Standardizing for microsatellite length in comparisons of genetic diversity

Molecular Ecology

Volumn 14, Issue 3, 2005, Pages 885-890

  Petit, Rémy J ^a   Deguilloux, Marie France ^a,b   Chat, Joëlle ^c   Grivet, Delphine ^a,d   Garnier Géré, Pauline ^a   Vendramini, Giovanni G ^e  

^a UMR 1202 BIOGECO   (France)

^b UNIVERSITÉ BORDEAUX 1   (France)

^c Ecologie Comportementale et Biologie des Populations de Poissons   (France)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e CNR   (Italy)

Author keywords

Allelic richness; Ascertainment bias; Genetic diversity; Rarefaction; Slippage; Standardization

Indexed keywords

CHLOROPLAST DNA; MICROSATELLITE DNA;

ANGIOSPERM; ARTICLE; BIOLOGICAL MODEL; COMPARATIVE STUDY; CONIFER; GENE FREQUENCY; GENETIC VARIABILITY; GENETICS; MUTATION; REGRESSION ANALYSIS;

ANGIOSPERMS; CONIFEROPHYTA; DNA, CHLOROPLAST; GENE FREQUENCY; MICROSATELLITE REPEATS; MODELS, GENETIC; MUTATION; REGRESSION ANALYSIS; VARIATION (GENETICS);

CONIFEROPHYTA; MAGNOLIOPHYTA;

EID: 14844331058     PISSN: 09621083     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2005.02446.x     Document Type: Article

References (35)

1. Adams RI, Brown KM, Hamilton MB (2004) The impact of microsatellite electromorph size homoplasy on multilocus population structure estimates in a tropical tree (Corythophora alta) and an anadromous fish (Morone saxatilis). Molecular Ecology, 13, 2579-2588.
2. Bachtrog D, Agis M, Imhof M, Schlötterer C (2000) Microsatellite variability differs between dinucleotide repeat motifs. Evidence from Drosophila melanogaster. Molecular Biology and Evolution, 17, 1277-1285.
3. Brinkmann B, Klintschar M, Neuhuber F, Hühne J, Rolf R (1998) Mutation rate in human microsatellites: influence of the structure and length of the tandem repeat. American Journal of Human Genetics, 62, 1408-1415.
4. Brohede J, Primmer CR, Moller A, Ellegren H (2002) Heterogeneity in the rate and pattern of germline mutation at individual microsatellite loci. Nucleic Acids Research, 30, 1997-2003.
5. Chakraborty R, Kimmel M, Stivers DN, Davison LJ, 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.
6. Cooper G, Rubinsztein DC, Amos W (1998) Ascertainment bias cannot entirely account for human microsatellites being longer than their chimpanzee homologues. Human Molecular Genetics, 7, 1425-1429.
7. Deguilloux M-F, Dumolin-Lapègue S, Gielly L, Grivet D, Petit RJ (2003) A set of primers for the amplification of chloroplast microsatellites in Quercus. Molecular Ecology Notes, 3, 24-27.
8. Ellegren H (2000) Microsatellite mutations in the germline: implication for evolutionary inference. Trends in Genetics, 16, 551-558.
9. Ellegren H, Primmer CR, Sheldon BC (1995) Microsatellite evolution: directionality or bias in locus selection. Nature Genetics, 11, 360-362.
10. El Mousadik A, Petit RJ (1996) High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco. Theoretical and Applied Genetics, 92, 832-839.
11. Ewens W (1972) The sampling theory of selectively neutral alleles. Theoretical Population Biology, 3, 87-112.
12. Hamrick JL, Linhart YB, Mitton JB (1979) Relationship between life history parameters and allozyme variation in plants. Annual Review of Ecology and Systematics, 10, 173-200.
13. Hurlbert SH (1971) The nonconcept of species diversity: a critique and alternative parameters. Ecology, 52, 577-586.
14. Innan H, Terauchi R, Miyashita NT (1997) Microsatellite polymorphism in natural populations of the wild plant Arabidopsis thaliana. Genetics, 146, 1441-1452.
15. 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.
16. Levinson G, Gutman GA (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Molecular Biology and Evolution, 4, 203-221.
17. Neff BD, Gross MR (2001) Microsatellite evolution in vertebrates: inference from AC dinucleotide repeats. Evolution, 55, 1717-1733.
18. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89, 583-590.
19. Petit RJ, Vendramin GG (2005) Phylogeography of organelle DNA in plants: an introduction. In: Phylogeography of Southern European Refugia (eds Weiss S, Ferrand N). Amsterdam, Kluwer, in press.
20. Petit RJ, Kremer A, Wagner DB (1993) Finite island model for organelle and nuclear genes in plants. Heredity, 71, 630-641.
21. Petit RJ, Duminil J, Fineschi S, Hampe A, Salvini D, Vendramin GG (2004) Comparative organisation of chloroplast, mitochondrial and nuclear diversity in plant populations. Molecular Ecology, doi: 10.1111/j.1365-294X.2005.02446.x
22. Primmer CR, Ellegren H, Saino N, Moller AP (1996) Directional evolution in germline microsatellites mutations. Nature Genetics, 13, 391-393.
23. Provan J, Powell W, Hollingsworth PM (2001) Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends in Ecology and Evolution, 16, 142-147.
24. Rose O, Falush D (1998) A threshold size for microsatellite expansion. Molecular Biology and Evolution, 15, 613-615.
25. SAS Institute (1989) SAS/STAT user's guide, 6.03 edn. SAS Institute Publishers, Cary, NC.
26. Sokal RR, Rohlf FJ (1995) Biometry, 3rd edn. Freeman, San Francisco.
27. Symonds VV, Lloyd AM (2003) An analysis of microsatellite loci in Arabidopsis thaliana: mutational dynamics and application. Genetics, 165, 1475-1488.
28. Vendramin GG, Ziegenhagen B (1997) Characterisation and inheritance of polymorphic plastid microsatellites in Abies. Genome, 40, 857-864.
29. Vendramin GG, Anzidei M, Madaghiele A, Bucci G (1998) Distribution of genetic diversity in Pinus pinaster Ait. as revealed by chloroplast microsatellites. Theoretical and Applied Genetics, 97, 446-563.
30. Vendramin GG, Lelli L, Rossi P, Morgante M (1996) A set of primers for the amplification of 20 chloroplast microsatellites in Pinaceae. Molecular Ecology, 5, 595-598.
31. Wakasugi TJ, Tsudzuki SI, Nakashima K, Tsudzuki T, Sugiura M (1994) Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine, Pinus thunbergii. Proceedings of the National Academy of Sciences of the United States of America, 91, 9794-9798.
32. n polymorphisms. Genomics, 7, 524-530.
33. Weising K, Gardner RG (1999) A set of conserved PCR primers for the analysis of single sequence repeat polymorphisms in chloroplast genomes of dicotyledonous angiosperms. Genome, 42, 9-19.
34. Whittaker JC, Harbord RM, Boxall N, Mackay I, Dawson G, Sibly RM (2003) Likelihood-based estimation of microsatellite mutation rates. Genetics, 164, 781-787.
35. Whittle C-A, Johnston MO (2002) Male-driven evolution of mitochondrial and chloroplastidial DNA sequences in plants. Molecular Biology and Evolution, 19, 938-949.