Abstract
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’.
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References
Nei, M. (1987) Molecular Evolutionary Genetics. Columbia University Press. NewYork.
Siatkin, M. (1993) Isolation by distance in equilibrium and non-equilibrium populations. Evolution 47: 264–279.
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.
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 — http://lotka.stanford.edu/distance.html
Siatkin, M. (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics 139: 457–462.
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.
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.
Wright S. (1978). Evolution and the Genetics of Popultions Vol 4. Variability Within and Among Natural Populations. University of Chicago Press, Chicago Ill.
Cavalli-Sforza L.L., Edwards A.W.F. (1967). Phylogentic analysis: Models and estimation procedures. American Journal of Human Genetics. 19: 233–257.
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.
Takezaki N and Nei M (1996). Genetic distances and reconstruction of phylogenetic trees from microsatellite data. Genetics 144: 389–399.
Weir, B.S. and Cockerham, C.C. (1984). Estimating F-statistics for the analysis of population structure. Evolution 38, 1358–1370.
Weir, B.S. (1996). Genetic Data Analysis II: Methods for Discrete Population Genetic Data. Sinauer Associates Inc., Sanderland, Massachusetts. GDA web site (β version): http://biology001.unm.edu/ ~ lewis/gda.htm
Lynch, M. and Milligan, B.G. (1994). Analysis of population genetic structure with RAPD markers. Molecular Ecology 3: 91–99.
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.
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.
Zhivotosky, L.A. and Feldman M.W. (1995) Microsatellite variability and genetic distances. Proceedings of the National Academy of Sciences USA 92: 11549–11552.
Lynch, M. and Crease, T.J. (1990) The analysis of population survey data on DNA sequence variation. Molecular Biology and Evolution 7: 377–394.
Excoffier, L. (1995). AMOVA 1.55 (Analysis of Molecular Variance) University of Geneva. Amova site — http://anthroplogie.unige.ch/ftp/comp/win/amova
Siatkin, M. and Madison, W.R (1990) Detecting isolation by distance using phytogenies of genes. Genetics 126: 249–260.
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.
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.
Higgins, D.G. and Sharp, P.M. (1989) Fast and sensitive multiple sequence alignments on a microcomputer. CABIOS 5, 151–153.
Li, W.-H. (1993). Unbiased estimation of the rates of synonymous and nonsynonymous substitution. Journal of Molecular Evolution 36: 96–99.
Felsenstein, J. (1991). PHYLIP (Phylogeny Inference Package) version 3.5. University of Washington, Seattle. Web site — http://evolution. genetics.washington.edu/phylip.html
Sudhir, K., Tamura, K., and Nei, M. (1993).“MEGA: Molecular Evolutionary Genetic Analysis, Version 1.01. The Pennsylvania State University, University Park, PA 16802.
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.
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.
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.
Goudet, J. (1995) FSTAT version 1.2: a computer program to calculate F-statistics. Journal of Heredity 86: 485–486.
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: ftp://ftp.cefe.cnrs-mop.fr/pub/msdos/genepop
Nei, M. and Tajima, F. (1981). DNA polymorphism detectable by restriction endonucleases. Genetics 97: 145–163.
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.
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.
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).
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 — http://www.rr.ualberta.ca/profs/yeh.htm
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 — http://www.bioc.rice.edu/ ~ kfg/GSoft.html
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Beaumont, M.A., Ibrahim, K.M., Boursot, P., Bruford, M.W. (1998). Measuring Genetic Distance. In: Karp, A., Isaac, P.G., Ingram, D.S. (eds) Molecular Tools for Screening Biodiversity. Springer, Dordrecht. https://doi.org/10.1007/978-94-009-0019-6_58
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DOI: https://doi.org/10.1007/978-94-009-0019-6_58
Publisher Name: Springer, Dordrecht
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