On the genealogy of a duplicated microsatellite

Genetics

Volumn 177, Issue 4, 2007, Pages 2109-2122

  Zhang, Kangyu ^a   Rosenberg, Noah A ^b  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICROSATELLITE DNA;

ALLELE; ARTICLE; DIPLOIDY; GENE AMPLIFICATION; GENE DUPLICATION; GENE LOCUS; GENE MUTATION; GENEALOGY; GENETIC MODEL; GENETIC PARAMETERS; GENETIC VARIABILITY; MUTATION RATE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROBABILITY; SHORT TANDEM REPEAT; SIMULATION;

DNA PRIMERS; EVOLUTION, MOLECULAR; GENE DUPLICATION; MICROSATELLITE REPEATS; MODELS, GENETIC; MUTATION; POLYMERASE CHAIN REACTION; VARIATION (GENETICS);

EID: 37249054206     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.106.063131     Document Type: Article

References (36)

1. ANTUNES, A., K. GHARBI, P. ALEXANDRINO and R. GUYOMARD, 2006 Characterization of transferrin-linked microsatellites in brown trout (Salmo trutta) and Atlantic salmon (Salmo salar). Mol. Ecol. Notes 6: 547-549.
2. BALARESQUE, P., A. SIBERT, E. HEYER and B. CROUAU-ROY, 2007 Unbiased interpretation of haplotypes at duplicated microsatellites. Ann. Hum. Genet. 71: 209-219.
3. BLUM, M. G. B., C. DAMERVAL, S. MANEL and O. FRANCOIS, 2004 Brownian models and coalescent structures. Theor. Popul. Biol. 65: 249-261.
4. CALABRESE, P., and R. SAINUDIIN, 2005 Models of microsatellite evolution, pp. 289-305 in Statistical Methods in Molecular Evolution, edited by R. NIELSEN. Springer, New York.
5. DAVID, L., S. BLUM, M. W. FELDMAN, U. LAVI and J. HILLEL, 2003 Recent duplication of the common carp (Cyprinus carpio L.) genome as revealed by analyses of microsatellite loci. Mol. Biol. Evol. 20: 1425-1434.
6. DAVID, L., N. A. ROSENBERG, U. LAVI, M. W. FELDMAN and J. HILLEL, 2007 Genetic diversity and population structure inferred from the partially duplicated genome of domesticated carp, Cyprinus carpio L. Genet. Sel. Evol. 39: 319-340.
7. DEMUTH, J. P., T. DE BIE, J. E. STAJICH, N. CRISTIANINI and M. W. HAHN, 2006 The evolution of mammalian gene families. PLoS ONE 1: e85.
8. ELLEGREN, H., 2004 Microsatellites: simple sequences with complex evolution. Nat. Rev. Genet. 5: 435-445.
9. ESTOUP, A., P. JARNE and J.-M. CORNUET, 2002 Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Mol. Ecol. 11: 1591-1604.
10. GOLDSTEIN, D. B., A. RUIZ LINARES, L. L. CAVALLI-SFORZA and M. W. FELDMAN, 1995 An evaluation of genetic distances for use with microsatellite loci. Genetics 139: 463-471.
11. GRADSHTEYN, I. S., and I. M. RYZHIK, 1980 Table of Integrals, Series, and Products. Academic Press, London.
12. INNAN, H., 2002 A method for estimating the mutation, gene conversion and recombination parameters in small multigene families. Genetics 161: 865-872.
13. INNAN, H., 2003 The coalescent and infinite-site model of a small multigene family. Genetics 163: 803-810.
14. INNAN, H., 2004 Theories for analyzing polymorphism data in duplicated genes. Genes Genet. Syst. 79: 65-75.
15. KIMMEL, M., and R. CHAKRABORTY, 1996 Measures of variation at DNA repeat loci under a general stepwise mutation model. Theor. Popul. Biol. 50: 345-367.
16. LYNCH, M., and J. S. CONERY, 2000 The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
17. LYNCH, M., and A. FORCE, 2000 The probability of duplicate gene preservation by subfunctionalization. Genetics 154: 459-473.
18. MATHIAS, N., M. BAYES and C. TYLER-SMITH, 1994 Highly informative compound haplotypes for the human Y chromosome. Hum. Mol. Genet. 3: 115-123.
19. MATSUOKA, Y., S. E. MITCHELL, S. KRESOVICH, M. GOODMAN and J. DOEBLEY, 2002 Microsatellites in Zea - variability, patterns of mutations, and use for evolutionary studies. Theor. Appl. Genet. 104: 436-450.
20. MORAN, P. A. P., 1975 Wandering distributions and the electrophoretic profile. Theor. Popul. Biol. 8: 318-330.
21. NIELSEN, R., 1997 A likelihood approach to populations samples of microsatellite alleles. Genetics 146: 711-716.
22. NORDBORG, M., 2001 Coalescent theory, pp. 179-212 in Handbook of Statistical Genetics, edited by D. J. BALDING, M. BISHOP and C. CANNINGS. Wiley, Chichester, UK.
23. OHNO, S., 1970 Evolution by Gene Duplication. Springer-Verlag, New York.
24. OHTA, T., and M. KIMURA, 1973 A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genet. Res. 22: 201-204.
25. O'MALLEY, K. G., T. SAKAMOTO, R. G. DANZMANN and M. M. FERGUSON, 2003 Quantitative trait loci for spawning date and body weight in rainbow trout: testing for conserved effects across ancestrally duplicated chromosomes. J. Hered. 94: 273-284.
26. PRITCHARD, J. K., and M. W. FELDMAN, 1996 Statistics for microsatellite variation based on coalescence. Theor. Popul. Biol. 50: 325-344.
27. SAINUDIIN, R., R. T. DURRETT, C. F. AQUADRO and R. NIELSEN, 2004 Microsatellite mutation models: insights from a comparison of humans and chimpanzees. Genetics 168: 383-395.
28. SLATKIN, M., 1995 A measure of population subdivision based on microsatellite allele frequencies. Genetics 139: 457-462.
29. TESHIMA, K. M., and H. INNAN, 2004 The effect of gene conversion on the divergence between duplicated genes. Genetics 166: 1553-1560.
30. WALSH, B., 2003 Population-genetic models of the fates of duplicate genes. Genetica 118: 279-294.
31. WARD, R., and R. DURRETT, 2004 Subfunctionalization: How often does it occur? How long does it take? Theor. Popul. Biol. 66: 93-100.
32. WEHRHAHN, C. F., 1975 The evolution of selectively similar electrophoretically detectable alleles in finite natural populations. Genetics 80: 375-394.
33. WHITTAKER, J. C., R. M. HARBORD, N. BOXALL, I. MACKAY, G. DAWSON et al., 2003 Likelihood-based estimation of microsatellite mutation rates. Genetics 164: 781-787.
34. WILSON, I. J., and D. J. BALDING, 1998 Genealogical inference from microsatellite data. Genetics 150: 499-510.
35. ZHANG, J., 2003 Evolution by gene duplication: an update. Trends Ecol. Evol. 18: 292-298.
36. ZHIVOTOVSKY, L. A., and M. W. FELDMAN, 1995 Microsatellite variability and genetic distances. Proc. Natl. Acad. Sci. USA 92: 11549-11552.