Measuring Genetic Distance

  • Mark A. Beaumont
  • Kamal M. Ibrahim
  • Pierre Boursot
  • Michael W. Bruford


A common assumption about genetic distance is that it is a measure of the evolutionary divergence between copies of homologous genes which share a common ancestor. Under this assumption. an ideal measure of genetic distance is where the difference between the two genes is proportional to the time since they shared a common ancestor. While this is true, it is important to remember that genetic distance was originally devised as a means to estimate the degree of genetic differentiation between populations. Indeed, in his landmark text ‘Molecular Evolutionary Genetics’ written in 1987, Nei (1) formally defines genetic distance in a way which embraces both of these ideas: ‘Genetic distance is the extent of gene differences... between populations or species that is measured by some numerical quantity’.


Genetic Distance Common Ancestor Distance Measure Ancestral Population Stepwise Mutation Model 
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  1. 1.
    Nei, M. (1987) Molecular Evolutionary Genetics. Columbia University Press. NewYork.Google Scholar
  2. 2.
    Siatkin, M. (1993) Isolation by distance in equilibrium and non-equilibrium populations. Evolution 47: 264–279.CrossRefGoogle Scholar
  3. 3.
    Ohta, T. and Kimura, M. (1973). A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genetical Research 22: 201–204.CrossRefGoogle Scholar
  4. 4.
    Goldstein, D.B., Ruíz-Linares, A., Feldman, M. and Cavalli-Sforza, L.L. (1995). An evaluation of genetic distances for use with microsatellite loci. Genetics 139:463–471. Microsat site — Scholar
  5. 5.
    Siatkin, M. (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics 139: 457–462.Google Scholar
  6. 6.
    Shriver, M.D., Jin, L., Boerwinkle, E., Deka, R., Ferrell, R.E., and Chakraborty, R. (1995). A novel measure of genetic distance for highly polymorphic tandem repeat loci. Molecular Biology and Evolution 12:914–920.Google Scholar
  7. 7.
    Michalakis, Y. and Excoffier, L. (1996). A generic estimation of population subdivision using distances between alleles with special reference for microsatellite loci. Genetics 142, 1061–1064.Google Scholar
  8. 8.
    Wright S. (1978). Evolution and the Genetics of Popultions Vol 4. Variability Within and Among Natural Populations. University of Chicago Press, Chicago Ill.Google Scholar
  9. 9.
    Cavalli-Sforza L.L., Edwards A.W.F. (1967). Phylogentic analysis: Models and estimation procedures. American Journal of Human Genetics. 19: 233–257.Google Scholar
  10. 10.
    Nei M, Tajima F. and Tateno Y (1983). Accuracy of estimated phylogenetic trees from molecular data II: Gene frequency data. Journal of Molecular Evolution. 19: 153–170.CrossRefGoogle Scholar
  11. 11.
    Takezaki N and Nei M (1996). Genetic distances and reconstruction of phylogenetic trees from microsatellite data. Genetics 144: 389–399.Google Scholar
  12. 12.
    Weir, B.S. and Cockerham, C.C. (1984). Estimating F-statistics for the analysis of population structure. Evolution 38, 1358–1370.CrossRefGoogle Scholar
  13. 13.
    Weir, B.S. (1996). Genetic Data Analysis II: Methods for Discrete Population Genetic Data. Sinauer Associates Inc., Sanderland, Massachusetts. GDA web site (β version): ~ lewis/gda.htmGoogle Scholar
  14. 14.
    Lynch, M. and Milligan, B.G. (1994). Analysis of population genetic structure with RAPD markers. Molecular Ecology 3: 91–99.CrossRefGoogle Scholar
  15. 15.
    Bowcock, A.M., Ruíz-Linares, A., Tomfohrde, J., Minch, E., Kidd, J.R. and Cavalli-Sforza, L.L. (1994) High resolution human evolutionary trees with polymorphic microsatellites. Nature, 368: 455–457.CrossRefGoogle Scholar
  16. 16.
    Goldstein, D.B., Ruíz-Linares, A., Feldman, M. and Cavalli-Sforza, L.L. (1995) Genetic absolute dating based on microsatellites and the origin of modern humans. Proceedings of the National Academy of Sciences USA, 92: 6720–6727.Google Scholar
  17. 17.
    Zhivotosky, L.A. and Feldman M.W. (1995) Microsatellite variability and genetic distances. Proceedings of the National Academy of Sciences USA 92: 11549–11552.Google Scholar
  18. 18.
    Lynch, M. and Crease, T.J. (1990) The analysis of population survey data on DNA sequence variation. Molecular Biology and Evolution 7: 377–394.Google Scholar
  19. 19.
    Excoffier, L. (1995). AMOVA 1.55 (Analysis of Molecular Variance) University of Geneva. Amova site — Scholar
  20. 20.
    Siatkin, M. and Madison, W.R (1990) Detecting isolation by distance using phytogenies of genes. Genetics 126: 249–260.Google Scholar
  21. 21.
    Higgins, D.G., Bleasby, A.J. and Fuchs, R. (1992). CLUSTAL V — Improved software for multiple sequence alignment. Computer Applications in the Biosciences. 8: 189–191.Google Scholar
  22. 22.
    Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22: 4673–4680.CrossRefGoogle Scholar
  23. 23.
    Higgins, D.G. and Sharp, P.M. (1989) Fast and sensitive multiple sequence alignments on a microcomputer. CABIOS 5, 151–153.Google Scholar
  24. 24.
    Li, W.-H. (1993). Unbiased estimation of the rates of synonymous and nonsynonymous substitution. Journal of Molecular Evolution 36: 96–99.CrossRefGoogle Scholar
  25. 25.
    Felsenstein, J. (1991). PHYLIP (Phylogeny Inference Package) version 3.5. University of Washington, Seattle. Web site — http://evolution. Scholar
  26. 26.
    Sudhir, K., Tamura, K., and Nei, M. (1993).“MEGA: Molecular Evolutionary Genetic Analysis, Version 1.01. The Pennsylvania State University, University Park, PA 16802.Google Scholar
  27. 27.
    Cooper, S.J.B., Ibrahim, K.M. and Hewitt, G.M. (1995). Postglacial expansion and genome subdivision in the European grasshopper Chorthippus parallelus. Molecular Ecology 4: 49–60.CrossRefGoogle Scholar
  28. 28.
    Hudson, R.R., Boos, D.D. and Kaplan, N.L. (1992). A statistical test for detecting geographic subdivision. Molecular Biology and Evolution 9: 138–151.Google Scholar
  29. 29.
    Swofford, DL and Seiander, RB (1981). BIOSYS-1: a FORTRAN program for the comprehensive analysis of electrophretic data in population genetics and systematics. Journal of Heredity 72: 281–283.Google Scholar
  30. 30.
    Goudet, J. (1995) FSTAT version 1.2: a computer program to calculate F-statistics. Journal of Heredity 86: 485–486.Google Scholar
  31. 31.
    Raymond, M. and Rousset, F. (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity 86 248–249. Genepop download site: Scholar
  32. 32.
    Nei, M. and Tajima, F. (1981). DNA polymorphism detectable by restriction endonucleases. Genetics 97: 145–163.Google Scholar
  33. 33.
    Nei M and Miller JC (1990) A simple method for estimating average number of nucleotide substitutions within and between populations from restricted data. Genetics 4: 873–879.Google Scholar
  34. 34.
    Roques, S (1996). Population Structure of the Whiting, Odontogandus merlangus in the North Atlantic: An Evaluation by Mitochndrial DNA Analysis. M.Sc. Thesis. School of Biology. University of East Anglia, Norwich, UK.Google Scholar
  35. 35.
    Rico C., Ibrahim K.M., Rico C., Hewitt, G.M. (1997). Stock composition in North Atlantic populations of whiting using microsatellite markers. Journal of Fish Biology (in press).Google Scholar
  36. 36.
    Yeh F.C., Boyle T (1997). POPGENE version 1.2. Microsoft Windows based software for population genetic analysis. University of Alberta, Department of Renewable Resources. Edmonton, Canada. Popgene site — Scholar
  37. 37.
    Goodnight, K.F., Queller, D.C. and Poznansky, T. (1997). KINSHIP 1.1.2. Department of Ecology and Evolutionary Biology, Rice University, Texas, USA. Kinship web site — ~ kfg/GSoft.htmlGoogle Scholar

Copyright information

© Chapman & Hall 1998

Authors and Affiliations

  • Mark A. Beaumont
  • Kamal M. Ibrahim
  • Pierre Boursot
  • Michael W. Bruford

There are no affiliations available

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