Multiple levels of single-strand slippage at cetacean tri- and tetranucleotide repeat microsatellite loci

Genetics

Volumn 151, Issue 1, 1999, Pages 285-296

  Palsbøll, Per J ^a,b,c   Bérubé, Martine ^b   Jørgensen, Hanne ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c BANGOR UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; GENE LOCUS; GENE MUTATION; NONHUMAN; PRIORITY JOURNAL; SPECIES DIFFERENCE; WHALE;

ALLELES; ANIMALS; GENOTYPE; MICROSATELLITE REPEATS; MUTATION; SEQUENCE ANALYSIS, DNA; TRINUCLEOTIDE REPEATS; WHALES;

ANIMALIA; BALAENOPTERA PHYSALUS; CETACEA; MAMMALIA; MEGAPTERA NOVAEANGLIAE; MYSTICETI; ONCORHYNCHUS GORBUSCHA;

EID: 0345129969     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (58)

1. AMOS, W., and A. R. HOELZEL, 1991 Long-term preservation of whale skin for DNA analysis. Rep. Int. Whaling Comm. Spec. Issue 13: 99-104.
2. AMOS, W., and D. C. RUBINSZTEIN, 1996a Microsalellites are subject to directional evolution. Nat. Genet. 12: 13-14.
3. AMOS, W., and D. C. RUBINSZTEIN, 1996b Microsatelliles showmutational bias and heterozygote instability. Nat. Genet. 13: 390-391.
4. ANGERS, B., and L. BERNATCHEZ, 1997 Complex evolution of a salmonid microsatellite locus and its consequences in inferring allelic divergence from size information. Mol. Biol. Evol. 14: 230-238.
5. BÉRUBE,́ M., and P. PALSBØLL, 1996a Erratum of identification of sex in cetaceans by multiplexing with three ZFX and ZFY specific primers. Mol. Ecol. 5: 602.
6. BÉRUBÉ, M., and P. J. PALSBØLL, 1996b Identification of sex in cetaceans by multiplexing with three ZFX and ZFY specific primers. Mol. Ecol. 5: 283-287.
7. BÉRUBÉ, M., A. AGUILAR, D. DENDANTO, F. LARSEN, G. NOTARBAR-TOKO-DI-SCIARA et al., 1998 Population genetic structure of North Atlantic, Mediterranean Sea and Sea of Cortez fin whales, Balaenoptera physalus (Linnaeus, 1758): analysis of mitochondrial and nuclear loci. Mol. Ecol. 7: 585-600.
8. CHAKRABORTY, R., and K. M. WEISS, 1991 Genetic variation of the mitochondrial DNA genome in American Indians is at mutation-drift equilibrium. Am. J. Phys. Anthropol. 86: 497-506.
9. CHAKRABORTY, R., M. KIMMEL, D. N. STIVERS, L. J. DAVISON and R. DEKA, 1997 Relative mutation rate at di-, tri-, and tetranucleotide microsatellite loci. Proc. Natl. Acad. Sci. USA 94: 1041-1046.
10. CLAPHAM, P. J., P. J. PALSBØLL and D. K. MATTILA, 1993 High-energy behaviors in humpback whales as a source of sloughed skin for molecular analysis. Mar. Mamm. Sci. 9: 213-220.
11. Di RIENZO, A., A. C. PETERSON, J. C. CARZA, A. M. VALDES, M. SLATKIN et al., 1994 Mutational processes of simple-sequence repeat loci in human populations. Proc. Natl. Acad. Sci. USA 91: 3166-3170.
12. DUYAO, M., C. AMBROSE, R. MYERS, A. NOVELLETTO, F. PERSICHETTI et al., 1993 Trinucleotide repeat length instability and age of onset in Huntington's disease. Nat. Genet. 4: 387-392.
13. ELLEGREN, H., C. R. PRIMMER and B. C. SHELDON, 1995 Microsatellite 'evolution': directional bias? Nat. Genet. 11: 360-362.
14. ESTOUP, A., C. TAILIEZ, J.-M. CORNUET and M. SOLIGNAC, 1995 Size homoplasy and mutational processes of interrupted microsatellites in two bee species, Apis mellifera and Bombus terrestris (Apidae). Mol. Biol. Evol. 12: 1074-1084.
15. GARZA, J. C., and N. B. FREIMER, 1996 Homoplasy for size at microsatellite loci in humans and chimpanzees. Genome Res. 6: 211-217.
16. GARZA, J. C., M. SLATKIN and N. B. FREIMER, 1995 Microsatellite allele frequencies in humans and chimpanzees, with implications for constraints on allele size. Mol. Biol. Evol. 12: 594-603.
17. GOLDSTEIN, D. B., A. R. LINARES, L. L. CAVELLI-SFORZA and M. W. FELDMAN, 1995a An evaluation of genetic distances for use with microsatellile loci. Genetics 139: 463-471.
18. GOLDSTEIN, D. B., A. RUIZ LINARES, L. L. GAVALLI-SFORZA and M. W. FELDMAN, 1995b Genetic absolute dating based upon microsatellites and the origin of modern humans. Proc. Natl. Acad. Sci. USA 92: 6723-6727.
19. GRIMALDI, M.-C., and B. CROUAU-ROY, 1997 Microsatellite allelic homoplasmy due to variable flanking sequences. J. Mol. Evol. 44: 336-340.
20. GYLLENSTEN, U. B., and H. A. ERLICH, 1988 Generation of single-stranded DNA by the polymerase reaction and its application to direct sequencing of the HLA-DQA locus. Proc. Natl. Acad. Sci. USA 85: 7652-7656.
21. HUDSON, R. R., 1990 Gene genealogies and the coalescent process, pp. 1-44 in Oxfords Surveys in Evolutionary Biology, edited by D. J. FUTUYMA and J. ANTONOVICS. Oxford University Press, Oxford.
22. HUDSON, R. R., and N. L. KAPLAN, 1986 On the divergence of alleles in nested subsamples from finite populations. Genetics 113: 1057-1076.
23. JIN, L., C. MACAUBAS, J. HALLMAYER, A. KIMURA and K. MIGNOT, 1996 Mutation rate varies among alleles at a microsatellite locus: phylogenetic evidence. Proc. Natl. Acad. Sci. USA 93: 15285-15288.
24. 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.
25. KIMMEL, M., R. CHAKRABORTY, D. N. STIVERS and R. DEKA, 1996 Dynamics of repeat polymorphisms under a forward-backward mutation model: within- and between-population variability at microsalellite loci. Genetics 143: 549-555.
26. KIMMEL, M., R. CHAKRABORTY, J. P. KING, M. BAMSHAD, W. S. WATKINS et al., 1998 Signatures of population expansion in microsatellite repeat data. Genetics 148: 1921-1930.
27. KUHNER, M. K., J. YAMATO and J. FELSENSTEIN, 1998 Maximum likelihood estimation of population growth rates based on the coalescent. Genetics 149: 429-434.
28. LEVINSON, G., and G. A. GUTMAN, 1987a High frequencies of short frameshifts in poly-CA/TG tandem repeats borne by bacteriophage M13 in Escherichia coli K-12. Nucleic Acids Res. 15: 5323-5339.
29. LEVINSON, G., and G. A. GUTMAN, 1987b Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol. Biol. Evol. 4: 203-221.
30. MAHTANI, M. M., and H. F. WILLARD, 1993 A polymorphic X-linked tetranucleotide repeat locus displaying a high rate of new mutation: implications for mechanisms of mutation at short tandem repeat loci. Hum. Mol. Genet. 2: 431-437.
31. MANIATIS, T., E. F. FRITSCH and J. SAMBROOK, 1982 Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
32. MESSIER, W., S.-H. LI and G.-B. STEWARD, 1996 The birth of microsatellites. Nature 381: 483.
33. MONCKTON, D. G., R. NEUMANN, T. GURAM, N. FRETWELL, K. TAMAKI et al., 1994 Minisatellite mutation rate variation associated with a flanking DNA sequence polymorphism. Nat. Genet. 8: 162-170.
34. MORAN, P. A. P., 1975 Wandering distribution and the electrophoretic profile. Theor. Popul. Biol. 8: 318-330.
35. NIELSEN, R., 1997 A likelihood approach to population samples of microsatellite alleles. Genetics 146: 711-716.
36. NIELSEN, R., and P. J. PALLBØLL, 1999 Single-locus tests of microsatellite evolution: multi-step mutations and constraints on allele size. Mol. Phylogenet. Evol. (in press).
37. ORTI, G., D. E. PEARSE and J. C. AVISE, 1997 Phylogenetic assessment of length variation at a microsatellite locus. Proc. Natl. Acad. Sci. USA 94: 10745-10749.
38. PALSBØLL, P. J., F. LARSEN and E. SIGURD HANSEN, 1991 Sampling of skin biopsies from free-ranging large cetaceans in West Greenland: development of new biopsy tips and bolt designs. Rep. Int. Whaling Comm. Spec. Issue 13: 71-79.
39. PALSBØLL, P. J., P. J. CLAPHAM, D. K. MATTILA, F. LARSEN, R. SEARS et al., 1995 Distribution of mtDNA haplotypes in North Atlantic humpback whales: the influence of behaviour on population structure. Marine Ecol. Prog. Sci, 116: 1-10.
40. PALSBØLL, P. J., J. ALLEN, M. BÉRUBÉ, P. J. CLAPHAM, T. P. FEDDERSEN et al., 1997a Genetic tagging of humpback whales. Nature 388: 676-679.
41. PALSBØLL, P. J., M. BÉRUBÉ, A. H. LARSEN and H. JØRGENSEN, 1997b Primers for the amplification of tri- and tetramer microsatellite loci in cetaceans. Mol. Ecol. 6: 893-895.
42. PRIMMER, C. R., N. SAINO and A. P. MØLLER, 1996 Directional evolution in germline microsatellite mutations. Nat. Genet. 13: 391-393.
43. RICO, C., I. RICO and G. HEWITT, 1994 An optimized method for isolating and sequencing large (CA/GT)n (n > 40) microsatellites from genomic DNA. Mol. Ecol. 3: 181-182.
44. RUBINSZTEIN, D. C., W. AMOS, J. LEGGO, S. GOODBURN, S. JAIN et al., 1995 Microsalellite evolution - evidence for directionality and variation in rate between species. Nat. Genet. 10: 337-343.
45. SCHLÖTTERER, C., and D. TAUTZ, 1992 Slippage synthesis of simple sequence DNA. Nucleic Acids Res. 20: 211-215.
46. SHRIVER, M. D., L. JIN, R. CHAKRABORTY and E. BOERWINKLE, 1993 VNTR allele frequency distributions under the stepwise mutation model: a computer simulation approach. Genetics 134: 983-993.
47. SHRIVER, M. D., L. JIN, E. BOERWINKLE, R. DEKA, R. E. FERRELL et al., 1995 A novel measure of genetic distance for highly polymorphic tandem repeat loci. Mol. Biol. Evol. 12: 914-920.
48. SLATKIN, M., 1995 A measure of population subdivision based on microsatellite allele frequencies. Genetics 139: 457-462.
49. SLATKIN, M., and R. R. HUDSON, 1991 Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129: 555-562.
50. TALBOT, C. C., D. AVRAMOPOULOS, S. GERKEN, A. CHAKRAVARTI, J. A. ARMOUR et al., 1995 The tetranucleotide repeat polymorphism D21S1245 demonstrates hypermutability in germline and somatic cells. Hum. Mol. Genet. 4: 1193-1199.
51. TAUTZ, D., 1989 Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res. 17: & 463-6471.
52. VALDES, A. M., M. SLATKIN and N. B. FREIMER, 1993 Allele frequencies at microsatellile loci: the stepwise mutation model revisited. Genetics 133: 737-749.
53. VALSECCHI, E., P. PALSBØLL, P. HALE, D. GLOCKNER-FERRARI, M. FERRARI et al., 1997 Microsatellite genetic distances between oceanic populations of the humpback whale (Megaptera novaeangliae). Mol. Biol. Evol. 14: 355-362.
54. n polymorphisms, Genomics 7: 524-530.
55. WEBER, J. L., and P. E., MAY, 1989 Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am. J. Hum. Genet. 44: 388-396.
56. WEBER, J. L., and C. WONG, 1993 Mutation of human short tandem repeats. Hum. Mol. Ginet. 2: 1123-1128.
57. WEIR, B. S., 1990 Genetic Data Analysis. Methods for Discrete Population Genetic Data. Sinauer Associates, Sunderland, MA.
58. ZHIVOTOVSKY, L. A., and M. W. FELDMAN, 1995 Microsatellite variability and genetic distances. Proc. Natl. Acad. Sci. USA 92:11549-11552.