paul, M., Delacy, I., et al. (2007). Applications of pedigree-based genome mapping in wheat and barley breeding programs. Euphytica, 154, 307–316.CrossRefGoogle Scholar
  25. 25.
    Goldstein, D. B., & Schlotterer, C. (1999). Microsatellites: Evolution and applications. Oxford: Oxford University Press.Google Scholar
  26. 26.
    Cummings, C. J., & Zoghbi, H. Y. (2000). Trinucleotide repeats: Mechanisms and pathophysiology. Annual Review of Genomics and Human Genetics, 1, 281–328.CrossRefGoogle Scholar
  27. 27.
    Masino, L., & Pastore, A. (2001). A structural approach to trinucleotide expansion diseases. Brain Research Bulletin, 56, 183–189.CrossRefGoogle Scholar
  28. 28.
    Kovtun, I. V., Goellner, G., & McMurray, C. T. (2001). Structural features of trinucleotide repeats associated with DNA expansion. Biochemistry and Cell Biology, 79, 325–326.CrossRefGoogle Scholar
  29. 29.
    Everett, C. M., & Wood, N. W. (2004). Trinucleotide repeats and neurodegenerative disease. Pain, 127, 2385–2405.Google Scholar
  30. 30.
    Oda, S., Maehara, Y., Sumiyoshi, Y., & Sugimachi, K. (2002). Microsatellite instability in cancer: What problems remain unanswered? Surgery, 131, S55–S62.CrossRefGoogle Scholar
  31. 31.
    Shaikh, L., Sagebiel, R. W., Ferreira, C. M. M., Nosrati, M., Miller, J. R., & Kashani-Sabet, M. (2005). The role of microsatellites as a prognostic factor in malignant melanoma. Archives of Dermatology, 141, 739–742.CrossRefGoogle Scholar
  32. 32.
    Powell, W., Machray, G., & Provan, G. (1996). Polymorphism revealed by simple sequence repeats. Trends in Plant Science, 1, 215–222.Google Scholar
  33. 33.
    Maughan, P. J., Saghai-Maroof, M. A., & Buss, G. R. (1995). Microsatellite and amplified sequence length polymorphisms in cultivated and wild soybean. Genome, 38, 715–723.CrossRefGoogle Scholar
  34. 34.
    Hancock, J. M. (1999). Microsatellites and other simple sequences: Genomic context and mutational mechanisms. In D. B. Goldstein & C. Schlotterer (Eds.), Microsatellites: Evolution and applications (pp. 1–9). Oxford: Oxford University Press.Google Scholar
  35. 35.
    Morgante, M., Hanafey, M., & Powell, W. (2002). Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nature Genetics, 30, 194–200.CrossRefGoogle Scholar
  36. 36.
    Schlötterer, C., & Harr, B. (2000). Drosophila virilis has long and highly polymorphic microsatellites. Molecular Biology and Evolution, 17, 1641–1646.Google Scholar
  37. 37.
    Katti, M. V., Ranjekar, P. K., & Gupta, V. S. (2001). Differential distribution of simple sequence repeats in eukaryotic genome sequences. Molecular Biology and Evolution, 18, 1161–1167.Google Scholar
  38. 38.
    Sharma, P. C., Grover, A., & Kahl, G. (2007). Mining microsatellites in eukaryotic genomes. Trends in Biotechnology, 25, 490–498.CrossRefGoogle Scholar
  39. 39.
    Cruz, F., Perez, M., & Presa, P. (2005). Distribution and abundance of microsatellites in the genome of bivalves. Gene, 346, 241–247.CrossRefGoogle Scholar
  40. 40.
    Brandstrom, M., & Ellegren, S. (2008). Genome wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias. Genome Research, 18, 881–887.CrossRefGoogle Scholar
  41. 41.
    Ellegren, H. (2000). Microsatellite mutations in the germline: Implications for evolutionary inference. Trends in Genetics, 16, 551–558.CrossRefGoogle Scholar
  42. 42.
    Ellegren, H. (2004). Microsatellites: Simple sequences with complex evolution. Nature Reviews Genetics, 5, 435–445.CrossRefGoogle Scholar
  43. 43.
    Webster, M. T., Smith, N. G., & Ellegren, H. (2002). Microsatellite evolution inferred from human–chimpanzee genomic sequence alignments. Proceedings of the National Academy of Sciences of the United States of America, 99, 8748–8753.CrossRefGoogle Scholar
  44. 44.
    Chakraborty, R., Kimmel, M., Stivers, D. N., Davison, L. J., & Deka, R. (1997). Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci. Proceedings of the National Academy of Sciences of the United States of America, 94, 1041–1046.CrossRefGoogle Scholar
  45. 45.
    Baldi, P., & Baisnee, P. F. (2000). Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths. Bioinformatics, 16, 865–889.CrossRefGoogle Scholar
  46. 46.
    Rolfsmeier, M. L., & Lahue, R. S. (2000). Stabilizing effects of interruptions on trinucleotide repeat expansions in Saccharomyces cerevisiae. Molecular Cell Biology, 20, 173–180.CrossRefGoogle Scholar
  47. 47.
    Pearson, C. E., Nichol-Edamura, K., & Cleary, J. D. (2005). Repeat instability: Mechanisms of dynamic mutations. Nature Reviews Genetics, 6, 729–742.CrossRefGoogle Scholar
  48. 48.
    Krasilnikova, M. M., Samadashwily, G. M., Krasilnikov, A. S., & Mirkin, S. M. (1998). Transcription through a simple DNA repeat blocks replication elongation. EMBO Journal, 17, 5095–5102.CrossRefGoogle Scholar
  49. 49.
    Rose, O., & Falush, D. (1998). A threshold size for microsatellite expansion. Molecular Biology and Evolution, 15, 613–615.Google Scholar
  50. 50.
    Schlotterer, C. (2000). Evolutionary dynamics of microsatellite DNA. Chromosoma, 109, 365–371.CrossRefGoogle Scholar
  51. 51.
    Sia, E. A., Butler, C. A., Dominska, M., Greenwell, P., Fox, T. D., & Petes, T. D. (2000). Analysis of microsatellite mutations in the mitochondrial DNA of Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America, 97, 250–255.CrossRefGoogle Scholar
  52. 52.
    Li, Y. C., Korol, A. B., Fahima, T., Beiles, A., & Novo, E. (2002). Microsatellites: Genomic distribution, putative functions and mutational mechanisms: A review. Molecular Ecology, 11, 2453–2465.CrossRefGoogle Scholar
  53. 53.
    Weber, J., & Wong, C. (1993). Mutation of human short tandem repeats. Human Molecular Genetics, 2, 1123–1128.CrossRefGoogle Scholar
  54. 54.
    Lai, Y., & Sun, F. (2003). The relationship between microsatellite slippage mutation rate and the number of repeat units. Molecular Biology and Evolution, 20, 2123–2131.CrossRefGoogle Scholar
  55. 55.
    Bachtrog, D., Agis, M., Imhof, M., & Schlotterer, C. (2000). Microsatellite variability differs between dinucleotide repeat motifs-evidence from Drosophila melanogaster. Molecular Biology and Evolution, 17, 1277–1285.Google Scholar
  56. 56.
    Primmer, C. R., Ellegren, H., Saino, N., & Moller, A. P. (1996). Directional evolution in germline microsatellite mutations. Nature Genetics, 13, 391–393.CrossRefGoogle Scholar
  57. 57.
    Ellegren, H. (2000). Heterogeneous mutation processes in humans microsatellite sequences. Nature Genetics, 24, 400–402.CrossRefGoogle Scholar
  58. 58.
    Whittaker, J. C., Harbord, R. M., Boxall, N., Mackay, I., & Dawson, G. (2003). Likelihood-based estimation of microsatellite mutation rates. Genetics, 164, 781–787.Google Scholar
  59. 59.
    Seyfert, A. L., Cristescu, M. E., Frisse, L., Schaack, S., Thomas, W. K., & Lynch, M. (2008). The rate and spectrum of microsatellite mutation in Caenorhabditis elegans and Daphnia pulex. Genetics, 178, 2113–2121.CrossRefGoogle Scholar
  60. 60.
    Amos, W., Flint, J., & Xu, X. (2008). Heterozygosity increases microsatellite mutation rate, linking it to demographic history. BMC Genetics, 9, 72.CrossRefGoogle Scholar
  61. 61.
    Di Rienzo, A., Peterson, A. C., Garza, J. C., Valdes, A. M., & Slatkin, M. (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.CrossRefGoogle Scholar
  62. 62.
    Harr, B., Zangerl, B., Brem, G., & Schlotterer, C. (1998). Conservation of locus specific microsatellite variability across species: A comparison of two Drosophila sibling species D. melanogaster and D. simulans. Molecular Biology and Evolution, 15, 176–184.Google Scholar
  63. 63.
    Buschiazzo, E., & Gemmell, N. J. (2006). The rise, fall and renaissance of microsatellites in eukaryotic genomes. Bioessays, 28, 1040–1050.CrossRefGoogle Scholar
  64. 64.
    Goldstein, D., & Clark, A. (1995). Microsatellite variation in North American populations of Drosophila melanogaster. Nucleic Acids Research, 23, 3882–3886.CrossRefGoogle Scholar
  65. 65.
    Wierdl, M., Dominska, M., & Petes, T. D. (1997). Microsatellite instability in yeast: Dependence on the length of the microsatellite. Genetics, 146, 769–779.Google Scholar
  66. 66.
    Brinkmann, B., Klintschar, M., Neuhuber, F., Huhne, J., & Rolf, B. (1998). Mutation rate in human microsatellites: Influence of the structure and length of the tandem repeat. The American Journal of Human Genetics, 62, 1408–1415.CrossRefGoogle Scholar
  67. 67.
    Hutter, C. M., Schug, M. D., & Aquadro, C. F. (1998). Microsatellite variation in Drosophila melanogaster and Drosophila simulans: A reciprocal test of the ascertainment bias hypothesis. Molecular Biology and Evolution, 15, 1620–1636.Google Scholar
  68. 68.
    Schlotterer, C., Ritter, R., Harr, B., & Brem, G. (1998). High mutation rates of a long microsatellite allele in Drosophila melanogaster provides evidence for allele-specific mutation rates. Molecular Biology and Evolution, 15, 1269–1274.Google Scholar
  69. 69.
    Schug, M., Hutter, C., Wetterstrand, K., Gaudette, M., & Mackay, T. (1998). The mutation rates of di-, tri- and tetranucleotide repeats in Drosophila melanogaster. Molecular Biology and Evolution, 15, 1751–1760.Google Scholar
  70. 70.
    Phillips, N., Saloman, M., Custer, A., Ostrow, D., & Baer, C. F. (2009). Spontaneous mutational and standing genetic co(variation) at dinucleotide microsatellites in Caenorhabditis briggsae and Caenorhabditis elegans. Molecular Biology and Evolution, 26, 659–669.CrossRefGoogle Scholar
  71. 71.
    Primmer, C. R., Saino, N., Moller, A. P., & Ellegren, H. (1998). Unraveling the processes of microsatellite evolution through analysis of germ line mutations in barn swallows Hirundo rustica. Molecular Biology and Evolution, 15, 1047–1054.Google Scholar
  72. 72.
    Vigouroux, Y., Jaqueth, J. S., Matsouka, Y., Smith, O. S., & Beavis, W. F. (2002). Rate and pattern of mutation at microsatellite loci in maize. Molecular Biology and Evolution, 19, 1251–1260.Google Scholar
  73. 73.
    Shinde, D., Lai, Y. L., Sun, F. Z., & Arnheim, N. (2003). Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis: (CA/GT)n and (A/T)n microsatellites. Nucleic Acids Research, 31, 974–980.CrossRefGoogle Scholar
  74. 74.
    Coenye, T., & Vandamme, P. (2005). Characterization of mononucleotide repeats in sequenced prokaryotic genomes. DNA Research, 12, 221–233.CrossRefGoogle Scholar
  75. 75.
    Zhu, Y., Queller, D. C., & Strassmann, J. E. (2000). A phylogenetic perspective on sequence evolution in microsatellite loci. Journal of Molecular Evolution, 50, 324–338.Google Scholar
  76. 76.
    Dettman, J. R., & Taylor, J. W. (2004). Mutation and evolution of microsatellite loci in Neurospora. Genetics, 168, 1231–1248.CrossRefGoogle Scholar
  77. 77.
    Bell, G. I., & Jurka, J. (1997). The length distribution of perfect dimer repetitive DNA is consistent with its evolution by an unbiased single step mutation process. Journal of Molecular Evolution, 44, 414–421.CrossRefGoogle Scholar
  78. 78.
    Kruglyak, S., Durrett, R. T., Schug, M. D., & Aquadro, C. F. (1998). Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proceedings of the National Academy of Sciences of the United States of America, 95, 10774–10778.CrossRefGoogle Scholar
  79. 79.
    Kruglyak, S., Durrett, R. T., Schug, M. D., & Aquadro, C. F. (2000). Distribution and abundance of microsatellites in the yeast genome can be explained by a balance between slippage events and point mutations. Molecular Biology and Evolution, 17, 1210–1219.Google Scholar
  80. 80.
    Calabrese, P. P., Durrett, R. T., & Aquadro, C. F. (2001). Dynamics of microsatellite divergence. Genetics, 159, 839–852.Google Scholar
  81. 81.
    Xu, X., Peng, M., Fang, Z., & Xu, X. (2000). The direction of microsatellite mutations is dependent upon allele length. Nature Genetics, 24, 396–399.CrossRefGoogle Scholar
  82. 82.
    Huang, Q. Y., Xu, F. H., Shen, H., Deng, H. Y., Liu, Y. J., Liu, Y. Z., et al. (2002). Mutation patterns at dinucleotide microsatellite loci in humans. The American Journal of Human Genetics, 70, 625–634.CrossRefGoogle Scholar
  83. 83.
    Eisen, J. A. (1999). Mechanistic basis for microsatellite instability. In D. B. Goldstein & C. Schlotterer (Eds.), Microsatellites: Evolution and applications (pp. 34–48). Oxford: Oxford University Press.Google Scholar
  84. 84.
    Messier, M., Li, S. H., & Stewart, C. B. (1996). The birth of microsatellites. Nature, 381, 483.CrossRefGoogle Scholar
  85. 85.
    Eckert, K. A., & Hile, S. E. (2009). Every microsatellite is different: Intrinsic DNA features dictate mutagenesis of common microsatellites present in the human genome. Molecular Carcinigenesis, 48, 379–388.CrossRefGoogle Scholar
  86. 86.
    Pupko, T., & Graur, D. (1999). Evolution of microsatellites in the yeast Saccharomyces cerevisiae: Role of length and number of repeated units. Journal of Molecular Evolution, 48, 313–316.CrossRefGoogle Scholar
  87. 87.
    Halangoda, A., Still, J. G., Hill, K. A., & Sommer, S. S. (2001). Spontaneous microdeletions and microinsertions in a transgenic mouse mutation detection system: Analysis of age, tissue, and sequence specificity. Environmental and Molecular Mutagenesis, 37, 311–323.CrossRefGoogle Scholar
  88. 88.
    Schlötterer, C., & Zangerl, B. (1999). The use of imperfect microsatellites for DNA fingerprinting and population genetics. In J. T. Epplen & T. Lubjuhn (Eds.), DNA profiling and DNA fingerprinting (pp. 153–165). Switzerland, Basel: Birkhäuser.Google Scholar
  89. 89.
    Boyer, J. C., Yamada, N. A., Roques, C. N., Hatch, S. B., Riess, K., & Farber, R. A. (2002). Sequence dependent instability of mononucleotide microsatellites in cultured mismatch repair proficient and deficient mammalian cells. Human Molecular Genetics, 11, 703–713.CrossRefGoogle Scholar
  90. 90.
    Sia, E. A., Jinks-Robertson, S., & Petes, T. D. (1997). Genetic control of microsatellite instability. Mutation Research, 383, 61–70.CrossRefGoogle Scholar
  91. 91.
    Jin, L., Macaubas, C., Hallmayer, J., Kimura, A., & Mignot, E. (1996). Mutation rate varies among alleles at a microsatellite locus: Phylogenetic evidence. Proceedings of the National Academy of Sciences of the United States of America, 93, 15285–15288.CrossRefGoogle Scholar
  92. 92.
    Zhu, Y., Strassmann, J. E., & Queller, D. C. (2000). Insertions, substitutions, and the origin of microsatellites. Genetics Research, 76, 227–236.CrossRefGoogle Scholar
  93. 93.
    Brock, G. J., Anderson, N. H., & Monckton, D. G. (1999). Cis-acting modifiers of expanded CAG/CTG triplet repeat expandability: Associations with flanking GC content and proximity to CpG islands. Human Molecular Genetics, 8, 1061–1067.CrossRefGoogle Scholar
  94. 94.
    Metzgar, D., Bytof, J., & Wills, C. (2000). Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Research, 10, 72–80.Google Scholar
  95. 95.
    Glenn, T. C., Stephan, W., Dessauer, H. C., & Braun, M. J. (1996). Allelic diversity in alligator microsatellite loci is negatively correlated with GC content of flanking sequences and evolutionary conservation of PCR amplifiability. Molecular Biology and Evolution, 13, 1151–1154.Google Scholar
  96. 96.
    Balloux, F., Ecoffey, E., Fumagalli, L., Goudet, J., Wyttenback, A., & Hausser, J. (1998). Microsatellite conservation, polymorphism and GC content in shrews of the genus Sorex (Insectivora, Mammalia). Molecular Biology and Evolution, 15, 473–475.Google Scholar
  97. 97.
    Begun, D. J., & Aquadro, C. F. (1992). Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature, 356, 519–520.CrossRefGoogle Scholar
  98. 98.
    Schug, M., Hutter, C. M., Wetterstrand, K. A., Gaudette, M. S., Mackay, T. F., & Aquadro, C. F. (1998). Mutation and evolution of microsatellites in Drosophila melanogaster. Genetica, 102(103), 359–367.CrossRefGoogle Scholar
  99. 99.
    Michalakis, Y., & Veuille, M. (1996). Length variation of CAG/CAA trinucleotide repeats in natural populations of Drosophila melanogaster and its relation to the recombination rate. Genetics, 143, 1713–1725.Google Scholar
  100. 100.
    Schug, M., Mackay, T. F. C., & Aquadro, C. F. (1997). Low mutation rates of microsatellite loci in Drosophila melanogaster. Nature Genetics, 15, 99–102.CrossRefGoogle Scholar
  101. 101.
    Payseur, B. A., & Nachman, M. W. (2000). Microsatellite variation and recombination rate in the human genome. Genetics, 156, 1285–1298.Google Scholar
  102. 102.
    Primmer, C. R., Raudsepp, T., Chowdhary, B. P., Mbller, A. P., & Ellegren, H. (1997). Low frequency of microsatellites in the avian genome. Genome Research, 7, 471–782.Google Scholar
  103. 103.
    Pearson, C. E., & Sinden, R. R. (1998). Trinucleotide repeat DNA structures: Dynamic mutations from dynamic DNA. Current Opinions in Structural Biology, 8, 321–330.CrossRefGoogle Scholar
  104. 104.
    Sinden, R. R. (1999). Trinucleotide repeats: Biological implications of the DNA structures associated with disease-causing triplet repeats. The American Journal of Human Genetics, 64, 346–353.CrossRefGoogle Scholar
  105. 105.
    Ellegren, H. (2002). Microsatellite evolution: A battle between replication slippage and point mutation. Trends in Genetics, 18, 70.CrossRefGoogle Scholar
  106. 106.
    Li, Y. C., Korol, A. B., Fahima, T., & Novo, E. (2004). Microsatellites within genes: Structure, function and evolution. Molecular Biology and Evolution, 21, 991–1007.CrossRefGoogle Scholar
  107. 107.
    Alba, M. M., Santibáñez-Koref, M. F., & Hancock, J. M. (2001). The comparative genomics of polyglutamine repeats: Extreme difference in the codon organization of repeat-encoding region between mammals and Drosophila. Journal of Molecular Evolution, 52, 249–259.Google Scholar
  108. 108.
    Ellegren, H. (2002). Mismatch repair and mutational bias in microsatellite DNA. Trends in Genetics, 18, 552.CrossRefGoogle Scholar
  109. 109.
    Streisinger, G., & Owen, J. (1985). Mechanisms of spontaneous and induced frameshift mutation in bacteriophage T4. Genetics, 109, 633–659.Google Scholar
  110. 110.
    Schlotterer, C., & Tautz, D. (1992). Slippage synthesis of simple sequence DNA. Nucleic Acids Research, 20, 211–215.CrossRefGoogle Scholar
  111. 111.
    Strand, M., Prolla, T. A., Liskay, R. M., & Petes, T. D. (1993). Destabilization of tracts of simple repetitive DNA in yeast by mutations affecting DNA mismatch repair. Nature, 365, 274–276.CrossRefGoogle Scholar
  112. 112.
    Li, Y. C., Röder, M. S., & Fahima, T. (2002). Climatic effect on microsatellite diversity in wild emmer wheat, Triticum dicoccoides, at Yehudiyya microsite, Israel. Heredity, 89, 127–132.CrossRefGoogle Scholar
  113. 113.
    Kolodner, R. D., & Marsischky, G. T. (1999). Eukaryotic DNA mismatch repair. Current Opinions in Genetics and Development, 9, 89–96.CrossRefGoogle Scholar
  114. 114.
    Atkin, N. B. (2001). Microsatellite instability. Cytogenetics and Cell Genetics, 92, 177–181.CrossRefGoogle Scholar
  115. 115.
    Chang, D. K., Metzgar, D., Wills, C., & Boland, C. R. (2001). Microsatellites in the eukaryotic DNA mismatch repair genes as modulators of evolutionary mutation rate. Genome Research, 11, 1145–1146.CrossRefGoogle Scholar
  116. 116.
    Harr, B., Todorova, J., & Schlotterer, C. (2002). Mismatch repair-driven mutational bias in D. melanogaster. Molecular Cell, 10, 199–205.CrossRefGoogle Scholar
  117. 117.
    Boyer, J. C., Umar, A., & Risinger, J. I. (1995). Microsatellite instability, mismatch repair deficiency, and genetic defects in human cancer cell lines. Cancer Research, 55, 6063–6070.Google Scholar
  118. 118.
    Clark, A. B., Cook, M. E., Tran, H. T., Gordenin, D. A., Resnick, M. A., & Kunkel, T. A. (1999). Functional analysis of human MutSalpha and MutSbeta complexes in yeast. Nucleic Acids Research, 27, 736–742.CrossRefGoogle Scholar
  119. 119.
    Jaworski, A., Rosche, W. A., & Gellibolian, R. (1995). Mismatch repair in Escherichia coli enhances instability of (CTG)n triplet repeats from human hereditary diseases. Proceedings of the National Academy of Sciences of the United States of America, 92, 11019–11023.CrossRefGoogle Scholar
  120. 120.
    Schumacher, S., Fuchs, R. P. P., & Bichara, M. (1998). Expansion of CTG repeats from human disease genes is dependent upon replication mechanisms in Escherichia coli: The effect of long patch mismatch repair revisited. Journal of Molecular Biology, 279, 1101–1110.CrossRefGoogle Scholar
  121. 121.
    Matic, I., Radman, M., & Taddei, F. (1997). Highly variable mutation rates in commensal and pathogenetic Escherichia coli. Science, 277, 1833–1834.CrossRefGoogle Scholar
  122. 122.
    Parniewski, P., Jaworski, A., Wells, R., & Bowater, R. (2000). Length of CTG CAG repeats determines the influence of mismatch repair on genetic instability. Journal of Molecular Biology, 299, 865–874.CrossRefGoogle Scholar
  123. 123.
    Charlesworth, B., Sniegowski, P., & Stephan, W. (1994). The evolutionary dynamics of repetitive DNA in eukaryotes. Nature, 371, 215–220.CrossRefGoogle Scholar
  124. 124.
    Brohede, J., & Ellegren, H. (1999). Microsatellite evolution: Polarity of substitutions within repeats and neutrality of flanking sequences. Proceedings of the Royal Society of London, 266, 825–833.CrossRefGoogle Scholar
  125. 125.
    Jakupciak, J. P., & Wells, R. D. (2000). Gene conversion (recombination) mediates expansions of CTG.CAG repeats. Journal of Biological Chemistry, 275, 4003–4013.CrossRefGoogle Scholar
  126. 126.
    Bagshaw, A. T. M., Pitt, J. P. W., & Gemmell, N. J. (2008). High frequency of microsatellites in Saccharomyces cerevisiae meiotic recombination hotspots. BMC Genomics, 9, 49.CrossRefGoogle Scholar
  127. 127.
    Myers, S., Bottolo, L., Freeman, C., McVean, G., & Donnelly, P. (2005). A fine-scale map of recombination rates and hotspots across the human genome. Science, 310, 321–324.CrossRefGoogle Scholar
  128. 128.
    Schultes, N. P., & Szostak, J. W. (1991). A poly(dA.dT) tract is a component of the recombination initiation site at the ARG4 locus in Saccharomyces cerevisiae. Molecular Cell Biology, 11, 322–328.Google Scholar
  129. 129.
    Treco, D., & Arnheim, N. (1986). The evolutionary conserved repetitive sequence d(TG·AC)n promotes reciprocal exchange and generates unusual recombinant tetrads during yeast meiosis. Molecular and Cellular Biology, 6, 3934–3947.Google Scholar
  130. 130.
    Gendrel, C. G., Boulet, A., & Dutreix, M. (2000). (CA/GT)(n) microsatellites affect homologous recombination during yeast meiosis. Genes and Development, 14, 1261–1268.Google Scholar
  131. 131.
    Kirkpatrick, D. T., Wang, Y. H., Dominska, M., Griffith, J. D., & Petes, T. D. (1999). Control of meiotic recombination and gene expression in yeast by a simple repetitive DNA sequence that excludes nucleosomes. Molecular Cell Biology, 19, 7661–7671.Google Scholar
  132. 132.
    Wahls, W. P., Wallace, L. J., & Moore, P. D. (1990). The Z-DNA motif d(TG)30 promotes reception of information during gene conversion events while stimulating homologous recombination in human cells in culture. Molecular Cell Biology, 10, 785–793.Google Scholar
  133. 133.
    Napierala, M., Parniewski, P., Pluciennik, A., & Wells, R. D. (2002). Long CTG•CAG repeat sequences markedly stimulate intramolecular recombination. Journal of Biological Chemistry, 277, 34087–34100.CrossRefGoogle Scholar
  134. 134.
    Stephan, W., & Cho, S. (1994). Possible role of natural selection in the formation of tandem-repetitive noncoding DNA. Genetics, 136, 333–341.Google Scholar
  135. 135.
    Bachtrog, D., Weiss, S., Zangerl, B., Brem, G., & Schlotterer, C. (1999). Distribution of dinucleotide microsatellites in the Drosophila melanogaster genome. Molecular Biology and Evolution, 16, 602–610.Google Scholar
  136. 136.
    Majewski, J., & Ott, J. (2000). GT repeats are associated with recombination on human chromosome 22. Genome Research, 10, 1108–1114.CrossRefGoogle Scholar
  137. 137.
    Heyer, E., Puymirat, J., Dielties, P., Bakker, E., & de Knijff, P. (1997). Estimating Y chromosome specific microsatellite mutation frequencies using deep rooted pedigrees. Human Molecular Genetics, 6, 799–803.CrossRefGoogle Scholar
  138. 138.
    Kayser, M., et al. (2000). Characteristics and frequency of germline mutations at microsatellite loci from the human Y chromosome, as revealed by direct observation in father/son pairs. The American Journal of Human Genetics, 66, 1580–1588.CrossRefGoogle Scholar
  139. 139.
    Arnheim, N., Calabrese, P., & Nordborg, M. (2003). Hot and cold spots of recombination in the human genome: The reason we should find them and how this can be achieved. The American Journal of Human Genetics, 73, 5–16.CrossRefGoogle Scholar
  140. 140.
    Jeffreys, A. J., Holloway, J. K., Kauppi, L., May, C. A., Neumann, R., Slingsby, M. T., et al. (2004). Meiotic recombination hot spots and human DNA diversity. Philosophical Transactions of the Royal Society B: Biological Sciences, 359, 141–152.CrossRefGoogle Scholar
  141. 141.
    Gerton, J. L., De Risi, J., Shroff, R., Lichten, M., Brown, P. O., & Petes, T. D. (2000). Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America, 97, 11383–11390.CrossRefGoogle Scholar
  142. 142.
    Jeffreys, A. J., Kauppi, L., & Neumann, R. (2001). Intensely punctuate meiotic recombination in the class II region of the major histocompatibility complex. Nature Genetics, 29, 217–272.CrossRefGoogle Scholar
  143. 143.
    Bailey, A. D., Pavelitz, T., & Weiner, A. M. (1998). The microsatellite (CT)n X (GA)n promotes stable chromosomal integration of large tandem arrays of functional human U2 small nuclear RNA genes. Molecular Cell Biology, 18, 2226–2271.Google Scholar
  144. 144.
    Rosenberg, S. M., Longerich, S., Gee, P., & Harris, R. S. (1994). Adaptive mutation by deletions in small mononucleotide repeats. Science, 265, 405–407.CrossRefGoogle Scholar
  145. 145.
    Jeffreys, A. J., Neuman, R., Panayi, M., Myers, S., & Donnelly, P. (2005). Human recombination hotspots hidden in regions of strong marker association. Nature Genetics, 37, 601–606.CrossRefGoogle Scholar
  146. 146.
    Hashem, V. I., Rosche, W. A., & Sinden, R. R. (2004). Genetic recombination destabilizes (CTG)n·(CAG)n repeats in E. coli. Mutation Research, 554, 95–109.Google Scholar
  147. 147.
    Li, Y. C., Fahima, T., & Korol, A. B. (2000). Microsatellite diversity correlated with ecological-edaphic and genetic factors in three microsites of wild emmer wheat in North Israel. Molecular Biology and Evolution, 17, 851–862.Google Scholar
  148. 148.
    Dieringer, D., & Schlotterer, C. (2003). Microsatellite Analyser (MSA): A platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes, 3, 167–169.CrossRefGoogle Scholar
  149. 149.
    Nishizawa, N., & Nishizawa, K. (2002). A DNA sequence evolution analysis generalized by simulation and the Markov Chain Monte Carlo method implicates strand slippage in a majority of insertions and deletions. Journal of Molecular Evolution, 55, 706–717.CrossRefGoogle Scholar
  150. 150.
    Wilder, J., & Hollocher, H. (2001). Mobile elements and the genesis of microsatellites in dipterans. Molecular Biology and Evolution, 18, 384–392.Google Scholar
  151. 151.
    Arcot, S. S., Wang, Z., Weber, J. L., Deininger, L., & Batzer, M. A. (1995). Alu repeats: A source for the genesis of primate microsatellites. Genomics, 29, 136–144.CrossRefGoogle Scholar
  152. 152.
    Alexander, L., Rohrer, G., & Beattie, C. (1995). Porcine SINE-associated microsatellite markers: Evidence for new artiodactyl SINEs. Mammalian Genome, 6, 464–468.CrossRefGoogle Scholar
  153. 153.
    Gallagher, P. C., Lear, T. L., Coogle, L. D., & Bailey, E. (1999). Two SINE families associated with equine microsatellite loci. Mammalian Genome, 10, 140–144.CrossRefGoogle Scholar
  154. 154.
    Nadir, E., Margalit, H., Gallily, T., & Ben-Sasson, S. A. (1996). Microsatellites spreading in the human genome: Evolutionary mechanisms and structural implications. Proceedings of the National Academy of Sciences of the United States of America, 93, 6470–6475.CrossRefGoogle Scholar
  155. 155.
    Lin, X., et al. (1999). Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature, 402, 761–768.CrossRefGoogle Scholar
  156. 156.
    Ramsay, L., Macaulay, M., Cardle, L., Morgante, M., Ivanissevich, S. D., Maestri, E., et al. (1999). Intimate association of microsatellite repeats with retrotransposons and other dispersed repetitive elements in barley. Plant Journal, 17, 415–425.CrossRefGoogle Scholar
  157. 157.
    Metzgar, D., Liu, L., Hansen, C., Dybrig, K., & Wills, C. (2002). Domain-level differences in microsatellite distribution and content result from different relative rates of insertion and deletion mutations. Genetics Research, 12, 408–413.Google Scholar
  158. 158.
    Zhang, L., Yuan, D., Yu, S., Li, Z., & Cao, Y. (2004). Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana. Bioinformatics, 20, 1081–1086.CrossRefGoogle Scholar
  159. 159.
    Robert, V. J., Sijen, T., van Wolfswinkel, J., & Plasterk, R. H. (2005). Chromatin and RNAi factors protect the C. elegans germline against repetitive sequences. Genes and Development, 19, 782–787.CrossRefGoogle Scholar
  160. 160.
    Bogerd, H. P., Wiegand, H. L., Hulme, A. E., Garcia-Perez, J. L., & O’Shea, K. S. (2006). Cellular inhibitors of long interspersed element 1 and Alu retrotransposition. Proceedings of the National Academy of Sciences of the United States of America, 103, 8780–8785.CrossRefGoogle Scholar
  161. 161.
    Taylor, J. S., Durkin, J. M., & Breden, F. (1999). The death of a microsatellite: A phylogenetic perspective on microsatellite interruptions. Molecular Biology and Evolution, 16, 567–572.Google Scholar
  162. 162.
    Amos, W. (1999). A relative approach to study the evolution of microsatellites. In D. B. Goldstein & C. Schlotterer (Eds.), Microsatellites: Evolution and applications (pp. 60–79). Oxford: Oxford University Press.Google Scholar
  163. 163.
    Chambers, G. K., & MacAvoy, E. S. (2000). Microsatellites: Consensus and controversy. Comparitive Biochemistry and Physiology. Part B. Biochemistry & Molecular Biology, 126, 455–476.CrossRefGoogle Scholar
  164. 164.
    Ewen, K. R., Bahlo, M., Treloar, S. A., Levinson, D. F., Mowry, B., Barlow, J. W., et al. (2000). Identification and analysis of error types in high-throughput genotyping. The American Journal of Human Genetics, 67, 727–736.CrossRefGoogle Scholar
  165. 165.
    Ohta, T., & Kimura, M. (1973). A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genetics Research, 22, 201–204.CrossRefGoogle Scholar
  166. 166.
    Shriver, M. D., Jin, L., Chakraborty, R., & Boerwinkle, E. (1993). VNTR allele frequency distributions under the stepwise mutation model: A computer simulation approach. Genetics, 134, 983–993.Google Scholar
  167. 167.
    Moran, P. A. P. (1975). Wandering distributions and the electrophoretic profile. Theoretical Population Biology, 8, 318–330.CrossRefGoogle Scholar
  168. 168.
    Kimmel, M., & Chakraborty, R. (1996). Measures of variation at DNA repeat loci under a general stepwise mutation model. Theoretical Population Biology, 50, 345–367.CrossRefGoogle Scholar
  169. 169.
    Pritchard, J. K., & Feldman, M. W. (1996). Statistics for microsatellite variation based on coalescence. Theoretical Population Biology, 50, 325–344.CrossRefGoogle Scholar
  170. 170.
    Zhivotovsky, L. A., & Feldman, M. W. (1995). Microsatellite variability and genetic distances. Proceedings of the National Academy of Sciences of the United States of America, 92, 11549–11552.CrossRefGoogle Scholar
  171. 171.
    Goldstein, D., Linares, A. R., Cavalli-Sforza, L. L., & Feldman, M. W. (1995). Genetic absolute dating based on microsatellites and the origin of modern humans. Proceedings of the National Academy of Sciences of the United States of America, 92, 6723–6727.CrossRefGoogle Scholar
  172. 172.
    Thuillet, A. C., Bataillon, T., Sourdille, P., & David, J. L. (2004). Factors affecting polymorphism at microsatellite loci in bread wheat [Triticum aestivum (L.) Thell]: Effects of mutation processes and physical distance from the centromere. Theoretical and Applied Genetics, 108, 368–377.CrossRefGoogle Scholar
  173. 173.
    Slatkin, M. (1995). A measure of population subdivision based on microsatellite allele frequencies. Genetics, 139, 457–462.Google Scholar
  174. 174.
    Goldstein, D. B., & Pollock, D. D. (1997). Launching microsatellites: A review of mutation processes and methods of phylogenetic inference. Journal of Heredity, 88, 335–342.Google Scholar
  175. 175.
    Pritchard, J. K., Seielstad, M. T., Perez-Lezaun, A., & Feldman, M. W. (1999). Population growth of human Y chromosome microsatellites. Molecular Biology and Evolution, 16, 1791–1798.Google Scholar
  176. 176.
    Estoup, A., & Cornuet, J. M. (1999). Microsatellite evolution: Inferences from population data. In D. B. Goldstein & C. Schlotterer (Eds.), Microsatellites: Evolution and applications (pp. 49–65). Oxford: Oxford University Press.Google Scholar
  177. 177.
    Leblois, R., Estoup, A., & Rousset, F. (2003). Influence of mutational and sampling factors on the estimation of demographic parameters in a “continuous” population under isolation by distance. Molecular Biology and Evolution, 20, 491–502.CrossRefGoogle Scholar
  178. 178.
    Fu, Y., & Chakraborty, R. (1998). Simultaneous estimation of all the parameters of a step-wise mutation model. Genetics, 150, 487–497.Google Scholar
  179. 179.
    Kimura, M., & Crow, J. F. (1964). The number of alleles that can be maintained in a finite population. Genetics, 49, 725–738.Google Scholar
  180. 180.
    Symonds, V. V., & Lloyd, A. M. (2003). An analysis of microsatellite loci in Arabidopsis thaliana: Mutational dynamics and application. Genetics, 165, 1475–1488.Google Scholar
  181. 181.
    Goldstein, D., Linares, A. R., Cavalli-Sforza, L. L., & Feldman, M. W. (1995). An evaluation of genetic distances for use with microsatellite loci. Genetics, 139, 463–471.Google Scholar
  182. 182.
    Brohede, J., Primmer, C. R., Moller, A., & Ellegren, H. (2002). Heterogeneity in the rate and pattern of germline mutation at individual microsatellite loci. Nucleic Acids Research, 30, 1997–2003.CrossRefGoogle Scholar
  183. 183.
    Thuillet, A. C., Bru, D., David, J., Roumet, P., & Santoni, S. (2002). Direct estimation of mutation rate for 10 microsatellite loci in durum wheat. Triticum turgidum (L.) Thell. ssp durum desf. Molecular Biology and Evolution, 19, 122–125.Google Scholar
  184. 184.
    Harr, B., & Schlotterer, C. (2000). Long microsatellite alleles in Drosophila melanogaster have a downward mutation bias and short persistence times, which cause their genome-wide under-representation. Genetics, 155, 1213–1220.Google Scholar
  185. 185.
    Garza, J. C., Slatkin, M., & Freimer, N. B. (1995). Microsatellite allele frequencies in humans and chimpanzees, with implications for constraints on allele size. Molecular Biology and Evolution, 12, 594–603.Google Scholar
  186. 186.
    Zhivotovsky, L. A., Feldman, M. W., & Grishechkin, S. A. (1997). Biased mutations and microsatellite variation. Molecular Biology and Evolution, 14, 926–933.Google Scholar
  187. 187.
    Crow, J., & Kimura, M. (1970). An introduction to population genetics theory. Minneapolis: Burgess Publishing Company.Google Scholar
  188. 188.
    Cooper, G., Burroughs, N. J., Rand, D. A., Rubinsztein, D. C., & Amos, W. (1999). Markov chain Monte Carlo analysis of human Y-chromosome microsatellite provides evidence of biased mutation. Proceedings of the National Academy of Sciences of the United States of America, 96, 11916–11921.CrossRefGoogle Scholar
  189. 189.
    Renwick, A., Davison, L., Spratt, H., King, J. P., & Kimmel, M. (2001). DNA dinucleotide evolution in humans: Fitting theory to facts. Genetics, 159, 737–747.Google Scholar
  190. 190.
    Xu, H., & Fu, Y. X. (2004). Estimating effective population size or mutation rate with microsatellites. Genetics, 166, 555–563.CrossRefGoogle Scholar
  191. 191.
    Grimaldi, M. C., & Crouau-Roy, B. (1997). Microsatellite allelic homoplasy due to variable flanking sequences. Journal of Molecular Evolution, 44, 336–340.CrossRefGoogle Scholar
  192. 192.
    Van Oppen, J. H., Rico, C., Turner, G. F., & Hewitt, G. M. (2000). Extensive homoplasy, non-step mutations and ancestral polymorphism at a complex microsatellite locus in lake Malawi Ciclids. Molecular Biology and Evolution, 17, 489–498.Google Scholar
  193. 193.
    Primmer, C. R., & Ellegren, H. (1998). Patterns of molecular evolution in avian microsatellites. Molecular Biology and Evolution, 15, 997–1008.Google Scholar
  194. 194.
    Colson, I., & Goldstein, D. B. (1999). Evidence for complex mutations at microsatellite loci in Drosophila. Genetics, 152, 617–627.Google Scholar
  195. 195.
    Estoup, A., Jarne, P., & Cornuet, J. M. (2002). Homoplasy and mutation model at microsatellite loci and their consequences for population genetic analysis. Molecular Ecology, 11, 1591–1604.CrossRefGoogle Scholar
  196. 196.
    Nauta, M. J., & Weissing, F. J. (1996). Constraints on allele size at microsatellite loci—Implications for genetic differentiation. Genetics, 143, 1021–1032.Google Scholar
  197. 197.
    Viard, F., Franck, P., Dubois, M. P., Estoup, A., & Jarne, P. (1998). Variation of microsatellite size homoplasy across electromorphs, loci and populations in three vertebrate species. Journal of Molecular Evolution, 47, 42–51.CrossRefGoogle Scholar
  198. 198.
    Taylor, J. S., Sanny, J. S. P., & Breden, F. (1999). Microsatellite allele size homoplasy in the guppy (Poecilia reticulata). Journal of Molecular Evolution, 48, 245–247.Google Scholar
  199. 199.
    Hartl, D. I. (2000). Molecular melodies in high and low C. Nature Reviews Genetics, 1, 145–149.CrossRefGoogle Scholar
  200. 200.
    Ohri, D., Bhargava, A., & Chatterjee, A. (2004). Nuclear DNA amounts in 112 species of tropical hardwoods—New estimates. Plant Biology, 6, 555–561.CrossRefGoogle Scholar
  201. 201.
    Bhargava, A., Shukla, S., & Ohri, D. (2007). Genome size variation in some cultivated and wild species of Chenopodium (Chenopodiaceae). Caryologia, 60, 245–250.Google Scholar
  202. 202.
    Hancock, J. M. (1996). Simple sequences and the expanding genome. BioEssays, 18, 421–425.CrossRefGoogle Scholar
  203. 203.
    Garner, T. W. (2002). Genome size and microsatellites: The effect of nuclear size on amplification potential. Genome, 45, 212–215.CrossRefGoogle Scholar
  204. 204.
    Ustinova, J., Achmann, R., Cremer, S., & Mayer, F. (2006). Long repeats in a huge genome: Microsatellite loci in the grasshopper Chorthippus biguttulus. Journal of Molecular Evolution, 62, 158–167.CrossRefGoogle Scholar
  205. 205.
    Tero, N., Neumeier, H., Gudavalli, R., & Schlotterer, C. (2006). Silene tatarica microsatellites are frequently located in repetitive DNA. Journal of Evolutionary Biology, 19, 1612–1619.CrossRefGoogle Scholar
  206. 206.
    Mrazek, J., Guo, X., & Shah, A. (2007). Simple sequence repeats in prokaryotic genomes. Proceedings of the National Academy of Sciences of the United States of America, 104, 8472–8477.CrossRefGoogle Scholar
  207. 207.
    Karaoglu, H., Lee, C. M. Y., & Meyer, W. (2005). Survey of simple sequence repeats in completed fungal genomes. Molecular Biology and Evolution, 22, 639–649.CrossRefGoogle Scholar
  208. 208.
    Levinson, G., & Gutman, G. A. (1987). Slipped strand mispairing: A major mechanism for DNA sequence evolution. Molecular Biology and Evolution, 4, 203–221.Google Scholar
  209. 209.
    Vasquez, F., Perez, T., Albornoz, J., & Dominguez, A. (2000). Estimation of the mutation rates in Drosophila melanogaster. Genetics Research, 76, 323–326.CrossRefGoogle Scholar
  210. 210.
    Serikawa, T., Kuramoto, T., Hilbert, P., Mori, M., & Yamada, J. (1992). Rat gene mapping using PCR-analyzed microsatellites. Genetics, 131, 701–721.Google Scholar
  211. 211.
    Dietrich, W. F., Miller, J. C., Steen, R. G., Merchant, M., & Damron, D. (1994). A genetic map of the mouse with 4,006 simple sequence length polymorphisms. Nature Genetics, 7, 220–245.CrossRefGoogle Scholar
  212. 212.
    Sajantilla, A., Lukka, M., & Syvanen, A. C. (1999). Experimentally observed germline mutations at human micro- and mini-satellite loci. European Journal of Human Genetics, 7, 263–266.CrossRefGoogle Scholar
  213. 213.
    Udupa, S. M., & Baum, M. (2001). High mutation rate and mutational bias at (TAA)n microsatellite loci in chickpea (Cicer arietinum L.). Molecular Genetics and Genomics, 265, 1097–1103.CrossRefGoogle Scholar
  214. 214.
    McConnell, R., Middlemist, S., Scala, C., Strassman, J. E., & Queller, D. C. (2007). An unusually low microsatellite mutation rate in Dictyostelium discoideum, an organism with unusually abundant microsatellites. Genetics, 177, 1499–1507.CrossRefGoogle Scholar
  215. 215.
    Raquin, A. L., Depaulis, F., Lambert, A., Galic, N., Brabant, P., & Goldringer, I. (2008). Experimental estimation of mutation rates in a wheat population with a gene genealogy approach. Genetics, 179, 2195–2211.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  1. 1.Amity Institute of Biotechnology, Amity University Uttar Pradesh (Lucknow Campus)LucknowIndia
  2. 2.Departemento de Agricultura del DesiertoUniversidad Arturo PratIquiqueChile

Personalised recommendations