A phylogenetic perspective on sequence evolution in microsatellite loci

Journal of Molecular Evolution

Volumn 50, Issue 4, 2000, Pages 324-338

  Zhu, Yong ^a   Queller, David C ^a   Strassmann, Joan E ^a  

^a RICE UNIVERSITY   (United States)

Author keywords

Ascertainment bias; Directionality; Evolution; Independent contrasts; Microsatellite; Phylogeny; Polistes; Slippage; Stepwise mutation; Vespidae

Indexed keywords

MICROSATELLITE DNA;

ARTICLE; CHROMOSOME SATELLITE; GENE LOCUS; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE;

POLISTES; POLISTINAE; VESPIDAE;

EID: 0033935516     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002399910036     Document Type: Article

References (58)

1. Amos W, Rubinsztein DC (1996) Microsatellites are subject to directional evolution. Nat Genet 12:13-14
2. Amos W, Sawcer SJ, Feakes RW, Rubinsztein DC (1996) Microsatellites show mutational bias and heterozygote instability. Nat Genet 13:390-391
3. Anger B, Bernatchez L (1997) Complex evolution of a salmonid microsatellite locus and its consequences in inferring allelic divergence from size formation. Mol Biol Evol 14:230-238
4. Bichara M, Schumacher S, Fuchs RPP (1995) Genetic instability within monotonous runs of CpG sequences in Escherichia coli. Genetics 140:897-907
5. Blanquer-Maumont A, Crouau-Roy B (1995) Polymorphism, monomorphism and sequences in conserved microsatellites in primate species. J Mol Evol 41:492-497
6. Bowcock AM, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd JR, Cavalli-Sforza LL (1994) High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368:455-457
7. Carpenter JM (1993) Biogeographic patterns in the Vespidae (Hymenoptera); two views of Africa and South America. In: Goldhlatt P (ed) Biological relationships between Africa and South America. Yale University Press, New Haven, CT, pp 139-155
8. Chung MY, Ranum LPW, Duvick LA, Servadio A, Zoghbi HY, Orr HT (1993) Evidence for a mechanism predisposing to intergenerational CAG repeat instability in spinocerebellar ataxia type I. Nat Genet 5:254-258
9. Cooper G, Rubinsztein DC, Amos W (1998) Ascertainment bias cannot entirely account for human microsatellites being longer than their chimpanzee homologues. Hum Molec Genet 7:1425-1429
10. Crawford AM, Kappes SM, Paterson KA, deGotari MJ, Dodds KG, Freking BA, Stone RT, Beattie CW (1998) Microsatellite evolution: testing the ascertainment bias hypothesis. J Mol Evol 46:256-260
11. Dib C, Faure S, Fizames C, Samson D, Drouot N, Vignal A, Millasseau P, Marc S, Hazan J, Seboun E, Lathrop M, Gyapay G, Morissette J, Weissenbach J (1996) A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 380:152-154
12. Di Rienzo A, Peterson AC, Garza JC, Valders AM, Slatkin M, Freimer NB (1994) Mutational processes of simple-sequence repeat loci in human populations. Proc Natl Acad Sci USA 91:3166-3170
13. Edwards A, Hammond HA, Jin L, Caskey CT, Chakraborty R (1992) Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups. Genomics 12:241-253
14. Ellegren H, Primmer CR, Sheldon BC (1995) Microsatellite evolution: directionality or bias. Nat Genet 11:360-362
15. Ezenwa VO, Peters JM, Zhu Y, Arévalo E, Hastings MD, Seppä P, Pederson JS, Zacchi F, Queller DC, Strassmann JE (1998) Ancient conservation of trinucleotide microsatellite loci in polistine wasps. Mol Phylogen Evol 10:168-177
16. Felsenstein J (1985) Phylogenies and the comparative method. Am Nat 125:1-15
17. FitzSimmons NN, Moritz C, Moore SS (1995) Conservation and dynamics of microsatellite loci over 300 million years of marine turtle evolution. Mol Biol Evol 12:432-440
18. Freund AM, Fuchs RPP, Bichara M (1989) Z-DNA-forming sequences are spontaneous deletion hot spots. Proc Natl Acad Sci USA 86: 7465-7469
19. Garza JC, Slatkin M, Freimer NB (1995) Microsatellite allele frequencies in humans and chimpanzees, with implications for constraints on allele size. Mol Biol Evol 12:594-603
20. Hamada H, Petrino MG, Kakunaga T (1982) A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes. Proc Natl Acad Sci USA 79:6465-6469
21. Hastings MD, Queller DC, Eischen F, Strassmann JE (1998) Kin selection, relatedness, and worker control of reproduction in a large-colony epiponine wasp, Brachygastra mellifica. Behav Ecol 9:573-581
22. Henderson ST, Petes TD (1992) Instability of simple sequence DNA in Sarcharomyces cerevisiae. Mol Cell Biol 12:2749-2757
23. Hutter CM, Schug MD, Aquadro CF (1998) Microsatellite variation in Drosophila melanogaster and Drosophila simulans: a reciprocal test of the ascertainment bias hypothesis. Mol Biol Evol 15:1620-1636
24. Jin L, Macaubas C, Hallmayer J, Kimura A, Mignot E (1996) Mutation rate varies among alleles at a microsatellite locus: phylogenetic evidence. Proc Natl Acad Sci USA 93:15285-15288
25. Kolodner R (1996) Biochemistry and genetics of eukaryotic mismatch repair. Genes Dev 10:1433-1442
26. Kroutil LC, Register K, Bebenek K, Kunkel TA (1996) Exonucleolytic proofreading during replication of repetitive DNA. Biochemistry 35:1046-1053
27. Kruglyak S, Durrett RT, Schug MD, Aquadro CF (1998) Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proc Natl Acad Sci USA 95:10774-10778
28. Levinson G, Gutman GA (1987) High frequencies of short frameshifts in poly-CA/TG tandem repeats borne by bacteriophage M13 in Escherichia coli K-12. Nucleic Acids Res 15:5289-5304
29. Li W-H (1997) Molecular evolution. Sinauer Associates, Sunderland, MA
30. Lorenzi MC, Turillazzi S (1986) Behavioural and ecological adaptations to the high mountain environment of Polistes biglumis bimaculatus. Ecol Entomol 11:199-204
31. Maddison WP, Maddison DR (1992) MacClade: analysis of phylogeny and character evolution, version 3.0. Sinauer, Sunderland, MA
32. Maurer DJ, O'Callaghan BL, Livingston DM (1996) Mapping the polarity of changes that occur in interrupted CAG repeat tracts in yeast. Mol Cell Biol 18:4597-4604
33. Messier W, Li SH, Stewart CB (1996) The birth of microsatellites. Nature 381:483
34. Pardi (1941) Ricerche sui Polistini 2. Nota sui Polistini della campagna. Att della Societa Toscana di Scienze Naturali 50:1-7
35. Pépin L, Amigues Y, Lépingle A, Berthier JL, Bensaids A, Vaiman D (1995) Sequence conservation of microsatellites between Bos taurus (cattle), Capra hircus (goat) and related species. Examples of use in parentage testing and phylogeny analysis. Heredity 74:53-61
36. Primmer CR, Ellegren H, Saino N, Moller AP (1996) Directional evolution in germline microsatellite mutations. Nat Genet 13:391-393
37. Purvis A, Rambaut A (1995) Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analyzing comparative data. Comp Appl Biosci 11:247-251
38. Purvis A, Gittleman JL, Luh HK (1994) Truth or consequences: effects of phylogenetic accuracy on two comparative methods. J Theor Biol 167:293-300
39. Queller DC, Strassmann JE, Hughes CR (1993) Microsatellites and kinship. Trends Ecol Evol 8:285-288
40. Richards OW (1978) The social wasps of the Americas excluding the Vespinae. British Museum (Natural History), London
41. Richards RI, Sutherland GR (1994) Simple repeat DNA is not replicated simply. Nat Genet 6:114-116
42. Rico C, Rico I, Hewitt G (1996) 470 million years of conservation of microsatellite loci among fish species. Proc Roy Soc Lond B 263: 540-557
43. Rubinsztein DC, Amos W, Leggo J, Goodburn S, Jain S, Li SH, Margolis RL, Ross CA, Ferguson-Smith MA (1995) Microsatellite evolution-evidence for directionality and variation in rate between species. Nat Genet 10:337-343
44. Schlötterer C, Tautz D (1992) Slippage synthesis of simple sequence DNA. Nucleic Acids Res 20:211-215
45. Shriver MD, Jin L, Chakraborty R, Boerwinkle E (1993) VNTR allele frequency distributions under the stepwise mutation model: a computer simulation approach. Genetics 134:983-993
46. Sia EA, Kokoska RJ, Dominska M, Greenwell P, Petes TD (1997) Microsatellite instability in yeast: dependence on repeat unit size and DNA mismatch repair genes. Mol Cell Biol 17:2851-2858
47. Stephan W, Cho S (1994) Possible role of natural selection in the formation of tandem-repetitive noncoding DNA. Genetics 136: 333-341
48. Strand M, Prolla TA, Liskay RM, Petes TD (1993) Destabilization of tracts of simple repetitive DNA in yeast by mutations affecting DNA mismatch repair. Nature 365:274-276
49. Strand M, Earley MC, Crouse GF, Petes TD (1995) Mutations in the MSH3 gene preferentially lead to deletions within tracts of simple repetitive DNA in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 92:10418-10421
50. Strassmann JE (1979) Honey caches help female paper wasps (Polistes annularis) survive Texas winter. Science 204:207-209
51. Strassman JE, Barefield K, Solís CR, Hughes CR, Queller DC (1997) Trinucleotide microsatellite loci for a social wasp, Polistes. Mol Ecol 6:97-100
52. Strassman JE, Solís CR, Peters JM, Queller DC (1996) Strategies for finding and using highly polymorphic DNA microsatellite loci for studies of genetic relatedness and pedigrees. In: Ferraris J, Palumbi S (eds) Molecular methods in zoology and evolution. Wiley, New York, NY, pp 163-180, pp 528-549
53. Streisinger G, Okada Y, Emrich J, Newton T, Tsugita A, Terzaghi E, Inouye M (1996) Frameshift mutations and the genetic code. Quant Biol 31:77-82
54. Tran HT, Keen JD, Kricker M, Resnick MA, Gordenin DA (1997) Hypermutability of homonucleotide runs in mismatch repair and DNA polymerase proofreading yeast mutants. Mol Cell Biol 17: 2859-2865
55. Weber JL (1990) Informativeness of human (dC-dA)n. (dG-dT)n polymorphisms. Genomics 7:524-530
56. Weber JL, Wong C (1993) Mutation of human short tandem repeats. Hum Mol Genet 2:1123-1128
57. Weissenbach J, Gyapay G, Dib C, Vignal A, Morissette J, Millasseau P, Vaysseix G, Lathrop M (1992) A second-generation linkage map of the human genome. Nature 359:794-801
58. Wierdl M, Dominska M, Petes TD (1997) Microsatellite instability in yeast: dependence on the length of the microsatellite. Genetics 146:769-779